Sample records for bound water molecules

  1. SPAM: A Simple Approach for Profiling Bound Water Molecules. (United States)

    Cui, Guanglei; Swails, Jason M; Manas, Eric S


    A method that identifies the hydration shell structure of proteins and estimates the relative free energies of water molecules within that hydration shell is described. The method, which we call "SPAM" (maps spelled in reverse), utilizes explicit solvent molecular dynamics (MD) simulations to capture discrete hydration sites at the water-protein interface and computes a local free energy measure from the distribution of interaction energies between water and the environment at a specific site. SPAM is able to provide a qualitative estimate of the thermodynamic profile of bound water molecules that correlates nicely with well-studied structure-activity relationships and observed binding "hot spots". This is demonstrated in retrospective analyses of HIV1 protease and hen egg white lysozyme, where the effects of water displacement and solvent binding have been studied extensively. The simplicity and effectiveness of SPAM allow for prospective application during the drug discovery process.

  2. Protein-bound water molecules in primate red- and green-sensitive visual pigments. (United States)

    Katayama, Kota; Furutani, Yuji; Imai, Hiroo; Kandori, Hideki


    Protein-bound water molecules play crucial roles in the structure and function of proteins. The functional role of water molecules has been discussed for rhodopsin, the light sensor for twilight vision, on the basis of X-ray crystallography, Fourier transform infrared (FTIR) spectroscopy, and a radiolytic labeling method, but nothing is known about the protein-bound waters in our color visual pigments. Here we apply low-temperature FTIR spectroscopy to monkey red (MR)- and green (MG)-sensitive color pigments at 77 K and successfully identify water vibrations using D(2)O and D(2)(18)O in the whole midinfrared region. The observed water vibrations are 6-8 for MR and MG, indicating that several water molecules are present near the retinal chromophore and change their hydrogen bonds upon retinal photoisomerization. In this sense, color visual pigments possess protein-bound water molecules essentially similar to those of rhodopsin. The absence of strongly hydrogen-bonded water molecules (O-D stretch at microbial rhodopsins. On the other hand, two important differences are observed in water signal between rhodopsin and color pigments. First, the water vibrations are identical between the 11-cis and 9-cis forms of rhodopsin, but different vibrational bands are observed at >2550 cm(-1) for both MR and MG. Second, strongly hydrogen-bonded water molecules (2303 cm(-1) for MR and 2308 cm(-1) for MG) are observed for the all-trans form after retinal photoisomerization, which is not the case for rhodopsin. These specific features of MR and MG can be explained by the presence of water molecules in the Cl(-)-biding site, which are located near positions C11 and C9 of the retinal chromophore. The averaged frequencies of the observed water O-D stretching vibrations for MR and MG are lower as the λ(max) is red-shifted, suggesting that water molecules are involved in the color tuning of our vision.

  3. Observation of water molecules bound to a protein using cold-spray ionization mass spectrometry. (United States)

    Sei, Yoshihisa; Shimotakahara, Sakurako; Ishii, Juri; Shindo, Heisaburo; Seki, Hiroko; Yamaguchi, Kentaro; Tashiro, Mitsuru


    The characterization of water molecules bound to ribonuclease T1 (RNase T1) was carried out using cold-spray ionization mass spectrometry (CSI-MS). CSI-MS is a variant of electrospray ionization mass spectrometry (ESI-MS) operating at low temperature, and is particularly suitable for investigating the weaker molecular associations, since the temperature at the spray interface is much lower than that in the conventional ESI-MS. In this approach, ion peaks due to the addition of nine water molecules were identified at a spray temperature of 48 degrees C. This result showed good agreement with that inferred by the combinational analysis of NMR and X-ray crystallography, indicating that CSI-MS is capable of rapidly providing reliable information to characterize the number of water molecules bound to a macromolecule.

  4. Two-dimensional description of surface-bounded exospheres with application to the migration of water molecules on the Moon (United States)

    Schorghofer, Norbert


    On the Moon, water molecules and other volatiles are thought to migrate along ballistic trajectories. Here, this migration process is described in terms of a two-dimensional partial differential equation for the surface concentration, based on the probability distribution of thermal ballistic hops. A random-walk model, a corresponding diffusion coefficient, and a continuum description are provided. In other words, a surface-bounded exosphere is described purely in terms of quantities on the surface, which can provide computational and conceptual advantages. The derived continuum equation can be used to calculate the steady-state distribution of the surface concentration of volatile water molecules. An analytic steady-state solution is obtained for an equatorial ring; it reveals the width and mass of the pileup of molecules at the morning terminator.

  5. sup 2 D NMR study of the dynamics of bound water molecules in dipalmitoyl-phosphatidylcholine-D sub 2 O system at a low water content

    CERN Document Server

    Takahashi, A; Takizawa, T


    We found two doublet signals A and B in sup 2 D-NMR of dipalmitoyl-phosphatidylcholine-D sub 2 O system at a low water content below the temperature of the onset of the main phase transition, i.e. in the beta'-crystalline (L subbeta sub ') phase. The splitting of each doublet becomes minimum at the onset of the transition. The signal A decreases in intensity with a slight increase of its splitting as the temperature increases further, accompanying the marked growth of the signal B in its intensity and splitting. These features of two doublets in the L subbeta sub ' phase and at higher temperatures have never been noticed. The signals A and B were ascribed to the tightly bound water and the loosely bound water, respectively. These assignments were confirmed by the theoretical calculations of the splitting of the doublet A for all possible number of the tightly bound water molecules. (author)

  6. More loosely bound hadron molecules at CDF?

    CERN Document Server

    Bignamini, C; Piccinini, F; Polosa, A D; Riquer, V; Sabelli, C


    In a recent paper we have proposed a method to estimate the prompt production cross section of X(3872) at the Tevatron assuming that this particle is a loosely bound molecule of a D and a D*bar meson. Under this hypothesis we find that it is impossible to explain the high prompt production cross section found by CDF at sigma(X(3872)) \\sim 30-70 nb as our theoretical prediction is about 300 times smaller than the measured one. Following our work, Artoisenet and Braaten, have suggested that final state interactions in the DD*bar system might be so strong to push the result we obtained for the cross section up to the experimental value. Relying on their conclusions we show that the production of another very narrow loosely bound molecule, the X_s=D_s D_s*bar, could be similarly enhanced. X_s should then be detectable at CDF with a mass of 4080 MeV and a prompt production cross section of sigma(X_s) \\sim 1-3 nb.

  7. Water, bound and mobile (United States)

    Resolving the global transpiration flux is critical to constraining global carbon cycle models because carbon uptake by photosynthesis in terrestrial plants (Gross Primary Productivity, GPP) is directly related to water lost through transpiration. Quantifying GPP globally is cha...

  8. Free and bound water in normal and cataractous human lenses. (United States)

    Heys, Karl R; Friedrich, Michael G; Truscott, Roger J W


    To analyze free and total water in human normal and cataractous lenses. Thermogravimetric analysis was used to determine total water, and differential scanning calorimetry was used for free water. In normal human lenses, the total water content of the nucleus remained unchanged with age, but the state of the water altered. The ratio of free to bound water increased steadily throughout adult life. In a 20-year-old person, there was approximately one bound water molecule for each free water molecule in the lens center, whereas in a 70- to 80-year-old person, there were two free water molecules for each bound water molecule. This conversion of bound to free water does not appear to be simply a consequence of the aggregation of soluble crystallins into high molecular weight aggregates because studies with intact pig lenses, in which such processes were facilitated by heat, did not show similar changes. The region of the lens in which the barrier to diffusion develops at middle age corresponds to a transition zone in which the protein concentration is intermediate between that of the cortex and the nucleus. In cataractous lenses, the free-to-bound water ratio was not significantly different from that of age-matched normal lenses; however, total water content in the center of advanced nuclear cataractous lenses was slightly lower than in normal lenses. As the human lens ages, bound water is progressively changed to free water. Advanced nuclear cataract may be associated with lower total hydration of the lens nucleus.

  9. Crystal Structure of Fatty Acid Amide Hydrolase Bound to the Carbamate Inhibitor URB597: Discovery of a Deacylating Water Molecule and Insight into Enzyme Inactivation

    Energy Technology Data Exchange (ETDEWEB)

    Mileni, Mauro; Kamtekar, Satwik; Wood, David C.; Benson, Timothy E.; Cravatt, Benjamin F.; Stevens, Raymond C. (Scripps); (Pfizer)


    The endocannabinoid system regulates a wide range of physiological processes including pain, inflammation, and cognitive/emotional states. URB597 is one of the best characterized covalent inhibitors of the endocannabinoid-degrading enzyme fatty acid amide hydrolase (FAAH). Here, we report the structure of the FAAH-URB597 complex at 2.3 {angstrom} resolution. The structure provides insights into mechanistic details of enzyme inactivation and experimental evidence of a previously uncharacterized active site water molecule that likely is involved in substrate deacylation. This water molecule is part of an extensive hydrogen-bonding network and is coordinated indirectly to residues lining the cytosolic port of the enzyme. In order to corroborate our hypothesis concerning the role of this water molecule in FAAH's catalytic mechanism, we determined the structure of FAAH conjugated to a urea-based inhibitor, PF-3845, to a higher resolution (2.4 {angstrom}) than previously reported. The higher-resolution structure confirms the presence of the water molecule in a virtually identical location in the active site. Examination of the structures of serine hydrolases that are non-homologous to FAAH, such as elastase, trypsin, or chymotrypsin, shows a similarly positioned hydrolytic water molecule and suggests a functional convergence between the amidase signature enzymes and serine proteases.

  10. Properties of Water Bound in Hydrogels

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    Vladimir M. Gun’ko


    Full Text Available In this review, the importance of water in hydrogel (HG properties and structure is analyzed. A variety of methods such as 1H NMR (nuclear magnetic resonance, DSC (differential scanning calorimetry, XRD (X-ray powder diffraction, dielectric relaxation spectroscopy, thermally stimulated depolarization current, quasi-elastic neutron scattering, rheometry, diffusion, adsorption, infrared spectroscopy are used to study water in HG. The state of HG water is rather non-uniform. According to thermodynamic features of water in HG, some of it is non-freezing and strongly bound, another fraction is freezing and weakly bound, and the third fraction is non-bound, free water freezing at 0 °C. According to structural features of water in HG, it can be divided into two fractions with strongly associated and weakly associated waters. The properties of the water in HG depend also on the amounts and types of solutes, pH, salinity, structural features of HG functionalities.

  11. Far-Infrared Spectroscopy of Weakly Bound Hydrated Cluster Molecules

    DEFF Research Database (Denmark)

    Andersen, Jonas

    -sized molecular clusters with water by means of far-infrared and terahertz neon matrix isolation spectroscopy. The embedding of non-covalent cluster molecules in solid cryogenic neon matrices at 2.8 K ensures a high sensitivity for direct spectroscopic observations of the large-amplitude intermolecular...

  12. Dynamics of water bound to crystalline cellulose

    Energy Technology Data Exchange (ETDEWEB)

    O’Neill, Hugh; Pingali, Sai Venkatesh; Petridis, Loukas; He, Junhong; Mamontov, Eugene; Hong, Liang; Urban, Volker; Evans, Barbara; Langan, Paul; Smith, Jeremy C.; Davison, Brian H.


    Interactions of water with cellulose are of both fundamental and technological importance. Here, we characterize the properties of water associated with cellulose using deuterium labeling, neutron scattering and molecular dynamics simulation. Quasi-elastic neutron scattering provided quantitative details about the dynamical relaxation processes that occur and was supported by structural characterization using small-angle neutron scattering and X-ray diffraction. We can unambiguously detect two populations of water associated with cellulose. The first is “non-freezing bound” water that gradually becomes mobile with increasing temperature and can be related to surface water. The second population is consistent with confined water that abruptly becomes mobile at ~260 K, and can be attributed to water that accumulates in the narrow spaces between the microfibrils. Quantitative analysis of the QENS data showed that, at 250 K, the water diffusion coefficient was 0.85 ± 0.04 × 10-10 m2sec-1 and increased to 1.77 ± 0.09 × 10-10 m2sec-1 at 265 K. MD simulations are in excellent agreement with the experiments and support the interpretation that water associated with cellulose exists in two dynamical populations. Our results provide clarity to previous work investigating the states of bound water and provide a new approach for probing water interactions with lignocellulose materials.

  13. Computed bound and continuum electronic states of the nitrogen molecule

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    Tennyson Jonathan


    Full Text Available The dissociative recombination (DR of N2+ is important for processes occurring in our atmosphere. However, it is not particularly well characterised, experimentally for the vibrational ground state and, theoretically for the v ≥ 4. We use the R-matrix method to compute potential energy curves for both the bound Rydberg states of nitrogen and for quasi-bound states lying in the continuum. Use of a fine mesh of internuclear separations allows the details of avoided crossings to be determined. The prospects for using the curves as the input for DR calculations is discussed.

  14. Cooperation between bound waters and hydroxyls in controlling isotope-exchange rates (United States)

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


    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

  15. Structure of the weakly bound triatomic He2Li and He2Na molecules (United States)

    Suno, Hiroya


    We study the structure of triatomic molecules containing two helium atoms and one alkali-metal atom X (X = Li, Na). The three-body Schrödinger equation is solved in hyperspherical coordinates using the He-He and He-X pair van der Waals potentials available in the literature. We calculate the structural properties of the He2Li and He2Na bound states, and analyze one-dimensional pair and angle distribution functions as well as two-dimensional pair-pair and angle-angle distribution functions. These bound states are characterized by so peculiar weakly bound structures that classifying them into particular sizes and geometrical shapes appears to be elusive. Particularly, the JΠ=0+ excited states of He426Li and He427Li are found to constitute giant triatomic molecules with their size amounting to several hundred bohrs.

  16. Bound states of water in gelatin discriminated by near-infrared spectroscopy (United States)

    Otsuka, Yukiko; Shirakashi, Ryo; Hirakawa, Kazuhiko


    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.

  17. Adsorption of Water Molecule on Silicene-FE System (United States)

    Ruiz Chavarria, Gregorio

    After graphene synthesis, there have been numerous studies on similar systems in two dimensions so, we have the borophene, germanene, silicene, phosphorene, etc. Following this line, I do a study that takes the silicene system at its starting point, system to which it add Fe atom. At first, the stability of SILICENE-Fe system is studied, which is stable. Then a water molecule is added to the SILICENE-Fe system, which is captured, as is bounded to the Fe atom. To make this study I used Functional Density Theory, Born-Openheimer Approximation, Atomic Pseudopotentials and Molecular Dynamics.

  18. Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

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    Marijn T J van Loenhout

    Full Text Available The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

  19. Determination of cellular lipids bound to human CD1d molecules.

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    Daryl Cox

    Full Text Available CD1 molecules are glycoproteins that present lipid antigens at the cell surface for immunological recognition by specialized populations of T lymphocytes. Prior experimental data suggest a wide variety of lipid species can bind to CD1 molecules, but little is known about the characteristics of cellular ligands that are selected for presentation. Here we have molecularly characterized lipids bound to the human CD1d isoform. Ligands were eluted from secreted CD1d molecules and separated by normal phase HPLC, then characterized by mass spectroscopy. A total of 177 lipid species were molecularly identified, comprising glycerophospholipids and sphingolipids. The glycerophospholipids included common diacylglycerol species, reduced forms known as plasmalogens, lyso-phospholipids (monoacyl species, and cardiolipins (tetraacyl species. The sphingolipids included sphingomyelins and glycosylated forms, such as the ganglioside GM3. These results demonstrate that human CD1d molecules bind a surprising diversity of lipid structures within the secretory pathway, including compounds that have been reported to play roles in cancer, autoimmune diseases, lipid signaling, and cell death.

  20. Assembly of membrane-bound protein complexes: detection and analysis by single molecule diffusion. (United States)

    Ziemba, Brian P; Knight, Jefferson D; Falke, Joseph J


    Protein complexes assembled on membrane surfaces regulate a wide array of signaling pathways and cell processes. Thus, a molecular understanding of the membrane surface diffusion and regulatory events leading to the assembly of active membrane complexes is crucial to signaling biology and medicine. Here we present a novel single molecule diffusion analysis designed to detect complex formation on supported lipid bilayers. The usefulness of the method is illustrated by detection of an engineered, heterodimeric complex in which two membrane-bound pleckstrin homology (PH) domains associate stably, but reversibly, upon Ca(2+)-triggered binding of calmodulin (CaM) to a target peptide from myosin light chain kinase (MLCKp). Specifically, when a monomeric, fluorescent PH-CaM domain fusion protein diffusing on a supported bilayer binds a dark MLCKp-PH domain fusion protein, the heterodimeric complex is observed to diffuse nearly 2-fold more slowly than the monomer because both of its twin PH domains can simultaneously bind to the viscous bilayer. In a mixed population of monomers and heterodimers, the single molecule diffusion analysis resolves, identifies and quantitates the rapidly diffusing monomers and slowly diffusing heterodimers. The affinity of the CaM-MLCKp interaction is measured by titrating dark MLCKp-PH construct into the system, while monitoring the changing ratio of monomers and heterodimers, yielding a saturating binding curve. Strikingly, the apparent affinity of the CaM-MLCKp complex is ~10(2)-fold greater in the membrane system than in solution, apparently due to both faster complex association and slower complex dissociation on the membrane surface. More broadly, the present findings suggest that single molecule diffusion measurements on supported bilayers will provide an important tool for analyzing the 2D diffusion and assembly reactions governing the formation of diverse membrane-bound complexes, including key complexes from critical signaling

  1. Tightly bound soil water introduces isotopic memory effects on mobile and extractable soil water pools. (United States)

    Newberry, Sarah L; Prechsl, Ulrich E; Pace, Matthew; Kahmen, Ansgar


    Cryogenic vacuum extraction is the well-established method of extracting water from soil for isotopic analyses of waters moving through the soil-plant-atmosphere continuum. We investigate if soils can alter the isotopic composition of water through isotope memory effects, and determined which mechanisms are responsible for it. Soils with differing physicochemical properties were re-wetted with reference water and subsequently extracted by cryogenic water distillation. Results suggest some reference waters bind tightly to the soil and not all of this tightly bound water is removed during cryogenic vacuum extraction. Kinetic isotopic fractionation occurring when reference water binds to the soil is likely responsible for the (18)O-depletion of re-extracted reference water, suggesting an enrichment of the tightly bound soil water pool. Further re-wetting of cryogenically extracted soils indicates an isotopic memory effect of tightly bound soil water on water added to the soil. The data suggest tightly bound soil water can influence the isotopic composition of mobile soil water. Findings show that soils influence the isotope composition of soil water by (i) kinetic fractionation when water is bound to the soil and (ii) equilibrium fractionation between different soil water pools. These findings could be relevant for plant water uptake investigations and complicate ecohydrological and paleohydrological studies.

  2. Single-molecule vibrational spectroscopy of water molecules using an LT-STM (United States)

    Matsumoto, Chikako; Kim, Yousoo; Motobayashi, Kenta; Kawai, Maki


    Single-molecule vibrational spectroscopy has attracted considerable attention as a powerful tool for nanoscale chemistry. The adsorption of water molecules on metal surfaces plays an important role in understanding many phenomena in nature, such as heterogeneous catalysis and corrosion, etc. The structure of water at low coverage has been investigated on a variety of transition-metal surfaces with various techniques. But the microscopic understanding of the adsorption feature of single water molecules is still unclear. We report molecular scale study of adsorption behaviors of water molecules on Pt (111) surface at 4.7 K by use of single-molecule vibrational spectroscopy with the scanning tunneling microscopy (STM). The Pt (111) surface was dosed with a small amount of water molecules (cherry blossom', which can be explained by one of the water molecules rotating around the other. Inelastic electron tunneling spectroscopy using the STM was utilized to determine vibrational modes of individual water dimers.

  3. Autodissociation of a water molecule in liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Geissler, Phillip L.; Dellago, Christoph; Chandler, David; Hutter, Jurg; Parrinello, Michele


    The dissociation of a water molecule in liquid water is the fundamental event in acid-base chemistry, determining the pH of water.Because the microscopic dynamics of this autodissociation are difficult to probe, both by experiment and by computer simulation, its mechanism has been unknown. Here we report several autodissociation trajectories generated by ab initio molecular dynamics [1]. These trajectories, which were harvested using transition path sampling [2-4], reveal the mechanism for the first time. Rare fluctuations in solvation energies destabilize an oxygen-hydrogen bond. Through the transfer of one or more protons along a hydrogen bond.

  4. Reactivity of Metal Ions Bound to Water-Soluble Polymers

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, N.N.; Watkins, J.G.; Lin, M.; Birnbaum, E.R.; Robison, T.W.; Smith, B.F.; Gohdes, J.W.; McDonald, J.G.


    The intent of this work is to determine the effectiveness of catalysts covalently bound to polymers and to understand the consequences of supporting the catalysts on catalyst efficiency and selectivity. Rhodium phosphine complexes with functional groups for coupling to polymers were prepared. These catalyst precursors were characterized using standard techniques including IR, NMR, and elemental analysis. Studies on the modified catalysts showed that they were still active hydrogenation catalysts. However, tethering of the catalysts to polyamines gave systems with low hydrogenation activity. Analogous biphasic systems were also explored. Phosphine ligands with a surfactant-like structure have been synthesized and used to prepare catalytically active complexes of palladium. The palladium complexes were utilized in Heck-type coupling reactions (e.g. coupling of iodobenzene and ethyl acrylate to produce ethyl cinnamate) under vigorously stirred biphasic reaction conditions, and were found to offer superior performance over a standard water-soluble palladium catalyst under analogous conditions.

  5. Ficolins and FIBCD1: Soluble and membrane bound pattern recognition molecules with acetyl group selectivity

    DEFF Research Database (Denmark)

    Thomsen, Theresa; Schlosser, Anders; Holmskov, Uffe


    A network of molecules, which recognizes pathogens, work together to establish a quick and efficient immune response to infectious agents. Molecules containing a fibrinogen related domain in invertebrates and vertebrates have been implicated in immune responses against pathogens, and characterize...

  6. The large quadrupole of water molecules (United States)

    Niu, Shuqiang; Tan, Ming-Liang; Ichiye, Toshiko


    Many quantum mechanical calculations indicate water molecules in the gas and liquid phase have much larger quadrupole moments than any of the common site models of water for computer simulations. Here, comparisons of multipoles from quantum mechanical/molecular mechanical (QM/MM) calculations at the MP2/aug-cc-pVQZ level on a B3LYP/aug-cc-pVQZ level geometry of a waterlike cluster and from various site models show that the increased square planar quadrupole can be attributed to the p-orbital character perpendicular to the molecular plane of the highest occupied molecular orbital as well as a slight shift of negative charge toward the hydrogens. The common site models do not account for the p-orbital type electron density and fitting partial charges of TIP4P- or TIP5P-type models to the QM/MM dipole and quadrupole give unreasonable higher moments. Furthermore, six partial charge sites are necessary to account reasonably for the large quadrupole, and polarizable site models will not remedy the problem unless they account for the p-orbital in the gas phase since the QM calculations show it is present there too. On the other hand, multipole models by definition can use the correct multipoles and the electrostatic potential from the QM/MM multipoles is much closer than that from the site models to the potential from the QM/MM electron density. Finally, Monte Carlo simulations show that increasing the quadrupole in the soft-sticky dipole-quadrupole-octupole multipole model gives radial distribution functions that are in good agreement with experiment.

  7. Cutaneous water loss and sphingolipids covalently bound to corneocytes in the stratum corneum of house sparrows Passer domesticus. (United States)

    Gu, Yu; Muñoz-Garcia, Agustí; Brown, Johnie C; Ro, Jennifer; Williams, Joseph B


    The barrier to water loss from the skin of birds and mammals is localized in the stratum corneum (SC), the outer layer of the epidermis. The SC consists of corneocytes, each surrounded by a protein envelope, and a lipid compartment, formed by an extracellular matrix of lipids and by lipids covalently bound to the protein envelope. In mammals, covalently bound lipids in the SC consist of omega-hydroxyceramides attached to the outer surface of corneocytes. Evidence suggests that covalently bound lipids in the SC might be crucial for the establishment of a competent permeability barrier. In this study we assessed the composition of covalently bound lipids of the avian SC and their relationship to cutaneous water loss (CWL) in two populations of house sparrows, one living in the deserts of Saudi Arabia and the other in mesic Ohio. Previously, we showed that CWL of adult desert sparrows was 25% lower than that of mesic birds. In the present study we characterize covalently bound lipids of the SC using thin layer chromatography and high performance liquid chromatography coupled with atmospheric pressure Photospray ionization mass spectrometry. Our study is the first to demonstrate the existence of sphingolipids covalently bound to corneocytes in the SC of birds. Although omega-hydroxyceramides occurred in the lipid envelope surrounding corneocytes, the major constituent of the covalently bound lipid envelope in house sparrows was omega-hydroxycerebrosides, ceramides with a hexose molecule attached. Sparrows from Saudi Arabia had more covalently bound cerebrosides, fewer covalently bound ceramides and a lower ceramide to cerebroside ratio than sparrows living in Ohio; these differences were associated with CWL.

  8. Depletion of water molecules during ethanol wet-bonding with etch and rinse dental adhesives

    Energy Technology Data Exchange (ETDEWEB)

    Gregoire, Genevieve, E-mail: [Department of Biomaterials, Faculty of Odontology, University Toulouse III, 31062, Toulouse (France); Sharrock, Patrick [Medical and Spatial Imaging Laboratory, University Toulouse III, Ave. Pompidou, 81104, Castres (France); Delannee, Mathieu [Department of Biomaterials, Faculty of Odontology, University Toulouse III, 31062, Toulouse (France); Delisle, Marie-Bernadette [Faculty of Medicine, University Toulouse III, 31062, Toulouse (France)


    The treatment of demineralized dentin with ethanol has been proposed as a way to improve hydrophobic monomer penetration into otherwise water saturated collagen fibrils. The ethanol rinse is expected to preserve the fibrils from collapsing while optimizing resin constituent infiltration for better long term adhesion. The physico-chemical investigations of demineralized dentin confirmed objectively these working hypotheses. Namely, Differential Scanning Calorimetry (DSC) measurements of the melting point of water molecules pointed to the presence of free and bound water states. Unfreezable water was the main type of water remaining following a rinsing step with absolute ethanol. Two different liquid water phases were also observed by Magic Angle Spinning (MAS) solid state Nuclear magnetic Resonance (NMR) spectroscopy. Infrared spectra of ethanol treated specimens illustrated differences with the fully hydrated specimens concerning the polar carbonyl vibrations. Optical microscopy observations as well as scanning electron microscopy showed an improved dentin-adhesive interface with ethanol wet bonding. The results indicate that water can be confined to strongly bound structural molecules when excess water is removed with ethanol prior to adhesive application. This should preserve collagen from hydrolysis upon aging of the hybrid layer. - Highlights: Black-Right-Pointing-Pointer Non-freezable water exists in demineralized dentine. Black-Right-Pointing-Pointer Free water can be removed by ethanol rinse of the demineralized collagen. Black-Right-Pointing-Pointer Ethanol wet bonding leads to a homogeneous hybrid layer free of defects.

  9. Composition of Phoebe and Iapetus: Bound Water and Possible Deuterated Water (United States)

    Clark, Roger Nelson; Brown, Robert H.; Lytle, Dyer M.; Cruikshank, Dale P.


    Cassini VIMS has obtained spatially resolved 0.35 to 5.1 micron reflectance spectra of Saturn's satellites beginning with the Phoebe fly-by in 2004. We report new discoveries of bound water absorptions on Iapetus and Phoebe, and a new narrow absorption at 3.61 microns thatis strong in Phoebe spectra and trace in Iapetus spectra. The bound water absorption is at 1.96 microns and is consistent with bound water in nano-hematite at cryogenic temperatures that Clark et al (Icarus 2012, v218 p831) used to match the 3-micron absorption in Iapetus dark material spectra. The bound water absorption in nano-hematite has a unique position and shape at least among the materials whose spectra have been measured so far. The new 3.61 micron absorption is not matched by organics, salts or other materials whose spectra have been measured that we can find. The best match so far is a D-O stretch. If so, this enrichment in deuterium may be due to stripping the water and dark material from Phoebe, preferentially leaving a deuterium-enriched surface. Alternatively, if Pheobe is indeed a captured outer solar system object, the source material from which Phoebe was formed may be enriched in deuterium.Some confusing interpretations of VIMS spectra have been due a shift in VIMS wavelengths with time with subsequent degradation of the calibration to radiance and I/F with time. A new calibration has been developed that tracks the time-varying calibration that resulted in patterns in the VIMS I/F calibration. Those patterns masked some spectral features and produced others that were not real. The new calibration fixes these problems, reducing pattern problems by a couple of orders of magnitude. With new tools for querying the growing massive VIMS data, we have averaged many pixels to obtain the highest precision spectra of objects in the Saturn system. Clark et al (JGR 2012) found a triplet at 1.9 microns in Phoebe and Iapetus dark material and attributed the triplet to bound water but could

  10. Bounding Analysis of Drinking Water Health Risks from a Spill of Hydraulic Fracturing Flowback Water. (United States)

    Rish, William R; Pfau, Edward J


    A bounding risk assessment is presented that evaluates possible human health risk from a hypothetical scenario involving a 10,000-gallon release of flowback water from horizontal fracturing of Marcellus Shale. The water is assumed to be spilled on the ground, infiltrates into groundwater that is a source of drinking water, and an adult and child located downgradient drink the groundwater. Key uncertainties in estimating risk are given explicit quantitative treatment using Monte Carlo analysis. Chemicals that contribute significantly to estimated health risks are identified, as are key uncertainties and variables to which risk estimates are sensitive. The results show that hypothetical exposure via drinking water impacted by chemicals in Marcellus Shale flowback water, assumed to be spilled onto the ground surface, results in predicted bounds between 10-10 and 10-6 (for both adult and child receptors) for excess lifetime cancer risk. Cumulative hazard indices (HICUMULATIVE ) resulting from these hypothetical exposures have predicted bounds (5th to 95th percentile) between 0.02 and 35 for assumed adult receptors and 0.1 and 146 for assumed child receptors. Predicted health risks are dominated by noncancer endpoints related to ingestion of barium and lithium in impacted groundwater. Hazard indices above unity are largely related to exposure to lithium. Salinity taste thresholds are likely to be exceeded before drinking water exposures result in adverse health effects. The findings provide focus for policy discussions concerning flowback water risk management. They also indicate ways to improve the ability to estimate health risks from drinking water impacted by a flowback water spill (i.e., reducing uncertainty). © 2017 Society for Risk Analysis.

  11. Ultrafast anisotropy dynamics of water molecules dissolved in acetonitrile

    NARCIS (Netherlands)

    Cringus, Dan; Jansen, Thomas L. C.; Pshenichnikov, Maxim S.; Wiersma, Douwe A.


    Infrared pump-probe experiments are performed on isolated H2O molecules diluted in acetonitrile in the spectral region of the OH stretching vibration. The large separation between water molecules excludes intermolecular interactions, while acetonitrile as a solvent provides substantial hydrogen

  12. On the Several Molecules and Nanostructures of Water

    Directory of Open Access Journals (Sweden)

    Cynthia Kolb Whitney


    Full Text Available This paper investigates the water molecule from a variety of viewpoints. Water can involve different isotopes of Hydrogen and Oxygen, it can form differently shaped isomer molecules, and, when frozen, it occupies space differently than most other substances do. The tool for conducting the investigation of all this is called ‘Algebraic Chemistry’. This tool is a quantitative model for predicting the energy budget for all sorts of changes between different ionization states of atoms that are involved in chemical reactions and in changes of physical state. The model is based on consistent patterns seen in empirical data about ionization potentials, together with rational scaling laws that can interpolate and extrapolate for situations where no data are available. The results of the investigation of the water molecule include comments, both positive and negative, about technologies involving heavy water, poly water, Brown’s gas, and cold fusion.

  13. Mechanistic pathway for controlled extraction of guest molecule bound to herring sperm DNA using α-cyclodextrin (United States)

    Jaffer, S. Syed; Ghosh, Prasun; Purkayastha, Pradipta


    trans-2-[4-(Dimethylamino)styryl]benzothiazole (DMASBT) is known to have dual emitting states where the locally excited (LE) state is responsible for fluorescence in less polar environment and in polar milieu fluorescence is from the twisted intramolecular charge transfer (TICT) state. This compound also undergoes minor groove binding to herring sperm DNA (hsDNA) evidenced by the absorption spectra before and after the binding process and an effect on DMASBT fluorescence by an anionic quencher. The binding occurs efficiently in a 1:1 manner, i.e. one guest molecule binds to one site on the hsDNA. Instead of following the DNA twist, the aromatic part seems to project outward. Thus, the bound molecule can be successfully extracted out from the DNA in a controlled way by the hydrophobic cavity of α-cyclodextrin (α-CD). The extraction starts even with a low concentration of α-CD and increases as the concentration is increased. Absorption, steady-state and time resolved fluorescence spectroscopic methods have been employed to explore the mechanistic pathway of binding of DMASBT to hsDNA. The mechanistic approach toward controlled extraction of the guest molecules from hsDNA by α-CD is reported and is expected to serve a significant purpose in treatment of drug overdose.

  14. Target molecules of food phytochemicals: food science bound for the next dimension. (United States)

    Murakami, Akira; Ohnishi, Kohta


    Phytochemicals are generally defined as secondary metabolites in plants that play crucial roles in their adaptation to a variety of environmental stressors. There is a great body of compelling evidence showing that these metabolites have pronounced potentials for regulating and modulating human health and disease onset, as shown by both experimental and epidemiological approaches. Concurrently, enormous efforts have been made to elucidate the mechanism of actions underlying their biological and physiological functions. For example, the pioneering work of Tachibana et al. uncovered the receptor for (-)-epigallocatechin-3-gallate (EGCg) as the 67 kDa laminin receptor, which was shown to partially mediate the functions of EGCg, such as anti-inflammatory, anti-allergic, and anti-proliferative activities. Thereafter, several protein kinases were identified as binding proteins of flavonoids, including myricetin, quercetin, and kaempferol. Isothiocyanates, sulfur-containing phytochemicals present in cruciferous plants, are well known to target Keap1 for activating the transcription factor Nrf2 for inducing self-defensive and anti-oxidative gene expression. In addition, we recently identified CD36 as a cell surface receptor for ursolic acid, a triterpenoid ubiquitously occurring in plants. Importantly, the above mentioned target proteins are indispensable for phytochemicals to exhibit, at least in part, their bioactivities. Nevertheless, it is reasonable to assume that some of the activities and potential toxicities of metabolites are exerted via their interactions with unidentified, off-target proteins. This notion may be supported by the fact that even rationally designed drugs occasionally display off-target effects and induce unexpected outcomes, including toxicity. Here we update the current status and future directions of research related to target molecules of food phytochemicals.

  15. Bound water in soybean seed and its relation to respiration and imbibitional damage. (United States)

    Vertucci, C W; Leopold, A C


    In an attempt to understand the initial stage of seed imbibition-the wetting stage-we have examined water binding in dry soybean cotyledon tissue using water sorption isotherm curves. The sorption isotherms show three levels of water affinity: a region of strongly bound water at moisture contents below 8%, a region of weakly bound water at moisture contents between 8 and 24%, and a region of very loosely bound water at contents greater than 24%. The enthalpies of the water binding for the three sectors were -6 to -12.5, about -2.5, and about -0.5 kilocalories per mole water, respectively.The degree of physiological activity in the tissue reflects the level of water binding. O(2) consumption is first detectable in the second region of water affinity (8-24% water), and increases dramatically with increasing water content above about 24%. Damage due to imbibing water is greatest when initial seed moisure contents are in the region of strongest water binding. Damage is lessened and finally absent when seed moisture contents are increased to the second and then to the third level of water affinity.

  16. Computational modeling of chemical reactions and interstitial growth and remodeling involving charged solutes and solid-bound molecules. (United States)

    Ateshian, Gerard A; Nims, Robert J; Maas, Steve; Weiss, Jeffrey A


    Mechanobiological processes are rooted in mechanics and chemistry, and such processes may be modeled in a framework that couples their governing equations starting from fundamental principles. In many biological applications, the reactants and products of chemical reactions may be electrically charged, and these charge effects may produce driving forces and constraints that significantly influence outcomes. In this study, a novel formulation and computational implementation are presented for modeling chemical reactions in biological tissues that involve charged solutes and solid-bound molecules within a deformable porous hydrated solid matrix, coupling mechanics with chemistry while accounting for electric charges. The deposition or removal of solid-bound molecules contributes to the growth and remodeling of the solid matrix; in particular, volumetric growth may be driven by Donnan osmotic swelling, resulting from charged molecular species fixed to the solid matrix. This formulation incorporates the state of strain as a state variable in the production rate of chemical reactions, explicitly tying chemistry with mechanics for the purpose of modeling mechanobiology. To achieve these objectives, this treatment identifies the specific theoretical and computational challenges faced in modeling complex systems of interacting neutral and charged constituents while accommodating any number of simultaneous reactions where reactants and products may be modeled explicitly or implicitly. Several finite element verification problems are shown to agree with closed-form analytical solutions. An illustrative tissue engineering analysis demonstrates tissue growth and swelling resulting from the deposition of chondroitin sulfate, a charged solid-bound molecular species. This implementation is released in the open-source program FEBio ( ). The availability of this framework may be particularly beneficial to optimizing tissue engineering culture systems by examining the

  17. Anisotropic diffusion of water molecules in hydroxyapatite nanopores (United States)

    Prakash, Muthuramalingam; Lemaire, Thibault; Caruel, Matthieu; Lewerenz, Marius; de Leeuw, Nora H.; Di Tommaso, Devis; Naili, Salah


    New insights into the dynamical properties of water in hydroxyapatite (HAP) nanopores, a model system for the fluid flow within nanosize spaces inside the collagen-apatite structure of bone, were obtained from molecular dynamics simulations of liquid water confined between two parallel HAP surfaces of different sizes (20 Å ≤ H ≤ 240 Å). Calculations were conducted using a core-shell interatomic potential for HAP together with the extended simple point charge model for water. This force field gives an activation energy for water diffusion within HAP nanopores that is in excellent agreement with available experimental data. The dynamical properties of water within the HAP nanopores were quantified in terms of the second-order water diffusion tensor. Results indicate that water diffuses anisotropically within the HAP nanopores, with the solvent molecules moving parallel to the surface twice as fast as the perpendicular direction. This unusual dynamic behaviour is linked to the strong polarizing effect of calcium ions, and the synergic interactions between the water molecules in the first hydration layer of HAP with the calcium, hydroxyl, and phosphate ions, which facilitates the flow of water molecules in the directions parallel to the HAP surface.

  18. Unprecedentedly rapid transport of single-file rolling water molecules (United States)

    Qiu, Tong; Huang, Ji-Ping


    The realization of rapid and unidirectional single-file water-molecule flow in nanochannels has posed a challenge to date. Here, we report unprecedentedly rapid unidirectional single-file water-molecule flow under a translational terahertz electric field, which is obtained by developing a Debye doublerelaxation theory. In addition, we demonstrate that all the single-file molecules undergo both stable translation and rotation, behaving like high-speed train wheels moving along a railway track. Independent molecular dynamics simulations help to confirm these theoretical results. The mechanism involves the resonant relaxation dynamics of H and O atoms. Further, an experimental demonstration is suggested and discussed. This work has implications for the design of high-efficiency nanochannels or smaller nanomachines in the field of nanotechnology, and the findings also aid in the understanding and control of water flow across biological nanochannels in biology-related research.

  19. Rotovibrational states of the water molecule on the sun. (United States)

    Leite, Bruno S; Bastos, Cristiano C; Pavão, Antonio C


    The infrared spectrum of water observed in sunspots is complex and dense, with bands separated by approximately 0.01 cm-1. For top asymmetrical molecules, there is no theoretical approach that allows for the calculation of rotovibrational energy with such precision. Experimentally derived rotovibracional energy levels of water at high temperatures combined with variational calculations have been used for the band assignments. These energy levels are employed to refine the analysis of a small portion of the infrared absorption spectrum. Such procedure has allowed for the identification of additional 55 bands to the 70 already identified as rotovibrational transitions of the water molecule. Our new assignments, which include pure and cross transitions, offer additional evidence of the existence of water on the sun, but above all they illustrate the complexity of the solar spectrum that involves states with higher levels of rotational excitation. Given the conditions on the sun, more molecules of water would occur in excited electronic states, which include apolar and paramagnetic states, generating intense bands in the spectrum. Since there is an analytical solution for the rotovibrational transitions of linear molecules, we were able to identify 16 bands relative to the excited electronic states 1B2 and 3A1 in the sunspot spectrum. Density functional B3LYP/AUG-cc-pVTZ calculations of the electric and magnetic dipole are employed to discuss some consequences of the presence of excited states of water in the dynamics of sunspots and solar magnetic field.

  20. Balancing Waste Water Treatment Plant Load Using Branch and Bound

    NARCIS (Netherlands)

    van Nooijen, R.R.P.; Kolechkina, A.G.


    The problem of smoothing dry weather inflow variations for
    a Waste Water Treatment Plant (WWTP) that receives sewage from
    multiple mixed sewer systems is presented, together with a first rough
    solution algorithm. A simplification followed by a naive translation into
    a zero-one linear

  1. Stable Isotope Analysis of Water Indicates that Mixing Occurs between Mobile and Tightly-Bound Soil Water (United States)

    Vargas, A. I.; Schaffer, B.; Yuhong, L.; Sternberg, L. O.


    Stable oxygen (δ18O) and hydrogen (δ2H) isotope composition of precipitation, soil and plants have been studied over the years to understand the mechanism of soil water movement and the depth of plant water uptake in the soil water profile. Recent studies have suggested that in soil during the wet season, tightly bound water does not mix with mobile water but is retained in the soil until the dry season when it is taken up by plants via the force of transpiration. To test this, we sampled δ18O and δ2H in plant stems as a proxy for wet season mobile water and dry season bound water in two types of soils to determine if mixing occurs between mobile and tightly bound soil water. Plastic pots were filled with clay or very gravelly loam soil and a Persea americana tree was planted in each pot. Soil in each pot was first saturated with tap water to fully label the bound water with the isotopic identity of tap water and then fully saturated with either tap water (T) or isotopically-enriched pool water (P) and covered with white polyethylene to prevent evaporation. After saturating the soil, δ18O and δ2H of water draining from each pot were similar to those of water added to each pot for both the T and P treatments. For each treatment, δ18O and δ2H in plant stems were sampled 2-3 days after soil was initially saturated (simulated wet season; soil tension 80.0 kPa). During the "dry season", there was a significant difference between T and P treatments for δ18O and δ2H in plant stems, indicating that bound water accessed by plants in the P treatment did not retain the tap water label and mixing occurred between mobile and bound water in the soil. Comparing P-T in the wet season with P-T in the dry season indicated that as much as 95% of water freely exchanged between the mobile and bound components of the soil. This is contrary to recent studies suggesting that no mixing occurs.

  2. On the polarity of buckminsterfullerene with a water molecule inside. (United States)

    Ensing, Bernd; Costanzo, Francesca; Silvestrelli, Pier Luigi


    Since the recent achievement of Kurotobi and Murata to capture a water molecule in a C(60) fullerene (Science 2011, 333, 613), there has been a debate about the properties of this H(2)O@C(60) complex. In particular, the polarity of the complex, which is thought to be underlying the easy separation of H(2)O@C(60) from the empty fullerene by HPLC, was calculated and found to be almost equal to that of an isolated water molecule. Here we present our detailed analysis of the charge distribution of the water-encapsulated C(60) complex, which shows that the polarity of the complex is, with 0.5 ± 0.1 D, indeed substantial, but significantly smaller than that of H(2)O. This may have important implications for the aim to design water-soluble and biocompatible fullerenes.

  3. On the polarity of buckminsterfullerene with a water molecule inside

    NARCIS (Netherlands)

    Ensing, B.; Costanzo, F.; Silvestrelli, P.L.


    Since the recent achievement of Kurotobi and Murata to capture a water molecule in a C60 fullerene (Science2011, 333, 613), there has been a debate about the properties of this H2O@C60 complex. In particular, the polarity of the complex, which is thought to be underlying the easy separation of

  4. Electrostatic deflection of the water molecule: A fundamental asymmetric rotor.

    NARCIS (Netherlands)

    Moro, M.J.; Bulthuis, J.; Heinrich, J.; Kresin, V. V.


    An inhomogeneous electric field is used to study the deflection of a supersonic beam of water molecules. The deflection profiles show strong broadening accompanied by a small net displacement towards higher electric fields. The profiles are in excellent agreement with a calculation of rotational

  5. Calculating pure rotational transitions of water molecule with a ...

    Indian Academy of Sciences (India)

    Abstract. We have calculated pure rotational transitions of water molecule from a kinetic energy operator (KEO) with the z-axis perpendicular to the molecular plane. We have used rotational basis functions which are linear combinations of symmetric top functions so that all matrix elements are real. The calculated spectra ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Goble, J.H. Jr.


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

  7. Quantitative determination of bound water in cardboard by measurement of dielectric permittivity (United States)

    Ben Ayoub, M. W.; Georgin, E.; Rochas, J. F.; Hubert, S.; Aro, R.; Neves, L.; Sabouroux, P.


    In this study we investigated the complex dielectric permittivity of cardboard with different water contents using a coaxial transmission/reflection technique from 10 MHz to 1.5 GHz. A relaxation process was analyzed to identify the bonding forms that exist in cardboard; this analysis was accompanied by a selective direct thermo-coulometric method. Two different types of bonding of water are found in cardboard (free and bound water) and both can be eliminated at 105 °C. The novelty of this work is the experimental correlation between the relaxation frequency situated in the radio-frequency band and the fraction of bound water in cardboard with a low water content.

  8. Towards a kinetic energy density functional for the water molecule (United States)

    Akin-Ojo, Omololu; Shittu, Doyin

    Development of an accurate kinetic energy kinetic energy density functional (KEDF) is a holy grail. In this work, local KEDFS are parameterized for the water molecule in order to reproduce Kohn-Sham density functional theory (KS-DFT) results. Energies, forces and dipole moments from these KEDFs are presented. Problems with the convergence of the self-consistent-field (SCF) calculations are discussed together with possible solutions. and: Theoretical and Applied Physics Dept. African Univ. of Science and Technology (AUST) Abuja, Nigeria.

  9. Electron and positron collisions with polar molecules: studies with the benchmark water molecule

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Rui; Tennyson, Jonathan [Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT (United Kingdom); Faure, Alexandre [Laboratoire d' Astrophysique, UMR 5571 CNRS, Universite Joseph-Fourier, BP 53, 38041 Grenoble cedex 09 (France)], E-mail:


    It is difficult to measure low-energy cross sections for collisions of charged particles with strongly dipolar systems since the magnitude of such cross sections is completely dominated by collisions in the forward direction. Theoretically, it is possible to account for the strong forward scattering using the Born approximation but the procedure for combining Born 'top-up' with the more sophisticated treatments required to treat the scattering in other directions is not unique. This comment describes recent progress in describing both electron and positron collisions with polar molecules taking the important water molecule as a benchmark. Previous calculations on electron water at collision energies below 7 eV are compared with new experiments. Positron water studies up to 10 eV are re-analysed based on given experimental acceptance profiles, which depend on the details of the apparatus and method used in the measurements. It is suggested that theory is capable of giving reliable results for elastic and rotationally inelastic electron/positron collisions with strongly dipolar species.

  10. The spontaneous synchronized dance of pairs of water molecules

    Energy Technology Data Exchange (ETDEWEB)

    Roncaratti, Luiz F. [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy); Instituto de Física, Universidade de Brasília, 70910-900 Brasília (Brazil); Cappelletti, David, E-mail:; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy)


    Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

  11. The spontaneous synchronized dance of pairs of water molecules (United States)

    Roncaratti, Luiz F.; Cappelletti, David; Pirani, Fernando


    Molecular beam scattering experiments have been performed to study the effect of long-range anisotropic forces on the collision dynamics of two small polar molecules. The main focus of this paper is on water, but also ammonia and hydrogen sulphide molecules have been investigated, and some results will be anticipated. The intermolecular distances mainly probed are of the order of 1 nm and therefore much larger than the molecular dimensions. In particular, we have found that the natural electric field gradient, generated by different spatial orientations of the permanent electric dipoles, is able to promote the transformation of free rotations into coupled pendular states, letting the molecular partners involved in the collision complex swinging to and fro around the field direction. This long-ranged concerted motion manifested itself as large increases of the magnitude of the total integral cross section. The experimental findings and the theoretical treatment developed to shed light on the details of the process suggest that the transformation from free rotations to pendular states depends on the rotational level of both molecules, on the impact parameter, on the relative collision velocity, on the dipole moment product and occurs in the time scale of picoseconds. The consequences of this intriguing phenomenon may be important for the interpretation and, in perspective, for the control of elementary chemical and biological processes, given by polar molecules, ions, and free radicals, occurring in several environments under various conditions.

  12. Bound water at protein-protein interfaces: partners, roles and hydrophobic bubbles as a conserved motif.

    Directory of Open Access Journals (Sweden)

    Mostafa H Ahmed

    Full Text Available There is a great interest in understanding and exploiting protein-protein associations as new routes for treating human disease. However, these associations are difficult to structurally characterize or model although the number of X-ray structures for protein-protein complexes is expanding. One feature of these complexes that has received little attention is the role of water molecules in the interfacial region.A data set of 4741 water molecules abstracted from 179 high-resolution (≤ 2.30 Å X-ray crystal structures of protein-protein complexes was analyzed with a suite of modeling tools based on the HINT forcefield and hydrogen-bonding geometry. A metric termed Relevance was used to classify the general roles of the water molecules.The water molecules were found to be involved in: a (bridging interactions with both proteins (21%, b favorable interactions with only one protein (53%, and c no interactions with either protein (26%. This trend is shown to be independent of the crystallographic resolution. Interactions with residue backbones are consistent for all classes and account for 21.5% of all interactions. Interactions with polar residues are significantly more common for the first group and interactions with non-polar residues dominate the last group. Waters interacting with both proteins stabilize on average the proteins' interaction (-0.46 kcal mol(-1, but the overall average contribution of a single water to the protein-protein interaction energy is unfavorable (+0.03 kcal mol(-1. Analysis of the waters without favorable interactions with either protein suggests that this is a conserved phenomenon: 42% of these waters have SASA ≤ 10 Å(2 and are thus largely buried, and 69% of these are within predominantly hydrophobic environments or "hydrophobic bubbles". Such water molecules may have an important biological purpose in mediating protein-protein interactions.

  13. Geometry-dependent atomic multipole models for the water molecule. (United States)

    Loboda, O; Millot, C


    Models of atomic electric multipoles for the water molecule have been optimized in order to reproduce the electric potential around the molecule computed by ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set. Different models of increasing complexity, from atomic charges up to models containing atomic charges, dipoles, and quadrupoles, have been obtained. The geometry dependence of these atomic multipole models has been investigated by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For several models, the atomic multipole components have been fitted as a function of the geometry by a Taylor series of fourth order in monomer coordinate displacements.

  14. Solution 1H, 15N NMR spectroscopic characterization of substrate-bound, cyanide-inhibited human heme oxygenase: water occupation of the distal cavity. (United States)

    Li, Yiming; Syvitski, Ray T; Auclair, Karine; Ortiz de Montellano, Paul; La Mar, Gerd N


    A solution NMR spectroscopic study of the cyanide-inhibited, substrate-bound complex of uniformly (15)N-labeled human heme oxygenase, hHO, has led to characterization of the active site with respect to the nature and identity of strong hydrogen bonds and the occupation of ordered water molecules within both the hydrogen bonding network and an aromatic cluster on the distal side. [(1)H-(15)N]-HSQC spectra confirm the functionalities of several key donors in particularly robust H-bonds, and [(1)H-(15)N]HSQC-NOESY spectra lead to the identification of three additional robust H-bonds, as well as the detection of two more relatively strong H-bonds whose identities could not be established. The 3D NMR experiments provided only a modest, but important, extension of assignments because of the loss of key TOCSY cross-peaks due to the line broadening from a dynamic heterogeneity in the active site. Steady-state NOEs upon saturating the water signal locate nine ordered water molecules in the immediate vicinity of the H-bond donors, six of which are readily identified in the crystal structure. The additional three are positioned in available spaces to account for the observed NOEs. (15)N-filtered steady-state NOEs upon saturating the water resonances and (15)N-filtered NOESY spectra demonstrate significant negative NOEs between water molecules and the protons of five aromatic rings. Many of the NOEs can be rationalized by water molecules located in the crystal structure, but strong water NOEs, particularly to the rings of Phe47 and Trp96, demand the presence of at least an additional two immobilized water molecules near these rings. The H-bond network appears to function to order water molecules to provide stabilization for the hydroperoxy intermediate and to serve as a conduit to the active site for the nine protons required per HO turnover.

  15. Influence of water on the properties of an Au/Mpy/Pd metal/molecule/metal junction

    Directory of Open Access Journals (Sweden)

    Jan Kučera


    Full Text Available The geometric and electronic structure of the metal–molecule interface in metal/molecule/metal junctions is of great interest since it affects the functionality of such units in possible nanoelectronic devices. We have investigated the interaction between water and a palladium monolayer of a Au(111/4-mercaptopyridine/Pd junction by means of DFT calculations. A relatively strong bond between water and the palladium monolayer of the Au/Mpy/Pd complex is observed via a one-fold bond between the oxygen atom of the water molecule and a Pd atom. An isolated H2O molecule adsorbs preferentially in a flat-lying geometry on top of a palladium atom that is at the same time also bound to the nitrogen atom of a Mpy molecule of the underlying self-assembled monolayer. The electronic structure of these Pd atoms is considerably modified which is reflected in a reduced local density of states at the Fermi energy. At higher coverages, water can be arranged in a hexagonal ice-like bilayer structure in analogy to water on bulk metal surfaces, but with a much stronger binding which is dominated by O–Pd bonds.

  16. The role of free and bound water in irradiation preservation: Free radical damage as a function of the physical state of water (United States)

    Wedemeyer, Gary; Dollar, A.M.


    English sole fillets previously equilibrated with aqueous 0.1% cysteine were dehydrated by three methods to moisture levels ranging from 2 to 72%. Model systems using cellulose to replace the fish tissue were also used. The samples were irradiated at 1 Mrad in an air, nitrogen, or oxygen atmosphere. The destruction of −SH groups was measured and related to the amount and physical state of the tissue water. As free water was removed, destruction steadily increased, reaching a maximum at about 20% moisture. Destruction decreased markedly at moisture levels below 10%, and calorimetric measurements confirmed that 10% moisture was about the level of bound water in this species. These data suggest that dehydration favors the reaction of solute molecules with free radicals formed in the free water of muscle cells. At moisture levels greater than about 20%, simple free radical recombination is more likely than reaction with solute molecules, while below 20% moisture the reverse is true. The calculated α values support this conclusion, as do the results from model systems using cellulose.

  17. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

    Popadic, A.; Praprotnik, M.; Koumoutsakos, P.


    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently by continuum flow...

  18. An upper-bound assessment of the benefits of reducing perchlorate in drinking water. (United States)

    Lutter, Randall


    The Environmental Protection Agency plans to issue new federal regulations to limit drinking water concentrations of perchlorate, which occurs naturally and results from the combustion of rocket fuel. This article presents an upper-bound estimate of the potential benefits of alternative maximum contaminant levels for perchlorate in drinking water. The results suggest that the economic benefits of reducing perchlorate concentrations in drinking water are likely to be low, i.e., under $2.9 million per year nationally, for several reasons. First, the prevalence of detectable perchlorate in public drinking water systems is low. Second, the population especially sensitive to effects of perchlorate, pregnant women who are moderately iodide deficient, represents a minority of all pregnant women. Third, and perhaps most importantly, reducing exposure to perchlorate in drinking water is a relatively ineffective way of increasing iodide uptake, a crucial step linking perchlorate to health effects of concern. © 2014 Society for Risk Analysis.

  19. Using a Water Balance Model to Bound Potential Irrigation Development in the Upper Blue Nile Basin (United States)

    Jain Figueroa, A.; McLaughlin, D.


    The Grand Ethiopian Renaissance Dam (GERD), on the Blue Nile is an example of water resource management underpinning food, water and energy security. Downstream countries have long expressed concern about water projects in Ethiopia because of possible diversions to agricultural uses that could reduce flow in the Nile. Such diversions are attractive to Ethiopia as a partial solution to its food security problems but they could also conflict with hydropower revenue from GERD. This research estimates an upper bound on diversions above the GERD project by considering the potential for irrigated agriculture expansion and, in particular, the availability of water and land resources for crop production. Although many studies have aimed to simulate downstream flows for various Nile basin management plans, few have taken the perspective of bounding the likely impacts of upstream agricultural development. The approach is to construct an optimization model to establish a bound on Upper Blue Nile (UBN) agricultural development, paying particular attention to soil suitability and seasonal variability in climate. The results show that land and climate constraints impose significant limitations on crop production. Only 25% of the land area is suitable for irrigation due to the soil, slope and temperature constraints. When precipitation is also considered only 11% of current land area could be used in a way that increases water consumption. The results suggest that Ethiopia could consume an additional 3.75 billion cubic meters (bcm) of water per year, through changes in land use and storage capacity. By exploiting this irrigation potential, Ethiopia could potentially decrease the annual flow downstream of the UBN by 8 percent from the current 46 bcm/y to the modeled 42 bcm/y.

  20. Adsorption of glyoxal molecules on atmospheric water ice nanoparticles (United States)

    Schrems, O.; Ignatov, S. K.; Gadzhiev, O. B.


    Ice nanoparticles play an important role in physics and chemistry of the Earth atmosphere. Knowledge about the uptake and incorporation of atmospheric trace gases in ice particles as well as their interactions with water molecules is very important for the understanding of processes at the air/ice interface. The interaction of the atmospheric trace gases with atmospheric nanoparticles is also an important issue for the development of modern physicochemical models. Usually, the interactions between trace gases and small particles considered theoretically apply small-size model complexes or the surface models representing only fragments of the ideal surface. In this study we used modern quantum chemical methods to study the interaction of glyoxal molecules (HCOCHO) with the full-size particles of crystalline water ice of nanoscale size. Glyoxal, the simplest a-dicarbonyl, is an atmospheric relevant carbonyl compound and is formed as product in the photooxidation of simple volatile organic compounds in air in the presence of NOx. The ice particles consisting of 48, 72, and 216 water molecules with a distorted structure of hexagonal water ice Ih were studied using the new SCC-DFTBA method combining well the advantages of the DFT theory and semiempirical methods of quantum chemistry. Typical sizes of the ice particles were in the range 1.5-2.6 nm. The glyoxal molecules were coordinated on different sites of the nanoparticles corresponding to different ice Ih crystal planes: (0001), (10-10), (11-20). The structure of coordination complexes, their vibrational frequencies, the corresponding adsorption energies and thermodynamic parameters (the enthalpy and the Gibbs free energy of adsorption) were evaluated using the full optimization followed by the frequency calculations. Additionally, the different modes of incorporation of the glyoxal molecules into the ice particles were considered and the corresponding structural and energetic parameters were evaluated. The

  1. Thermodynamics of water condensation on a primary marine aerosol coated by surfactant organic molecules. (United States)

    Djikaev, Yuri S; Ruckenstein, Eli


    A large subset of primary marine aerosols can be initially (immediately upon formation) treated using an "inverted micelle" model. We study the thermodynamics of heterogeneous water condensation on such a marine aerosol. Its hydrophobic organic coating can be processed by chemical reactions with atmospheric species; this enables the marine aerosol to serve as a nucleating center for water condensation. The most probable pathway of such "aging" involves atmospheric hydroxyl radicals that abstract hydrogen atoms from organic molecules coating the aerosol (first step), the resulting radicals being quickly oxidized by ubiquitous atmospheric oxygen molecules to produce surface-bound peroxyl radicals (second step). Taking these two reactions into account, we derive an expression for the free energy of formation of an aqueous droplet on a marine aerosol. The model is illustrated by numerical calculations. The results suggest that the formation of aqueous droplets on marine aerosols is most likely to occur via Köhler activation rather than via nucleation. The model allows one to determine the threshold parameters necessary for the Köhler activation of such aerosols. Numerical results also corroborate previous suggestions that one can omit some chemical species of aerosols (and other details of their chemical composition) in investigating aerosol effects on climate.

  2. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials (United States)

    Liao, Rui-Jin; Zhu, Meng-Zhao; Yang, Li-Jun; Zhou, Xin; Gong, Chun-Yan


    Moisture is an important factor that influences the safe operation of transformers. In this study, molecular dynamics was employed to investigate the diffusion behavior of water molecules in the oil-paper insulation materials of transformers. Two oil-cellulose models were built. In the first model, water molecules were initially distributed in oil, and in the second model, water molecules were distributed in cellulose. The non-bonding energies of interaction between water molecules and oil, and between water molecules and cellulose, were calculated by the Dreiding force field. The interaction energy was found to play a dominant role in influencing the equilibrium distribution of water molecules. The radial direction functions of water molecules toward oil and cellulose indicate that the hydrogen bonds between water molecules and cellulose are sufficiently strong to withstand the operating temperature of the transformer. Mean-square displacement analysis of water molecules diffusion suggests that water molecules initially distributed in oil showed anisotropic diffusion; they tended to diffuse toward cellulose. Water molecules initially distributed in cellulose diffused isotropically. This study provides a theoretical contribution for improvements in online monitoring of water in transformers, and for subsequent research on new insulation materials.

  3. Distribution of binding energies of a water molecule in the water liquid-vapor interface

    Energy Technology Data Exchange (ETDEWEB)

    Chempath, Shaji [Los Alamos National Laboratory; Pratt, Lawrence R [TULANE UNIV


    Distributions of binding energies of a water molecule in the water liquid-vapor interface are obtained on the basis of molecular simulation with the SPC/E model of water. These binding energies together with the observed interfacial density profile are used to test a minimally conditioned Gaussian quasi-chemical statistical thermodynamic theory. Binding energy distributions for water molecules in that interfacial region clearly exhibit a composite structure. A minimally conditioned Gaussian quasi-chemical model that is accurate for the free energy of bulk liquid water breaks down for water molecules in the liquid-vapor interfacial region. This breakdown is associated with the fact that this minimally conditioned Gaussian model would be inaccurate for the statistical thermodynamics of a dilute gas. Aggressive conditioning greatly improves the performance of that Gaussian quasi-chemical model. The analogy between the Gaussian quasi-chemical model and dielectric models of hydration free energies suggests that naive dielectric models without the conditioning features of quasi-chemical theory will be unreliable for these interfacial problems. Multi-Gaussian models that address the composite nature of the binding energy distributions observed in the interfacial region might provide a mechanism for correcting dielectric models for practical applications.

  4. Rapid and accurate prediction and scoring of water molecules in protein binding sites.

    Directory of Open Access Journals (Sweden)

    Gregory A Ross

    Full Text Available Water plays a critical role in ligand-protein interactions. However, it is still challenging to predict accurately not only where water molecules prefer to bind, but also which of those water molecules might be displaceable. The latter is often seen as a route to optimizing affinity of potential drug candidates. Using a protocol we call WaterDock, we show that the freely available AutoDock Vina tool can be used to predict accurately the binding sites of water molecules. WaterDock was validated using data from X-ray crystallography, neutron diffraction and molecular dynamics simulations and correctly predicted 97% of the water molecules in the test set. In addition, we combined data-mining, heuristic and machine learning techniques to develop probabilistic water molecule classifiers. When applied to WaterDock predictions in the Astex Diverse Set of protein ligand complexes, we could identify whether a water molecule was conserved or displaced to an accuracy of 75%. A second model predicted whether water molecules were displaced by polar groups or by non-polar groups to an accuracy of 80%. These results should prove useful for anyone wishing to undertake rational design of new compounds where the displacement of water molecules is being considered as a route to improved affinity.

  5. Single-molecule studies reveal a hidden key step in the activation mechanism of membrane-bound protein kinase C-α. (United States)

    Ziemba, Brian P; Li, Jianing; Landgraf, Kyle E; Knight, Jefferson D; Voth, Gregory A; Falke, Joseph J


    Protein kinase C-α (PKCα) is a member of the conventional family of protein kinase C isoforms (cPKCs) that regulate diverse cellular signaling pathways, share a common activation mechanism, and are linked to multiple pathologies. The cPKC domain structure is modular, consisting of an N-terminal pseudosubstrate peptide, two inhibitory domains (C1A and C1B), a targeting domain (C2), and a kinase domain. Mature, cytoplasmic cPKCs are inactive until they are switched on by a multistep activation reaction that occurs largely on the plasma membrane surface. Often, this activation begins with a cytoplasmic Ca(2+) signal that triggers C2 domain targeting to the plasma membrane where it binds phosphatidylserine (PS) and phosphatidylinositol 4,5-bisphosphate (PIP2). Subsequently, the appearance of the signaling lipid diacylglycerol (DAG) activates the membrane-bound enzyme by recruiting the inhibitory pseudosubstrate and one or both C1 domains away from the kinase domain. To further investigate this mechanism, this study has utilized single-molecule total internal reflection fluorescence microscopy (TIRFM) to quantitate the binding and lateral diffusion of full-length PKCα and fragments missing specific domain(s) on supported lipid bilayers. Lipid binding events, and events during which additional protein is inserted into the bilayer, were detected by their effects on the equilibrium bound particle density and the two-dimensional diffusion rate. In addition to the previously proposed activation steps, the findings reveal a major, undescribed, kinase-inactive intermediate. On bilayers containing PS or PS and PIP2, full-length PKCα first docks to the membrane via its C2 domain, and then its C1A domain embeds itself in the bilayer even before DAG appears. The resulting pre-DAG intermediate with membrane-bound C1A and C2 domains is the predominant state of PKCα while it awaits the DAG signal. The newly detected, membrane-embedded C1A domain of this pre-DAG intermediate

  6. Dynamics of water molecules in the active-site cavity of human cytochromes P450

    DEFF Research Database (Denmark)

    Rydberg, Patrik; Rod, Thomas Holm; Olsen, Lars


    We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot. In the...... molecules close to the heme iron ion in these simulations of the high-spin ferric state (the average distance to the closest water molecule is 3.3-5 A), and there are few ordered water molecules in the active sites, none of which is conserved in all proteins.......We have studied the dynamics of water molecules in six crystal structures of four human cytochromes P450, 2A6, 2C8, 2C9, and 3A4, with molecular dynamics simulations. In the crystal structures, only a few water molecules are seen and the reported sizes of the active-site cavity vary a lot....... In the simulations, the cavities are completely filled with water molecules, although with approximately 20% lower density than in bulk water. The 2A6 protein differs from the other three in that it has a very small cavity with only two water molecules and no exchange with the surroundings. The other three proteins...

  7. Building better water models using the shape of the charge distribution of a water molecule (United States)

    Dharmawardhana, Chamila Chathuranga; Ichiye, Toshiko


    The unique properties of liquid water apparently arise from more than just the tetrahedral bond angle between the nuclei of a water molecule since simple three-site models of water are poor at mimicking these properties in computer simulations. Four- and five-site models add partial charges on dummy sites and are better at modeling these properties, which suggests that the shape of charge distribution is important. Since a multipole expansion of the electrostatic potential describes a charge distribution in an orthogonal basis set that is exact in the limit of infinite order, multipoles may be an even better way to model the charge distribution. In particular, molecular multipoles up to the octupole centered on the oxygen appear to describe the electrostatic potential from electronic structure calculations better than four- and five-site models, and molecular multipole models give better agreement with the temperature and pressure dependence of many liquid state properties of water while retaining the computational efficiency of three-site models. Here, the influence of the shape of the molecular charge distribution on liquid state properties is examined by correlating multipoles of non-polarizable water models with their liquid state properties in computer simulations. This will aid in the development of accurate water models for classical simulations as well as in determining the accuracy needed in quantum mechanical/molecular mechanical studies and ab initio molecular dynamics simulations of water. More fundamentally, this will lead to a greater understanding of how the charge distribution of a water molecule leads to the unique properties of liquid water. In particular, these studies indicate that p-orbital charge out of the molecular plane is important.

  8. Chemical reactions of water molecules on Ru(0001) induced by selective excitation of vibrational modes

    Energy Technology Data Exchange (ETDEWEB)

    Mugarza, Aitor; Shimizu, Tomoko K.; Ogletree, D. Frank; Salmeron, Miquel


    Tunneling electrons in a scanning tunneling microscope were used to excite specific vibrational quantum states of adsorbed water and hydroxyl molecules on a Ru(0 0 0 1) surface. The excited molecules relaxed by transfer of energy to lower energy modes, resulting in diffusion, dissociation, desorption, and surface-tip transfer processes. Diffusion of H{sub 2}O molecules could be induced by excitation of the O-H stretch vibration mode at 445 meV. Isolated molecules required excitation of one single quantum while molecules bonded to a C atom required at least two quanta. Dissociation of single H{sub 2}O molecules into H and OH required electron energies of 1 eV or higher while dissociation of OH required at least 2 eV electrons. In contrast, water molecules forming part of a cluster could be dissociated with electron energies of 0.5 eV.

  9. A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC50 determination (United States)

    Yin, Liusong; Stern, Lawrence J.


    HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC50 (change in 50% inhibition concentration) value. We simulated binding competition reactions of peptides with various intrinsic and DM-catalyzed kinetic parameters and found that under a wide range of conditions the delta-IC50 value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC50 is comparable to that measured by traditional off-rate assay for peptides with known DM-susceptibility hierarchy. The major advantage of this method is that it allows simple, fast and high throughput measurement of DM-susceptibility for a large set of unlabeled peptides in studies of the mechanism of DM action and for identification of CD4+ T cell epitopes. PMID:24583195

  10. A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC(50) determination. (United States)

    Yin, Liusong; Stern, Lawrence J


    HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC(50) (change in 50% inhibition concentration) value. We simulated binding competition reactions of peptides with various intrinsic and DM-catalyzed kinetic parameters and found that under a wide range of conditions the delta-IC(50) value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC(50) is comparable to that measured by traditional off-rate assay for peptides with known DM-susceptibility hierarchy. The major advantage of this method is that it allows simple, fast and high throughput measurement of DM-susceptibility for a large set of unlabeled peptides in studies of the mechanism of DM action and for identification of CD4+ T cell epitopes. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Contamination of boreholes water by 76 pesticides molecules in the ...

    African Journals Online (AJOL)


    Analysis campaign of underground water was done in 2010 on five boreholes water samples situated in agricultural cotton zone. ... contamination of the underground water by pesticides were those areas where the cotton faming is practiced. Keywords: Kérou ..... center, Richardson, Texas, pp.87-89. Hani K, Narcisse A, ...

  12. Encapsulation and Characterization of Proton-Bound Amine Homodimers in a Water Soluble, Self-Assembled Supramolecular Host

    Energy Technology Data Exchange (ETDEWEB)

    Pluth, Michael; Fiedler, Dorothea; Mugridge, Jeffrey; Bergman, Robert; Raymond, Kenneth


    Cyclic amines can be encapsulated in a water-soluble self-assembled supramolecular host upon protonation. The hydrogen bonding ability of the cyclic amines, as well as the reduced degrees of rotational freedom, allows for the formation of proton-bound homodimers inside of the assembly which are otherwise not observable in aqueous solution. The generality of homodimer formation was explored with small N-alkyl aziridines, azetidines, pyrrolidines and piperidines. Proton-bound homodimer formation is observed for N-alkylaziridines (R = methyl, isopropyl, tert-butyl), N-alkylazetidines (R = isopropyl, tertbutyl), and N-methylpyrrolidine. At high concentration, formation of a proton-bound homotrimer is observed in the case of N-methylaziridine. The homodimers stay intact inside the assembly over a large concentration range, thereby suggesting cooperative encapsulation. Both G3(MP2)B3 and G3B3 calculations of the proton-bound homodimers were used to investigate the enthalpy of the hydrogen bond in the proton-bound homodimers and suggest that the enthalpic gain upon formation of the proton-bound homodimers may drive guest encapsulation.

  13. Incident energy dependence of scattering behavior of water molecules on Si (100) and graphite surfaces (United States)

    Kihara, G.; Kotsubo, Y.; Yoshimoto, Y.; Kinefuchi, I.; Takagi, S.


    The interaction between water molecules and solid surfaces has a great impact on water vapor flows in nanostructures. We conduct molecular beam scattering experiments covering the incident energy range corresponding to the thermal energy at room temperature to investigate the scattering behavior of water molecules on silicon and graphite surfaces. The incident energy dependence of the scattering distributions exhibits opposite trends on these surfaces. Molecular dynamics simulations reveal that the difference is caused by the inertia effect of the incident molecules and the surface corrugations.

  14. Preparation and characterization of water-soluble albumin-bound curcumin nanoparticles with improved antitumor activity. (United States)

    Kim, Tae Hyung; Jiang, Hai Hua; Youn, Yu Seok; Park, Chan Woong; Tak, Kyung Kook; Lee, Seulki; Kim, Hyungjun; Jon, Sangyong; Chen, Xiaoyuan; Lee, Kang Choon


    Curcumin (CCM), a yellow natural polyphenol extracted from turmeric (Curcuma longa), has potent anti-cancer properties as has been demonstrated in various human cancer cells. However, the widespread clinical application of this efficient agent in cancer and other diseases has been limited by its poor aqueous solubility and bioavailability. In this study, we prepared novel CCM-loaded human serum albumin (HSA) nanoparticles (CCM-HSA-NPs) for intravenous administration using albumin bound technology. Field emission scanning electron microscopy (FE-SEM) and dynamic light scattering (DLS) investigation confirmed a narrow size distribution in the 130-150nm range. Furthermore, CCM-HSA-NPs showed much greater water solubility (300-fold) than free CCM, and on storage, the biological activity of CCM-HSA-NPs was preserved with negligible activity loss. In vivo distributions and vascular endothelial cells transport studies demonstrated the superiority of CCM-HSA-NPs over CCM. Amounts of CCM in tumors after treatment with CCM-HSA-NPs were about 14 times higher at 1h after injection than that achieved by CCM. Furthermore, vascular endothelial cell binding of CCM increased 5.5-fold, and transport of CCM across a vascular endothelial cell monolayer by Transwell testing was 7.7-fold greater for CCM-HSA-NPs than CCM. Finally, in vivo antitumor tests revealed that CCM-HSA-NPs (10 or 20mg/kg) had a greater therapeutic effect (50% or 66% tumor growth inhibition vs. PBS-treated controls) than CCM (18% inhibition vs. controls) in tumor xenograft HCT116 models without inducing toxicity. We attribute this potent antitumor activity of CCM-HSA-NPs to enhanced water solubility, increased accumulation in tumors, and an ability to traverse vascular endothelial cell. Copyright © 2010 Elsevier B.V. All rights reserved.

  15. First Principles Study on the Interaction Mechanisms of Water Molecules on TiO₂ Nanotubes. (United States)

    Dai, Jianhong; Song, Yan


    The adsorption properties of water molecules on TiO₂ nanotubes (TiO₂NT) and the interaction mechanisms between water molecules are studied by first principles calculations. The adsorption preferences of water molecules in molecular or dissociated states on clean and H-terminated TiO₂NT are evaluated. Adsorption of OH clusters on (0, 6) and (9, 0) TiO₂ nanotubes are first studied. The smallest adsorption energies are -1.163 eV and -1.383 eV, respectively, by examining five different adsorption sites on each type of tube. Eight and six adsorption sites were considered for OH adsorbtion on the H terminated (0, 6) and (9, 0) nanotubes. Water molecules are reformed with the smallest adsorption energy of -4.796 eV on the former and of -5.013 eV on the latter nanotube, respectively. For the adsorption of a single water molecule on TiO₂NT, the molecular state shows the strongest adsorption preference with an adsorption energy of -0.660 eV. The adsorption of multiple (two and three) water molecules on TiO₂NT is also studied. The calculated results show that the interactions between water molecules greatly affect their adsorption properties. Competition occurs between the molecular and dissociated states. The electronic structures are calculated to clarify the interaction mechanisms between water molecules and TiO₂NT. The bonding interactions between H from water and oxygen from TiO₂NT may be the reason for the dissociation of water on TiO₂NT.

  16. First Principles Study on the Interaction Mechanisms of Water Molecules on TiO2 Nanotubes (United States)

    Dai, Jianhong; Song, Yan


    The adsorption properties of water molecules on TiO2 nanotubes (TiO2NT) and the interaction mechanisms between water molecules are studied by first principles calculations. The adsorption preferences of water molecules in molecular or dissociated states on clean and H-terminated TiO2NT are evaluated. Adsorption of OH clusters on (0, 6) and (9, 0) TiO2 nanotubes are first studied. The smallest adsorption energies are −1.163 eV and −1.383 eV, respectively, by examining five different adsorption sites on each type of tube. Eight and six adsorption sites were considered for OH adsorbtion on the H terminated (0, 6) and (9, 0) nanotubes. Water molecules are reformed with the smallest adsorption energy of −4.796 eV on the former and of −5.013 eV on the latter nanotube, respectively. For the adsorption of a single water molecule on TiO2NT, the molecular state shows the strongest adsorption preference with an adsorption energy of −0.660 eV. The adsorption of multiple (two and three) water molecules on TiO2NT is also studied. The calculated results show that the interactions between water molecules greatly affect their adsorption properties. Competition occurs between the molecular and dissociated states. The electronic structures are calculated to clarify the interaction mechanisms between water molecules and TiO2NT. The bonding interactions between H from water and oxygen from TiO2NT may be the reason for the dissociation of water on TiO2NT. PMID:28774138

  17. The dynamic behavior of ethanol and water mixtures inside an Au nanotube molecule filter. (United States)

    Wang, Yao-Chun; Ju, Shin-Pon


    Molecular dynamics (MD) simulation was used to investigate the behavior of water and ethanol molecules, which were mixed with five water-ethanol weight fractions (100:0, 0:100, 25:75, 50:50, and 75:25) inside the Au nanotube. To investigate the nano-confinement effect on water and ethanol molecules, the data of both molecules were analyzed by the probability of the number H-bonds per water and ethanol molecule and radial density distribution. Our results reveal that the radial density distributions and the number of H-bonds are significantly influenced by the Au nanotube, and the molecules also display different behavior from those in the bulk environment. In addition, the interaction between water molecules and the Au nanotube is stronger than that between ethanol molecules and the Au nanotube, from the profile of radial density distribution. Finally, both the number of H-bonds per water and per ethanol will be affected by the weight fraction, because the H-bond not only forms between the same material, but also between different materials.

  18. Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion. (United States)

    Nguyen, Trung Hai; Zhang, Chao; Weichselbaum, Ewald; Knyazev, Denis G; Pohl, Peter; Carloni, Paolo


    Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence. Hence, the specific water-proton interaction may help explain the proton mobility experimentally observed at the membrane interface.

  19. Theoretical investigation of the ultrafast dissociation of core-ionized water and uracil molecules immersed in liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Stia, C.R.; Fojon, O.A. [Instituto de Fisica Rosario - CONICET-Universidad Nacional de Rosario, Rosario (Argentina); Gaigeot, M.P. [Laboratoire Analyse et Modelisation pour la Biologie et l' Environnement, LAMBE, UMR-CNRS 8587, Universite d' Evry-Val-d' Essonne, 91 - Evry (France); Institut Universitaire de France, 75 - Paris (France); Vuilleumier, R. [Departement de chimie, Ecole Normale Superieure, 75 - Paris (France); Herve du Penhoat, M.A.; Politis, M.F. [Institut de Mineralogie et de Physique des Milieux Condenses, IMPMC, UMR-CNRS 7590, Universite Pierre et Marie Curie, 75 - Paris (France)


    We present a series of ab initio density functional based calculations of the fragmentation dynamics of core-ionized biomolecules. The computations are performed for pure liquid water, aqueous and isolated Uracil. Core ionization is described by replacing the 1s{sup 2} pseudopotential of one atom of the target molecule (C, N or O) with a pseudopotential for a 1s{sup 1} core-hole state. Our results predict that the dissociation of core-ionized water molecules may be reached during the lifetime of inner-shell vacancy (less than 10 fs), leading to OH bond breakage as a primary outcome. We also observe a second fragmentation channel in which total Coulomb explosion of the ionized water molecule occurs. Fragmentation pathways are found similar for pure water or when the water molecule is in the primary hydration shell of the uracil molecule. In the latter case, the proton may be transferred towards the uracil oxygen atoms. When the core hole is located on the uracil molecule, ultrafast dissociation is only observed in the aqueous environment and for nitrogen-K vacancies, resulting in proton transfers towards the hydrogen-bonded water molecule. (authors)

  20. Contamination of boreholes water by 76 pesticides molecules in the ...

    African Journals Online (AJOL)

    Analysis campaign of underground water was done in 2010 on five boreholes water samples situated in agricultural cotton zone. The obtained results showed the presence of various active matters of at least 76 residues of pesticides, especially insecticides, herbicides and fungicides, with accumulated contents which could ...

  1. The exothermic HCl + OH·(H2O) reaction: removal of the HCl + OH barrier by a single water molecule. (United States)

    Li, Guoliang; Wang, Hui; Li, Qian-Shu; Xie, Yaoming; Schaefer, Henry F


    The entrance complex, transition state, and exit complex for the title reaction have been investigated using the CCSD(T) method with correlation consistent basis sets up to cc-pVQZ. The stationary point geometries for the reaction are related to but different from those for the water monomer reaction HCl + OH → Cl + H2O. Our most important conclusion is that the hydrogen-bonded water molecule removes the classical barrier entirely. For the endothermic reverse reaction Cl + (H2O)2, the second water molecule lowers the relative energies of the entrance complex, transition state, and exit complex by about 4 kcal/mol. The title reaction is exothermic by 17.7 kcal/mol. The entrance complex HCl⋯OH·(H2O) is bound by 6.9 kcal/mol relative to the separated reactants. The classical barrier height for the reverse reaction is predicted to be 16.5 kcal/mol. The exit complex Cl⋯(H2O)2 is found to lie 6.8 kcal/mol below the separated products. The potential energy surface for the Cl + (H2O)2 reaction is radically different from that for the valence isoelectronic F + (H2O)2 system.

  2. Incipient ferroelectricity of water molecules confined to nano-channels of beryl


    Gorshunov, B. P.; Torgashev, V. I.; Zhukova, E. S.; Thomas, V. G.; Belyanchikov, M. A.; Kadlec, C.; Kadlec, F.; Savinov, M.; Ostapchuk, T.; Petzelt, J.; Prokle?ka, J.; Tomas, P. V.; Pestrjakov, E. V.; Fursenko, D. A.; Shakurov, G. S.


    Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole?dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they...

  3. MRI-derived bound and pore water concentrations as predictors of fracture resistance. (United States)

    Manhard, Mary Kate; Uppuganti, Sasidhar; Granke, Mathilde; Gochberg, Daniel F; Nyman, Jeffry S; Does, Mark D


    Accurately predicting fracture risk in the clinic is challenging because the determinants are multi-factorial. A common approach to fracture risk assessment is to combine X-ray-based imaging methods such as dual-energy X-ray absorptiometry (DXA) with an online Fracture Risk Assessment Tool (FRAX) that includes additional risk factors such as age, family history, and prior fracture incidents. This approach still does not adequately diagnose many individuals at risk, especially those with certain diseases like type 2 diabetes. As such, this study investigated bound water and pore water concentrations (Cbw and Cpw) from ultra-short echo time (UTE) magnetic resonance imaging (MRI) as new predictors of fracture risk. Ex vivo cadaveric arms were imaged with UTE MRI as well as with DXA and high-resolution micro-computed tomography (μCT), and imaging measures were compared to both whole-bone structural and material properties as determined by three-point bending tests of the distal-third radius. While DXA-derived areal bone mineral density (aBMD) and μCT-derived volumetric BMD correlated well with structural strength, they moderately correlated with the estimate material strength with gender being a significant covariate for aBMD. MRI-derived measures of Cbw and Cpw had a similar predictive ability of material strength as aBMD but did so independently of gender. In addition, Cbw was the only imaging parameter to significantly correlate with toughness, the energy dissipated during fracture. Notably, the strength of the correlations with the material properties of bone tended to be higher when a larger endosteal region was used to determine Cbw and Cpw. These results indicate that MRI measures of Cbw and Cpw have the ability to probe bone material properties independent of bone structure or subject gender. In particular, toughness is a property of fracture resistance that is not explained by X-ray based methods. Thus, these MRI-derived measures of Cbw and Cpw in cortical

  4. Roles of water molecules in bacteria and viruses (United States)

    Cox, C. S.


    In addition to water, microbes mainly comprise lipids, carbohydrates, proteins and nucleic acids. Their structure and function singularly and conjointly is affected by water activity. Desiccation leads to dramatic lipid phase changes whereas carbohydrates, proteins and nucleic acids initially suffer spontaneous, reversible low activation energy Maillard reactions forming products that more slowly re-arrange, cross-link etc. to give non-native states. While initial products spontaneously may reverse to native states by raising water activity, later products only do so through energy consumption and enzymatic activity eg. repair. Yet, native states of lipid membranes and associated enzymes are required to generate energy. Consequently, good reserves of high energy compounds (e.g. ATP) and of membrane stabilisers (e.g. trehalose) may be expected to enhance survival following drying and rehydration (e.g. anhydrobiotic organisms).

  5. Visualizing water molecule distribution by atomic force microscopy. (United States)

    Kimura, Kenjiro; Ido, Shinichiro; Oyabu, Noriaki; Kobayashi, Kei; Hirata, Yoshiki; Imai, Takashi; Yamada, Hirofumi


    Hydration structures at biomolecular surfaces are essential for understanding the mechanisms of the various biofunctions and stability of biomolecules. Here, we demonstrate the measurement of local hydration structures using an atomic force microscopy system equipped with a low-noise deflection sensor. We applied this method to the analysis of the muscovite mica/water interface and succeeded in visualizing a hydration structure that is site-specific on a crystal. Furthermore, at the biomolecule/buffer solution interface, we found surface hydration layers that are more packed than those at the muscovite mica/water interface.

  6. Effects of Helicobacter pylori Water Extract on Expression of Endothelial Adhesion Molecules

    Directory of Open Access Journals (Sweden)

    Norimasa Yoshida


    Full Text Available The present study investigated whether Helicobacter pylori water extract induces the upregulation of intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin on human umbilical vein endothelial cells, using an ELISA. The nature of the substances mediating this upregulation was also analyzed. H pylori water extract derived from type strain (NCTC 11637 significantly upregulated intercellular adhesion molecule-1, vascular cell adhesion molecule-1 and E-selectin to the same extent as interleukin-1. Treatments with extracts from clinical strains showed no significant increases in expression of these adhesion molecules. In a fractionation study, approximately 7 kDa fraction showed peak activity. This activity was tolerant to heating and trypsin digestion. These results indicate that H pylori water extract contains water-soluble, low-molecular, nonprotein substances which induce upregulation of adhesion molecules on human umbilical vein endothelial cells, suggesting that products of H pylori may elicit gastric mucosal inflammation by promoting expression of endothelial adhesion molecules.

  7. Contamination of boreholes water by 76 pesticides molecules in the ...

    African Journals Online (AJOL)


    76 residues of pesticides, especially insecticides, herbicides and fungicides, with accumulated contents which could average 0.350 or 350 ... cide residues of weed killers and fungicides were already detected in water reserves, ..... lithographic structure, its high content in organic matter and the depth of the underground ...

  8. Bounding the marginal cost of producing potable water including the use of seawater desalinization as a backstop potable water production technology

    Energy Technology Data Exchange (ETDEWEB)

    Dooley, James J.


    The analysis presented in this technical report should allow for the creation of high, medium, and low cost potable water prices for GCAM. Seawater reverse osmosis (SWRO) based desalinization should act as a backstop for the cost of producing potable water (i.e., the literature seems clear that SWRO should establish an upper bound for the plant gate cost of producing potable water). Transporting water over significant distances and having to lift water to higher elevations to reach end-users can also have a significant impact on the cost of producing water. The three potable fresh water scenarios describe in this technical report are: low cost water scenario ($0.10/m3); medium water cost scenario ($1.00/m3); and high water cost scenario ($2.50/m3).

  9. Combined quantum mechanics/molecular mechanics (QM/MM) simulations for protein-ligand complexes: free energies of binding of water molecules in influenza neuraminidase. (United States)

    Woods, Christopher J; Shaw, Katherine E; Mulholland, Adrian J


    The applicability of combined quantum mechanics/molecular mechanics (QM/MM) methods for the calculation of absolute binding free energies of conserved water molecules in protein/ligand complexes is demonstrated. Here, we apply QM/MM Monte Carlo simulations to investigate binding of water molecules to influenza neuraminidase. We investigate five different complexes, including those with the drugs oseltamivir and peramivir. We investigate water molecules in two different environments, one more hydrophobic and one hydrophilic. We calculate the free-energy change for perturbation of a QM to MM representation of the bound water molecule. The calculations are performed at the BLYP/aVDZ (QM) and TIP4P (MM) levels of theory, which we have previously demonstrated to be consistent with one another for QM/MM modeling. The results show that the QM to MM perturbation is significant in both environments (greater than 1 kcal mol(-1)) and larger in the more hydrophilic site. Comparison with the same perturbation in bulk water shows that this makes a contribution to binding. The results quantify how electronic polarization differences in different environments affect binding affinity and also demonstrate that extensive, converged QM/MM free-energy simulations, with good levels of QM theory, are now practical for protein/ligand complexes.

  10. Changes in content of free, conjugated and bound polyamines and osmotic adjustment in adaptation of vetiver grass to water deficit. (United States)

    Zhou, Qiang; Yu, Bingjun


    Osmotic adjustment and alteration of polyamines (PAs) have been suggested to play roles in plant adaptation to water deficit/drought stress. In this study, the changes in cell intactness, photosynthesis, compatible solutes and PAs [including putrescine (Put), spermidine (Spd) and spermine (Spm) each in free, conjugated and bound forms] were investigated in leaves of vetiver grass exposed to different intensity of water deficit stress and subsequent rewatering. The results showed that, when vetiver grass was exposed to the moderate (20% and 40% PEG-6000 solutions) and severe (60% PEG solution) water deficit for 6days, the plant injury degree (expressed as the parameters of plant growth, cell membrane integrity, water relations and photosynthesis) increased and contents of free and conjugated Put decreased with the rise of PEG concentration. Under the moderate water deficit, the plants could survive by the reduced osmotic potential (psi(s)), increased free and conjugated Spd and Spm in leaves. After subsequent rewatering, the osmotic balance was re-established, most of the above investigated physiological parameters were fully or partly recovered to the control levels. However, it was not the case for the severely-stressed and rewatering plants. It indicates that, vetiver grass can cope well with the moderate water deficit/drought stress by using the strategies of osmotic adjustment and maintenance of total contents of free, conjugated and bound PAs in leaves.

  11. Incipient ferroelectricity of water molecules confined to nano-channels of beryl (United States)

    Gorshunov, B. P.; Torgashev, V. I.; Zhukova, E. S.; Thomas, V. G.; Belyanchikov, M. A.; Kadlec, C.; Kadlec, F.; Savinov, M.; Ostapchuk, T.; Petzelt, J.; Prokleška, J.; Tomas, P. V.; Pestrjakov, E. V.; Fursenko, D. A.; Shakurov, G. S.; Prokhorov, A. S.; Gorelik, V. S.; Kadyrov, L. S.; Uskov, V. V.; Kremer, R. K.; Dressel, M.


    Water is characterized by large molecular electric dipole moments and strong interactions between molecules; however, hydrogen bonds screen the dipole-dipole coupling and suppress the ferroelectric order. The situation changes drastically when water is confined: in this case ordering of the molecular dipoles has been predicted, but never unambiguously detected experimentally. In the present study we place separate H2O molecules in the structural channels of a beryl single crystal so that they are located far enough to prevent hydrogen bonding, but close enough to keep the dipole-dipole interaction, resulting in incipient ferroelectricity in the water molecular subsystem. We observe a ferroelectric soft mode that causes Curie-Weiss behaviour of the static permittivity, which saturates below 10 K due to quantum fluctuations. The ferroelectricity of water molecules may play a key role in the functioning of biological systems and find applications in fuel and memory cells, light emitters and other nanoscale electronic devices.

  12. Hydroxyl and water molecule orientations in trypsin: Comparison to molecular dynamics structures

    Energy Technology Data Exchange (ETDEWEB)

    McDowell, R.S.; Kossiakoff, A.A. [Genentech, Inc., South San Francisco, CA (United States)


    A comparison is presented of experimentally observed hydroxyl and water hydrogens in trypsin determined from neutron density maps with the results of a 140ps molecular dynamics (MD) simulation. Experimental determination of hydrogen and deuterium atom positions in molecules as large as proteins is a unique capability of neutron diffraction. The comparison addresses the degree to which a standard force-field approach can adequately describe the local electrostatic and van der Waals forces that determine the orientations of these hydrogens. Neutron densities, derived from 2.1{Angstrom} D{sub 2}O-H{sub 2}O difference Fourier maps, provide a database of 27 well-ordered hydroxyl hydrogens. Most of the simulated hydroxyl orientations are within a standard deviation of the experimentally-observed positions, including several examples in which both the simulation and the neutron density indicate that a hydroxyl group is shifted from a {open_quote}standard{close_quote} rotamer. For the most highly ordered water molecules, the hydrogen distributions calculated from the trajectory were in good agreement with neutron density; simulated water molecules that displayed multiple hydrogen bonding networks had correspondingly broadened neutron density profiles. This comparison was facilitated by development of a method to construct a pseudo 2{Angstrom} density map based on the hydrogen atom distributions from the simulation. The degree of disorder of internal water molecules is shown to result primarily from the electrostatic environment surrounding that water molecule as opposed to the cavity size available to the molecule. A method is presented for comparing the discrete observations sampled in a dynamics trajectory with the time- averaged data obtained from X-ray or neutron diffraction studies. This method is particularly useful for statically-disordered water molecules, in which the average location assigned from a trajectory may represent a site of relatively low occupancy.

  13. Cramér–Rao bounds for three‐point decomposition of water and fat

    National Research Council Canada - National Science Library

    Pineda, Angel R; Reeder, Scott B; Wen, Zhifei; Pelc, Norbert J


    .... This generalization leads to a nonlinear estimation problem. The Crámer–Rao bound (CRB) was used to study the variance of the estimates of the magnitude, phase, and field map by computing the maximum effective number of signals averaged (NSA...

  14. Molecular Dynamics Study of the Disruption of H-BONDS by Water Molecules and its Diffusion Behavior in Amorphous Cellulose (United States)

    Liao, Ruijin; Zhu, Mengzhao; Zhou, Xin; Zhang, Fuzhou; Yan, Jiaming; Zhu, Wenbin; Gu, Chao


    Hydrolysis is an important component of the aging of cellulose, and it severely affects the insulating performance of cellulosic materials. The diffusion behavior of water molecules in amorphous cellulose and their destructive effect on the hydrogen bonding structure of cellulose were investigated by molecular dynamics. The change in the hydrogen bonding structure indicates that water molecules have a considerable effect on the hydrogen bonding structure within cellulose: both intermolecular and intramolecular hydrogen bonds decreased with an increase in ingressive water molecules. Moreover, the stabilities of the cellulose molecules were disrupted when the number of intermolecular hydrogen bonds declined to a certain degree. Both the free volumes of amorphous cells and water molecule-cellulose interaction affect the diffusion of water molecules. The latter, especially the hydrogen bonding interaction between water molecules and cellulose, plays a predominant role in the diffusion behavior of water molecules in the models of which the free volume rarely varies. The diffusion coefficient of water molecules has an excellent correlation with water molecule-cellulose interaction and the average hydrogen bonds between each water molecule and cellulose; however, this relationship was not apparent between the diffusion coefficient and free volume.

  15. Laser Induced Molecular Micro-Jet Implantation of Perylene Molecules through Water or Diiodomethane Layers (United States)

    Goto, Masahiro; Pihosh, Yuriy; Kasahara, Akira; Tosa, Masahiro


    Laser-induced molecular micro-jets of perylene molecules have been successfully generated in water and diiodomethane layers. The perylene molecules were ejected from a thin film of perylene molecules used as a source by photoexcitation using 4-ns laser pulses onto a borosilicate glass substrate used as a target. The gap between the source and the target was filled with water or diiodomethane. After the ejection, the perylene molecules passed through the liquid layer and were implanted into the target. The focusing of the molecular micro-jet and consequently the shape of the implanted molecular dots depends on the molecular species and type of liquid. This novel technique can be used for the fabrication of a pattern of functional molecular dots on a designated region of hard materials and can be used to manufacture molecular devices, molecular sensors, and optoelectronic devices.

  16. Deficiency of water molecules in the crystallographic structure of vauxite (United States)

    Van Alboom, A.; da Costa, G. M.; De Grave, E.


    A vauxite mineral sample from Huanuni, Bolivia, was studied by XRD, TGA and Mössbauer spectroscopy. The XRD revealed the sample as having the typical triclinic structure of vauxite. The chemical formula was determined as (Fe0.88Mn0.01)Al1.99(PO4)2(OH)1.75(H2O)5.31, implying some Fe2+, OH- and H2O deficiencies. The TGA curve showed ca. 27% loss of weight over a temperature range from 80 to 400 °C, supposedly due to the loss of water and hydroxyl groups. For the first time, Mössbauer spectra for vauxite were collected over a wide temperature range between 9 and 310 K. No magnetic ordering was detected. The spectra could be successfully and consistently analyzed by a superposition of four doublet subspectra. On the basis of the relation between the center shift and the mean Fe-ligand distance on the one hand and the center shift values for the various doublets on the other hand, one doublet was assigned to Fe(2). For the other doublets, it is proposed that, as a result of the H2O deficiency in the structure of the present vauxite sample, vacancies are present in the second coordination spheres of some Fe(1) and that these vacancies affect the quadrupole splitting of the corresponding Fe(1) cations, thus causing three Fe(1) doublet components in the Mössbauer spectra. The temperature variations of center shift and quadrupole splitting of the various doublet contributions are presented and discussed.

  17. Water molecule network and active site flexibility of apo protein tyrosine phosphatase 1B

    DEFF Research Database (Denmark)

    Pedersen, A.K.; Peters, Günther H.J.; Møller, K.B.


    Protein tyrosine phosphatase 1B (PTP1B) plays a key role as a negative regulator of insulin and leptin signalling and is therefore considered to be an important molecular target for the treatment of type 2 diabetes and obesity. Detailed structural information about the structure of PTP1B, including...... the conformation and flexibility of active-site residues as well as the water-molecule network, is a key issue in understanding ligand binding and enzyme kinetics and in structure-based drug design. A 1.95 Angstrom apo PTP1B structure has been obtained, showing four highly coordinated water molecules in the active......-site pocket of the enzyme; hence, the active site is highly solvated in the apo state. Three of the water molecules are located at positions that approximately correspond to the positions of the phosphate O atoms of the natural substrate phosphotyrosine and form a similar network of hydrogen bonds. The active...

  18. Influences of water molecules on the electronic properties of atomically thin molybdenum disulfide (United States)

    Zhang, Kang; Wang, Xingli; Sun, Leimeng; Zou, Jianping; Wang, Jingyuan; Liu, Zheng; Chen, Tupei; Tay, Beng Kang; Zhang, Qing


    Although it is well known that the performances of two-dimensional transition metal dichalcogenide (2D-TMD) based devices are strongly affected by humidity, the roles of water molecules in the electronic properties of 2D-TMDs are still unclear. In this work, the influence of water molecules on the electrical properties of monolayer molybdenum disulfide (MoS2) is studied systemically using the dielectric force microscopy (DFM) technique. Taking the advantage of the DFM technique and other nondestructive characterization techniques, the electronic properties (surface potential, dielectrics, and carrier mobility) of atomically thin MoS2 exposed to different levels of humidity are investigated. Furthermore, Raman spectroscopy manifested the correlation between the optical phonon and the mobility drop of MoS2 flakes when subjected to humidity variations. Our results provide an in-depth understanding of the mechanism of water molecules interacting with MoS2.

  19. Interaction of water molecules with hexagonal 2D systems. A DFT study (United States)

    Rojas, Ángela; Rey, Rafael

    Over the years water sources have been contaminated with many chemical agents, becoming issues that affect health of the world population. The advances of the nanoscience and nanotechnology in the development new materials constitute an alternative for design molecular filters with great efficiencies and low cost for water treatment and purification. In the nanoscale, the process of filtration or separation of inorganic and organic pollutants from water requires to study interactions of these atoms or molecules with different nano-materials. Specifically, it is necessary to understand the role of these interactions in physical and chemical properties of the nano-materials. In this work, the main interest is to do a theoretical study of interaction between water molecules and 2D graphene-like systems, such as silicene (h-Si) or germanene (h-Ge). Using Density Functional Theory we calculate total energy curves as function of separation between of water molecules and 2D systems. Different spatial configurations of water molecules relative to 2D systems are considered. Structural relaxation effects and changes of electronic charge density also are reported. Universidad Nacional de Colombia.

  20. Catalytic effect of a single water molecule on the OH + CH2NH reaction. (United States)

    Akbar Ali, Mohamad; M, Balaganesh; Lin, K C


    In recent work, there has been considerable speculation about the atmospheric reaction of methylenimine (CH 2 NH), because this compound is highly reactive, soluble in water, and sticky, thus posing severe experimental challenges. In this work, we have revisited the kinetics of the OH + CH 2 NH reaction assisted by a single water molecule. The potential energy surfaces (PESs) for the water-assisted OH + CH 2 NH reaction were calculated using the CCSD(T)//BH&HLYP/aug-cc-pVTZ levels of theory. The rate coefficients for the bimolecular reaction pathways CH 2 NHH 2 O + OH and CH 2 NH + H 2 OHO were computed using canonical variational transition state theory (CVT) with small curvature tunneling correction. The reaction without water has four elementary reaction pathways, depending on how the hydroxyl radical approaches CH 2 NH. In all cases, the reaction begins with the formation of a single pre-reactive complex before producing abstraction and addition products. When water is added, the products of the reaction do not change, and the reaction becomes quite complex, yielding four different pre-reactive complexes and eight reaction pathways. The calculated rate coefficient for the OH + CH 2 NH (water-free) reaction at 300 K is 1.7 × 10 -11 cm 3 molecule -1 s -1 and for OH + CH 2 NH (water-assisted), it is 5.1 × 10 -14 cm 3 molecule -1 s -1 . This result is similar to the isoelectronic analogous reaction OH + CH 2 O (water-assisted). In general, the effective rate coefficients of the water-assisted reaction are 2∼3 orders of magnitude smaller than water-free. Our results show that the water-assisted OH + CH 2 NH reaction cannot accelerate the reaction because the dominated water-assisted process depends parametrically on water concentration. As a result, the overall reaction rate coefficients are smaller.

  1. Spatial distribution of organic contaminants in three rivers of Southern England bound to suspended particulate material and dissolved in water. (United States)

    Wilkinson, John L; Hooda, Peter S; Swinden, Julian; Barker, James; Barton, Stephen


    The spatial distribution of pharmaceuticals, personal care products (PPCPs) and other emerging contaminants (ECs) such as plasticisers, perflourinated compounds (PFCs) and illicit drug metabolites in water and bound to suspended particulate material (SPM) is not well-understood. Here, we quantify levels of thirteen selected contaminants in water (n=88) and their partition to suspended particulate material (SPM, n=16) in three previously-unstudied rivers of Greater London and Southern England during a key reproduction/spawning period. Analysis was conducted using an in-house validated method for Solid Phase Extraction followed by High-Performance Liquid Chromatography-Tandem Mass-Spectrometry. Analytes were extracted from SPM using an optimised method for ultrasonic-assisted solvent extraction. Detection frequencies of contaminants dissolved in water ranged from 3% (ethinylestradiol) to 100% (bisphenol-A). Overall mean concentrations in the aqueous-phase ranged from 14.7ng/L (benzoylecgonine) to 159ng/L (bisphenol-A). Sewage treatment works (STW) effluent was the predominant source of pharmaceuticals, while plasticisers/perfluorinated compounds may additionally enter rivers via other sources. In SPM, detection frequencies ranged from 44% (PFOA) to 94% (hydroxyacetophenone). Mean quantifiable levels of analytes bound to SPM ranged from 13.5ng/g dry SPM (0.33ng bound/L water) perfluorononanoic acid to 2830ng/g dry SPM (14.3ng bound/L water) perfluorooctanesulfonic acid. Long chain (>C7) amphipathic and acidic PFCs were found to more preferentially bind to SPM than short chain PFCs and other contaminants (Kd=34.1-75.5 vs work (n=104) enabled ANOVA followed by Tukey HSD post-hoc tests to establish significant trends in PPCP/EC spatial distribution from headwaters through downstream stretches of studied rivers. Novel findings include environmental Kd calculations, the occurrence of contaminants in river headwaters, increases in contaminant metabolite concentrations

  2. A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01

    DEFF Research Database (Denmark)

    Pedersen, Lasse Eggers; Rasmussen, Michael; Harndahl, Mikkel


    Affinity and stability of peptides bound by major histocompatibility complex (MHC) class I molecules are important factors in presentation of peptides to cytotoxic T lymphocytes (CTLs). In silico prediction methods of peptide-MHC binding followed by experimental analysis of peptide-MHC interactions...... constitute an attractive protocol to select target peptides from the vast pool of viral proteome peptides. We have earlier reported the peptide binding motif of the porcine MHC-I molecules SLA-1*04:01 and SLA-2*04:01, identified by an ELISA affinity-based positional scanning combinatorial peptide library...

  3. Investigations of water bounded in clam mussels (Mytilius edulis) by nuclear magnetic relaxation for protons; Badanie wody zwiazanej w muszlach omulka (Mytillus edulls) metoda magnetycznej relaksacji dla protonow

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, H.; Niziol, J. [Inst. Fizyki, Uniwersytet Jagiellonski, Cracow (Poland); Falniowski, A. [Inst. Zoologii, Uniwersytet Jagiellonski, Cracow (Poland)


    The process of water bounding in clam shells has been investigated by nuclear magnetic relaxation of protons measurements. Decomposition of measured relaxation functions have been done using the specially constructed computer program. 4 refs, 4 figs, 3 tabs.

  4. Identification of intrinsic catalytic activity for electrochemical reduction of water molecules to generate hydrogen

    KAUST Repository

    Shinagawa, Tatsuya


    Insufficient hydronium ion activities at near-neutral pH and under unbuffered conditions induce diffusion-limited currents for hydrogen evolution, followed by a reaction with water molecules to generate hydrogen at elevated potentials. The observed constant current behaviors at near neutral pH reflect the intrinsic electrocatalytic reactivity of the metal electrodes for water reduction. This journal is © the Owner Societies.

  5. Reduced coupling of water molecules near the surface of reverse micelles

    NARCIS (Netherlands)

    Bakulin, Artem A.; Pshenichnikov, Maxim S.


    We report on vibrational dynamics of water near the surface of AOT reverse micelles studied by narrow-band excitation, mid-IR pump-probe spectroscopy. Evidence of OH-stretch frequency splitting into the symmetric and asymmetric modes is clearly observed for the interfacial H2O molecules. The

  6. Supplementary Material Table 1: H2O molecule as example. Water ...

    Indian Academy of Sciences (India)


    Table 1: H2O molecule as example. Water has 3N-6=3 frequencies. So we need three force constants. the f4 is automatically fixed from f1,f2 and f3. In C1 symmetry, all the off- diagonal elements are fixed by the diagonal force constants because 3N-6=number of frequencies= number of diagonal force constants.

  7. Ab initio treatment of ion-water molecule collisions with a three-center pseudo potential


    Martínez, Pablo A.; Errea, L. F.; Méndez, Laura González; Rabadán, Ismanuel


    We calculate electron capture cross sections in collisions of protons with water molecules, using two simple ab initio approaches. The formalism involves the calculation of one-electron scattering wave functions and the use of three-center pseudo potential to represent the electron H2O+ interaction. Several methods to obtain many-electron cross sections are considered

  8. Transport properties of water molecules confined between hydroxyapaptite surfaces: A Molecular dynamics simulation approach (United States)

    Prakash, Muthuramalingam; Lemaire, Thibault; Di Tommaso, Devis; de Leeuw, Nora; Lewerenz, Marius; Caruel, Matthieu; Naili, Salah


    Water diffusion in the vicinity of hydroxyapatite (HAP) crystals is a key issue to describe biomineralization process. In this study, a configuration of parallel HAP platelets mimicking bone nanopores is proposed to characterize the nanoscopic transport properties of water molecules at HAP-water surface and interfaces using various potential models such as combination of the Core-Shell (CS) model, Lennard-Jones (LJ) potentials with SPC or SPC/E water models. When comparing all these potentials models, it appears that the core-shell potential for HAP together with the SPC/E water model more accurately predicts the diffusion properties of water near HAP surface. Moreover, we have been able to put into relief the possibility of observing hydroxyl (OH-) ion dissociation that modifies the water structure near the HAP surface.

  9. Effects of Water Molecule on CO Oxidation by OH: Reaction Pathways, Kinetic Barriers, and Rate Constants. (United States)

    Zhang, Linyao; Yang, Li; Zhao, Yijun; Zhang, Jiaxu; Feng, Dongdong; Sun, Shaozeng


    The water dilute oxy-fuel combustion is a clean combustion technology for near-zero emission power; and the presence of water molecule could have both kinetic and dynamic effects on combustion reactions. The reaction OH + CO → CO 2 + H, one of the most important elementary reactions, has been investigated by extensive electronic structure calculations. And the effects of a single water molecule on CO oxidation have been studied by considering the preformed OH(H 2 O) complex reacts with CO. The results show little change in the reaction pathways, but the additional water molecule actually increases the vibrationally adiabatic energy barriers (V a G ). Further thermal rate constant calculations in the temperature range of 200 to 2000 K demonstrate that the total low-pressure limit rate constant for the water assisted OH(H 2 O) + CO → CO 2 + H 2 O + H reaction is 1-2 orders lower than that of the water unassisted one, which is consistent with the change of V a G . Therefore, the hydrated radical OH(H 2 O) would actually slow down the oxidation of CO. Meanwhile, comparisons show that the M06-2X/aug-cc-pVDZ method gives a much better estimation in energy and thus is recommended to be employed for direct dynamics simulations.

  10. [WTP guidance technology: a comparison of payment card, single-bounded and double-bounded dichotomous formats for evaluating non-use values of Sanjiang Plain ecotourism water resources]. (United States)

    Chen, Hong-Guang; Wang, Qiu-Dan; Li, Chen-Yang


    Contingent valuation method (CVM) is the most widespread method to assess resources and value of environmental goods and services. The guidance technology of willingness to pay (WTP) is an important means of CVM. Therefore, the study on the WTP guidance technology is an important approach to improve the reliability and validity of CVM. This article conducted comprehensive evaluation on non-use value of eco-tourism water resources in Sanjiang Plain by using payment card, single-bound dichotomous choice and double-bound dichotomous choice. Results showed that the socio-economic attributes were consistent with the willingness to pay in the three formats, and the tender value, age, educational level, annual income and the concern level had significant effect on the willingness to pay, while gender and job did not have significant influence. The WTP value was 112.46 yuan per capita with the payment card, 136.15 with the single-bound dichotomous choice, and 168.74 with the double-bound dichotomous choice. Comprehensive consideration of the nature of the investigation, investigation costs and statistical techniques, the result of double-bound dichotomous choice (47.86 x 10(8) yuan · a(-1)) was best in accordance with the reality, and could be used as non-use value of eco-tourism water resources in Sanjiang Plain. The format of questionnaire was very important to improve its validity, and made a great influence on the WTP.

  11. Preliminary bounds on the water composition and secondary mineral development that may influence the near-field environment

    Energy Technology Data Exchange (ETDEWEB)

    Whitbeck, M.; Glassley, W.


    The evolution of the water chemistry and secondary mineral development in the vicinity of the near-field of a potential Yucca Mountain high level nuclear waste repository will be controlled by temperature, and interaction of water with rock over time. This report describes initial bounds on water composition and secondary mineral development, as a function of time, temperature, and rock type (devitrified, welded tuff and vitrophyre). The code EQ3/6 was used in the calculations, with explicit use of transition state theory models for mineral dissolution rates for the framework minerals of the tuff. Simulations were run for time durations sufficient to achieve steady state conditions. Uncertainty in the calculations, due to uncertainty in the measured dissolution rates, was considered by comparing results in simulations in which rates were varied within the range of known uncertainties for dissolution rate constants. The results demonstrate that the steady state mineralogy and water compositions are relatively insensitive to the rock unit modeled, which is consistent with the fact that the compositions of the rock units in the vicinity if the potential repository are similar, and will tend toward similar thermodynamic free energy minima, for similar rock:water ratios. Significant differences are observed, however, for large differences in rock: water ratios. The rates at which this end point condition are approached are a function of the rate parameters used, and can vary by orders of magnitude.

  12. Lipid carbonyl groups terminate the hydrogen bond network of membrane-bound water. (United States)

    Ohto, Tatsuhiko; Backus, Ellen H G; Hsieh, Cho-Shuen; Sulpizi, Marialore; Bonn, Mischa; Nagata, Yuki


    We present a combined experimental sum-frequency generation (SFG) spectroscopy and ab initio molecular dynamics simulations study to clarify the structure and orientation of water at zwitterionic phosphatidylcholine (PC) lipid and amine N-oxide (AO) surfactant monolayers. Simulated O-H stretch SFG spectra of water show good agreement with the experimental data. The SFG response at the PC interface exhibits positive peaks, whereas both negative and positive bands are present for the similar zwitterionic AO interface. The positive peaks at the water/PC interface are attributed to water interacting with the lipid carbonyl groups, which act as efficient hydrogen bond acceptors. This allows the water hydrogen bond network to reach, with its (up-oriented) O-H groups, into the headgroup of the lipid, a mechanism not available for water underneath the AO surfactant. This highlights the role of the lipid carbonyl group in the interfacial water structure at the membrane interface, namely, stabilizing the water hydrogen bond network.

  13. Measurements of water molecule density by tunable diode laser absorption spectroscopy in dielectric barrier discharges with gas–water interface (United States)

    Tachibana, Kunihide; Nakamura, Toshihiro; Kawasaki, Mitsuo; Morita, Tatsuo; Umekawa, Toyofumi; Kawasaki, Masahiro


    We measured water molecule (H2O) density by tunable diode-laser absorption spectroscopy (TDLAS) for applications in dielectric barrier discharges (DBDs) with a gas–water interface. First, the effects of water temperature and presence of gas flow were tested using a Petri dish filled with water and a gas injection nozzle. Second, the TDLAS system was applied to the measurements of H2O density in two types of DBDs; one was a normal (non-inverted) type with a dielectric-covered electrode above a water-filled counter electrode and the other was an inverted type with a water-suspending mesh electrode above a dielectric-covered counter electrode. The H2O density in the normal DBD was close to the density estimated from the saturated vapor pressure, whereas the density in the inverted DBD was about half of that in the former type. The difference is attributed to the upward gas flow in the latter type, that pushes the water molecules up towards the gas–water interface.

  14. Polarization induced water molecule dissociation below the first-order electronic-phase transition temperature

    CERN Document Server

    Arulsamy, Andrew Das; Elersic, Kristina; Modic, Martina; Subramani, Uma Shankar


    Hydrogen produced from the photocatalytic splitting of water is one of the reliable alternatives to replace the polluting fossil and the radioactive nuclear fuels. Here, we provide unequivocal evidence for the existence of blue- and red-shifting O$-$H covalent bonds within a single water molecule adsorbed on MgO surface as a result of asymmetric displacement polarizabilities. The adsorbed H-O-H on MgO gives rise to one weaker H-O bond, while the other O-H covalent bond from the same adsorbed water molecule compensates this effect with a stronger bond. The weaker bond (nearest to the surface), the interlayer tunneling electrons and the silver substrate are shown to be the causes for the smallest dissociative activation energy on MgO monolayer. The origin that is responsible to initiate the splitting mechanism is proven to be due to the changes in the polarizability of an adsorbed water molecule, which are further supported by the temperature-dependent static dielectric constant measurements for water below the...

  15. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface (United States)

    Murina, Ezequiel L.; Fernández-Prini, Roberto; Pastorino, Claudio


    We studied the behavior of long chain alkanes (LCAs) as they were transferred from gas to bulk water, through the liquid-vapor interface. These systems were studied using umbrella sampling molecular dynamics simulation and we have calculated properties like free energy profiles, molecular orientation, and radius of gyration of the LCA molecules. The results show changes in conformation of the solutes along the path. LCAs adopt pronounced molecular orientations and the larger ones extend appreciably when partially immersed in the interface. In bulk water, their conformations up to dodecane are mainly extended. However, larger alkanes like eicosane present a more stable collapsed conformation as they approach bulk water. We have characterized the more probable configurations in all interface and bulk regions. The results obtained are of interest for the study of biomatter processes requiring the transfer of hydrophobic matter, especially chain-like molecules like LCAs, from gas to bulk aqueous systems through the interface.

  16. Structure detection in a libration vibration spectrum of water molecules by methods of nonlinear optics

    Energy Technology Data Exchange (ETDEWEB)

    Babenko, V A; Sychev, Andrei A [P N Lebedev Physical Institute, Russian Academy of Sciences, Moscow (Russian Federation)


    In exciting water possessing an enhanced optical strength by the radiation of a YAG : Nd{sup 3+} laser with 20-ps pulses, nonlinear scattering of light was detected in the frequency range of the optical second harmonic. A relationship was established of the signal of the nonlinear scattering with a stimulated Raman scattering (SRS) of the laser radiation in water. Near the SRS threshold, the structure was observed in the spectrum of nonlinear scattering, which is related to intermolecular libration vibrations of water molecules. (laser applications and other topics in quantum electronics)

  17. Molecular Dynamics Study of Water Molecules in Interlayer of 14 ^|^Aring; Tobermorite

    KAUST Repository

    Yoon, Seyoon


    The molecular structure and dynamics of interlayer water of 14 Å tobermorite are investigated based on molecular dynamics (MD) simulations. Calculated structural parameters of the interlayer water configuration are in good agreement with current knowledge of the refined structure. The MD simulations provide detailed information on the position and mobility of the hydrogen and oxygen of interlayer water, as well as its self-diffusion coefficient, through the interlayer of 14 Å tobermorite. Comparison of the MD simulation results at 100 and 300 K demonstrates that water molecules in the interlayer maintain their structure but change their mobility. The dominant configuration and self-diffusion coefficient of interlayer water are obtained in this study. Copyright © 2013 Japan Concrete Institute.

  18. Single-molecule folding mechanisms of the apo- and Mg2+-bound states of human neuronal calcium sensor-1

    DEFF Research Database (Denmark)

    Naqvi, Mohsin M; Heiðarsson, Pétur Orri; Otazo, Mariela R


    were reconstructed through hidden Markov model analysis. Unlike what has been observed with the Ca(2+)-bound state, the presence of Mg(2+) allows both the N- and C-domain to fold through all-or-none transitions with similar refolding rates. In the absence of divalent ions, NCS-1 unfolds and refolds...

  19. Adhesion of alumina surfaces through confined water layers containing various molecules. (United States)

    Rossetto, Hebert L; Bowen, James; Kendall, Kevin


    When two surfaces confine water layers between them at the nanoscale, the behavior of these confined water molecules can deviate significantly from the behavior of bulk water, and it could reflect on the adhesion of such surfaces. Thus, the aim of this study is to assess the role of confined water layers on the adhesion of hydrophilic surfaces and how sensitive this adhesion is to the presence of contaminants. Our methodology used under water AFM force measurements with an alumina-sputtered sphere-tipped cantilever and a flat alumina single crystal and then added fractions of ethanol, dimethylformamide, formamide, trimethylamine, and trehalose to water as contaminants. Such solutions were designed to illuminate the influences of dielectric constant, molecular size, refractive index, and number of hydrogen bonds from donors and acceptors of solutes to water. Apart from very dilute solutions of dimethylformamide, all solutions decreased the ability of confined water to give adhesion of the alumina surfaces. The predicted theoretical contribution of van der Waals and electrostatic forces was not observed when the contaminants distorted the way water organizes itself in confinement. The conclusion was that adhesion was sensitive mostly to the hydrogen-bonding network within water layers confined by the hydrophilic alumina surfaces.


    Sorption, co-precipitation, and oxidation-reduction reactions of arsenic at the sorbent-water interface are importent factors affecting the fate and transport of arsenic in aqueous systems. Numerous studies have concluded that arsenite (As(III) is more soluble and mobile than ar...

  1. Partition Coefficients of Organic Molecules in Squalane and Water/Ethanol Mixtures by Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Lundsgaard, Rasmus; Kontogeorgis, Georgios; Economou, Ioannis G.


    on the calculations. It was found that the combination of the TraPPE-UA force field and the TIP4p water model gave the best results. Based on the methodology proposed in this article, it is possible to obtain good partition coefficients only knowing the chemical structure of the molecules in the system.......Accurate partition coefficient data of migrants between a polymer and a solvent are of paramount importance for estimating the migration of the migrant over time, including the concentration of the migrant at infinite time in the two solvents. In this article it is shown how this partition...... coefficient can be estimated for both a small hydrophilic and a hydrophobic organic molecules between squalane (used here to mimic low density poly ethylene) and water/ethanol solutes using thermodynamic integration to calculate the free energy of solvation. Molecular dynamics simulations are performed, using...

  2. DFT study on the water molecule adsorption and the surface dissolution behavior of Mg alloys

    Energy Technology Data Exchange (ETDEWEB)

    Nezafati, Marjan [Materials Science and Engineering Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211 (United States); Cho, Kyu [U.S. Army Research Laboratory, Weapons and Materials Research Directorate, Aberdeen Proving Ground, MD 21005 (United States); Giri, Anit [U.S. Army Research Laboratory, Weapons and Materials Research Directorate, Aberdeen Proving Ground, MD 21005 (United States); TKC Global, Herndon, VA 20171 (United States); Kim, Chang-Soo, E-mail: [Materials Science and Engineering Department, University of Wisconsin-Milwaukee, Milwaukee, WI 53211 (United States)


    Mg-based alloys have a strong potential for various structural and biomedical applications. A critical issue associated with Mg-based alloys is their high degradation (corrosion) rates in oxidation environments. It is known that both the internal crystal structures and the impurity compositions/contents in the Mg alloys can affect the degradation rates. In the present work, we employed the density-functional theory (DFT) computation technique to understand the surface degradation behaviors with different crystallographic orientations and impurity elements from an atomistic point of view. Here, we studied the adsorption response of a water molecule to the Mg alloy surface and the dissolution of surface atoms that can be potentially applied to describe the degradation behavior of Mg/Mg alloy. The tendency for water molecule adsorption was quantified for Mg-based slab systems with low-index surface planes and various alloying elements including Al, Zn, Ca, and Y. The trends for surface degradation from these systems were examined using surface energy analysis and electrode potential shift analysis. The results show that adding Ca and/or Y increases the propensity to attract a water molecule to the alloy surface. Also, it was generally found that the relative electrode potential shift of Mg-Y alloys is positive while those of all other alloys are negative. - Highlights: • DFT was used to study the dissolution behavior of Mg atoms from Mg/Mg alloy surface. • Degree of a water molecule adsorption in Mg/Mg alloy surfaces was quantified. • Electrode potential shift trend in Mg alloy surfaces with Al, Zn, Ca, or Y was predicted.

  3. Size distribution of total and water-soluble fractions of particle-bound elements-assessment of possible risks via inhalation. (United States)

    Voutsa, D; Anthemidis, A; Giakisikli, G; Mitani, K; Besis, A; Tsolakidou, A; Samara, C


    The size distribution of total and water-soluble elemental concentrations in six particle sizes particle mode (0.97-1.5 μm), whereas Al, Ba, Ca, Fe, and Mn occurred predominately in the coarse particle mode (3.0-7.2 μm). The water-soluble elemental fractions exhibited significant spatiotemporal variations and particle size dependence. Possible non-carcinogenic and carcinogenic risks associated with inhalation of particle-bound elements based on total and water-soluble concentrations were in acceptable levels. However, the cumulative risk for all potential particle-bound constituents has to be considered.

  4. Investigation of the Hydantoin Monomer and its Interaction with Water Molecules (United States)

    Gruet, Sébastien; Perez, Cristobal; Schnell, Melanie


    Hydantoin (Imidazolidine-2,4-dione, C_3H_4N_2O_2) is a five-membered heterocyclic compound of astrobiological interest. This molecule has been detected in carbonaceous chondrites [1], and its formation can rise from the presence of glycolic acid and urea, two prebiotic molecules [2]. The hydrolysis of hydantoin under acidic conditions can also produce glycine [3], an amino acid actively searched for in the interstellar medium. Spectroscopic data of hydantoin is very limited and mostly dedicated to the solid phase. The high resolution study in gas phase is restricted to the work recently published by Ozeki et al. reporting the pure rotational spectra of the ground state and two vibrational states of the molecule in the millimeter-wave region (90-370 GHz)[4]. Using chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy, we recorded the jet-cooled rotational spectra of hydantoin with water between 2 to 8 GHz. We observed the ground state of hydantoin monomer and several water complexes with one or two water molecules. All the observed species exhibit a hyperfine structure due to the two nitrogen atoms present in the molecule, which were fully resolved and analyzed. Additional experiments with a ^{18}O enriched water sample were realized to determine the oxygen-atom positions of the water monomers. These experiments yielded accurate structural information on the preferred water binding sites. The observed complexes and the interactions that hold them together, mainly strong directional hydrogen bonds, will be presented and discussed. [1] Shimoyama, A. and Ogasawara, R., Orig. Life Evol. Biosph., 32, 165-179, 2002. DOI:10.1023/A:1016015319112. [2] Menor-Salván, C. and Marín-Yaseli, M.R., Chem. Soc. Rev., 41(16), 5404-5415, 2012. DOI:10.1039/c2cs35060b. [3] De Marcellus P., Bertrand M., Nuevo M., Westall F. and Le Sergeant d'Hendecourt L., Astrobiology. 11(9), 847-854, 2011. DOI:10.1089/ast.2011.0677. [4] Ozeki, H., Miyahara R., Ihara H., Todaka S., Kobayashi

  5. Biphasic and SAPC Hydroformylation Catalyzed by Rh-phosphines Bound to Water-Soluble Polymers

    DEFF Research Database (Denmark)

    Malmstrøm, Torsten; Andersson, Carlaxel; Hjortkjær, Jes


    Coupling of the triphenylphosphine moiety to poly-acrylic acid and poly-ethyleneimine respectively afford the macromolecular ligands PAA-PNH and PEI-PNH. Reaction of the ligands with Rh(CO)2(acac) give water-soluble complexes that are active as catalysts in the hydroformylation ofdifferent olefin...... PEI-PNH as ligands show lower stability and activity in both SAPC and biphasic applications....

  6. Colloid-bound and dissolved phosphorus species in topsoil water extracts along a grassland transect from Cambisol to Stagnosol (United States)

    Jiang, Xiaoqian; Bol, Roland; Cade-Menun, Barbara J.; Nischwitz, Volker; Willbold, Sabine; Bauke, Sara L.; Vereecken, Harry; Amelung, Wulf; Klumpp, Erwin


    Phosphorus (P) species in colloidal and dissolved soil fractions may have different distributions. To understand which P species are potentially involved, we obtained water extracts from the surface soils of a gradient from Cambisol, Stagnic Cambisol to Stagnosol from temperate grassland in Germany. These were filtered to dissolved P ( Stagnic Cambisol > Stagnosol. Across all soil types, elevated proportions of inositol hexakisphosphate (IHP) species (e.g., myo-, scyllo- and D-chiro-IHP) were associated with soil mineral particles (i.e., bulk soil and small-sized soil colloids), whereas other orthophosphate monoesters and phosphonates were found in the dissolved P fraction. We conclude that P species composition varies among colloidal and dissolved soil fractions after characterization using advanced techniques, i.e., AF4 and NMR. Furthermore, stagnic properties affect P speciation and availability by potentially releasing dissolved inorganic and ester-bound P forms as well as nano-sized organic matter-Fe/Al-P colloids.

  7. Adsorption of water molecules on selected charged sodium-chloride clusters. (United States)

    Bradshaw, James A; Gordon, Sidney L; Leavitt, Andrew J; Whetten, Robert L


    The adsorption of water molecules (H(2)O) on sodium chloride cluster cations and anions was studied at 298 K over a mass range of 100-1200 amu using a custom-built laser desorption ionization reactor and mass spectrometer. Under the conditions used, the cations Na(3)Cl(2)(+) and Na(4)Cl(3)(+) bind up to three water molecules, whereas the larger cations, Na(5)Cl(4)(+) to Na(19)Cl(18)(+), formed hydrates with one or two only. The overall trend is a decrease in hydration with increasing cluster size, with an abrupt drop occurring at the closed-shell Na(14)Cl(13)(+). As compared to the cluster cations, the cluster anions showed almost no adsorption. Among smaller clusters, a weak adsorption of one water molecule was observed for the cluster anions Na(6)Cl(7)(-) and Na(7)Cl(8)(-). In the higher mass region, a substantial adsorption of one water molecule was observed for Na(14)Cl(15)(-). Density functional theory (DFT) computations were carried out for the adsorption of one molecule of H(2)O on the cations Na(n)Cl(n-1)(+), for n = 2-8, and the anions Na(n)Cl(n+1)(-), for n = 1-7. For each ion, the structure of the hydrate, the hydration energy, and the standard-state enthalpy, entropy, and Gibbs energy of hydration at 298 K were computed. In addition, it was useful to compute the distortion energy, defined as the electronic energy lost due to weakening of the Na-Cl bonds upon adsorption of H(2)O. The results show that strong adsorption of a H(2)O molecule occurs for the linear cations only at an end Na ion and for the nonlinear cations only at a corner Na ion bonded to two Cl ions. An unexpected result of the theoretical investigation for the anions is that certain low-energy isomers of Na(6)Cl(7)(-) and Na(7)Cl(8)(-) bind H(2)O strongly enough to produce the observed weak adsorption. The possible implications of these results for the initial hydration of extended NaCl surfaces are discussed.

  8. Effects of an electric field on the adsorption of water molecules on the Cd(0001) surface (United States)

    Tu, Yu-Bing; Tao, Min-Long; Sun, Kai; Wang, Jun-Zhong


    The adsorption of water molecules on the Cd(0001) surface has been systematically investigated in the absence or presence of the electric field using first principles calculations based on density functional theory. It has been determined that the adsorption is enhanced by the electric field. From the geometries and energetics, we find that the water-cadmium interaction become stronger (weaker) under a negative (positive) field in the adsorbed monomer. Otherwise, the formation of the hydrogen bonds makes it difficult for molecules in the water clusters to response the electric field. Most importantly, the stability of the water bilayers depends on the strength of the negative electric field. Instead of the H-up bilayer, the H-down bilayer is more stable when the negative field is sufficiently strong. In this case, the dipole-field interaction is the dominant interaction in the change of stability. These results are helpful in the understanding of the fundamental processes at the water-electrode interfaces.

  9. Probing the Intermolecular Hydrogen Bonding of Water Molecules at the CCl sub 4 Water Interface in the Presence of Charged Soluble Surfactant

    National Research Council Canada - National Science Library

    Gragson, D


    The molecular structure and hydrogen bonding of water molecules at the CCl sub 4/water interface in the presence of a charged soluble surfactant has been explored in this study using vibrational sum frequency generation...

  10. Ion association in aqueous solutions probed through vibrational energy transfers among cation, anion, and water molecules. (United States)

    Li, Jiebo; Bian, Hongtao; Chen, Hailong; Wen, Xiewen; Hoang, Bryan T; Zheng, Junrong


    KSCN and NH4SCN aqueous solutions were investigated with intermolecular vibrational energy transfer methods. In a KSCN/H2O (1/10 molar ratio) solution, 90% of the initial excitation of the CN stretch (~2066 cm(-1)) of the SCN(-) anion is transferred to the HOH bending mode (~1636 cm(-1)) of water molecules with an energy transfer time constant 3.1 ps. In a NH4SCN/H2O (1/10 molar ratio) solution, only 49% of the CN excitation flows to the water HOH bending mode with a time constant 6.3 ps. Most of the remaining CN excitation goes to the NH bending mode (~1460 cm(-1)) of the NH(+) cation with a time constant of 7.0 ps. The results indicate that about 50% of the energy transfer channel from the CN stretch to the HOH bending observed in the KSCN solution is overpowered by the NH4(+) cations in the NH4SCN/H2O solution. Ion concentration dependent measurements support this argument. According to the dipole/dipole approximation, the CN/OH energy transfer occurs most efficiently between SCN(-) anions and the water molecules closest to them. The experimental results therefore suggest that more than 50% of the water molecules closest to the SCN(-) anions are replaced by the NH4(+) cations in the NH4SCN/H2O (1/10 molar ratio) solution. The percentage is much larger than the NH4(+)/water ratio of 10%, indicating that the ion association between NH4(+) and SCN(-) is caused by the chemical nature of the solution rather than the statistical "forced contact" because of the high ion concentration.

  11. Implantation of Perylene Molecules into Glass Plates through a Water Layer Using a Laser Induced Molecular Micro-Jet (United States)

    Goto, Masahiro; Pihosh, Yuriy; Kasahara, Akira; Tosa, Masahiro


    Perylene molecules have been successfully implanted onto borosilicate glass plates, forming fluorescent features of 420 nm in diameter, using a method involving laser induced molecular micro-jet ejection through a water layer. The technique utilises a polymer source film in which perylene molecules are dispersed, a borosilicate glass substrate as a target and a pulsed laser. The space gap between the source film and the target is filled with liquid water. Perylene molecules dispersed in the polymer source films are photo-excited using 4-ns laser pulses resulting in the ejection of the molecules from the source matrix after which they become implanted into the target after passing through the water layer. This new advanced implantation method, using a laser induced molecular micro-jet through water, gives fine spatial control for fixing functional organic molecules in a designated region on hard dielectric materials and will have application in the fabrication of molecular devices, molecular sensors, and opto-electronics.

  12. Raman spectral classification of mineral- and collagen-bound water's associations to elastic and post-yield mechanical properties of cortical bone. (United States)

    Unal, Mustafa; Akkus, Ozan


    Water that is bound to bone's matrix is implied as a predictor of fracture resistance; however, bound water is an elusive variable to be measured nondestructively. To date, the only nondestructive method used for studying bone hydration status is magnetic resonance variants (NMR or MRI). For the first time, bone hydration status was studied by short-wave infrared (SWIR) Raman spectroscopy to investigate associations of mineral-bound and collagen-bound water compartments with mechanical properties. Thirty cortical bone samples were used for quantitative Raman-based water analysis, gravimetric analysis, porosity measurement, and biomechanical testing. A sequential dehydration protocol was developed to replace unbound (heat drying) and bound (ethanol treatment) water in bone. Raman spectra were collected serially to track the OH-stretch band during dehydration. Four previously identified peaks were investigated: I3220/I2949, I3325/I2949 and I3453/I2949 reflect status of organic-matrix related water (mostly collagen-related water) compartments and collagen portion of bone while I3584/I2949 reflects status of mineral-related water compartments and mineral portion of bone. These spectroscopic biomarkers were correlated with elastic and post-yield mechanical properties of bone. Collagen-water related biomarkers (I3220/I2949 and I3325/I2949) correlated significantly and positively with toughness (R(2)=0.81 and R(2)=0.79; pproperties of wet bone and the reported correlations of Raman-based water measurements to mechanical properties underline the necessity for enabling approaches to assess these new biomarkers noninvasively in vivo to improve the current diagnosis of those who may be at risk of bone fracture due to aging and diseases. Published by Elsevier Inc.

  13. Release of mineral-bound water prior to subduction tied to shallow seismogenic slip off Sumatra. (United States)

    Hüpers, Andre; Torres, Marta E; Owari, Satoko; McNeill, Lisa C; Dugan, Brandon; Henstock, Timothy J; Milliken, Kitty L; Petronotis, Katerina E; Backman, Jan; Bourlange, Sylvain; Chemale, Farid; Chen, Wenhuang; Colson, Tobias A; Frederik, Marina C G; Guèrin, Gilles; Hamahashi, Mari; House, Brian M; Jeppson, Tamara N; Kachovich, Sarah; Kenigsberg, Abby R; Kuranaga, Mebae; Kutterolf, Steffen; Mitchison, Freya L; Mukoyoshi, Hideki; Nair, Nisha; Pickering, Kevin T; Pouderoux, Hugo F A; Shan, Yehua; Song, Insun; Vannucchi, Paola; Vrolijk, Peter J; Yang, Tao; Zhao, Xixi


    Plate-boundary fault rupture during the 2004 Sumatra-Andaman subduction earthquake extended closer to the trench than expected, increasing earthquake and tsunami size. International Ocean Discovery Program Expedition 362 sampled incoming sediments offshore northern Sumatra, revealing recent release of fresh water within the deep sediments. Thermal modeling links this freshening to amorphous silica dehydration driven by rapid burial-induced temperature increases in the past 9 million years. Complete dehydration of silicates is expected before plate subduction, contrasting with prevailing models for subduction seismogenesis calling for fluid production during subduction. Shallow slip offshore Sumatra appears driven by diagenetic strengthening of deeply buried fault-forming sediments, contrasting with weakening proposed for the shallow Tohoku-Oki 2011 rupture, but our results are applicable to other thickly sedimented subduction zones including those with limited earthquake records. Copyright © 2017, American Association for the Advancement of Science.

  14. Bounding Limitations in the Practical Design of Adsorption Heat Pump Water Heaters

    Energy Technology Data Exchange (ETDEWEB)

    Ally, Moonis Raza [ORNL; Sharma, Vishaldeep [ORNL; Gluesenkamp, Kyle R [ORNL


    The boundary temperatures for any sorption-based technology can be estimated on the basis of Trouton s hypothesis that isosteres, extrapolated to infinite pressure (or analogously to infinite temperature) meet at a single point. In this paper we discuss the consequences of this hypothesis for many sorption devices that are thermally operated, suitable for exploiting renewable energy resources, or making better use of high or low level thermal energy. Trouton s hypothesis is independent of the working fluids making it particularly useful to both liquid-vapor and solid-vapor systems. We exemplify the use of the derived boundary temperatures derived from Trouton s hypothesis to important processes such as ice making, space cooling in hot climates, deep freezing, and residential hot water production. The boundary temperatures help determine which sorption or solar heating technology may be better suited to serve the given application, or whether it is beyond the scope of sorption systems.

  15. Modeling the Release Kinetics of Poorly Water-Soluble Drug Molecules from Liposomal Nanocarriers

    Directory of Open Access Journals (Sweden)

    Stephan Loew


    Full Text Available Liposomes are frequently used as pharmaceutical nanocarriers to deliver poorly water-soluble drugs such as temoporfin, cyclosporine A, amphotericin B, and paclitaxel to their target site. Optimal drug delivery depends on understanding the release kinetics of the drug molecules from the host liposomes during the journey to the target site and at the target site. Transfer of drugs in model systems consisting of donor liposomes and acceptor liposomes is known from experimental work to typically exhibit a first-order kinetics with a simple exponential behavior. In some cases, a fast component in the initial transfer is present, in other cases the transfer is sigmoidal. We present and analyze a theoretical model for the transfer that accounts for two physical mechanisms, collisions between liposomes and diffusion of the drug molecules through the aqueous phase. Starting with the detailed distribution of drug molecules among the individual liposomes, we specify the conditions that lead to an apparent first-order kinetic behavior. We also discuss possible implications on the transfer kinetics of (1 high drug loading of donor liposomes, (2 attractive interactions between drug molecules within the liposomes, and (3 slow transfer of drugs between the inner and outer leaflets of the liposomes.

  16. Single-Molecule Imaging of DNAs with Sticky Ends at Water/Fused Silica Interface

    Energy Technology Data Exchange (ETDEWEB)

    Isailovic, Slavica [Iowa State Univ., Ames, IA (United States)


    Total internal reflection fluorescence microscopy (TIRFM) was used to study intermolecular interactions of DNAs with unpaired (sticky) ends of different lengths at water/fused silica interface at the single-molecule level. Evanescent field residence time, linear velocity and adsorption/desorption frequency were measured in a microchannel for individual DNA molecules from T7, Lambda, and PSP3 phages at various pH values. The longest residence times and the highest adsorption/desorption frequencies at the constant flow at pH 5.5 were found for PSP3 DNA, followed by lower values for Lambda DNA, and the lowest values for T7 DNA. Since T7, Lambda, and PSP3 DNA molecules contain none, twelve and nineteen unpaired bases, respectively, it was concluded that the affinity of DNAs for the surface increases with the length of the sticky ends. This confirms that hydrophobic and hydrogen-bonding interactions between sticky ends and fused-silica surface are driving forces for DNA adsorption at the fused-silica surface. Described single-molecule methodology and results therein can be valuable for investigation of interactions in liquid chromatography, as well as for design of DNA hybridization sensors and drug delivery systems.

  17. Reactions of water and C1 molecules on carbide and metal-modified carbide surfaces. (United States)

    Wan, Weiming; Tackett, Brian M; Chen, Jingguang G


    The formation of carbides can significantly modify the physical and chemical properties of the parent metals. In the current review, we summarize the general trends in the reactions of water and C1 molecules over transition metal carbide (TMC) and metal-modified TMC surfaces and thin films. Although the primary focus of the current review is on the theoretical and experimental studies of reactions of C1 molecules (CO, CO2, CH3OH, etc.), the reactions of water will also be reviewed because water plays an important role in many of the C1 transformation reactions. This review is organized by discussing separately thermal reactions and electrochemical reactions, which provides insights into the application of TMCs in heterogeneous catalysis and electrocatalysis, respectively. In thermal reactions, we discuss the thermal decomposition of water and methanol, as well as the reactions of CO and CO2 over TMC surfaces. In electrochemical reactions, we summarize recent studies in the hydrogen evolution reaction, electrooxidation of methanol and CO, and electroreduction of CO2. Finally, future research opportunities and challenges associated with using TMCs as catalysts and electrocatalysts are also discussed.

  18. Bioaccumulation of tritiated water in phytoplankton and trophic transfer of organically bound tritium to the blue mussel, Mytilus edulis. (United States)

    Jaeschke, Benedict C; Bradshaw, Clare


    Large releases of tritium are currently permitted in coastal areas due to assumptions that it rapidly disperses in the water and has a low toxicity due to its low energy emissions. This paper presents a laboratory experiment developed to identify previously untested scenarios where tritium may concentrate or transfer in biota relevant to Baltic coastal communities. Phytoplankton populations of Dunaliella tertiolecta and Nodularia spumigena were exposed at different growth-stages, to tritiated water (HTO; 10 MBq l(-1)). Tritiated D. tertiolecta was then fed to mussels, Mytilus edulis, regularly over a period of three weeks. Activity concentrations of phytoplankton and various tissues from the mussel were determined. Both phytoplankton species transformed HTO into organically-bound tritium (OBT) in their tissues. D. tertiolecta accumulated significantly more tritium when allowed to grow exponentially in HTO than if it had already reached the stationary growth phase; both treatments accumulated significantly more than the corresponding treatments of N. spumigena. No effect of growth phase on bioaccumulation of tritium was detectable in N. spumigena following exposure. After mussels were given 3 feeds of tritiated D. tertiolecta, significant levels of tritium were detected in the tissues. Incorporation into most mussel tissues appeared to follow a linear relationship with number of tritiated phytoplankton feeds with no equilibrium, highlighting the potential for biomagnification. Different rates of incorporation in species from a similar functional group highlight the difficulties in using a 'representative' species for modelling the transfer and impact of tritium. Accumulations of organic tritium into the mussel tissues from tritiated-phytoplankton demonstrate an environmentally relevant transfer pathway of tritium even when water-concentrations are reduced, adding weight to the assertion that organically bound tritium acts as a persistent organic pollutant. The

  19. Calculations for ion-impact induced ionization and fragmentation of water molecules (United States)

    Kirchner, Tom; Murakami, Mitsuko; Horbatsch, Marko; Jürgen Lüdde, Hans


    Charge-state correlated cross sections for single- and multiple-electron removal processes in proton-water-molecule collisions are calculated by using the non-perturbative basis generator method adapted for ion-molecule collisions [1,2]. A fragmentation model is then applied to calculate the yields of H2O^+, OH^+, H^+, and O^+ ions emerging after H2O^q+ formation [3]. A detailed comparison is made with experimental data from three groups covering the energy range from 20--5000 keV. It is found that multiple electron processes with qMurakami et al, Phys. Rev. A 85, 052704 (2012)[0pt] [3] M. Murakami et al, Phys. Rev. A 85, 052713 (2012)

  20. Ab Initio Density Functional Theory Investigation of the Interaction between Carbon Nanotubes and Water Molecules during Water Desalination Process

    Directory of Open Access Journals (Sweden)

    Loay A. Elalfy


    Full Text Available Density functional theory calculations using B3LYP/3-21G level of theory have been implemented on 6 carbon nanotubes (CNTs structures (3 zigzag and 3 armchair CNTs to study the energetics of the reverse osmosis during water desalination process. Calculations of the band gap, interaction energy, highest occupied molecular orbital, lowest unoccupied molecular orbital, electronegativity, hardness, and pressure of the system are discussed. The calculations showed that the water molecule that exists inside the CNT is about 2-3 Å away from its wall. The calculations have proven that the zigzag CNTs are more efficient for reverse osmosis water desalination process than armchair CNTs as the reverse osmosis process requires pressure of approximately 200 MPa for armchair CNTs, which is consistent with the values used in molecular dynamics simulations, while that needed when using zigzag CNTs was in the order of 60 MPa.

  1. Influence of the water molecules near surface of viral protein on virus activation process (United States)

    Shepelenko, S. O.; Salnikov, A. S.; Rak, S. V.; Goncharova, E. P.; Ryzhikov, A. B.


    The infection of a cell with influenza virus comprises the stages of receptor binding to the cell membrane, endocytosis of virus particle, and fusion of the virus envelope and cell endosome membrane, which is determined by the conformational changes in hemagglutinin, a virus envelope protein, caused by pH decrease within the endosome. The pH value that induces conformation rearrangements of hemagglutinin molecule considerably varies for different influenza virus strains, first and foremost, due to the differences in amino acid structure of the corresponding proteins. The main goal of this study was to construct a model making it possible to assess the critical pH value characterizing the fusogenic activity of influenza virus hemagglutinin from the data on hemagglutinin structure and experimental verification of this model. Under this model, we assume that when the electrostatic force between interacting hemagglutinin molecules in the virus envelop exceeds a certain value, the hemagglutinin HA1 subunits are arranged so that they form a cavity sufficient for penetration of water molecules. This event leads to an irreversible hydration of the inner fragments of hemagglutinin molecule in a trimer and to the completion of conformational changes. The geometry of electrostatic field in hemagglutinin trimer was calculated taking into account the polarization effects near the interface of two dielectrics, aqueous medium and protein macromolecule. The critical pH values for the conformational changes in hemagglutinin were measured by the erythrocyte hemolysis induced by influenza virus particles when decreasing pH. The critical pH value conditionally separating the pH range into the regions with and without the conformational changes was calculated for several influenza virus H1N1 and H3N2 strains based on the data on the amino acid structure of the corresponding hemagglutinin molecules. Comparison of the theoretical and experimental values of critical pH values for

  2. Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines (United States)

    Bernatskiy, A. V.; Ochkin, V. N.


    A new approach is considered to detect the water leaks in inert plasma-forming gas present in the reactor chamber. It is made up of the intensity ratio of D α and H α spectral lines in combination with O, Ar and Xe lines intensity. The concentrations of H2O, O, H and D particles have been measured with high sensitivity. At the D2 admixture pressure {{p}{{\\text{D}\\text{2}}}}   =  0.025 mbar, we used the acquisition time of 10 s to measure the rate of water molecules injected from the outside, Γ0  =  1.4 · 10-9 mbar · m3 · s-1, and the incoming water molecules to plasma, Γ  =  5 ·10-11 mbar · m3 · s-1. The scaling proves that at small D2 admixtures (10-4 mbar), the leaks with the rates Γ0  ≈  6 · 10-12 mbar · m3 · s-1 and Γ  ≈  2 · 10-13 mbar · m3 · s-1 can be detected and measured. The difference between Γ0 and Γ values is due to the high degree of H2O dissociation, which can be up to 97-98%.

  3. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study (United States)

    Takahashi, Ohgi; Kirikoshi, Ryota


    Aspartic acid (Asp) residues in peptides and proteins (l-Asp) are known to undergo spontaneous nonenzymatic reactions to form l-β-Asp, d-Asp, and d-β-Asp residues. The formation of these abnormal Asp residues in proteins may affect their three-dimensional structures and hence their properties and functions. Indeed, the reactions have been thought to contribute to aging and pathologies. Most of the above reactions of the l-Asp residues proceed via a cyclic succinimide intermediate. In this paper, a novel three-water-assisted mechanism is proposed for cyclization of an Asp residue (forming a gem-diol precursor of the succinimide) by the B3LYP/6-31 + G(d,p) density functional theory calculations carried out for an Asp-containing model compound (Ace-Asp-Nme, where Ace = acetyl and Nme = NHCH3). The three water molecules act as catalysts by mediating ‘long-range’ proton transfers. In the proposed mechanism, the amide group on the C-terminal side of the Asp residue is first converted to the tautomeric iminol form (iminolization). Then, reorientation of a water molecule and a conformational change occur successively, followed by the nucleophilic attack of the iminol nitrogen on the carboxyl carbon of the Asp side chain to form the gem-diol species. A satisfactory agreement was obtained between the calculated and experimental energetics.

  4. Two-dimensional crystallography of amphiphilic molecules at the air-water interface

    DEFF Research Database (Denmark)

    Jacquemain, D.; Grayer Wolf, S.; Leveiller, F.


    time the determination of the in-plane and vertical structure of such monolayers with a resolution approaching the atomic level. We briefly describe these methods, including grazing incidence X-ray diffraction, specular reflectivity, Bragg rods, standing waves, and surface fluorescence techniques......, and review recent results obtained from them for Langmuir films. The methods have been successfully applied in the elucidation of the structure of crystalline aggregates of amphiphilic molecules such as alcohols, carboxylic acids and their salts, alpha-amino acids, and phospholipids at the water surface...

  5. Continuum Navier-Stokes modelling of water ow past fullerene molecules

    DEFF Research Database (Denmark)

    Walther, J. H.; Popadic, A.; Koumoutsakos, P.

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently...

  6. Continuum Navier-Stokes modelling of water flow past fullerene molecules

    DEFF Research Database (Denmark)

    Walther, J. H.; Popadic, A.; Koumoutsakos, P.

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip boundary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...... as computed by the present model are in good agreement with results from atomistic and atomistic-continuum simulations at a fraction of the computational cost. We simulate the flow past a single fullerene and an array of fullerenes and demonstrate that such nanoscale flows can be computed efficiently...

  7. Structure and dynamics of water and lipid molecules in charged anionic DMPG lipid bilayer membranes

    DEFF Research Database (Denmark)

    Rønnest, A. K.; Peters, Günther H.J.; Hansen, Flemming Yssing


    Molecular dynamics simulations have been used to investigate the influence of the valency of counter-ions on the structure of freestanding bilayer membranes of the anionic 1,2-dimyristoyl-sn-glycero-3-phosphoglycerol (DMPG) lipid at 310 K and 1 atm. At this temperature, the membrane is in the fluid...... phase with a monovalent counter-ion and in the gel phase with a divalent counter-ion. The diffusion constant of water as a function of its depth in the membrane has been determined from mean-square-displacement calculations. Also, calculated incoherent quasielastic neutron scattering functions have been...... compared to experimental results and used to determine an average diffusion constant for all water molecules in the system. On extrapolating the diffusion constants inferred experimentally to a temperature of 310 K, reasonable agreement with the simulations is obtained. However, the experiments do not have...

  8. Energy deposition model based on electron scattering cross section data from water molecules

    Energy Technology Data Exchange (ETDEWEB)

    Munoz, A; Oiler, J C [Centra de Investigaciones Energeticas, Medioambientales y Tecnologicas (CIEMAT), Avenida Complutense 22, 28040 Madrid (Spain); Blanco, F [Departamento de Fisica Atomica, Molecular y Nuclear, Universidad Complutense de Madrid, Avenida Complutense s.n., 28040 Madrid (Spain); Gorfinkiel, J D [Department of Physiscs and Astronomy, The Open University, Walton Hall, Milton Keynes MK7 6AA (United Kingdom); Limao-Vieira, P [Departamento de Fisica, Universidade Nova de Lisboa, 2829-516 Caparica (Portugal); Maira-Vidal, A; Borge, M J G; Tengblad, O [Instituto de Estructura de la Materia, Consejo Superior de Investigaciones Cientificas (CSIC), Serrano 113-bis, 28006 Madrid, Spam (Spain); Huerga, C; Tellez, M [Hospital Universitario La Paz, paseo de la Castellana 261, 28046 Madrid (Spain); Garcia, G [Instituto de Matematicas y Fisica Fundamental, Consejo Superior de Investigaciones CientifIcas (CSIC), Serrano 113-bis, 28006 Madrid (Spain)], E-mail:


    A complete set of electrons scattering cross sections by water molecules over a broad energy range, from the me V to the Me V ranges, is presented in this study. These data have been obtained by combining experiments and calculations and cover most relevant processes, both elastic and inelastic, which can take place in the considered energy range. A new Monte Carlo simulation programme has been developed using as input parameter these cross sectional data as well as experimental energy loss spectra. The simulation procedure has been applied to obtain electron tracks and energy deposition plots in water when irradiated by a Ru-106 plaque as those used for brachytherapy of ocular tumours. Finally, the low energy electron tracks provided by the present model have been compared with those obtained with other codes available in the literature.

  9. Conserved hydrogen bonds and water molecules in MDR HIV-1 protease substrate complexes

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Zhigang [Wayne State Univ., Detroit, MI (United States); Case Western Reserve Univ., Cleveland, OH (United States); Harbor Hospital Baltimore, MD (United States); Wang, Yong [Wayne State Univ., Detroit, MI (United States); Yedidi, Ravikiran S. [Wayne State Univ., Detroit, MI (United States); National Institutes of Health, Bethesda, MD (United States); Dewdney, Tamaria G. [Wayne State Univ., Detroit, MI (United States); Reiter, Samuel J. [Wayne State Univ., Detroit, MI (United States); Brunzelle, Joseph S. [Northwestern Univ. Feinberg School of Medicine, Chicago, IL (United States); Kovari, Iulia A. [Wayne State Univ., Detroit, MI (United States); Kovari, Ladislau C. [Wayne State Univ., Detroit, MI (United States)


    Success of highly active antiretroviral therapy (HAART) in anti-HIV therapy is severely compromised by the rapidly developing drug resistance. HIV-1 protease inhibitors, part of HAART, are losing their potency and efficacy in inhibiting the target. Multi-drug resistant (MDR) 769 HIV-1 protease (resistant mutations at residues 10, 36, 46, 54, 62, 63, 71, 82, 84, 90) was selected for the present study to understand the binding to its natural substrates. The nine crystal structures of MDR769 HIV-1 protease substrate hepta-peptide complexes were analyzed in order to reveal the conserved structural elements for the purpose of drug design against MDR HIV-1 protease. Our structural studies demonstrated that highly conserved hydrogen bonds between the protease and substrate peptides, together with the conserved crystallographic water molecules, played a crucial role in the substrate recognition, substrate stabilization and protease stabilization. Additionally, the absence of the key flap-ligand bridging water molecule might imply a different catalytic mechanism of MDR769 HIV-1 protease compared to that of wild type (WT) HIV-1 protease.

  10. On the Importance of Water Molecules in the Theoretical Study of Polyphenols Reactivity toward Superoxide Anion

    Directory of Open Access Journals (Sweden)

    Laure Lespade


    Full Text Available Numerous studies have shown the benefits of a diet rich in fruits and vegetables. These benefits are partly due to the radical scavenging properties of polyphenols contained in fruits and vegetables since polyphenols can fight against an excess of radicals which goes along inflammation in a certain number of diseases. This pathological state, called oxidative stress, results from the aerobic condition of human organism when OH radical, hydrogen peroxide, superoxide anion, or peroxynitrite is produced in excess. If hydrogen peroxide is easily handled by human defense against radicals, the other radicals can cause damage to biological constituents like lipids, cell membranes, and other biomolecules. This paper is devoted to the theoretical study of the interaction of superoxide anion (O2•- with a very potent radical scavenger, 1,2,4,6,8-pentahydroxynaphthalene. The importance of hydration of superoxide radical for the reactivity is analyzed. Potential energy surfaces (PES are calculated for different number of water molecules around the radical and it is shown that the transition barrier vanishes when complete hydration with six water molecules is explicitly handled. The nature of the reactivity is determined by using the natural bond orbital (NBO analysis.

  11. Confocal fluorescence microscope studies of the adsorptive behavior of dioctadecyl-rhodamine B molecules at a cyclohexane-water interface. (United States)

    Zheng, X Y; Harata, A


    The capabilities of using a confocal fluorescence microscope (CFM) for the interface-selective observation of dye molecules at an oil-water interface were evaluated. A simple expression for a criterion of interface selectivity was derived. The adsorptive behavior of dioctadecyl-rhodamine B at a cyclohexane-water interface was investigated experimentally to demonstrate the interface-selective observation with a CFM. The minimum number of detectable molecules in the probe area at the interface was estimated to be 82 for the present system. Preliminary experimental results of co-adsorption systems composed of adsorbed dye molecules and charged surfactants are also presented.

  12. Electrocatalytic Water Oxidation by a Water-Soluble Copper(II) Complex with a Copper-Bound Carbonate Group Acting as a Potential Proton Shuttle. (United States)

    Chen, Fangfang; Wang, Ni; Lei, Haitao; Guo, Dingyi; Liu, Hongfei; Zhang, Zongyao; Zhang, Wei; Lai, Wenzhen; Cao, Rui


    Water-soluble copper(II) complexes of the dianionic tridentate pincer ligand N,N'-2,6-dimethylphenyl-2,6-pyridinedicarboxamidate (L) are catalysts for water oxidation. In [L-Cu II -DMF] (1, DMF = dimethylformamide) and [L-Cu II -OAc] - (2, OAc = acetate), ligand L binds Cu II through three N atoms, which define an equatorial plane. The fourth coordination site of the equatorial plane is occupied by DMF in 1 and by OAc - in 2. These two complexes can electrocatalyze water oxidation to evolve O 2 in 0.1 M pH 10 carbonate buffer. Spectroscopic, titration, and crystallographic studies show that both 1 and 2 undergo ligand exchange when they are dissolved in carbonate buffer to give [L-Cu II -CO 3 H] - (3). Complex 3 has a similar structure as those of 1 and 2 except for having a carbonate group at the fourth equatorial position. A catalytic cycle for water oxidation by 3 is proposed based on experimental and theoretical results. The two-electron oxidized form of 3 is the catalytically active species for water oxidation. Importantly, for these two oxidation events, the calculated potential values of E p,a = 1.01 and 1.59 V vs normal hydrogen electrode (NHE) agree well with the experimental values of E p,a = 0.93 and 1.51 V vs NHE in pH 10 carbonate buffer. The potential difference between the two oxidation events is 0.58 V for both experimental and calculated results. With computational evidence, this Cu-bound carbonate group may act as a proton shuttle to remove protons for water activation, a key role resembling intramolecular bases as reported previously.

  13. Identification of Carboxylate, Phosphate, and Phenoxide Functionalities in Deprotonated Molecules Related to Drug Metabolites via Ion-Molecule Reactions with water and Diethylhydroxyborane (United States)

    Zhu, Hanyu; Ma, Xin; Kong, John Y.; Zhang, Minli; Kenttämaa, Hilkka I.


    Tandem mass spectrometry based on ion-molecule reactions has emerged as a powerful tool for structural elucidation of ionized analytes. However, most currently used reagents were designed to react with protonated analytes, making them suboptimal for acidic analytes that are preferentially detected in negative ion mode. In this work we demonstrate that the phenoxide, carboxylate, and phosphate functionalities can be identified in deprotonated molecules by use of a combination of two reagents, diethylmethoxyborane (DEMB) and water. A novel reagent introduction setup that allowed DEMB and water to be separately introduced into the ion trap region of the mass spectrometer was developed to facilitate fundamental studies of this reaction. A new reagent, diethylhydroxyborane (DEHB), was generated inside the ion trap by hydrolysis of DEMB on introduction of water. Most carboxylates and phenoxides formed a DEHB adduct, followed by addition of one water molecule and subsequent ethane elimination (DEHB adduct +H2O - CH3CH3) as the major product ion. Phenoxides with a hydroxy group adjacent to the deprotonation site and phosphates formed a DEHB adduct, followed by ethane elimination (DEHB adduct - CH3CH3). Deprotonated molecules with strong intramolecular hydrogen bonds or without the aforementioned functionalities, including sulfates, were unreactive toward DEHB/H2O. Reaction mechanisms were explored via isotope labeling experiments and quantum chemical calculations. The mass spectrometry method allowed the differentiation of phenoxide-, carboxylate-, phosphate-, and sulfate-containing analytes. Finally, it was successfully coupled with high-performance liquid chromatography for the analysis of a mixture containing hymecromone, a biliary spasm drug, and its three possible metabolites. [Figure not available: see fulltext.

  14. Bounded Rationality

    National Research Council Canada - National Science Library

    Ballester Pla, Coralio; Hernández, Penélope


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

  15. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data]. (United States)

    Gonzalez, E; Lino, J; Deriabina, A; Herrera, J N F; Poltev, V I


    To elucidate details of the DNA-water interactions we performed the calculations and systemaitic search for minima of interaction energy of the systems consisting of one of DNA bases and one or two water molecules. The results of calculations using two force fields of molecular mechanics (MM) and correlated ab initio method MP2/6-31G(d, p) of quantum mechanics (QM) have been compared with one another and with experimental data. The calculations demonstrated a qualitative agreement between geometry characteristics of the most of local energy minima obtained via different methods. The deepest minima revealed by MM and QM methods correspond to water molecule position between two neighbor hydrophilic centers of the base and to the formation by water molecule of hydrogen bonds with them. Nevertheless, the relative depth of some minima and peculiarities of mutual water-base positions in' these minima depend on the method used. The analysis revealed insignificance of some differences in the results of calculations performed via different methods and the importance of other ones for the description of DNA hydration. The calculations via MM methods enable us to reproduce quantitatively all the experimental data on the enthalpies of complex formation of single water molecule with the set of mono-, di-, and trimethylated bases, as well as on water molecule locations near base hydrophilic atoms in the crystals of DNA duplex fragments, while some of these data cannot be rationalized by QM calculations.

  16. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A


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

  17. Finite-bias electronic transport of molecules in a water solution

    KAUST Repository

    Rungger, Ivan


    The effects of water wetting conditions on the transport properties of molecular nanojunctions are investigated theoretically by using a combination of empirical-potential molecular-dynamics and first-principles electronic-transport calculations. These are at the level of the nonequilibrium Green’s-function method implemented for self-interaction corrected density-functional theory. We find that water effectively produces electrostatic gating to the molecular junction with a gating potential determined by the time-averaged water dipole field. Such a field is large for the polar benzene-dithiol molecule, resulting in a transmission spectrum shifted by about 0.6 eV with respect to that of the dry junction. The situation is drastically different for carbon nanotubes (CNTs). In fact, because of their hydrophobic nature the gating is almost negligible so that the average transmission spectrum of wet Au/CNT/Au junctions is essentially the same as that in dry conditions. This suggests that CNTs can be used as molecular interconnects also in water-wet situations, for instance, as tips for scanning tunnel microscopy in solution or in biological sensors.

  18. Cation effects on rotational dynamics of anions and water molecules in alkali (Li+, Na+, K+, Cs+) thiocyanate (SCN-) aqueous solutions. (United States)

    Bian, Hongtao; Chen, Hailong; Zhang, Qiang; Li, Jiebo; Wen, Xiewen; Zhuang, Wei; Zheng, Junrong


    Waiting time dependent rotational anisotropies of SCN(-) anions and water molecules in alkali thiocyanate (XSCN, X = Li, Na, K, Cs) aqueous solutions at various concentrations were measured with ultrafast infrared spectroscopy. It was found that cations can significantly affect the reorientational motions of both water molecules and SCN(-) anions. The dynamics are slower in a solution with a smaller cation. The reorientational time constants follow the order of Li(+) > Na(+) > K(+) ~/= Cs(+). The changes of rotational time constants of SCN(-) at various concentrations scale almost linearly with the changes of solution viscosity, but those of water molecules do not. In addition, the concentration-dependent amplitudes of dynamical changes are much more significant in the Li(+) and Na(+) solutions than those in the K(+) and Cs(+) solutions. Further investigations on the systems with the ultrafast vibrational energy exchange method and molecular dynamics simulations provide an explanation for the observations: the observed rotational dynamics are the balanced results of ion clustering and cation/anion/water direct interactions. In all the solutions at high concentrations (>5 M), substantial amounts of ions form clusters. The structural inhomogeneity in the solutions leads to distinct rotational dynamics of water and anions. The strong interactions of Li(+) and Na(+) because of their relatively large charge densities with water molecules and SCN(-) anions, in addition to the likely geometric confinements because of ion clustering, substantially slow down the rotations of SCN(-) anions and water molecules inside the ion clusters. The interactions of K(+) and Cs(+) with water or SCN(-) are much weaker. The rotations of water molecules inside ion clusters of K(+) and Cs(+) solutions are not significantly different from those of other water species so that the experimentally observed rotational relaxation dynamics are only slightly affected by the ion concentrations.

  19. Probing the Structure of Water Molecules at an Oil/Water Interface in the Presence of a Charged Soluble Surfactant Through Isotopic Dilution Studies

    National Research Council Canada - National Science Library

    Gragson, D


    .... By examining OH stretching modes that are highly sensitive to the local hydrogen bonding environment, we have been able to compare the structure of interfacial water molecules with the structure...

  20. Formation of the weakly bound muonic molecule (4Heμt) 01 2 + in the three-body (tμ) 1 s +4He +4He collision (United States)

    Czapliński, Wilhelm; Rybski, Michał


    Formation of the weakly bound muonic molecule (4He μt)012+ in the excited rotational-vibrational state (J , ν) = (0 , 1) due to the three-body collision (tμ)1 s +4He +4He is considered for the first time. It is assumed that the process occurs in T-4He gaseous mixture in thermal equilibrium containing thermalized muonic tritium atoms. The corresponding reaction rate is calculated in the frame of the distorted wave Born approximation (DWBA) method using the dipole approximation for the interaction of tμ +4He system with the incoming helium atom. The obtained formation rate (normalized to helium density equal to the liquid hydrogen density) increases with temperature from 7.8 ṡ106 s-1 for 1000 K to 4.8 ṡ107 s-1 for 3000 K.

  1. Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide* (United States)

    Yin, Liusong; Trenh, Peter; Guce, Abigail; Wieczorek, Marek; Lange, Sascha; Sticht, Jana; Jiang, Wei; Bylsma, Marissa; Mellins, Elizabeth D.; Freund, Christian; Stern, Lawrence J.


    HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides interacting nonoptimally in the P1 pocket exhibited low MHCII binding affinity and kinetic instability and were highly susceptible to HLA-DM-mediated peptide exchange. These changes were accompanied by conformational alterations detected by surface plasmon resonance, SDS resistance assay, antibody binding assay, gel filtration, dynamic light scattering, small angle x-ray scattering, and NMR spectroscopy. Surprisingly, all of those changes could be reversed by substitution of the P9 pocket anchor residue. Moreover, MHCII mutations outside the P1 pocket and the HLA-DM interaction site increased HLA-DM susceptibility. These results indicate that a dynamic MHCII conformational determinant rather than P1 pocket occupancy is the key factor determining susceptibility to HLA-DM-mediated peptide exchange and provide a molecular mechanism for HLA-DM to efficiently target unstable MHCII-peptide complexes for editing and exchange those for more stable ones. PMID:25002586

  2. Susceptibility to HLA-DM protein is determined by a dynamic conformation of major histocompatibility complex class II molecule bound with peptide. (United States)

    Yin, Liusong; Trenh, Peter; Guce, Abigail; Wieczorek, Marek; Lange, Sascha; Sticht, Jana; Jiang, Wei; Bylsma, Marissa; Mellins, Elizabeth D; Freund, Christian; Stern, Lawrence J


    HLA-DM mediates the exchange of peptides loaded onto MHCII molecules during antigen presentation by a mechanism that remains unclear and controversial. Here, we investigated the sequence and structural determinants of HLA-DM interaction. Peptides interacting nonoptimally in the P1 pocket exhibited low MHCII binding affinity and kinetic instability and were highly susceptible to HLA-DM-mediated peptide exchange. These changes were accompanied by conformational alterations detected by surface plasmon resonance, SDS resistance assay, antibody binding assay, gel filtration, dynamic light scattering, small angle x-ray scattering, and NMR spectroscopy. Surprisingly, all of those changes could be reversed by substitution of the P9 pocket anchor residue. Moreover, MHCII mutations outside the P1 pocket and the HLA-DM interaction site increased HLA-DM susceptibility. These results indicate that a dynamic MHCII conformational determinant rather than P1 pocket occupancy is the key factor determining susceptibility to HLA-DM-mediated peptide exchange and provide a molecular mechanism for HLA-DM to efficiently target unstable MHCII-peptide complexes for editing and exchange those for more stable ones. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Chemopreventive effects of free and bound phenolics associated to steep waters (nejayote) obtained after nixtamalization of different maize types. (United States)

    Rojas-García, Carlos; García-Lara, Silverio; Serna-Saldivar, Sergio O; Gutiérrez-Uribe, Janet A


    Free and bound phenolics extracts from nejayote solids were obtained after optimally lime-cooking blue, normal white, red, normal yellow, high-carotenoid and quality protein maize types. The extraction yield ranged from 4.47 to 10.05%. Bound phenolics extracts had higher content of total phenolics, antioxidant activity and ferulic acid compared to the free phenolics extracts. In general, free phenolics extracts were less cytotoxic than the bound phenolics counterparts. Bound phenolics extracts had higher induction of quinone reductase (QR) and particularly the normal yellow nejayote exerted the highest chemopreventive index tested in Hepa1c1c7 cells. When tested for monofunctional phase 2 induction capacity in BPrc1 cells, the bound phenolics extracts of blue, normal white and quality protein nejayotes were better inducers than the normal yellow counterpart. Particularly, the free phenolics extract of the white maize nejayote induced BPrc1 cells QR and exerted a higher chemopreventive index compared to the bound phenolics extract. Therefore, the nejayote of the normal white maize was the best source of monofunctional phase 2 enzyme inducers.

  4. Quantifying Macroscopic Friction of Diamond-like Carbon Films by Microscopic Adsorption and Removal of Water Molecules. (United States)

    Wang, Jingjing; Shang, Lunlin; Li, Xia; Lu, Zhibin; Zhang, Guangan


    The adsorption and desorption of water molecules, which affect the physical and chemical properties of the sliding interface, are critical for the friction behaviors of two solid contacts in atmosphere environment. The amount of water adsorbed on the open surface is a function of gas pressure according to an adsorption equation. However, for a confined sliding interface, the variation of surface fraction covered by gas molecules with water vapor pressure and its induced effects on friction have not been figured out. In this work, the macroscopic friction of diamond-like carbon (DLC) films in a water vapor atmosphere is quantified on the basis of microscopic adsorption and removal of water molecules. The studies correlate the fraction of water molecules adsorbed on the interface of self-mated DLC films with water vapor pressure to illustrate the direct relationship between friction coefficient and gas pressure by first-principles calculations and model fitting. The calculated results revealed that chemisorption and physisorption of water molecules occur on the surfaces of hydrogen-free DLC films (ta-C) and hydrogenated DLC films (HCF). Then, the relation between friction and gas pressure was built by employing a fractional coverage model based on the linear adsorption equation and gas removal. The obtained model agrees well with the typical experimental results about the steady-state friction coefficient of both highly hydrogenated DLC film (HCF) and tetrahedral amorphous carbon (ta-C) film during sliding at various water vapor pressures. In addition, it gave the curves of fractional surface coverage as a function of water vapor pressure. These results show that the frictional coefficient of DLC films could be predicted on the basis of fractional surface coverage as well as the intrinsic characters on surface chemistry. We suggest that the model may be thus extended to understand and predict the friction of DLC films under a specific gas pressure at a low load and

  5. Study of the adsorptive behavior of water-soluble dye molecules (rhodamine 6G) at the air-water interface using confocal fluorescence microscope. (United States)

    Zheng, X Y; Harata, A; Ogawa, T


    A confocal fluorescence microscope was applied to directly study the characteristic behaviors of adsorbed molecules at the air-water interface for a water-soluble chromophore, rhodamine 6G (R6G), in its extremely low-concentration region (below 10(-10) M). Significant photon bursts were observed only from the surface, and their width, height, and frequency were found to depend on the bulk concentration, suggesting the inhomogeneous distribution of R6G molecules at the air-water interface. This property of the adsorbed molecules is different from that of the bulk one. The influence of the ionic strength on photon bursts from the interface was investigated. It was found that the addition of NaCl to the R6G solution caused a decrease of the fluorescence signal. A change in the size of the aggregate and in the fluorescence quantum yield of the adsorbed molecules was suggested to be responsible for this experimental result.

  6. Regulation of a Coupled MARCKS-PI3K Lipid Kinase Circuit by Calmodulin: Single-Molecule Analysis of a Membrane-Bound Signaling Module. (United States)

    Ziemba, Brian P; Swisher, G Hayden; Masson, Glenn; Burke, John E; Williams, Roger L; Falke, Joseph J


    Amoeboid cells that employ chemotaxis to travel up an attractant gradient possess a signaling network assembled on the leading edge of the plasma membrane that senses the gradient and remodels the actin mesh and cell membrane to drive movement in the appropriate direction. In leukocytes such as macrophages and neutrophils, and perhaps in other amoeboid cells as well, the leading edge network includes a positive feedback loop in which the signaling of multiple pathway components is cooperatively coupled. Cytoplasmic Ca(2+) is a recently recognized component of the feedback loop at the leading edge where it stimulates phosphoinositide-3-kinase (PI3K) and the production of its product signaling lipid phosphatidylinositol 3,4,5-trisphosphate (PIP3). A previous study implicated Ca(2+)-activated protein kinase C (PKC) and the phosphatidylinositol 4,5-bisphosphate (PIP2) binding protein MARCKS as two important players in this signaling, because PKC phosphorylation of MARCKS releases free PIP2 that serves as the membrane binding target and substrate for PI3K. This study asks whether calmodulin (CaM), which is known to directly bind MARCKS, also stimulates PIP3 production by releasing free PIP2. Single-molecule fluorescence microscopy is used to quantify the surface density and enzyme activity of key protein components of the hypothesized Ca(2+)-CaM-MARCKS-PIP2-PI3K-PIP3 circuit. The findings show that CaM does stimulate PI3K lipid kinase activity by binding MARCKS and displacing it from PIP2 headgroups, thereby releasing free PIP2 that recruits active PI3K to the membrane and serves as the substrate for the generation of PIP3. The resulting CaM-triggered activation of PI3K is complete in seconds and is much faster than PKC-triggered activation, which takes minutes. Overall, the available evidence implicates both PKC and CaM in the coupling of Ca(2+) and PIP3 signals and suggests these two different pathways have slow and fast activation kinetics, respectively.

  7. A proactive role of water molecules in acceptor recognition by Protein-O-fucosyltransferase 2 (United States)

    Valero-González, Jessika; Leonhard-Melief, Christina; Lira-Navarrete, Erandi; Jiménez-Osés, Gonzalo; Hernández-Ruiz, Cristina; Pallarés, María Carmen; Yruela, Inmaculada; Vasudevan, Deepika; Lostao, Anabel; Corzana, Francisco; Takeuchi, Hideyuki; Haltiwanger, Robert S.; Hurtado-Guerrero, Ramon


    Protein O-fucosyltransferase 2 (POFUT2) is an essential enzyme that fucosylates serine/threonine residues of folded thrombospondin type 1 repeats (TSRs). To date, the mechanism by which this enzyme recognizes very dissimilar TSRs remained unclear. By engineering of a fusion protein, we report the crystal structure of Caenorhabditis elegans POFUT2 (CePOFUT2) in complex with GDP and human TSR1 that suggests an inverting mechanism for fucose transfer assisted by a catalytic base, and shows that nearly half of the TSR1 is embraced by CePOFUT2. A small number of direct interactions and a large network of water molecules maintain the complex. Site-directed mutagenesis demonstrates that POFUT2 fucosylates threonine preferentially over serine and relies on folded TSRs containing the minimal consensus sequence CXX(S/T)C. Crystallographic and mutagenesis data together with atomic-level simulations uncover an unprecedented binding mechanism by which POFUT2 promiscuously recognizes the structural fingerprint of poorly homologous TSRs through a dynamic network of water-mediated interactions. PMID:26854667

  8. Synthesis of ZnO particles using water molecules generated in esterification reaction (United States)

    Šarić, Ankica; Gotić, Marijan; Štefanić, Goran; Dražić, Goran


    Zinc oxide particles were synthesized without the addition of water by autoclaving (anhydrous) zinc acetate/alcohol and zinc acetate/acetic acid/alcohol solutions at 160 °C. The solvothermal synthesis was performed in ethanol or octanol. The structural, optical and morphological characteristics of ZnO particles were investigated by X-ray diffraction (XRD), UV-Vis spectroscopy, FE-SEM and TEM/STEM microscopy. 13C NMR spectroscopy revealed the presence of ester (ethyl- or octyl-acetate) in the supernatants which directly indicate the reaction mechanism. The formation of ester in this esterification reaction generated water molecule in situ, which hydrolyzed anhydrous zinc acetate and initiated nucleation and formation of ZnO. It was found that the size and shape of ZnO particles depend on the type of alcohol used as a solvent and on the presence of acetic acid in solution. The presence of ethanol in the ;pure; system without acetic acid favoured the formation of fine and uniform spherical ZnO nanoparticles (∼20 nm). With the addition of small amount of acetic acid the size of these small nanoparticles increased significantly up to a few hundred nanometers. The addition of small amount of acetic acid in the presence of octanol caused even more radical changes in the shape of ZnO particles, favouring the growth of huge rod-like particles (∼3 μm).

  9. Molecular organization of hydrophobic molecules and co-adsorbed water in SBA-15 ordered mesoporous silica material. (United States)

    Mellaerts, Randy; Roeffaers, Maarten B J; Houthoofd, Kristof; Van Speybroeck, Michiel; De Cremer, Gert; Jammaer, Jasper A G; Van den Mooter, Guy; Augustijns, Patrick; Hofkens, Johan; Martens, Johan A


    The purpose of this study was to improve our understanding of the molecular organization of hydrophobic guest molecules in the presence of co-adsorbed water inside SBA-15 ordered mesoporous silica material. Understanding this adsorption competition is essential in the development of applications of controlled adsorption and desorption. The poorly water soluble drug compound itraconazole and the fluorescent probe Nile red were selected for the study. The interaction between itraconazole and SBA-15 was investigated using FT-IR, (1)H MAS NMR and (29)Si MAS NMR spectroscopy, by determination of adsorption isotherms and release kinetics in simulated gastric fluid. The distribution and migration of the hydrophobic fluorescent probe Nile red was visualized in situ using confocal fluorescence microscopy. For both molecules, there was a pronounced influence of the co-adsorbed water on adsorption, hydrophobic aggregation and migration in SBA-15 pores. These insights contribute to the development of practical methods for loading ordered mesoporous silica materials with hydrophobic molecules.

  10. Transfer of lipid molecules and polycyclic aromatic hydrocarbons to open marine waters by dense water cascading events (United States)

    Salvadó, Joan A.; Grimalt, Joan O.; López, Jordi F.; Palanques, Albert; Heussner, Serge; Pasqual, Catalina; Sanchez-Vidal, Anna; Canals, Miquel


    Settling particles were collected by a set of moored sediment traps deployed during one year in the western Gulf of Lion along Cap de Creus and Lacaze-Duthiers submarine canyons and on the adjacent southern open slope. These traps collected particles during periods of pelagic settling and also during events of deep water flushing by dense shelf water cascading (DSWC). Analyses of lipid biomarkers (n-alkanes, n-alkan-1-ols, sterols and C37-C38 alkenones) and polycyclic aromatic hydrocarbons (PAHs) showed much higher transfer of terrestrial lipids and PAHs to open deep waters during DSWC than in the absence of cascading. The area of highest lateral fluxes was mostly located at 1000 m depth but also at 1500 m depth and extended along the canyons and to the adjacent slope. Higher fluxes were observed near the bottom (30 m above bottom; mab) than at intermediate waters (500 mab) which is consistent with the formation and sinking of dense water over the continental shelf, and its transport through the canyons towards the continental slope and deep basin. DSWC involved the highest settling fluxes of terrestrial lipids and PAHs ever described in marine continental slopes and the pelagic domain, as illustrated by peak values of C23-C33 odd carbon numbered alkanes (405 ng m-2 d-1), C22-C32 even carbon numbered alkan-1-ols (850 ng m-2 d-1), β-sitosterol+sitostanol (4800 ng m-2 d-1) and PAHs (55 μg m-2 d-1). The algal lipids also showed higher transfer to deep waters during DSWC but to a lower extent than the terrigenous compounds. However, the C37-C38 alkenones constituted an exception and their settling fluxes were not influenced by DSWC. The lack of influence of the DSWC on the C37-C38 alkenone settling is consistent with absence of haptophyte algal inputs from the continental shelf and reinforces the reliability of these molecules for palaeothermometry and palaeoproductivity measurements in pelagic systems.

  11. Association of Catechin Molecules in Water: Quantitative Binding Study and Complex Structure Analysis. (United States)

    Ujihara, Tomomi; Hayashi, Nobuyuki


    Associations between catechin molecules were investigated by (1)H NMR titration experiments. Eight green tea catechins formed self-assembled dimers in water, and gallate-type catechins had a greater tendency to self-associate than non-gallate-type catechins. All eight catechins also associated as 1:1 heterodimer complexes. Investigation of complex formation of epigallocatechin-3-O-gallate (EGCg) and epigallocatechin (EGC) with the other catechins showed that the affinity between EGCg and 2,3-trans-gallate-type catechins was remarkably high, and the binding affinity of EGCg for ECg was also rather strong. In contrast, the non-gallate-type catechin EGC exhibited generally low binding affinity for other catechins. Structural analyses of the complexes by ROESY experiments and density functional theory calculations demonstrated that the higher binding abilities of gallate-type catechins are due to providing multiple intermolecular interactions that remain effective in an aqueous environment, such as aromatic/aromatic or CH/π interactions.

  12. [Study of biological molecules in water by using the resonance raman spectra in liquid-core optical fiber]. (United States)

    Jia, Li-Hua; Wang, Yi-Ding; Sun, Cheng-Lin; Li, Zhan-Long; Li, Zuo-Wei; Wang, Li-Jun


    Raman spectrum is an important and effective method for the study of biological molecules in water. Measuring the Raman spectra for biological molecules in water, however, is very difficult because of the small Raman scattering cross section and the high electronic excitation energy of water molecules. In the present paper, the authors applied both technologies of liquid-core optical fiber and the resonance Raman spectra, then the intensity of Raman spectra was enhanced to a great extent. In this experiment, we chose the laser wavelength 514.5 of Ar+ ion laser as excitation laser, because we could obtain the maximal intensity of resonance Raman spectra at this wavelength. The experiment results show that, for the trace inspecting study of beta-carotene biological molecules in water, the concentration in the range of 10(-7)-10(-9) mol x L(-1) can be detected by quartz liquid-core optical fiber and the concentration in the range of 10(-9)-10(-10) mol x L(-1) by Teflon liquid-core optical fiber. The detecting utmost will be further reduced if improving the quality of optical fiber.

  13. The δ18O of Atmospheric Water Vapour is Recorded in the Oxygen Isotope Ratios of Leaf water and Organic Molecules at High Relative Humidity (United States)

    Lehmann, M. M.; Goldsmith, G. R.; Schmid, L.; Siegwolf, R. T.; Gessler, A.; Saurer, M.


    The oxygen stable isotope ratios (δ18O) of water and organic molecules in plants hold information about plant physiology, ecohydrology, and environmental conditions. For instance, the δ18O ratio of leaf water reflects both the δ18O ratios of water in the soil and in the atmosphere. This water, which is incorporated into organic molecules at the time of synthesis, thus serves to record the environment in which the plant was growing. However, how δ18O of atmospheric water vapour affects the δ18O ratio of organic molecules remains poorly understood. In order to investigate the effects of fog and rain (e.g. high atmospheric water availability) on δ18O ratios of leaf water and organic molecules, we exposed oak tree saplings (Quercus robur) in wet and dry soil treatments to 18O-depleted water vapour at ca. 90% relative humidity for 5 h. We harvested plant material over 24 h to trace the movement of the isotopic label in water and organics throughout the plant from the leaves to the stem. The atmospheric water vapour caused a strong 18O-depletion in leaf and xylem water, as well as in leaf carbohydrates, with the most negative ratios observed at the end of the fogging. Moreover, the label was clearly observed in twig and stem phloem carbohydrates following a short delay. A detailed compound-specific isotope analysis of the leaf carbohydrates revealed that the label caused an 18O-depletion in fructose, glucose, and sucrose. Quercitol, an oak-specific alditol, did not show 18O-depletion. Clear soil moisture treatment effects were only observed for twig phloem carbohydrates, with a stronger 18O-depletion in wet plants than in dry plants, suggesting retarded leaf-to-phloem sugar export in trees under drought. We demonstrate that labelling with 18O-depleted water is a potential tool to trace the movement and incorporation of oxygen stable isotopes in plants. We clearly show that changes in δ18O of atmospheric water vapour are quickly imprinted on leaf water and

  14. Bounded seas


    Kurš Jan; Lungu Mircea; Iyadurai Rathesan; Nierstrasz Oscar


    Abstract Imprecise manipulation of source code (semi parsing) is useful for tasks such as robust parsing error recovery lexical analysis and rapid development of parsers for data extraction. An island grammar precisely defines only a subset of a language syntax (islands) while the rest of the syntax (water) is defined imprecisely. Usually water is defined as the negation of islands. Albeit simple such a definition of water is naive and impedes composition of islands. When developing an island...

  15. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio


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

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

  16. Degradation of Bacterial Quorum Sensing Signaling Molecules by the Microscopic Yeast Trichosporon loubieri Isolated from Tropical Wetland Waters (United States)

    Wong, Cheng-Siang; Koh, Chong-Lek; Sam, Choon-Kook; Chen, Jian Woon; Chong, Yee Meng; Yin, Wai-Fong; Chan, Kok-Gan


    Proteobacteria produce N-acylhomoserine lactones as signaling molecules, which will bind to their cognate receptor and activate quorum sensing-mediated phenotypes in a population-dependent manner. Although quorum sensing signaling molecules can be degraded by bacteria or fungi, there is no reported work on the degradation of such molecules by basidiomycetous yeast. By using a minimal growth medium containing N-3-oxohexanoylhomoserine lactone as the sole source of carbon, a wetland water sample from Malaysia was enriched for microbial strains that can degrade N-acylhomoserine lactones, and consequently, a basidiomycetous yeast strain WW1C was isolated. Morphological phenotype and molecular analyses confirmed that WW1C was a strain of Trichosporon loubieri. We showed that WW1C degraded AHLs with N-acyl side chains ranging from 4 to 10 carbons in length, with or without oxo group substitutions at the C3 position. Re-lactonisation bioassays revealed that WW1C degraded AHLs via a lactonase activity. To the best of our knowledge, this is the first report of degradation of N-acyl-homoserine lactones and utilization of N-3-oxohexanoylhomoserine as carbon and nitrogen source for growth by basidiomycetous yeast from tropical wetland water; and the degradation of bacterial quorum sensing molecules by an eukaryotic yeast. PMID:24072030

  17. Crystalline Supramolecular Gyroscope with a Water Molecule as an Ultrasmall Polar Rotator Modulated by Charge-Assisted Hydrogen Bonds. (United States)

    Li, Wang; He, Chun-Ting; Zeng, Ying; Ji, Cheng-Min; Du, Zi-Yi; Zhang, Wei-Xiong; Chen, Xiao-Ming


    A new strategy for the construction of crystalline molecular rotors is presented. The combination of a conformation-modifiable macrocyclic host and two cooperative guests affords one supramolecular gyroscope-like compound, (t-BuNH 3 )(18-crown-6)[ZnCl 3 (H 2 O)], in which the coordinated water molecule functions as an ultrasmall polar rotator, revealed by its significant dielectric relaxation and the molecular dynamics simulations. In addition, such a compound can reversibly undergo a polar-to-polar phase transition triggered by the changed conformation of the 18-crown-6 host, leading to a switchable on/off rotation of water molecule, well controlled by strength and direction of charge-assisted hydrogen bonds.

  18. Self-assembly of neuroprotective carbazolium based small molecules at octane/water interface: A simulation investigation (United States)

    Zolghadr, Amin Reza; Heydari Dokoohaki, Maryam


    The self-assembly of dibromocarbazole based small molecule (P7C3) and its analogues is studied at the octane/water interface by using molecular dynamics simulations. P7C3 protects newborn neurons from apoptotic cell death and enhances neurogenesis. The bromines on the carbazole appear particularly important, as the derivatives with dichloro and parent carbazole did not appear active at the concentrations tested. We are mainly focused on the question that why is dibromocarbazole derivative an effective neuroprotective drug, but not dichlorocarbazole or parent carbazole? It was found that P7C3 and P7C3-Cl were concentrated in the interfacial region, whereas the parent carbazole derivative were distributed throughout the water phase. The diffusion of P7C3 molecules in the interfacial region are higher than P7C3-Cl. This approach could use by experimentalist to evaluate the permeability of drug candidates prior to their synthesis.

  19. How water molecules affect the catalytic activity of hydrolases - A XANES study of the local structures of peptide deformylase (United States)

    Cui, Peixin; Wang, Yu; Chu, Wangsheng; Guo, Xiaoyun; Yang, Feifei; Yu, Meijuan; Zhao, Haifeng; Dong, Yuhui; Xie, Yaning; Gong, Weimin; Wu, Ziyu


    Peptide deformylase (PDF) is a prokaryotic enzyme that catalyzes the deformylation of nascent peptides generated during protein synthesis and water molecules play a key role in these hydrolases. Using X-ray absorption near edge spectroscopy (XANES) and ab initio calculations we accurately probe the local atomic environment of the metal ion binding in the active site of PDF at different pH values and with different metal ions. This new approach is an effective way to monitor existing correlations among functions and structural changes. We show for the first time that the enzymatic activity depends on pH values and metal ions via the bond length of the nearest coordinating water (Wat1) to the metal ion. Combining experimental and theoretical data we may claim that PDF exhibits an enhanced enzymatic activity only when the distance of the Wat1 molecule with the metal ion falls in the limited range from 2.15 to 2.55 Å.

  20. Cutaneous water loss and covalently bound lipids of the stratum corneum in nestling house sparrows (Passer domesticus L.) from desert and mesic habitats. (United States)

    Clement, Michelle E; Muñoz-Garcia, Agustí; Williams, Joseph B


    Lipids of the stratum corneum (SC), the outer layer of the epidermis of birds and mammals, provide a barrier to water vapor diffusion through the skin. The SC of birds consists of flat dead cells, called corneocytes, and two lipid compartments: an intercellular matrix and a monolayer of covalently bound lipids (CBLs) attached to the outer surface of the corneocytes. We previously found two classes of sphingolipids, ceramides and cerebrosides, covalently bound to corneocytes in the SC of house sparrows (Passer domesticus L.); these lipids were associated with cutaneous water loss (CWL). In this study, we collected adult and nestling house sparrows from Ohio and nestlings from Saudi Arabia, acclimated them to either high or low humidity, and measured their rates of CWL. We also measured CWL for natural populations of nestlings from Ohio and Saudi Arabia, beginning when chicks were 2 days old until they fledged. We then evaluated the composition of the CBLs of the SC of sparrows using thin layer chromatography. We found that adult house sparrows had a greater diversity of CBLs in their SC than previously described. During ontogeny, nestling sparrows increased the amount of CBLs and developed their CBLs differently, depending on their habitat. Acclimating nestlings to different humidity regimes did not alter the ontogeny of the CBLs, suggesting that these lipids represent a fundamental component of SC organization that does not respond to short-term environmental change.

  1. Computation Results from a Parametric Study to Determine Bounding Critical Systems of Homogeneously Water-Moderated Mixed Plutonium--Uranium Oxides

    Energy Technology Data Exchange (ETDEWEB)

    Shimizu, Y.


    This report provides computational results of an extensive study to examine the following: (1) infinite media neutron-multiplication factors; (2) material bucklings; (3) bounding infinite media critical concentrations; (4) bounding finite critical dimensions of water-reflected and homogeneously water-moderated one-dimensional systems (i.e., spheres, cylinders of infinite length, and slabs that are infinite in two dimensions) that were comprised of various proportions and densities of plutonium oxides and uranium oxides, each having various isotopic compositions; and (5) sensitivity coefficients of delta k-eff with respect to critical geometry delta dimensions were determined for each of the three geometries that were studied. The study was undertaken to support the development of a standard that is sponsored by the International Standards Organization (ISO) under Technical Committee 85, Nuclear Energy (TC 85)--Subcommittee 5, Nuclear Fuel Technology (SC 5)--Working Group 8, Standardization of Calculations, Procedures and Practices Related to Criticality Safety (WG 8). The designation and title of the ISO TC 85/SC 5/WG 8 standard working draft is WD 14941, ''Nuclear energy--Fissile materials--Nuclear criticality control and safety of plutonium-uranium oxide fuel mixtures outside of reactors.'' Various ISO member participants performed similar computational studies using their indigenous computational codes to provide comparative results for analysis in the development of the standard.

  2. Influence of cations on catalytic properties of silica gel in radiolysis of adsorbed water molecules. [Gamma radiation

    Energy Technology Data Exchange (ETDEWEB)

    Garibov, A.A.; Melikzade, M.M.; Bakirov, M.Ya.; Ramazanova, M.Kh.

    Kinetics of hydrogen formation during gamma-radiolysis of water, adsorbed on the surface of silica gels: KSK, hyghly pure SiO/sub 2/-J and its SiO/sub 2/-Ca, SiO/sub 2/-Al cation exchange forms has been studied. Of all the studied samples SiO/sub 2/-Al possesses the highest catalytic activity. It is established that temperature increase from 25 to 250 deg causes the decrease in radiation-chemical yield of hydrogen molecules from 1.12 to 0.28 per 100 eV of energy, absorbed in system KSK/sup +/ adsorbed water.

  3. A linearized path integral description of the collision process between a water molecule and a graphite surface. (United States)

    Marković, Nikola; Poulsen, Jens A


    Quantum effects in the scattering and desorption process of a water molecule from a graphite surface are investigated using the linearized path integral model. The graphite surface is quantized rigorously using the fully quantum many-body Wigner transform of the surface Boltzmann operator, while the water molecule is treated as rigid. Classical dynamics with these quantized initial conditions show that quantizing the surface at 100 and 300 K results in markedly different results, compared to a fully classical analysis. The trapping probability (defined as the probability of multiple encounters with the surface) is not sensitive to the choice of dynamical treatment, but the residence time on the surface is much shorter in the quantum case. At 300 K the transiently trapped molecules desorb from the surface with a rate constant which is 60-70% larger than the corresponding classical value. Lowering the surface temperature to 100 K decreases the quantum rate constant by approximately a factor of 3 while all trapped molecules stick to the surface in the classical case. The stability of the quantum initial state for the highly anisotropic graphite crystal is discussed in detail as well as the dynamical consequences of energy redistribution during the scattering process. The graphite surface application demonstrates that the Boltzmann operator Wigner transform for a system with 900 degrees of freedom can be obtained by the so-called gradient implementation [Poulsen et al. J. Chem. Theory Comput. 2006, 2, 1482] of the underlying Feynman-Kleinert effective frequency theory, an implementation that only requires a force and potential routine for the system at hand, and hence is applicable to any molecule-surface collision problem.

  4. Performance Characterization of the Free Molecule Micro-Resistojet Utilizing Water Propellant (Preprint)

    National Research Council Canada - National Science Library

    Lee, R. H; Bauer, A. M; Killingsworth, M. D; Lilly, T. C; Duncan, J. A; Ketsdever, Andrew D


    .... The Free Molecule Micro-Resistojet (FMMR), a low cost, low power, high propellant storage density, and green propulsion system, has been analyzed in this study to determine its ability to provide a slew maneuver for a typical 10 kg nanosatellite...

  5. A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qiang [School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China); Gao, Jun, E-mail: [Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070 (China); School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China); Zhang, Dongju; Liu, Chengbu [School of Chemistry & Chemical Engineering, Shandong University, Jinan 250100 (China)


    Highlights: • We theoretical studied peptide bond formation reaction mechanism with two water molecules. • The first water molecule can decrease the reaction barriers by forming hydrogen bonds. • The water molecule mediated three-proton transfer mechanism is the favorable mechanism. • Our calculation supports the two-step and eight membered ring mechanism. - Abstract: The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9′ and H15′ in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.

  6. QTLs for cell wall-bound phenolics in relation to the photosynthetic apparatus activity and leaf water status under drought stress at different growth stages of triticale. (United States)

    Hura, Tomasz; Tyrka, Mirosław; Hura, Katarzyna; Ostrowska, Agnieszka; Dziurka, Kinga


    The present study aimed at identifying the regions of triticale genome responsible for cell wall saturation with phenolic compounds under drought stress during vegetative and generative growth. Moreover, the loci determining the activity of the photosynthetic apparatus, leaf water content (LWC) and osmotic potential (Ψ o) were identified, as leaf hydration and functioning of the photosynthetic apparatus under drought are associated with the content of cell wall-bound phenolics (CWPh). Compared with LWC and Ψ o, CWPh fluctuations were more strongly associated with changes in chlorophyll fluorescence. At the vegetative stage, CWPh fluctuations were due to the activity of three loci, of which only QCWPh.4B was also related to changes in F v/F m and ABS/CSm. In the other QTLs (QCWPh.6R.2 and QCWPh.6R.3), the genes of these loci determined also the changes in majority of chlorophyll fluorescence parameters. At the generative stage, the changes in CWPh in loci QCWPh.4B, QCWPh.3R and QCWPh.6R.1 corresponded to those in DIo/CSm. The locus QCWPh.6R.3, active at V stage, controlled majority of chlorophyll fluorescence parameters. This is the first study on mapping quantitative traits in triticale plants exposed to drought at different stages of development, and the first to present the loci for cell wall-bound phenolics.

  7. Quasi-bounded sets

    Directory of Open Access Journals (Sweden)

    Jan Kucera


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

  8. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket (United States)

    Debler, Erik W.; Müller, Roger; Hilvert, Donald; Wilson, Ian A.


    Design of catalysts featuring multiple functional groups is a desirable, yet formidable goal. Antibody 13G5, which accelerates the cleavage of unactivated benzisoxazoles, is one of few artificial enzymes that harness an acid and a base to achieve efficient proton transfer. X-ray structures of the Fab-hapten complexes of wild-type 13G5 and active-site variants now afford detailed insights into its mechanism. The parent antibody preorganizes AspH35 and GluL34 to abstract a proton from substrate and to orient a water molecule for leaving group stabilization, respectively. Remodeling the environment of the hydrogen bond donor with a compensatory network of ordered waters, as seen in the GluL34 to alanine mutant, leads to an impressive 109-fold rate acceleration over the nonenzymatic reaction with acetate, illustrating the utility of buried water molecules in bifunctional catalysis. Generalization of these design principles may aid in creation of catalysts for other important chemical transformations. PMID:19846764

  9. Investigation of N-acyl homoserine lactone (AHL) molecule production in Gram-negative bacteria isolated from cooling tower water and biofilm samples. (United States)

    Haslan, Ezgi; Kimiran-Erdem, Ayten


    In this study, 99 Gram-negative rod bacteria were isolated from cooling tower water, and biofilm samples were examined for cell-to-cell signaling systems, N-acyl homoserine lactone (AHL) signal molecule types, and biofilm formation capacity. Four of 39 (10 %) strains isolated from water samples and 14 of 60 (23 %) strains isolated from biofilm samples were found to be producing a variety of AHL signal molecules. It was determined that the AHL signal molecule production ability and the biofilm formation capacity of sessile bacteria is higher than planktonic bacteria, and there was a statistically significant difference between the AHL signal molecule production of these two groups (p tower water and biofilm samples produced different types of AHL signal molecules and that there were different types of AHL signal molecules in an AHL extract of bacteria. In the present study, it was observed that different isolates of the same strains did not produce the same AHLs or did not produce AHL molecules, and bacteria known as AHL producers did not produce AHL. These findings suggest that detection of signal molecules in bacteria isolated from cooling towers may contribute to prevention of biofilm formation, elimination of communication among bacteria in water systems, and blockage of quorum-sensing controlled virulence of these bacteria.

  10. Attributes of aerosol bound water soluble ions and carbon, and their relationships with AOD over the Brahmaputra Valley (United States)

    Bhuyan, Pranamika; Barman, Nivedita; Bora, Jayanta; Daimari, Rebecca; Deka, Pratibha; Hoque, Raza Rafiqul


    The present study is a ground based investigation of chemical properties of aerosol as PM10 and its relationship with the upper air optical properties. A total of 161 aerosol samples collected during 2010-2014 were characterized for water soluble ions viz. SO42-, NO3-, Cl-, F-, NH4+, K+, Ca2+, Mg2+and Na+ and water soluble carbon factions - water soluble organic carbon (WSOC) and water soluble inorganic carbon (WSIC). The entire study period was subdivided into four distinct seasons -pre-monsoon, monsoon, post-monsoon and winter to assess the characteristics of chemical species in different times of the year contributing to the particulate loading over the study site. To understand the relationship between chemical species and optical properties, aerosol optical depth (AOD) data of the study area have been retrieved from MODIS satellite data at 550 nm. Mean mass concentration of PM10 was found to be 49.3 ± 37 μg/m3 for the whole study period with an explicit seasonal variation and winter maximum of mass concentration. Also, secondary ions have strong influence on the total aerosol loading in the region. Vivid seasonal variability was found in the concentrations of ions and carbons. The winter season showed maximum loading of ionic and carbonaceous species and the presence of crustal derived ions - Ca2+ and Mg2+ - remained uniform all through the seasons. The anions were found to be dominant over the cations during the study period. Interestingly, K+, originating mostly from biomass burning emissions, also play important neutralizing role together with NH4+. Significant relationships between AOD with PM10 and attributes were observed. Strong correlation of anthropogenic (SO42-, NO3-, NH4+), biomass burning (K+) and organic carbon fraction of PM10 with AOD was observed, which indicated the influence of these fractions on the attenuation of incoming light over the study region. HYSPLIT backward trajectories of air masses, which were computed for the study area

  11. Comprehensive analysis of the Cramer–Rao bounds for magnetic resonance temperature change measurement in fat–water voxels using multi-echo imaging (United States)

    Wyatt, Cory; Soher, Brian J.; Arunachalam, Kavitha; MacFall, James


    Object The aim of this paper is to characterize the noise propagation for MRI temperature change measurement with emphasis on finding the best echo time combinations that yield the lowest temperature noise. Materials and methods A Cramer–Rao lower-bound (CRLB) calculation was used to estimate the temperature noise for a model of the MR signal in fat–water voxels. The temperature noise CRLB was then used to find a set of echo times that gave the lowest temperature change noise for a range of fat–water frequency differences, temperature changes, fat/water signal ratios, and T2* values. CRLB estimates were verified by Monte Carlo simulation and in phantoms using images acquired in a 1.5 T magnet. Results Results show that regions exist where the CRLB predicts minimal temperature variation as a function of the other variables. The results also indicate that the CRLB values calculated in this paper provide excellent guidance for predicting the variation of temperature measurements due to changes in the signal parameters. For three echo scans, the best noise characteristics are seen for TE values of 20.71, 23.71, and 26.71 ms. Results for five and seven echo scans are also presented in the text. Conclusion The results present a comprehensive analysis of the effects of different scan parameters on temperature noise, potentially benefiting the selection of scan parameters for clinical MRI thermometry. PMID:21442434

  12. Possible interstellar formation of glycine from the reaction of CH2=NH, CO and H2O: catalysis by extra water molecules through the hydrogen relay transport. (United States)

    Nhlabatsi, Zanele P; Bhasi, Priya; Sitha, Sanyasi


    "How the fundamental life elements are created in the interstellar medium (ISM)?" is one of the intriguing questions related to the genesis of life. Using computational calculations, we have discussed the reaction of CH2=NH, CO and H2O for the formation of glycine, the simplest life element. This reaction proceeds through a concerted mechanism with reasonably large barriers for the cases with one and two water molecules as reactants. For the two water case we found that the extra water molecule exhibits some catalytic role through the hydrogen transport relay effect and the barrier height is reduced substantially compared to the case with one water molecule. These two cases can be treated as ideal cases for the hot-core formation of the interstellar glycine. With an increasing number of water molecules as the reactants, we found that when the numbers of water molecules are three or more than three, the barrier height reduced so drastically that the transition states were more stable than the reactants. Such a situation gives a clear indication that with excess water molecules as the reactants, this reaction will be feasible even under the low temperature conditions existing in the cold interstellar clouds and the exothermic nature of the reaction will be the driving force.

  13. The added value of a water footprint approach: Micro- and macroeconomic analysis of cotton production, processing and export in water bound Uzbekistan (United States)

    Rudenko, I.; Bekchanov, M.; Djanibekov, U.; Lamers, J. P. A.


    Since independence from the former Soviet Union in 1991, Uzbekistan is challenged to consolidate its efforts and identify and introduce suitable agricultural policies to ease the threat of advancing land, water and ecosystem deterioration. On the one hand, irrigated cotton production provides income, food and energy sources for a large part of the rural households, which accounts for about 70% of the total population. On the other hand, this sector is considered a major driver of the on-going environmental degradation. Due to this dual nature, an integrated approach is needed that allows the analyses of the cotton sector at different stages and, consequently, deriving comprehensive options for action. The findings of the economic based value chain analysis and ecologically-oriented water footprint analysis on regional level were complemented with the findings of an input-output model on national level. This combination gave an added value for better-informed decision-making to reach land, water and ecosystem sustainability, compared to the individual results of each approach. The synergy of approaches pointed at various options for actions, such as to (i) promote the shift of water use from the high water consuming agricultural sector to a less water consuming cotton processing sector, (ii) increase overall water use efficiency by expanding the highly water productive industrial sectors and concurrently decreasing sectors with inefficient water use, and (iii) reduce agricultural water use by improving irrigation and conveyance efficiencies. The findings showed that increasing water use efficiency, manufacturing products with higher value added and raising water users' awareness of the real value of water are essential for providing water security in Uzbekistan.

  14. Reactivity of ionic oxides through water molecules adsorption process; MgO-V sub 2 O sub 5 behaviour

    Energy Technology Data Exchange (ETDEWEB)

    Goni-Elizalde, S. (Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Instituto de Ciencias de la Construccion Eduardo Torroja); Garcia-Clavel, M.E. (Consejo Superior de Investigaciones Cientificas, Madrid (Spain). Instituto de Edafologia)


    Crystalline V{sub 2}O{sub 5} reactivity is strongly dependent on both particle size and relative humidity surrounding the sample. To study the increase of reactivity of crystalline V{sub 2}O{sub 5} (grain size<0.05 mm), a mixture of MgO-V{sub 2}O{sub 5} (1:1) has been kept in a watervapour saturated atmosphere for different periods of time. X-ray diffraction is employed to follow the structural evolution of the mixture, the adsorption process of water molecules has been studied by infrared spectroscopy as well as by thermogravimetry. (author). 11 refs.; 5 figs.; 1 tab.

  15. A theoretical model investigation of peptide bond formation involving two water molecules in ribosome supports the two-step and eight membered ring mechanism (United States)

    Wang, Qiang; Gao, Jun; Zhang, Dongju; Liu, Chengbu


    The ribosome is the macromolecular machine that catalyzes protein synthesis. The kinetic isotope effect analysis reported by Strobel group supports the two-step mechanism. However, the destination of the proton originating from the nucleophilic amine is uncertain. A computational simulation of different mechanisms including water molecules is carried out using the same reaction model and theoretical level. Formation the tetrahedral intermediate with proton transfer from nucleophilic nitrogen, is the rate-limiting step when two water molecules participate in peptide bond formation. The first water molecule forming hydrogen bonds with O9‧ and H15‧ in the A site can decrease the reaction barriers. Combined with results of the solvent isotope effects analysis, we conclude that the three-proton transfer mechanism in which water molecule mediate the proton shuttle between amino and carbon oxygen in rate-limiting step is the favorable mechanism. Our results will shield light on a better understand the reaction mechanism of ribosome.

  16. The key role of meteorites in the formation of relevant prebiotic molecules in a formamide/water environment (United States)

    Rotelli, Luca; Trigo-Rodríguez, Josep M.; Moyano-Cambero, Carles E.; Carota, Eleonora; Botta, Lorenzo; di Mauro, Ernesto; Saladino, Raffaele


    We show that carbonaceous chondrite meteorites actively and selectively catalyze the formation of relevant prebiotic molecules from formamide in aqueous media. Specific catalytic behaviours are observed, depending on the origin and composition of the chondrites and on the type of water present in the system (activity: thermal > seawater > pure). We report the one-pot synthesis of all the natural nucleobases, of aminoacids and of eight carboxylic acids (forming, from pyruvic acid to citric acid, a continuous series encompassing a large part of the extant Krebs cycle). These data shape a general prebiotic scenario consisting of carbonaceous meteorites acting as catalysts and of a volcanic-like environment providing heat, thermal waters and formamide. This scenario also applies to the other solar system locations that experienced rich delivery of carbonaceous materials, and whose physical-chemical conditions could have allowed chemical evolution.

  17. Ligand uptake inMycobacterium tuberculosistruncated hemoglobins is controlled by both internal tunnels and active site water molecules. (United States)

    Boron, Ignacio; Bustamante, Juan Pablo; Davidge, Kelly S; Singh, Sandip; Bowman, Lesley Ah; Tinajero-Trejo, Mariana; Carballal, Sebastián; Radi, Rafael; Poole, Robert K; Dikshit, Kanak; Estrin, Dario A; Marti, Marcelo A; Boechi, Leonardo


    Mycobacterium tuberculosis, the causative agent of human tuberculosis, has two proteins belonging to the truncated hemoglobin (trHb) family. Mt-trHbN presents well-defined internal hydrophobic tunnels that allow O 2 and • NO to migrate easily from the solvent to the active site, whereas Mt-trHbO possesses tunnels interrupted by a few bulky residues, particularly a tryptophan at position G8. Differential ligand migration rates allow Mt-trHbN to detoxify • NO, a crucial step for pathogen survival once under attack by the immune system, much more efficiently than Mt-trHbO. In order to investigate the differences between these proteins, we performed experimental kinetic measurements, • NO decomposition, as well as molecular dynamics simulations of the wild type Mt-trHbN and two mutants, VG8F and VG8W. These mutations affect both the tunnels accessibility as well as the affinity of distal site water molecules, thus modifying the ligand access to the iron. We found that a single mutation allows Mt-trHbN to acquire ligand migration rates comparable to those observed for Mt-trHbO, confirming that ligand migration is regulated by the internal tunnel architecture as well as by water molecules stabilized in the active site.

  18. Prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium: DFT and Car-Parrinello molecular dynamics study (United States)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep


    The ground state prototropic tautomerism of 4-Methyl 1,2,4-Triazole-3-Thione molecule in solvent water medium has been investigated with the aid of DFT and Car-Parrinello molecular dynamics (CPMD) simulation studies. The CPMD simulations envisage the possibility of proton transfer reactions of the molecule through the solvent water medium. Probable proton transfer pathways have been predicted from the DFT calculations which are substantiated by the natural bond orbital analyses. The evolution and breaking of the concerned bonds of the molecule for different proton transfer reaction pathways are also estimated.

  19. Proposed Photosynthesis Method for Producing Hydrogen from Dissociated Water Molecules Using Incident Near-Infrared Light (United States)

    Li, Xingxing; Li, Zhenyu; Yang, Jinlong


    Highly efficient solar energy utilization is very desirable in photocatalytic water splitting. However, until now, the infrared part of the solar spectrum, which constitutes almost half of the solar energy, has not been used, resulting in significant loss in the efficiency of solar energy utilization. Here, we propose a new mechanism for water splitting in which near-infrared light can be used to produce hydrogen. This ability is a result of the unique electronic structure of the photocatalyst, in which the valence band and conduction band are distributed on two opposite surfaces with a large electrostatic potential difference produced by the intrinsic dipole of the photocatalyst. This surface potential difference, acting as an auxiliary booster for photoexcited electrons, can effectively reduce the photocatalyst's band gap required for water splitting in the infrared region. Our electronic structure and optical property calculations on a surface-functionalized hexagonal boron-nitride bilayer confirm the existence of such photocatalysts and verify the reaction mechanism.

  20. On the properties of a single OPLS-UA model curcumin molecule in water, methanol and dimethyl sulfoxide. Molecular dynamics computer simulation results

    Directory of Open Access Journals (Sweden)

    T. Patsahan


    Full Text Available The properties of model solutions consisting of a solute — single curcumin molecule in water, methanol and dimethyl sulfoxide solvents have been studied using molecular dynamics (MD computer simulations in the isobaric-isothermal ensemble. The united atom OPLS force field (OPLS-UA model for curcumin molecule proposed by us recently [J. Mol. Liq., 2016, 223, 707] in combination with the SPC/E water, and the OPLS-UA type models for methanol and dimethyl sulfoxide have been applied. We have described changes of the internal structure of the solute molecule induced by different solvent media in very detail. The pair distribution functions between particular fragments of a solute molecule with solvent particles have been analyzed. Statistical features of the hydrogen bonding between different species were explored. Finally, we have obtained a self-diffusion coefficient of curcumin molecules in three model solvents.

  1. Manganese compounds as catalysts for water oxidation and as CO releasing molecules


    Berends, Hans-Martin


    This PhD thesis deals with several aspects of manganese chemistry and is divided into three parts. The first two concern the synthesis and characterization of manganese-based water oxidation catalysts. The four-electron oxidation of water to dioxygen is a key process of oxygenic photosynthesis in which solar energy is captured and stored in the form of carbohydrates. In nature, this reaction is catalyzed by a µ-oxido-Mn4Ca cluster, the oxygen evolving complex (OEC). Mimicking this reacti...

  2. Back to the roots: photodynamic inactivation of bacteria based on water-soluble curcumin bound to polyvinylpyrrolidone as a photosensitizer. (United States)

    Winter, Sandra; Tortik, Nicole; Kubin, Andreas; Krammer, Barbara; Plaetzer, Kristjan


    Photodynamic inactivation (PDI), the light-induced and photosensitizer-mediated overproduction of reactive oxygen species in microorganisms, represents a convincing approach to treat infections with (multi-resistant) pathogens. Due to its favourable photoactive properties combined with excellent biocompatibility, curcumin derived from the roots of turmeric (Curcuma longa) has been identified as an advantageous photosensitizer for PDI. To overcome the poor water solubility and the rapid decay of the natural substance at physiological pH, we examined the applicability of polyvinylpyrrolidone curcumin (PVP-C) in an acidified aqueous solution (solubility of PVP-C up to 2.7 mM) for photoinactivation of Gram(+) and Gram(-) bacteria. Five micromolar PVP-C incubated for 5 minutes and illuminated using a blue light LED array (435 ± 10 nm, 33.8 J cm(-2)) resulted in a >6 log10 reduction of the number of viable Staphylococcus aureus. At this concentration, longer incubation periods result in a lower phototoxicity, most likely due to degeneration of curcumin. Upon an increase of the PVP-C concentration to 50 μM (incubation for 15 or 25 min) a complete eradication of Staphylococcus aureus can be achieved. As expected for a non-cationic photosensitizer, cell wall permeabilization with CaCl2 prior to addition of 50 μM PVP-C for 15 min is necessary to induce a drop in the count of the Gram(-) Escherichia coli for more than 3 log10. As both constituents of the formulation, curcumin (E number E100) and polyvinylpyrrolidone (E1201), have been approved as food additives, a PDI based on PCP-C might allow for a very sparing clinical application (e.g. for disinfection of wounds) or even for employment in aseptic production of foodstuffs.

  3. Recombination time of an RF discharge plasma in the presence of water molecules

    Energy Technology Data Exchange (ETDEWEB)

    Protasevich, E.T.


    The authors show that the introduction of water vapor into an electrodeless rf discharge noticeably reduces the excitation temperature and substantially increases the recombination time of the plasma. An attempt is made to explain the physical processes associated with these phenomena.

  4. Cell Wall Proteome in the Maize Primary Root Elongation Zone. II. Region-Specific Changes in Water Soluble and Lightly Ionically Bound Proteins under Water Deficit

    National Research Council Canada - National Science Library

    Jinming Zhu; Sophie Alvarez; Ellen L. Marsh; Mary E. LeNoble; In-Jeong Cho; Mayandi Sivaguru; Sixue Chen; Henry T. Nguyen; Yajun Wu; Daniel P. Schachtman; Robert E. Sharp


    Previous work on the adaptation of maize (Zea mays) primary roots to water deficit showed that cell elongation is maintained preferentially toward the apex, and that this response involves modification of cell wall extension properties...

  5. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study (United States)

    Pohorille, Andrew; Benjamin, Ilan


    A molecular dynamics study of adsorption of p-n-pentylphenol at infinite dilution at the water liquid-vapor interface is reported. The calculated free energy of adsorption is -8.8 +/- 0.7 kcal/mol, in good agreement with the experimental value of -7.3 kcal/mol. The transition between the interfacial region and the bulk solution is sharp and well-defined by energetic, conformational, and orientational criteria. At the water surface, the phenol head group is mostly immersed in aqueous solvent. The most frequent orientation of the hydrocarbon tail is parallel to the interface, due to dispersion interactions with the water surface. This arrangement of the phenol ring and the alkyl chain requires that the chain exhibits a kink. As the polar head group is being moved into the solvent, the chain length increases and the tail becomes increasingly aligned toward the surface normal, such that the nonpolar part of the molecule exposed to water is minimized. The same effect was achieved when phenol was replaced by a more polar head group, phenolate.

  6. Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5

    DEFF Research Database (Denmark)

    Meinild, A K; Klærke, Dan Arne; Zeuthen, T


    for the osmotic water permeability (L p) were obtained in swelling as in shrinkage experiments demonstrating, for the first time, that aquaporins are bidirectional. The reflection coefficients (¿) of urea, glycerol, acetamide, and formamide at 23¿°C were: AQP0: 1, 1, 0.8, 0.6; AQP1: 1, 0.8, 1, 1; AQP2: 1, 0.8, 1...

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

    Energy Technology Data Exchange (ETDEWEB)

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


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

  8. The mobility of single-file water molecules is governed by the number of H-bonds they may form with channel-lining residues


    Horner, Andreas; Zocher, Florian; Preiner, Johannes; Ollinger, Nicole; Siligan, Christine; Akimov, Sergey A.; Pohl, Peter


    Channel geometry governs the unitary osmotic water channel permeability, p f, according to classical hydrodynamics. Yet, p f varies by several orders of magnitude for membrane channels with a constriction zone that is one water molecule in width and four to eight molecules in length. We show that both the p f of those channels and the diffusion coefficient of the single-file waters within them are determined by the number N H of residues in the channel wall that may form a hydrogen bond with ...

  9. Water and oxygen induced degradation of small molecule organic solar cells

    DEFF Research Database (Denmark)

    Hermenau, Martin; Riede, Moritz; Leo, Karl


    by the donor material zinc-phthalocyanine (ZnPc) and the acceptor material Buckminsterfullerene (C60) followed by 30 nm C60 for additional absorption. The active layers are sandwiched between 6 nm 4,7-diphenyl-1,10-phenanthroline (Bphen) and 30 nm N,N′-diphenyl-N,N′-bis(3-methylphenyl)-[1,1′-biphenyl]-4......,4′-diamine p-doped with C60F36 (MeO-TPD:C60F36), which acted as hole transporting layer. Indium-tin-oxide (ITO) and aluminum served as hole and electron collecting electrode, respectively. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) and X-ray photoelectron spectroscopy (XPS) in conjunction...... that were kept in the dark and devices that were subjected to illumination under simulated sunlight. It was found that water significantly causes the device to degrade. The two most significant degradation mechanisms are diffusion of water through the aluminum electrode resulting in massive formation...

  10. Influence of the Raman laser power on the opto-electronics properties in graphene with water molecule (United States)

    Rey-GonzáLez, R. R.; Champi, A.; Rojas Cuervo, A. M.

    The study of physical and chemical properties of nanostructures has contributed in great part with advance of the nanotechnology, which is important for the development of present and future technological applications. An important key in this purpose is the interaction of atoms and molecules with nanostructures. The principal interest of this experimental work is to study these processes on the interaction between liquid and vapor phases water with a graphene bilayer which is obtained through micromechanical exfoliation technique from a sample of natural graphite deposited on a SiO2 substrate. The number of layers and the interaction water-bilayer are analyzed systematically by means of Raman spectroscopy λ = 532nm). Also, the influence of variation of the Raman laser power and its effects in the opto-electronic properties of the system are studied. From the usual G, D and 2D bands of these spectra, we analyze the relation between the laser power and some band parameters, such as its area, position and wide. Finally, these results permit us to quantify the density of defects and the distance among them as function of Raman power before and after of the water vapor incorporation in bilayers Authors would like to thank the Programa Latino Americano de Física of Sociedade Brasileira de Física for their financial support. A. M. Rojas-Cuervo would also like to thank the Colciencias, Colombia.

  11. CO2 and C2H2 in cold nanodroplets of oxygenated organic molecules and water (United States)

    Devlin, J. Paul; Balcı, F. Mine; Maşlakcı, Zafer; Uras-Aytemiz, Nevin


    Recent demonstrations of subsecond and microsecond timescales for formation of clathrate hydrate nanocrystals hint at future methods of control of environmental and industrial gases such as CO2 and methane. Combined results from cold-chamber and supersonic-nozzle [A. S. Bhabhe, "Experimental study of condensation and freezing in a supersonic nozzle," Ph.D. thesis (Ohio State University, 2012), Chap. 7] experiments indicate extremely rapid encagement of components of all-vapor pre-mixtures. The extreme rates are derived from (a) the all-vapor premixing of the gas-hydrate components and (b) catalytic activity of certain oxygenated organic large-cage guests. Premixing presents no obvious barrier to large-scale conditions of formation. Further, from sequential efforts of the groups of Trout and Buch, a credible defect-based model of the catalysis mechanism exists for guidance. Since the catalyst-generated defects are both mobile and abundant, it is often unnecessary for a high percentage of the cages to be occupied by a molecular catalyst. Droplets represent the liquid phase that bridges the premixed vapor and clathrate hydrate phases but few data exist for the droplets themselves. Here we describe a focused computational and FTIR spectroscopic effort to characterize the aerosol droplets of the all-vapor cold-chamber methodology. Computational data for CO2 and C2H2, hetero-dimerized with each of the organic catalysts and water, closely match spectroscopic redshift patterns in both magnitude and direction. Though vibrational frequency shifts are an order of magnitude greater for the acetylene stretch mode, both CO2 and C2H2 experience redshift values that increase from that for an 80% water-methanol solvent through the solvent series to approximately doubled values for tetrahydrofuran and trimethylene oxide (TMO) droplets. The TMO solvent properties extend to a 50 mol.% solution of CO2, more than an order of magnitude greater than for the water-methanol solvent mixture

  12. Electric Power Generation through the Direct Interaction of Pristine Graphene-Oxide with Water Molecules. (United States)

    Xu, Tong; Ding, Xiaoteng; Shao, Changxiang; Song, Long; Lin, Tengyu; Gao, Xue; Xue, Jiangli; Zhang, Zhipan; Qu, Liangti


    Converting ubiquitous environmental energy into electric power holds tremendous social and financial interests. Traditional energy harvesters and converters are limited by the specific materials and complex configuration of devices. Herein, it is presented that electric power can be directly produced from pristine graphene oxide (GO) without any pretreatment or additives once encountering the water vapor, which will generate an open-circuit-voltage of up to 0.4-0.7 V and a short-circuit-current-density of 2-25 µA cm -2 on a single piece of GO film. This phenomenon results from the directional movement of charged hydrogen ions through the GO film. The present work demonstrates and provides an extremely simple method for electric energy generation, which offers more applications of graphene-based materials in green energy converting field. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Physical capture and release of drug molecules, water and cations by a smectite clay

    DEFF Research Database (Denmark)

    Carvalho dos Santos, Éverton

    Clay minerals have been widely applied through human history. For instance research in archaeological sites shows their use to build tools or applied as medicine from prehistoric times. This wide range of applications results from the unique clay minerals properties, such as porosity, water......-fluorohectorite (LiFh, Li1.2(Mg4.8Li1.2)Si8O20F4), a synthetic clay mineral from the smectite family, have been experimentally analyzed. By means of X-rays powder diffraction (XRD), using both an in-house instrument and synchrotron radiation, UV-Vis spectroscopy, Thermogravimetric Analysis coupled to an Infrared...... spectrometer (TGA/IR), Differential Scanning Calorimetry (DSC), Energy Dispersive X-ray Spectroscopy (EDS) and Inelastic Neutron Scattering using the Elastic Fixed Window approach (EFW), the dynamics of cation exchange process, hydration behavior as a function of interlayer cation and, most importantly, CIPRO...

  14. Ubiquitous water-soluble molecules in aquatic plant exudates determine specific insect attraction.

    Directory of Open Access Journals (Sweden)

    Julien Sérandour

    Full Text Available Plants produce semio-chemicals that directly influence insect attraction and/or repulsion. Generally, this attraction is closely associated with herbivory and has been studied mainly under atmospheric conditions. On the other hand, the relationship between aquatic plants and insects has been little studied. To determine whether the roots of aquatic macrophytes release attractive chemical mixtures into the water, we studied the behaviour of mosquito larvae using olfactory experiments with root exudates. After testing the attraction on Culex and Aedes mosquito larvae, we chose to work with Coquillettidia species, which have a complex behaviour in nature and need to be attached to plant roots in order to obtain oxygen. This relationship is non-destructive and can be described as commensal behaviour. Commonly found compounds seemed to be involved in insect attraction since root exudates from different plants were all attractive. Moreover, chemical analysis allowed us to identify a certain number of commonly found, highly water-soluble, low-molecular-weight compounds, several of which (glycerol, uracil, thymine, uridine, thymidine were able to induce attraction when tested individually but at concentrations substantially higher than those found in nature. However, our principal findings demonstrated that these compounds appeared to act synergistically, since a mixture of these five compounds attracted larvae at natural concentrations (0.7 nM glycerol, <0.5 nM uracil, 0.6 nM thymine, 2.8 nM uridine, 86 nM thymidine, much lower than those found for each compound tested individually. These results provide strong evidence that a mixture of polyols (glycerol, pyrimidines (uracil, thymine, and nucleosides (uridine, thymidine functions as an efficient attractive signal in nature for Coquillettidia larvae. We therefore show for the first time, that such commonly found compounds may play an important role in plant-insect relationships in aquatic eco-systems.

  15. Constructing a Pipe-Bound City : A History of Water Supply, Sewerage, and Excreta Removal in Norrköping and Linköping, Sweden, 1860-1910


    Hallström, Jonas


    In the mid- to late 19th century, modern pipe-bound water and sewer systems proliferated in European cities, a development that has sometimes been regarded as a necessary result of a sanitary awakening and the progress of science and technology. By analyzing the introduction and subsequent expansion of water, sewerage, and excreta collection on the local level, in the Swedish cities Norrköping and Linköping, this oversimplified picture is questioned. The main problematique of this dissertatio...

  16. Forming nanoparticles of water-soluble ionic molecules and embedding them into polymer and glass substrates

    Directory of Open Access Journals (Sweden)

    Stella Kiel


    Full Text Available This work describes a general method for the preparation of salt nanoparticles (NPs made from an aqueous solution of ionic compounds (NaCl, CuSO4 and KI. These nanoparticles were created by the application of ultrasonic waves to the aqueous solutions of these salts. When the sonication was carried out in the presence of a glass microscope slide, a parylene-coated glass slide, or a silicon wafer the ionic NPs were embedded in these substrates by a one-step, ultrasound-assisted procedure. Optimization of the coating process resulted in homogeneous distributions of nanocrystals, 30 nm in size, on the surfaces of the substrates. The morphology and structure of each of the coatings were characterized by physical and chemical methods, such as X-ray diffraction (XRD, scanning electron microscopy (SEM, atomic force microscopy (AFM, Raman spectroscopy and X-ray photoelectron spectroscopy (XPS. After 24 h of leaching into water the nanoparticles of the inorganic salts were still present on the slides, and complete leaching of nanoparticles occurred only after 96 h. A mechanism of the ultrasound-assisted coating is proposed.

  17. On quark molecules

    CERN Document Server

    Dolgov, A D; Okun, Lev Borisovich


    A nonrelativistic quark model with three triplets and an octet of coloured gluons is considered. The interaction energy is calculated for some quark molecules. It is shown that states of the type qqqq and qqqqq are bounded more tightly than qq and qqq, respectively. This may indicate an existence of exotic particles in the nature or, perhaps, that the model is invalid. (11 refs).

  18. Detecting Darwinism from Molecules in the Enceladus Plumes, Jupiter's Moons, and Other Planetary Water Lagoons. (United States)

    Benner, Steven A


    To the astrobiologist, Enceladus offers easy access to a potential subsurface biosphere via the intermediacy of a plume of water emerging directly into space. A direct question follows: If we were to collect a sample of this plume, what in that sample, through its presence or its absence, would suggest the presence and/or absence of life in this exotic locale? This question is, of course, relevant for life detection in any aqueous lagoon that we might be able to sample. This manuscript reviews physical chemical constraints that must be met by a genetic polymer for it to support Darwinism, a process believed to be required for a chemical system to generate properties that we value in biology. We propose that the most important of these is a repeating backbone charge; a Darwinian genetic biopolymer must be a "polyelectrolyte." Relevant to mission design, such biopolymers are especially easy to recover and concentrate from aqueous mixtures for detection, simply by washing the aqueous mixtures across a polycharged support. Several device architectures are described to ensure that, once captured, the biopolymer meets two other requirements for Darwinism, homochirality and a small building block "alphabet." This approach is compared and contrasted with alternative biomolecule detection approaches that seek homochirality and constrained alphabets in non-encoded biopolymers. This discussion is set within a model for the history of the terran biosphere, identifying points in that natural history where these alternative approaches would have failed to detect terran life. Key Words: Enceladus-Life detection-Europa-Icy moon-Biosignatures-Polyelectrolyte theory of the gene. Astrobiology 17, 840-851.

  19. Heavy exotic molecules (United States)

    Liu, Yizhuang; Zahed, Ismail

    We briefly review the formation of pion-mediated heavy-light exotic molecules with both charm and bottom, under the general structures of chiral and heavy quark symmetries. The charm isosinglet exotic molecules with JPC = 1++ binds, which we identify as the reported neutral X(3872). The bottom isotriplet exotic with JPC = 1+1 binds, and is identified as a mixed state of the reported charged exotics Zb+(10610) and Zb-(10650). The bound bottom isosinglet molecule with JPC = 1++ is a possible neutral Xb(10532) to be observed.

  20. Bound states and the Bekenstein bound

    Energy Technology Data Exchange (ETDEWEB)

    Bousso, Raphael


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

  1. Benchmark reaction rates, the stability of biological molecules in water, and the evolution of catalytic power in enzymes. (United States)

    Wolfenden, Richard


    The rates of enzyme reactions fall within a relatively narrow range. To estimate the rate enhancements produced by enzymes, and their expected affinities for transition state analog inhibitors, it is necessary to measure the rates of the corresponding reactions in water in the absence of a catalyst. This review describes the spontaneous cleavages of C-C, C-H, C-N, C-O, P-O, and S-O bonds in biological molecules, as well as the uncatalyzed reactions that correspond to phosphoryl transfer reactions catalyzed by kinases and to peptidyl transfer in the ribosome. The rates of these reactions, some with half-lives in excess of one million years, span an overall range of 10¹⁹-fold. Moreover, the slowest reactions tend to be most sensitive to temperature, with rates that increase as much as 10⁷-fold when the temperature is raised from 25° to 100°C. That tendency collapses, by many orders of magnitude, the time that would have been required for chemical evolution on a warm earth. If the catalytic effect of primitive enzymes, like that of modern enzymes and many nonenzymatic catalysts, were mainly to reduce a reaction's enthalpy of activation, then the resulting rate enhancement would have increased automatically as the surroundings cooled. By reducing the time required for early chemical evolution in a warm environment, these findings counter the view that not enough time has passed for terrestrial life to have evolved to its present level of complexity.

  2. Near infrared light-driven water oxidation in a molecule-based artificial photosynthetic device using an upconversion nano-photosensitizer

    NARCIS (Netherlands)

    Liu, X.; Chen, H.C.; Kong, X.; Zhang, Y.; Tu, L.; Chang, Y.; Wu, F.; Wang, T.; Reek, J.N.H.; Brouwer, A.M.; Zhang, H.


    We provide the first demonstration of a near infrared light driven water oxidation reaction in a molecule-based artificial photosynthetic device using an upconversion nano-photosensitizer. One very attractive advantage of this system is that using NIR light irradiation does not cause significant

  3. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

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


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

  4. The DMM Bound

    DEFF Research Database (Denmark)

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


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

  5. Photoionization of water molecules by a train of attosecond pulses assisted by a near-infrared laser: delay and polarization control (United States)

    Martini, Lara; Boll, Diego I. R.; Fojón, Omar A.


    Basic reactions involving water molecules are essential to understand the interaction between radiation and the biological tissue because living cells are composed mostly by water. Therefore, the knowledge of ionization of the latter is crucial in many domains of Biology and Physics. So, we study theoretically the photoionization of water molecules by extreme ultraviolet attopulse trains assisted by lasers in the near-infrared range. We use a separable Coulomb-Volkov model in which the temporal evolution of the system can be divided into three stages allowing spatial and temporal separation for the Coulomb and Volkov final state wavefunctions. First, we analyze photoelectron angular distributions for different delays between the attopulse train and the assistant laser field. We compare our results for water and Ne atoms as they belong to the same isoelectronic series. Moreover, we contrast our calculations with previous theoretical and experimental work for Ar atoms due to the similarities of the orbitals involved in the reaction. Second, we study the effect of varying the relative orientations of the attopulse and laser field polarizations and we compare our predictions with other theories and experiments. We expect these studies contribute to the improvement of polarization experiments and the development of the attopulse trains and assistant laser fields technologies. Finally, we hope our work promote progress on the control of the chemical reactivity of water molecules since this could be useful in different fields such as radiobiology and medical physics.

  6. Distinct Conformation of ATP Molecule in Solution and on Protein. (United States)

    Kobayashi, Eri; Yura, Kei; Nagai, Yoshinori


    Adenosine triphosphate (ATP) is a versatile molecule used mainly for energy and a phosphate source. The hydrolysis of γ phosphate initiates the reactions and these reactions almost always start when ATP binds to protein. Therefore, there should be a mechanism to prevent spontaneous hydrolysis reaction and a mechanism to lead ATP to a pure energy source or to a phosphate source. To address these questions, we extensively analyzed the effect of protein to ATP conformation based on the sampling of the ATP solution conformations obtained from molecular dynamics simulation and the sampling of ATP structures bound to protein found in a protein structure database. The comparison revealed mainly the following three points; 1) The ribose ring in ATP molecule, which puckers in many ways in solution, tends to assume either C2' exo or C2' endo when it binds to protein. 2) The adenine ring in ATP molecule, which takes open-book motion with the two ring structures, has two distinct structures when ATP binds to protein. 3) The glycosyl-bond and the bond between phosphate and the ribose have unique torsion angles, when ATP binds to protein. The combination of torsion angles found in protein-bound forms is under-represented in ATP molecule in water. These findings suggest that ATP-binding protein exerts forces on ATP molecule to assume a conformation that is rarely found in solution, and that this conformation change should be a trigger for the reactions on ATP molecule.

  7. Crystal structure of a class-mu glutathione S-transferase from whiteleg shrimp Litopenaeus vannamei: structural changes in the xenobiotic binding H-site may alter the spectra of molecules bound. (United States)

    Juárez-Martínez, Ariadna B; Sotelo-Mundo, Rogerio R; Rudiño-Piñera, Enrique


    Glutathione S-transferases (GSTs) are dimeric proteins that play a key role in phase II cellular detoxification. Here, the first crystal structure of a GST class-mu from marine crustacean shrimp Litopenaeus vannamei is reported at a resolution of 2.0 Å. The coordinates reported here have the lowest sequence identity with previously reported GSTs class-mu deposited at the Protein Data Bank (PDB), although they have subtle conformational differences. One key feature of GST class-mu from L. vannamei is the active site crevice markedly reduced when it is compared with other GSTs class-mu. This finding together with the chemical change of residues into the cavity (F112 and Y210) points to a particular specialization in which smallest xenobiotics with nonstandard chemical characteristics can be bound to the H-site. This suggests that marine organisms have evolved structural strategies to provide efficient selectivity toward xenobiotics to be disposed of by the phase II detoxification process. © 2016 Wiley Periodicals, Inc.

  8. The influence of water molecules on NdCl3·3C3H8O in the properties: A DFT study (United States)

    Li, Na; Sun, Fuquan; Chen, Jiaping; Li, Kelu; Li, Shiyi; Zhao, Liang; Liu, Zhichang; Gao, Jinsen


    The catalytic activity of NdCl3-ROH-AlR3 is closely related to the amount of water in NdCl3. Usually NdCl3·6H2O has been dehydrated step by step to NdCl3·2H2O, however, the further dehydration process will be very difficult. In this work, we investigated the effect of added water molecules on structures and properties of NdCl3·3C3H8O, NdCl3·3C3H8O·H2O, and NdCl3·3C3H8O·2H2O, including bond length, angle, mulliken atomic charge, molecular electrostatic potential (MEP), HOMO (Highest Occupied Molecular Orbital) and LUMO (Lowest Unoccupied Molecular Orbital) energy, and natural bond orbital (NBO). All properties were calculated by density functional theory (DFT) using B3PW91 functional and basis set of 6-31G++**/SDDALL. It was found that the bond length of Ndsbnd Cl bond and bond angles of Cl3-Ndsbnd Cl2, O9-Ndsbnd O5, Cl3-Ndsbnd Cl4 could be directly affected due to the addition of water molecule. The MEP analysis revealed that the molecular reaction site should be located around Cl atom. Furthermore, analysis of mulliken atomic charges showed that charge of Nd atom as the active center of the reaction changed from 0.956 to 1.238 and then to 1.301 after addition of one water molecule and two water molecules respectively. HOMO and LUMO orbitals were carried out to investigate the stability of the system, the addition of two water molecules in the system enhanced the electron flow in the system. Also, NBO analysis was further performed to supply an in depth insight into the electronic structure, the distribution of valence electrons and bond orders, which all changed after the addition of water molecule. Therefore, it was necessary to convert NdCl3·2H2O to NdCl3 in order to achieve a higher catalytic activity.

  9. Bounded Parikh Automata

    Directory of Open Access Journals (Sweden)

    Michaël Cadilhac


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

  10. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

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


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

  11. Bounding Species Distribution Models (United States)

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


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

  12. A hot water extract of Curcuma longa inhibits adhesion molecule protein expression and monocyte adhesion to TNF-α-stimulated human endothelial cells. (United States)

    Kawasaki, Kengo; Muroyama, Koutarou; Yamamoto, Norio; Murosaki, Shinji


    The recruitment of arterial leukocytes to endothelial cells is an important step in the progression of various inflammatory diseases. Therefore, its modulation is thought to be a prospective target for the prevention or treatment of such diseases. Adhesion molecules on endothelial cells are induced by proinflammatory cytokines, including tumor necrosis factor-α (TNF-α), and contribute to the recruitment of leukocytes. In the present study, we investigated the effect of hot water extract of Curcuma longa (WEC) on the protein expression of adhesion molecules, monocyte adhesion induced by TNF-α in human umbilical vascular endothelial cells (HUVECs). Treatment of HUVECs with WEC significantly suppressed both TNF-α-induced protein expression of adhesion molecules and monocyte adhesion. WEC also suppressed phosphorylation and degradation of nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha (IκBα) induced by TNF-α in HUVECs, suggesting that WEC inhibits the NF-κB signaling pathway.

  13. Changes in the hydrogen-bonding strength of internal water molecules and cysteine residues in the conductive state of channelrhodopsin-1 (United States)

    Lórenz-Fonfría, Víctor A.; Muders, Vera; Schlesinger, Ramona; Heberle, Joachim


    Water plays an essential role in the structure and function of proteins, particularly in the less understood class of membrane proteins. As the first of its kind, channelrhodopsin is a light-gated cation channel and paved the way for the new and vibrant field of optogenetics, where nerve cells are activated by light. Still, the molecular mechanism of channelrhodopsin is not understood. Here, we applied time-resolved FT-IR difference spectroscopy to channelrhodopsin-1 from Chlamydomonas augustae. It is shown that the (conductive) P2380 intermediate decays with τ ≈ 40 ms and 200 ms after pulsed excitation. The vibrational changes between the closed and the conductive states were analyzed in the X-H stretching region (X = O, S, N), comprising vibrational changes of water molecules, sulfhydryl groups of cysteine side chains and changes of the amide A of the protein backbone. The O-H stretching vibrations of "dangling" water molecules were detected in two different states of the protein using H218O exchange. Uncoupling experiments with a 1:1 mixture of H2O:D2O provided the natural uncoupled frequencies of the four O-H (and O-D) stretches of these water molecules, each with a very weakly hydrogen-bonded O-H group (3639 and 3628 cm-1) and with the other O-H group medium (3440 cm-1) to moderately strongly (3300 cm-1) hydrogen-bonded. Changes in amide A and thiol vibrations report on global and local changes, respectively, associated with the formation of the conductive state. Future studies will aim at assigning the respective cysteine group(s) and at localizing the "dangling" water molecules within the protein, providing a better understanding of their functional relevance in CaChR1.

  14. The effect of water molecules on the thiol collector interaction on the galena (PbS) and sphalerite (ZnS) surfaces: A DFT study

    Energy Technology Data Exchange (ETDEWEB)

    Long, Xianhao [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Chen, Ye, E-mail: [College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China); Chen, Jianhua, E-mail: [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); College of Resources and Metallurgy, Guangxi University, Nanning 530004 (China); Xu, Zhenghe; Liu, Qingxia [Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 2V4 (Canada); Du, Zheng [National Supercomputing Center in Shenzhen, Shenzhen 518055 (China)


    Highlights: • Water adsorption has a greater effect on the electron distribution of ZnS surface than PbS surface. • Water adsorption decreases the reactivity of ZnS surface atoms but improves that of PbS. • Thiol collectors cannot interact with the hydrated ZnS surface. • The hydration has little influence on the interaction of thiol collectors with PbS surface. - Abstracts: In froth flotation the molecular interaction between reagents and mineral surfaces take place at the solid liquid interface. In this paper, the effect of water molecule on the three typical thiol collectors (xanthate, dithiocarbomate and dithiophosphate) interactions at the galena (PbS) and sphalerite (ZnS) surfaces has been studied adopting density functional theory (DFT). The results suggests that the presence of water molecule shows a greater influence on the electron distribution of ZnS surface than PbS surface, and reduce the reactivity of ZnS surface atoms but improves the reactivity of PbS surface atoms during the reaction with xanthate. Water adsorption could also reduce the covalent binding between Zn and S atoms but have little influence on Pb-S bond. In the presence of water, xanthate, dithiocarbomate (DTC) and dithiophosphate (DTP) could not adsorb on the sphalerite surface. And for galena (PbS) surface, the interaction of DTP is the strongest, then the DTC and the interaction of xanthate is the weakest. These results agree well with the flotation practice.

  15. KETERKAITAN BERBAGAI KONSEP INTERAKSI AIR DALAM PRODUK PANGAN [Interrelation on Water Interaction Concepts in Foods]--Komunikasi Singkat

    Directory of Open Access Journals (Sweden)

    Dede R. Adawiyah


    Full Text Available The idea of water interaction with chemicals in the food dry matter or solid was inspired from gas interaction with surface active chemicals, almost a hundred years ago, such as association of gases with active carbon. However, until now the mechanisms and consequences of water molecule associated with chemicals in food solid is still in debate among the food scientists. The concept of water interaction or association with chemicals in the food solid or dry matter was initially introduced as water activity (aw, then in the terminology of “Bound Water”. Water activity concept was further developed by Labuza in 1960s. The concept or idea of glass transition temperature (Tg from Polymers Science discipline was applied to foods in decade of 1980 by Slade & Levine, who denied or negated the earlier concepts of bound water and water activity. In glass transition concept of food products, water functions as a plasticizer related to the textural properties and safety of the products. Knowledge of structure and behaviours of water molecule is required to understand how water interacts or associates with chemicals in food solid. The unique nature of water molecule is a tetrahedral structure with 4 polar angles, which behaves strongly binding or being bound by polar or ionic chemicals in food solid. A number of physicochemical forces act how water molecules interact in complex ways with chemicals in food solid, and the interaction among water molecules in foods. Both types of water interaction lead to the consept of three fractions of bound water as well as to the varities of food characteristics, including preservability and food qualities, either appraisable or unacceptable by consummers. Relationship analyses among various parameter data of associated water in foods such as aw, Me, Tg, and enriched by NMR data, specific weight and specific heat of bound water, indicated that among the different concepts of water interaction in foods were

  16. Tuning the Redox Properties of a Nonheme Iron(III)-Peroxo Complex Binding Redox-Inactive Zinc Ions by Water Molecules. (United States)

    Lee, Yong-Min; Bang, Suhee; Yoon, Heejung; Bae, Seong Hee; Hong, Seungwoo; Cho, Kyung-Bin; Sarangi, Ritimukta; Fukuzumi, Shunichi; Nam, Wonwoo


    Redox-inactive metal ions play important roles in tuning chemical properties of metal-oxygen intermediates. Herein we report the effect of water molecules on the redox properties of a nonheme iron(III)-peroxo complex binding redox-inactive metal ions. The coordination of two water molecules to a Zn(2+) ion in (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 (1-Zn(2+) ) decreases the Lewis acidity of the Zn(2+) ion, resulting in the decrease of the one-electron oxidation and reduction potentials of 1-Zn(2+) . This further changes the reactivities of 1-Zn(2+) in oxidation and reduction reactions; no reaction occurred upon addition of an oxidant (e.g., cerium(IV) ammonium nitrate (CAN)) to 1-Zn(2+) , whereas 1-Zn(2+) coordinating two water molecules, (TMC)Fe(III) -(O2 )-Zn(CF3 SO3 )2 -(OH2 )2 [1-Zn(2+) -(OH2 )2 ], releases the O2 unit in the oxidation reaction. In the reduction reactions, 1-Zn(2+) was converted to its corresponding iron(IV)-oxo species upon addition of a reductant (e.g., a ferrocene derivative), whereas such a reaction occurred at a much slower rate in the case of 1-Zn(2+) -(OH2 )2 . The present results provide the first biomimetic example showing that water molecules at the active sites of metalloenzymes may participate in tuning the redox properties of metal-oxygen intermediates. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Site-specific binding of a water molecule to the sulfa drugs sulfamethoxazole and sulfisoxazole: a laser-desorption isomer-specific UV and IR study. (United States)

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


    To determine the preferred water molecule binding sites of the polybasic sulfa drugs sulfamethoxazole (SMX) and sulfisoxazole (SIX), we have studied their monomers and monohydrated complexes through laser-desorption conformer-specific UV and IR spectroscopy. Both the SMX and SIX monomer adopt a single conformer in the molecular beam. On the basis of their conformer-specific IR spectra in the NH stretch region, these conformers were assigned to the SMX and SIX global minimum structures, both exhibiting a staggered sulfonamide group and an intramolecular C-HO[double bond, length as m-dash]S hydrogen bond. The SMX-H 2 O and SIX-H 2 O complexes each adopt a single isomer in the molecular beam. Their isomeric structures were determined based on their isomer-specific IR spectra in the NH/OH stretch region. Quantum Theory of Atoms in Molecules analysis of the calculated electron densities revealed that in the SMX-H 2 O complex the water molecule donates an O-HN hydrogen bond to the heterocycle nitrogen atom and accepts an N-HO hydrogen bond from the sulfonamide NH group. In the SIX-H 2 O complex, however, the water molecule does not bind to the heterocycle but instead donates an O-HO[double bond, length as m-dash]S hydrogen bond to the sulfonamide group and accepts an N-HO hydrogen bond from the sulfonamide NH group. Both water complexes are additionally stabilized by a C ph -HOH 2 hydrogen bond. Interacting Quantum Atoms analysis suggests that all intermolecular hydrogen bonds are dominated by the short-range exchange-correlation contribution.

  18. Deprotonation states of the two active site water molecules regulate the binding of protein phosphatase 5 with its substrate: A molecular dynamics study. (United States)

    Wang, Lingyun; Yan, Feng


    Protein phosphatase 5 (PP5), mainly localized in human brain, can dephosphorylate tau protein whose high level of phosphorylation is related to Alzheimer's disease. Similar to other protein phosphatases, PP5 has a conserved motif in the catalytic domain that contains two binding sites for manganese (Mn2+ ) ions. Structural data indicate that two active site water molecules, one bridging the two Mn2+ ions and the other terminally coordinated with one of the Mn2+ ions (Mn1), are involved in catalysis. Recently, a density functional theory study revealed that the two water molecules can be both deprotonated to keep a neutral active site for catalysis. The theoretical study gives us an insight into the catalytic mechanism of PP5, but the knowledge of how the deprotonation states of the two water molecules affect the binding of PP5 with its substrate is still lacking. To approach this problem, molecular dynamics simulations were performed to model the four possible deprotonation states. Through structural, dynamical and energetic analyses, the results demonstrate that the deprotonation states of the two water molecules affect the structure of the active site including the distance between the two Mn2+ ions and their coordination, impact the interaction energy of residues R275, R400 and H304 which directly interact with the substrate phosphoserine, and mediate the dynamics of helix αJ which is involved in regulation of the enzyme's activity. Furthermore, the deprotonation state that is preferable for PP5 binding of its substrate has been identified. These findings could provide new design strategy for PP5 inhibitor. © 2017 The Protein Society.

  19. Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxyl via charge compensation†


    Lassalle-Kaiser, Benedikt; Hureau, Christelle; Pantazis, Dimitrios A.; Pushkar, Yulia; Guillot, Régis; Yachandra, Vittal K.; Yano, Junko; Neese, Frank; Anxolabéhère-Mallart, Elodie


    Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water mo...

  20. Molecule nanoweaver (United States)

    Gerald, II; Rex, E [Brookfield, IL; Klingler, Robert J [Glenview, IL; Rathke, Jerome W [Homer Glen, IL; Diaz, Rocio [Chicago, IL; Vukovic, Lela [Westchester, IL


    A method, apparatus, and system for constructing uniform macroscopic films with tailored geometric assemblies of molecules on the nanometer scale. The method, apparatus, and system include providing starting molecules of selected character, applying one or more force fields to the molecules to cause them to order and condense with NMR spectra and images being used to monitor progress in creating the desired geometrical assembly and functionality of molecules that comprise the films.

  1. Molecule Matters

    Indian Academy of Sciences (India)

    Fluorescence usually originates from the lowest excited electronic state (singlet) irrespective of the excitation and hence, the fluorescence spectrum of a molecule is characterized by a single band. However, what makes DMABN a very special molecule is that it exhibits dual fluorescence (i.e. emission of. Molecule Matters.

  2. Virial Expansion Bounds (United States)

    Tate, Stephen James


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

  3. The optimization of single mode basis functions for polyatomic vibrational problems with application to the water molecule (United States)

    Schwenke, David W.


    The optimization of the wave functions is considered for coupled vibrations represented by linear combinations of products of functions depending only on a single vibrational coordinate. The functions themselves are optimized as well as configuration list. For the H2O molecule highly accurate results are obtained for the lowest 15 levels using significantly shorter expansions than would otherwise be possible.

  4. Interactions between Asphaltenes and Water in Solutions in Toluene

    DEFF Research Database (Denmark)

    Khvostichenko, Daria; Andersen, Simon Ivar


    Binding of water by asphaltenes dissolved in toluene was investigated for two asphaltene samples, OMV1 and OMV2, from the same reservoir deposit. Solubility of water in asphaltene solutions in toluene was found to increase with an increasing asphaltene concentration, indicative of solubilization...... of water by asphaltenes. Fourier transform infrared (FTIR) spectroscopy of stretching modes of OH groups in the region of 3800-3100 cm(-1) was used to obtain insight into the state of water in water-unsaturated asphaltene solutions in toluene. The number of water molecules bound to one asphaltene molecule...... was determined for water-saturated solutions (OMV1 and OMV2) and for water-unsaturated solutions (OMV1 only). These numbers were found to decrease from several water molecules per asphaltene molecule to below unity upon an increase of the asphaltene concentration in toluene from 0.1 to 20 g/L, suggesting...

  5. Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxyl via charge compensation† (United States)

    Lassalle-Kaiser, Benedikt; Hureau, Christelle; Pantazis, Dimitrios A.; Pushkar, Yulia; Guillot, Régis; Yachandra, Vittal K.; Yano, Junko; Neese, Frank; Anxolabéhère-Mallart, Elodie


    Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water molecule in the Mn(O) complex is confirmed by electrochemical data while the analysis of EXAFS data reveals a gradual shortening of an Mn–O bond upon oxidation from Mn(II)OH2 to Mn(III)OH and Mn(O). Reactivity experiments, DFT calculations and XANES pre-edge features provide strong evidence that the bonding in Mn(O) is best characterized by a Mn(III)-oxyl description. Such oxyl species could play a crucial role in natural and artificial water splitting reactions. We provide here a synthetic example for such species, obtained by electrochemical activation of a water ligand. PMID:24772190

  6. Activation of a water molecule using a mononuclear Mn complex: from Mn-aquo, to Mn-hydroxo, to Mn-oxylviacharge compensation. (United States)

    Lassalle-Kaiser, Benedikt; Hureau, Christelle; Pantazis, Dimitrios A; Pushkar, Yulia; Guillot, Régis; Yachandra, Vittal K; Yano, Junko; Neese, Frank; Anxolabéhère-Mallart, Elodie


    Activation of a water molecule by the electrochemical oxidation of a Mn-aquo complex accompanied by the loss of protons is reported. The sequential (2 × 1 electron/1 proton) and direct (2 electron/2 proton) proton-coupled electrochemical oxidation of a non-porphyrinic six-coordinated Mn(II)OH 2 complex into a mononuclear Mn(O) complex is described. The intermediate Mn(III)OH 2 and Mn(III)OH complexes are electrochemically prepared and analysed. Complete deprotonation of the coordinated water molecule in the Mn(O) complex is confirmed by electrochemical data while the analysis of EXAFS data reveals a gradual shortening of an Mn-O bond upon oxidation from Mn(II)OH 2 to Mn(III)OH and Mn(O). Reactivity experiments, DFT calculations and XANES pre-edge features provide strong evidence that the bonding in Mn(O) is best characterized by a Mn(III)-oxyl description. Such oxyl species could play a crucial role in natural and artificial water splitting reactions. We provide here a synthetic example for such species, obtained by electrochemical activation of a water ligand.

  7. Gibbs Free Energy of Hydrolytic Water Molecule in Acyl-Enzyme Intermediates of a Serine Protease: A Potential Application for Computer-Aided Discovery of Mechanism-Based Reversible Covalent Inhibitors. (United States)

    Masuda, Yosuke; Yamaotsu, Noriyuki; Hirono, Shuichi


    In order to predict the potencies of mechanism-based reversible covalent inhibitors, the relationships between calculated Gibbs free energy of hydrolytic water molecule in acyl-trypsin intermediates and experimentally measured catalytic rate constants (kcat) were investigated. After obtaining representative solution structures by molecular dynamics (MD) simulations, hydration thermodynamics analyses using WaterMap™ were conducted. Consequently, we found for the first time that when Gibbs free energy of the hydrolytic water molecule was lower, logarithms of kcat were also lower. The hydrolytic water molecule with favorable Gibbs free energy may hydrolyze acylated serine slowly. Gibbs free energy of hydrolytic water molecule might be a useful descriptor for computer-aided discovery of mechanism-based reversible covalent inhibitors of hydrolytic enzymes.

  8. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins. (United States)

    Mihailescu, Mihail; Meirovitch, Hagai


    A mobile loop changes its conformation from "open" (free enzyme) to "closed" upon ligand binding. The difference in the Helmholtz free energy, ΔF(loop) between these states sheds light on the mechanism of binding. With our "hypothetical scanning molecular dynamics" (HSMD-TI) method ΔF(loop) = F(free) - F(bound) where F(free) and F(bound) are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI) procedure. In previous work the free and bound loop structures were both attached to the same "template" which was "cut" from the crystal structure of the free protein. Our results for loop 287-290 of AcetylCholineEsterase agree with the experiment, ΔF(loop)~ -4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., N(water) = 140 - 180 waters in a sphere of a 18 Å radius. Here we calculate ΔF(loop) for the more realistic case, where two templates are "cut" from the crystal structures, 2dfp.pdb (bound) and 2ace.pdb (free), where N(water) = 40 - 160; this requires adding a computationally more demanding (second) TI procedure. While the results for N(water) ≤ 140 are computationally sound, ΔF(loop) is always positive (18 ± 2 kcal/mol for N(water) = 140). These (disagreeing) results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å(2) for 2ace). While this conformational uncertainty is an inherent difficulty, the (unstable) results for N(water) = 160 suggest that it might be alleviated by applying different (initial) structural optimizations to each template.

  9. Intermolecular potential functions from spectroscopic properties of weakly bound complexes

    Energy Technology Data Exchange (ETDEWEB)

    Muenter, J.S.


    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  10. Phase-Transfer Energetics of Small-Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulation Using Charge Equilibration Models (United States)

    Bauer, Brad A.; Zhong, Yang; Meninger, David J.; Davis, Joseph E.; Patel, Sandeep


    We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 g/cm3 and 0.6378±0.0001 g/cm3, demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ε∥) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ε∥ for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13mV and 198.7±0.01mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than

  11. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

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


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

  12. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

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


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

  13. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José


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

  14. Born Level Bound States (United States)

    Hoyer, Paul


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

  15. Probing the continuous radio frequency spectrum of water relaxation using a carbon nanotube. (United States)

    Kim, H T; Kim, D W; Hwang, J S; Shin, J S; Whang, D; Ahn, D; Hwang, S W


    We have obtained the continuous radio frequency spectrum of water molecule relaxation using carbon nanotubes (CNT) as a high-speed nanoprobe. Three sets of characteristic time scales are clearly identified. Two sets are attributed to the electric-field-driven polarization of water molecules bound to CNTs and the collective relaxation of water layers in the vicinity of CNTs, respectively. The third set is appreciable only in air, and can be related to triplet oxygen relaxation. © 2011 IOP Publishing Ltd

  16. A Model of Ball Lightning as a Formation of Water Molecules Confining an Electric Charge and the Classical Theory of the Electron (United States)

    Tennakone, K.


    Ball lightning or faintly luminous floating spheres with radii of the order of ten centimeters appearing transiently in air notably during stormy weather continue to remain an unresolved phenomenon. It is suggested that these objects are organized structures constituted of an electrically charged spherical thin shell of electro-frozen dipole oriented water molecules carrying an electric charge, balanced by the internal negative pressure and outward electrostatic stress. A model presented, resembling the classical theory of the electron with Poincare stresses explain almost all observed attributes of this phenomenon. The possibility of realizing macroscopic spherical surface charge distributions in the vacuum and their implication on the problem of electron are commented.

  17. Supramolecular Amino Acid Based Hydrogels: Probing the Contribution of Additive Molecules using NMR Spectroscopy (United States)

    Ramalhete, Susana M.; Nartowski, Karol P.; Sarathchandra, Nichola; Foster, Jamie S.; Round, Andrew N.; Angulo, Jesús


    Abstract Supramolecular hydrogels are composed of self‐assembled solid networks that restrict the flow of water. l‐Phenylalanine is the smallest molecule reported to date to form gel networks in water, and it is of particular interest due to its crystalline gel state. Single and multi‐component hydrogels of l‐phenylalanine are used herein as model materials to develop an NMR‐based analytical approach to gain insight into the mechanisms of supramolecular gelation. Structure and composition of the gel fibres were probed using PXRD, solid‐state NMR experiments and microscopic techniques. Solution‐state NMR studies probed the properties of free gelator molecules in an equilibrium with bound molecules. The dynamics of exchange at the gel/solution interfaces was investigated further using high‐resolution magic angle spinning (HR‐MAS) and saturation transfer difference (STD) NMR experiments. This approach allowed the identification of which additive molecules contributed in modifying the material properties. PMID:28401991

  18. Molecule Matters

    Indian Academy of Sciences (India)

    is such an innocuous molecule that you might not think it worthy of special attention. We take this molecule for granted because it is abundantly available on earth. About 80 % of the earth's atmosphere, which means a total of 4×1018 kg, is dinitrogen![1] Secondly, it is ignored because it is quite un- reactive. Nitrogen is such ...

  19. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 4. Molecule Matters – van der Waals Molecules - History and Some Perspectives on Intermolecular Forces. E Arunan. Feature Article Volume 14 Issue 4 April 2009 pp 346-356 ...

  20. Doping ZnO with Water/Alcohol-Soluble Small Molecules as Electron Transport Layers for Inverted Polymer Solar Cells. (United States)

    Liu, Chang; Zhang, Lin; Xiao, Liangang; Peng, Xiaobin; Cao, Yong


    By doping ZnO with porphyrin small molecules (FNEZnP-OE and FNEZnP-T) as cathode electron transport layers (ETLs), the inverted polymer solar cells (i-PSC) with PTB7:PC71BM (PTB7: polythieno[3,4-b]-thiophene-co-benzodithiophene, PC71BM: [6, 6]-phenyl-C71-butyric acid methyl ester) as the active materials exhibit enhanced device performance. While the power conversion efficiency (PCE) of the PSCs with pure ZnO ETL is 7.52%, that of the devices with FNEZnP-T-doped ZnO ETL shows a slightly improved PCE of 8.09%, and that of the PSCs with FNEZnP-OE-doped ZnO ETL is further enhanced up to 9.24% with an over 20% improvement compared to that with pure ZnO ETL. The better performance is contributed by the better interfacial contact and reduced work function induced by 9,9-bis(30-(N,N-dimethylamino)propyl)-2,7-fluorenes and 3,4-bis-(2-(2-methoxy-ethoxy)-ethoxy)-phenyls in the porphyrin small molecules. More importantly, the PCE is still higher than 8% even when the thickness of FNEZnP-OE-doped ZnO ETL is up to 110 nm, which are important criteria for eventually making organic photovoltaic modules with roll-to-roll coat processing.

  1. In-situ X-ray diffraction reveals the degradation of crystalline CH3NH3PbI3 by water-molecule collisions at room temperature (United States)

    Hada, Masaki; Hasegawa, Yoichi; Nagaoka, Ryota; Miyake, Tomoya; Abdullaev, Ulugbek; Ota, Hiromi; Nishikawa, Takeshi; Yamashita, Yoshifumi; Hayashi, Yasuhiko


    We have developed a vacuum-compatible chamber for in-situ X-ray diffraction (XRD) studies and have used it to characterize the changing crystal structure of an inorganic–organic hybrid perovskite material, CH3NH3PbI3 (MAPbI3), during interactions with water vapor at room temperature. In the XRD spectra, we have observed the degradation of MAPbI3 and the creation of MAPbI3 hydrates, which follow simple rate equations. The time constant for the degradation of MAPbI3 during accelerated aging suggests that multiple collisions of water molecules with the MAPbI3 crystal trigger the degradation of the crystal.

  2. A novel strategy to produce highly stable and transparent aqueous 'nanosolutions' of water-insoluble drug molecules (United States)

    Wang, Jie-Xin; Zhang, Zhi-Bing; Le, Yuan; Zhao, Hong; Chen, Jian-Feng


    A surprisingly large proportion of new drug candidates emerging from drug discovery programmes are water-insoluble and, as a result, have poor oral bioavailability. To overcome insolubility, the drug particles are usually dispersed in a medium during product formation, but large particles that are formed may affect product performance and safety. Many techniques have been used to produce nanodispersions—dispersions with nanometre-scale dimensions—that have properties similar to solutions. However, making nanodispersions requires complex processing, and it is difficult to achieve stability over long periods. In this paper, we report a generic method for preparing drug nanoparticles with a combination of antisolvent precipitation in the presence of water-soluble matrices and spray-drying. The spray-dried powder composites (solid dispersion) are microspherical, highly stable and thus form transparent nanodispersions or so-called 'nanosolutions' of water-insoluble drug when simply added to water. Aqueous nanodispersions of silybin (a kind of water-insoluble drug for liver protection) with an average size of 25 nm produced with this approach display a 10 times faster dissolution rate than that of raw drug. This has great potential to offer a novel solution for innovative drugs of the future.

  3. Effect of H-bonding interactions of water molecules in the self assembly of supramolecular architecture-joint experimental and computational studies (United States)

    Jassal, Amanpreet Kaur; Kaur, Rajwinder; Islam, Nasarul; Anu; Mudsainiyan, Rahul Kumar


    A new {[Cu(4,4‧-BP)2.(H2O)4].2,6-NDC.3(H2O)} complex has been synthesized by refluxing Cu(NO3)2, 2,6-NDC and 4,4‧-BP (1:1:1 ratio) (2,6-NDC = 2,6-Naphthalene Dicarboxylic acid, 4,4‧-BP = 4,4'-bipyridine) in methanol/ammonia mixture and characterized by various spectroscopic techniques. The geometry around Cu2+ ion is typical octahedral in cationic complex, while the deprotonated 2,6-NDC act as a charge balancing counter anionic part. Water molecules (lattice and coordinated) also play important role in the self-assembly by forming Hsbnd bonded supramolecular architecture involving strong inter/intramolecular secondary interactions. The luminescence property and thermogravimetric analyses were also investigated. Both the intermolecular interactions of molecular and crystal structures of this complex were compared and discussed using Hirshfeld surface analysis and 2D-fingerprint plots. Hirshfeld surface analysis indicates that H⋯H, O⋯H and π···π contacts can account for 40.4, 19.3 and 7.7% respectively of the total Hirshfeld surface area. The DFT calculation at the CAM-B3LYP level of theory revealed the existence of three hydrogens binds in the complex. These hydrogen bonds exist between the oxygen atom of ligand and the hydrogen of coordinated water molecules.

  4. Cold molecules, collisions and reactions (United States)

    Hecker Denschlag, Johannes


    I will report on recent experiments of my group where we have been studying the formation of ultracold diatomic molecules and their subsequent inelastic/reactive collisions. For example, in one of these experiments we investigate collisions of triplet Rb2 molecules in the rovibrational ground state. We observe fast molecular loss and compare the measured loss rates to predictions based on universality. In another set of experiments we investigate the formation of (BaRb)+ molecules after three-body recombination of a single Ba+ ion with two Rb atoms in an ultracold gas of Rb atoms. Our investigations indicate that the formed (BaRb)+ molecules are weakly bound and that several secondary processes take place ranging from photodissociation of the (BaRb)+ molecule to reactive collisions with Rb atoms. I will explain how we can experimentally distinguish these processes and what the typical reaction rates are. Support from the German Research foundation DFG and the European Community is acknowledged.

  5. Bound Exciton Complexes (United States)

    Meyer, B. K.

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

  6. Atkins' molecules

    CERN Document Server

    Atkins, Peters


    Originally published in 2003, this is the second edition of a title that was called 'the most beautiful chemistry book ever written'. In it, we see the molecules responsible for the experiences of our everyday life - including fabrics, drugs, plastics, explosives, detergents, fragrances, tastes, and sex. With engaging prose Peter Atkins gives a non-technical account of an incredible range of aspects of the world around us, showing unexpected connections, and giving an insight into how this amazing world can be understood in terms of the atoms and molecules from which it is built. The second edition includes dozens of extra molecules, graphical presentation, and an even more accessible and enthralling account of the molecules themselves.

  7. Interstellar Molecules (United States)

    Solomon, Philip M.


    Radioastronomy reveals that clouds between the stars, once believed to consist of simple atoms, contain molecules as complex as seven atoms and may be the most massive objects in our Galaxy. (Author/DF)

  8. Epitaxy of the bound water phase on hydrophilic surfaces of biopolymers as key mechanism of microwave radiation effects on living objects. (United States)

    Kuznetsov, Denis B; Orlova, Ekaterina V; Neschislyaev, Valery A; Volkhin, Igor L; Izmestiev, Igor V; Lunegov, Igor V; Balandina, Alevtina V; Dianova, Dina G


    The research investigates the mechanism of microwave radiation effects on biological characteristics and structural-dynamic parameters of a sensor bioluminescence system. The research objects are a sterile growth medium (fish meal hydrolisate) and a bacterial culture. It has been established that irradiation causes changes of the growth medium spectral properties within the range of 200-350nm. Changes take place in the intensity and character of luminescence, as well as in relaxation parameters of nuclear magnetic resonance, growth characteristics of the bacterial culture, its cellular morphology and surface topology. The research results enabled us to establish the mechanisms of primary molecular processes that occur when the bacterial culture is exposed to microwave radiation. Transformation of the dynamic-structural state of adsorbed water phases on biopolymer surfaces has been found to be the key factor in the mechanism of microwave effects on living and water-containing objects. Copyright © 2017 Elsevier B.V. All rights reserved.

  9. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

    Visco, Donald Patrick, Jr. (, . Tennessee Technological University, Cookeville, TN); Faulon, Jean-Loup Michel; Roe, Diana C.


    This report is a comprehensive review of the field of molecular enumeration from early isomer counting theories to evolutionary algorithms that design molecules in silico. The core of the review is a detail account on how molecules are counted, enumerated, and sampled. The practical applications of molecular enumeration are also reviewed for chemical information, structure elucidation, molecular design, and combinatorial library design purposes. This review is to appear as a chapter in Reviews in Computational Chemistry volume 21 edited by Kenny B. Lipkowitz.

  10. Correlation between mechanical behavior of protein films at the air/water interface and intrinsic stability of protein molecules

    NARCIS (Netherlands)

    Martin, A.H.; Cohen Stuart, M.A.; Bos, M.A.; Vliet, van T.


    The relation between mechanical film properties of various adsorbed protein layers at the air/water interface and intrinsic stability of the corresponding proteins is discussed. Mechanical film properties were determined by surface deformation in shear and dilation. In shear, fracture stress, ¿f,

  11. Correlation between mechanical behavior of protein films at the air/water interface and intrinsic stability of protein molecules

    NARCIS (Netherlands)

    Martin, A.H.; Cohen Stuart, M.A.; Bos, M.A.; Vliet, T. van


    The relation between mechanical film properties of various adsorbed protein layers at the air/water interface and intrinsic stability of the corresponding proteins is discussed. Mechanical film properties were determined by surface deformation in shear and dilation. In shear, fracture stress, σf,

  12. Annual Variations in Water Storage and Precipitation in the Amazon Basin: Bounding Sink Terms in the Terrestrial Hydrological Balance using GRACE Satellite Gravity Data (United States)

    Crowley, John W.; Mitrovica, Jerry X.; Bailey, Richard C.; Tamisiea, Mark E.; Davis, James L.


    We combine satellite gravity data from the Gravity Recovery and Climate Experiment (GRACE) and precipitation measurements from the National Oceanic and Atmospheric Administration (NOAA) Climate Prediction Center's (CPC) Merged Analysis of Precipitation (CMAP) and the Tropical Rainfall Measuring Mission (TRMM), over the period from mid-2002 to mid-2006, to investigate the relative importance of sink (runoff and evaporation) and source (precipitation) terms in the hydrological balance of the Amazon Basin. When linear and quadratic terms are removed, the time series of land water storage variations estimated from GRACE exhibits a dominant annual signal of 250 mm peak-to-peak, which is equivalent to a water volume change of approximately 1800 cubic kilometers. A comparison of this trend with accumulated (i.e., integrated) precipitation shows excellent agreement and no evidence of basin saturation. The agreement indicates that the net runoff and evaporation contributes significantly less than precipitation to the annual hydrological mass balance. Indeed, raw residuals between the detrended water storage and precipitation anomalies range from plus or minus 40 mm. This range is consistent with streamflow measurements from the region, although the latter are characterized by a stronger annual signal than ow residuals, suggesting that runoff and evaporation may act to partially cancel each other.

  13. Density Functional Theory Calculation of pKa's of Thiols in Aqueous Solution Using Explicit Water Molecules and the Polarizable Continuum Model. (United States)

    Thapa, Bishnu; Schlegel, H Bernhard


    The pKa's of substituted thiols are important for understanding their properties and reactivities in applications in chemistry, biochemistry, and material chemistry. For a collection of 175 different density functionals and the SMD implicit solvation model, the average errors in the calculated pKa's of methanethiol and ethanethiol are almost 10 pKa units higher than for imidazole. A test set of 45 substituted thiols with pKa's ranging from 4 to 12 has been used to assess the performance of 8 functionals with 3 different basis sets. As expected, the basis set needs to include polarization functions on the hydrogens and diffuse functions on the heavy atoms. Solvent cavity scaling was ineffective in correcting the errors in the calculated pKa's. Inclusion of an explicit water molecule that is hydrogen bonded with the H of the thiol group (in neutral) or S(-) (in thiolates) lowers error by an average of 3.5 pKa units. With one explicit water and the SMD solvation model, pKa's calculated with the M06-2X, PBEPBE, BP86, and LC-BLYP functionals are found to deviate from the experimental values by about 1.5-2.0 pKa units whereas pKa's with the B3LYP, ωB97XD and PBEVWN5 functionals are still in error by more than 3 pKa units. The inclusion of three explicit water molecules lowers the calculated pKa further by about 4.5 pKa units. With the B3LYP and ωB97XD functionals, the calculated pKa's are within one unit of the experimental values whereas most other functionals used in this study underestimate the pKa's. This study shows that the ωB97XD functional with the 6-31+G(d,p) and 6-311++G(d,p) basis sets, and the SMD solvation model with three explicit water molecules hydrogen bonded to the sulfur produces the best result for the test set (average error -0.11 ± 0.50 and +0.15 ± 0.58, respectively). The B3LYP functional also performs well (average error -1.11 ± 0.82 and -0.78 ± 0.79, respectively).

  14. Hydrogen-bond network formation of water molecules and its effects on the glass transitions in the ethylene glycol aqueous solutions: failure of the Gordon-Taylor law in the water-rich range and absence of the T(g) = 115 K rearrangement process in bulk pure water. (United States)

    Nagoe, Atsushi; Oguni, Masaharu


    Enthalpy relaxation processes proceeding in ethylene glycol (EG) aqueous solutions [(EG)(x)(H(2)O)(1 - x)] within silica-gel nanopores were studied by adiabatic calorimetry. While the x = 0.25 solution within pores with diameter of 52 nm showed a glass transition at T(g) = 139 K, ageing of the solution at 160 K caused a phase separation to reveal glass transitions at T(g) = 145 and 160 K for EG-rich and water-rich regions, respectively: the water molecules are understood to form a more developed hydrogen-bond network, and consequently force the EG molecules in between the water-rich regions. The T(g) = 160 K is in good agreement with the T(g) value of the internal (not interfacial) water confined within pores with thickness of 1.1 nm. The ageing further remarkably diminished the T(g) = 115 K glass transition. This indicates that, while the molecules responsible for the glass transition are the mobile water ones forming a lower number of hydrogen bonds than four, the fraction of such water molecules is reduced in association with the development of the network and the glass transition is absent in bulk pure water. When the same x = 0.25 solution was confined within 1.1- and 12 nm pores, the water molecules developed a hydrogen-bond network in the pore centre due to the presence of the pore wall and pushed the EG molecules onto the pore surface even at higher temperatures: the water-rich region gave T(g) = 155 K close to 160 K. It is concluded that the hydrogen-bond network inherent to water structure is developed/collapsed remarkably in the range near x = 0; consequently, the composition dependence of T(g) in the bulk system deviates sharply in the range from the Gordon-Taylor empirical law followed for large x > 0.2.

  15. Dromions bound states

    Energy Technology Data Exchange (ETDEWEB)

    Maccari, Attilio


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

  16. A comparative study of thermo-sensitive hydrogels with water-insoluble paclitaxel in molecule, nanocrystal and microcrystal dispersions (United States)

    Lin, Zhiqiang; Mei, Dong; Chen, Meiwan; Wang, Yitao; Chen, Xianhui; Wang, Zhaoyang; He, Bing; Zhang, Hua; Wang, Xueqing; Dai, Wenbing; Yin, Yuxin; Zhang, Qiang


    In situ thermo-sensitive hydrogels have attracted increasing attention for alternative cancer therapies due to their long-term and effective drug levels at local sites. Besides synthesizing new thermo-sensitive polymers, we can also fabricate this delivery system by combining a hydrogel with a thermo-response and drug in a different dispersion state, such as drug nanocrystals. However, the impact of the drug dispersion state or dimension on the quality of such a local injectable system is still unknown. So, here we developed and compared three types of F127 hydrogel systems with either paclitaxel or the near infra-red probe DiR in molecules (MOs), nanocrystals (NCs) and microcrystals (MCs), respectively. With 120 nm rod-shape nanocrystals, the NCs-Gel achieved a high drug loading, moderate drug release rate and gel erosion in vitro and in vivo, medium intratumoral drug residue but the best anti-tumor efficacy in 4T1 tumor bearing BALB/c mice. With the free drug solubilized in 20 nm micelles of the gel, the MOs-Gel system demonstrated the least drug loading and the fastest drug release and gel erosion, leading to the least intratumoral residue as well as the lowest anti-tumor effect. Finally, when dispersed in micron-grade rod-shape drug crystals, the MCs-Gel exhibited a high drug loading but poor stability, precipitating in vitro and in vivo, the highest intratumoral residue but the least drug release, resulting in moderate tumor inhibition. In conclusion, this study clarifies the effect of the drug dispersion state and scale on the behavior of a thermo-sensitive hydrogel, indicating the advantage of the NCs-Gel system, and it provides a basis for the future design of the local delivery of hydrophobic anti-cancer agents.

  17. High rates and substrate selectivities in water by polyvinylimidazoles as transaminase enzyme mimics with hydrophobically bound pyridoxamine derivatives as coenzyme mimics. (United States)

    Skouta, Rachid; Wei, Sujun; Breslow, Ronald


    Free-radical polymers of 4-vinylimidazole and copolymers with 1-dodecyl-4-vinylimidazole were used as enzyme mimics to transaminate pyruvic acid to alanine, phenylpyruvic acid to phenylalanine, and indole-3-pyruvic acid to tryptophan in water at pH 7.5 and 20 degrees C using pyridoxamines carrying hydrophobic side chains as coenzyme mimics. The best enzyme mimic accelerated the transamination of indole-3-pyruvic acid by a factor of 4 million relative to the rate without the polymer, a higher rate ratio than we had previously achieved with a polyaziridine-based enzyme mimic. The properties of various polyvinylimidazoles were compared, including those prepared with the RAFT modification of the polymerization process.

  18. Delivery of antisense oligonucleotides using HPMA polymer: synthesis of A thiol polymer and its conjugation to water-soluble molecules. (United States)

    Wang, L; Kristensen, J; Ruffner, D E


    Here, we report the synthesis and characterization of an HPMA-based polymer for use as a carrier for the delivery of water soluble drugs. The polymer contains active-sulfhydryl groups for coupling of ligands through a disulfide linkage. The polymer can also be prepared containing pendant amino groups in addition to the active-sulfhydryl moiety. This allows the use of different chemistries to conjugate a variety of ligands to the polymer. We demonstrate that a sulfhydryl-terminated antisense oligonucleotide can be efficiently and rapidly conjugated to the polymer. The polymer-oligonucleotide conjugate is efficiently taken up by cultured cells.

  19. Fabrication of PLA/CaCO3 hybrid micro-particles as carriers for water-soluble bioactive molecules. (United States)

    Kudryavtseva, Valeriya L; Zhao, Li; Tverdokhlebov, Sergei I; Sukhorukov, Gleb B


    We propose the use of polylactic acid/calcium carbonate (PLA/CaCO3) hybrid micro-particles for achieving improved encapsulation of water-soluble substances. Biodegradable porous CaCO3 microparticles can be loaded with wide range of bioactive substance. Thus, the formation of hydrophobic polymeric shell on surface of these loaded microparticles results on encapsulation and, hence, sealing internal cargo and preventing their release in aqueous media. In this study, to encapsulate proteins, we explore the solid-in-oil-in-water emulsion method for fabricating core/shell PLA/CaCO3 systems. We used CaCO3 particles as a protective core for encapsulated bovine serum albumin, which served as a model protein system. We prepared a PLA coating using dichloromethane as an organic solvent and polyvinyl alcohol as a surfactant for emulsification; in addition, we varied experimental parameters such as surfactant concentration and polymer-to-CaCO3 ratio to determine their effect on particle-size distribution, encapsulation efficiency and capsule permeability. The results show that the particle size decreased and the size distribution narrowed as the surfactant concentration increased in the external aqueous phase. In addition, when the CaCO3/PLA mass ratio dropped below 0.8, the hybrid micro-particles were more likely to resist treatment by ethylenediaminetetraacetic acid and thus retained their bioactive cargos within the polymer-coated micro-particles. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Assessment of CCSD(T), MP2, and DFT methods for the calculations of structures and interaction energies of the peptide backbone with water molecules (United States)

    Kang, Nam Sook; Kang, Young Kee


    The CCSD(T), MP2, and DFT levels of theory with various basis sets are assessed for the structures and interaction energies of N-methylacetamide (NMA) and water molecules. The ωB97X-D/6-311++G(d,p) and ωB97X-D/6-31+G(2d,p) levels of theory seem to be adequate for optimization of the structures of NMA-water complexes. For seven NMA-water complexes, the best performances were obtained using the double-hybrid DSD-PBEP86-D3BJ and B2PLYP-D3BJ functionals with half-counterpoise corrections against the CCSD(T)/CBS-aTQ limit energies. However, the ωB97X-D/def2-QZVP//ωB97X-D/6-31+G(2d,p) level of theory can be an alternative method to calculate the interaction energies of the larger models.

  1. Sorption Characteristics of Mixed Molecules of Glutaraldehyde from Water on Mesoporous Acid-Amine Modified Low-Cost Activated Carbon: Mechanism, Isotherm, and Kinetics

    Directory of Open Access Journals (Sweden)

    Mukosha Lloyd


    Full Text Available The environmental discharge of inefficiently treated waste solutions of the strong biocide glutaraldehyde (GA from hospitals has potential toxic impact on aquatic organisms. The adsorption characteristics of mixed polarized monomeric and polymeric molecules of GA from water on mesoporous acid-amine modified low-cost activated carbon (AC were investigated. It was found that the adsorption strongly depended on pH and surface chemistry. In acidic pH, the adsorption mechanism was elaborated to involve chemical sorption of mainly hydroxyl GA monomeric molecules on acidic surface groups, while in alkaline pH, the adsorption was elaborated to involve both chemical and physical sorption of GA polymeric forms having mixed functional groups (aldehyde, carboxyl, and hydroxyl on acidic and amine surface groups. The optimum pH of adsorption was about 12 with significant contribution by cooperative adsorption, elucidated in terms of hydrogen bonding and aldol condensation. Freundlich and Dubinin-Radushkevich models were fitted to isotherm data. The adsorption kinetics was dependent on initial concentration and temperature and described by the Elovich model. The adsorption was endothermic, while the intraparticle diffusion model suggested significant contribution by film diffusion. The developed low-cost AC could be used to supplement the GA alkaline deactivation process for efficient removal of residual GA aquatic toxicity.

  2. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip


    Explores the atoms that govern chemical processes. This book shows how the interactions between simple substances such as salt and water are crucial to life on Earth and how those interactions are predestined by the atoms that make up the molecules.

  3. Degradation process by effect of water molecules during negative bias temperature stress in amorphous-InGaZnO thin-film transistor (United States)

    Lee, Yeol-Hyeong; Cho, Yong-Jung; Kim, Woo-Sic; Park, Jeong Ki; Kim, Geon Tae; Kim, Ohyun


    We explained how H2O degrades amorphous-InGaZnO thin-film transistors. H2O caused serious degradation only during negative bias temperature stress (NBTS). Degradation was caused by molecules that were absorbed or diffused from the outside. We suggest that degradation under NBTS is caused by the migration of hydrogen ions among oxygen vacancies. Under illumination, the soaking time t S did not affect the threshold voltage shift ΔV th. We consider that this independence occurred because illumination caused ionization from the oxygen vacancy VO state to VO 2+, which impeded hydrogen migration induced by electric field and thereby protected the device from degradation after exposure to water.

  4. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 9. Molecule Matters - A Chromium Compound with a Quintuple Bond. K C Kumara Swamy. Feature Article Volume 11 Issue 9 September 2006 pp 72-75. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 13; Issue 5. Molecule Matters - N-Heterocyclic Carbenes - The Stable Form of R2 C: Anil J Elias. Feature Article Volume 13 Issue 5 May 2008 pp 456-467. Fulltext. Click here to view fulltext PDF. Permanent link:

  6. Molecule Matters

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 11; Issue 11. Molecule Matters - Carbon Dioxide: Molecular States and Beyond. T P Radhakrishnan. Feature Article Volume 11 Issue 11 November 2006 pp 88-92. Fulltext. Click here to view fulltext PDF. Permanent link:

  7. Refining Multivariate Value Set Bounds (United States)

    Smith, Luke Alexander

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

  8. Specific Electrostatic Molecular Recognition in Water

    DEFF Research Database (Denmark)

    Li, Ming; Hoeck, Casper; Schoffelen, Sanne


    The identification of pairs of small peptides that recognize each other in water exclusively through electrostatic interactions is reported. The target peptide and a structure-biased combinatorial ligand library consisting of ≈78 125 compounds were synthesized on different sized beads. Peptide...... simulations binding also seemed to involve three tightly bound water molecules in the interface between the binding partners. Binding constants in the submicromolar range, useful for biomolecular adhesion and in nanostructure design, were measured....

  9. Photonic Molecule Lasers Revisited (United States)

    Gagnon, Denis; Dumont, Joey; Déziel, Jean-Luc; Dubé, Louis J.


    Photonic molecules (PMs) formed by coupling two or more optical resonators are ideal candidates for the fabrication of integrated microlasers, photonic molecule lasers. Whereas most calculations on PM lasers have been based on cold-cavity (passive) modes, i.e. quasi-bound states, a recently formulated steady-state ab initio laser theory (SALT) offers the possibility to take into account the spectral properties of the underlying gain transition, its position and linewidth, as well as incorporating an arbitrary pump profile. We will combine two theoretical approaches to characterize the lasing properties of PM lasers: for two-dimensional systems, the generalized Lorenz-Mie theory will obtain the resonant modes of the coupled molecules in an active medium described by SALT. Not only is then the theoretical description more complete, the use of an active medium provides additional parameters to control, engineer and harness the lasing properties of PM lasers for ultra-low threshold and directional single-mode emission. We will extend our recent study and present new results for a number of promising geometries. The authors acknowledge financial support from NSERC (Canada) and the CERC in Photonic Innovations of Y. Messaddeq.

  10. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

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


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

  11. Radiolysis of adsorbed water molecules on Al/sub 2/O/sub 3/, La/sub 2/O/sub 3/, Er/sub 2/O/sub 3/ and BeO. [Gamma Radiation

    Energy Technology Data Exchange (ETDEWEB)

    Garibov, A.A.; Melikzade, M.M.; Bakirov, M.Ya.; Ramazanova, M.K.

    The oxides were studied by first conditioning them at 500/sup 0/C for 12 h, and then processing them in a vacuum for 5 h at 350/sup 0/C. Double-distilled water was used for the adsorption tests. Ampules containing the oxides were irradiated with gamma radiation from /sup 60/Co. Analysis of radiolysis products showed H/sub 2/ and O/sub 2/ content in proportions above stoichiometric norms, indicating oxygen entrapment in the oxide structures. Hydrogen yield corresponded to the quantity of water molecules subjected to radiolysis. The oxides had a catalytic effect on the radiation chemical decomposition of the water, and were able to transmit absorbed energy from ionizing radiation to molecules adsorbed on their surfaces. BeO had relatively high catalytic activity, apparently due to a recombination mechanism of the decomposition of adsorbed molecules. 10 references, 1 figure.

  12. Anion binding by biotin[6]uril in water

    DEFF Research Database (Denmark)

    Lisbjerg, Micke; Nielsen, Bjarne Enrico; Milhøj, Birgitte Olai


    In this contribution we show that the newly discovered 6 + 6 biotin-formaldehyde macrocycle Biotin[6]uril binds a variety of anionic guest molecules in water. We discuss how and why the anions are bound based on data obtained using NMR spectroscopy, mass spectrometry, isothermal titration...

  13. selective excitation of vibrational modes of polyatomic molecule

    Indian Academy of Sciences (India)

    Abstract. Mode-selective dynamics of triatomic molecule in the electronic ground state under continuous wave laser pulse is investigated for the discrete vibrational bound states. A non-perturbative approach has been used to analyse the vibrational couplings and dynamics of the molecule. Keywords. Polyatomic molecule ...

  14. Understanding water: Molecular dynamics simulations of solubilized and crystallized myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P. [Los Alamos National Laboratory, NM (United States)


    Molecular dynamics simulations were performed on CO myoglobin to evaluate the stability of the bound water molecules as determined in a neutron diffraction analysis. The myoglobin structure derived from the neutron analysis provided the starting coordinate set used in the simulations. The simulations show that only a few water molecules are tightly bound to protein atoms, while most solvent molecules are labile, breaking and reforming hydrogen bonds. Comparison between myoglobin in solution and in a single crystal highlighted some of the packing effects on the solvent structure and shows that water solvent plays an indispensable role in protein dynamics and structural stability. The described observations explain some of the differences in the experimental results of protein hydration as observed in NMR, neutron and X-ray diffraction studies.

  15. Bounding approaches to system identification

    CERN Document Server

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


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

  16. with Bounded Failure Intensity

    Directory of Open Access Journals (Sweden)

    Preeti Wanti Srivastava


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

  17. ExtremeBounds: Extreme Bounds Analysis in R

    Directory of Open Access Journals (Sweden)

    Marek Hlavac


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

  18. A tool for cost-effectiveness analysis of field scale sediment-bound phosphorus mitigation measures and application to analysis of spatial and temporal targeting in the Lunan Water catchment, Scotland. (United States)

    Vinten, Andy; Sample, James; Ibiyemi, Adekunle; Abdul-Salam, Yakubu; Stutter, Marc


    The cost-effectiveness of six edge-of-field measures for mitigating diffuse pollution from sediment bound phosphorus (P) runoff from temperate arable farmland is analysed at catchment/field scales. These measures were: buffer strips, permanent grassland in the lowest 7% of arable fields, dry detention bunds, wetlands, and temporary barriers such as sediment fences. Baseline field P export was estimated using export coefficients (low risk crops) or a modified Universal Soil Loss Equation (high risk crops). The impact of measures was estimated using simple equations. Costs were estimated from gross margin losses or local data on grants. We used a net cost:benefit (NCB) factor to normalise the costs and impacts of each measure over time. Costs minimisation for target impact was done using PuLP, a linear programming module for Python, across 1634 riparian and non-riparian fields in the Lunan Water, a mixed arable catchment in Eastern Scotland. With all measures in place, average cost-effectiveness increases from £9 to £48/kg P as target P mitigation increases from 500 to 2500kg P across the catchment. Costs increase significantly when the measures available are restricted only to those currently eligible for government grants (buffers, bunds and wetlands). The assumed orientation of the average field slope makes a strong difference to the potential for storage of water by bunds and overall cost-effectiveness, but the non-funded measures can substitute for the extra expense incurred by bunds, where the slope orientation is not suitable. Economic discounting over time of impacts and costs of measures favours those measures, such as sediment fences, which are strongly targeted both spatially and temporally. This tool could be a useful guide for dialogue with land users about the potential fields to target for mitigation to achieve catchment targets. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  19. An optical conveyor for molecules. (United States)

    Weinert, Franz M; Braun, Dieter


    Trapping single ions under vacuum allows for precise spectroscopy in atomic physics. The confinement of biological molecules in bulk water is hindered by the lack of comparably strong forces. Molecules have been immobilized to surfaces, however often with detrimental effects on their function. Here, we optically trap molecules by creating the microscale analogue of a conveyor belt: a bidirectional flow is combined with a perpendicular thermophoretic molecule drift. Arranged in a toroidal geometry, the conveyor accumulates a hundredfold excess of 5-base DNA within seconds. The concentrations of the trapped DNA scale exponentially with length, reaching trapping potential depths of 14 kT for 50 bases. The mechanism does not require microfluidics, electrodes, or surface modifications. As a result, the trap can be dynamically relocated. The optical conveyor can be used to enhance diffusion-limited surface reactions, redirect cellular signaling, observe individual biomolecules over a prolonged time, or approach single-molecule chemistry in bulk water.

  20. Bounds for Asian basket options (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle


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

  1. Hadron-nucleus bound states

    CERN Document Server

    Yamazaki, T


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

  2. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

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

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

  3. Market access through bound tariffs

    DEFF Research Database (Denmark)

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


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

  4. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 12. Molecule Matters van der Waals Molecules - Noble Gas Clusters are London Molecules! E Arunan. Feature Article Volume 14 Issue 12 December 2009 pp 1210-1222 ...

  5. Protein-bound toxins: has the Cinderella of uraemic toxins turned into a princess? (United States)

    Liabeuf, Sophie; Villain, Cédric; Massy, Ziad A


    Chronic kidney disease (CKD) has emerged as a global public health problem. Although the incidence and prevalence of CKD vary from one country to another, the estimated worldwide prevalence is 8-16%. The complications associated with CKD include progression to end-stage renal disease (ESRD), mineral and bone disorders, anaemia, cognitive decline and elevated all-cause and cardiovascular (CV) mortality. As a result of progressive nephron loss, patients with late-stage CKD are permanently exposed to uraemic toxins. These toxins have been classified into three groups as a function of the molecular mass: small water-soluble molecules, middle molecules and protein-bound uraemic toxins. The compounds can also be classified according to their origin (i.e. microbial or not) or their protein-binding ability. The present review will focus on the best-characterized protein-bound uraemic toxins, namely indoxylsulfate (IS), indole acetic acid (IAA) and p-cresylsulfate (PCS, a cresol metabolite). Recent research suggests that these toxins accelerate the progression of CV disease, kidney disease, bone disorders and neurological complications. Lastly, we review therapeutic approaches that can be used to decrease toxin levels. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

  6. Hangman Catalysis for Photo–and Photoelectro–Chemical Activation of Water Proton-Coupled Electron Transfer Mechanisms of Small Molecule Activation

    Energy Technology Data Exchange (ETDEWEB)

    Nocera, Daniel G. [Harvard Univ., Cambridge, MA (United States)


    The weakest link for the large-scale deployment of solar energy and for that matter, any renewable energy source, is its storage. The energy needs of future society demands are so large that storage must be in the form of fuels owing to their high energy density. Indeed, society has intuitively understood this disparity in energy density as it has developed over the last century as all large-scale energy storage in our society is in the form of fuels. But these fuels are carbon-based. The imperative for the discipline of chemistry, and more generally science, is to develop fuel storage methods that are easily scalable, carbon-neutral and sustainable. These methods demand the creation of catalysts to manage the multi-electron, multi-proton transformations of the conversion of small molecules into fuels. The splitting of water using solar light is a fuel-forming reaction that meets the imperative of large scale energy storage. As light does not directly act on water to engender its splitting into its elemental components, we have designed “hangman” catalysts to effect the energy conversion processes needed for the fuel forming reactions. The hangman construct utilizes a pendant acid/base functionality within the secondary coordination sphere that is “hung” above the redox platform onto which substrate binds. In this way, we can precisely control the delivery of a proton to the substrate, thus ensuring efficient coupling between the proton and electron. An emphasis was on the coupling of electron and proton in the hydrogen evolution reaction (HER) on Ni, Co and Fe porphyrin platforms. Electrokinetic rate laws were developed to define the proton-coupled electron transfer (PCET) mechanism. The HER of Co and Fe porphyrins was metal-centered. Surprisingly, HER this was not the case for Ni porphyrins. In this system, the PCET occurred at the porphyrin platform to give rise to a phlorin. This is one of the first examples of an HER occurring via ligand non

  7. Watching single molecules dance (United States)

    Mehta, Amit Dinesh

    Molecular motors convert chemical energy, from ATP hydrolysis or ion flow, into mechanical motion. A variety of increasingly precise mechanical probes have been developed to monitor and perturb these motors at the single molecule level. Several outstanding questions can be best approached at the single molecule level. These include: how far does a motor progress per energy quanta consumed? how does its reaction cycle respond to load? how many productive catalytic cycles can it undergo per diffusional encounter with its track? and what is the mechanical stiffness of a single molecule connection? A dual beam optical trap, in conjunction with in vitro ensemble motility assays, has been used to characterize two members of the myosin superfamily: muscle myosin II and chick brain myosin V. Both move the helical polymer actin, but myosin II acts in large ensembles to drive muscle contraction or cytokinesis, while myosin V acts in small numbers to transport vesicles. An optical trapping apparatus was rendered sufficiently precise to identify a myosin working stroke with 1nm or so, barring systematic errors such as those perhaps due to random protein orientations. This and other light microscopic motility assays were used to characterize myosin V: unlike myosin II this vesicle transport protein moves through many increments of travel while remaining strongly bound to a single actin filament. The step size, stall force, and travel distance of myosin V reveal a remarkably efficient motor capable of moving along a helical track for over a micrometer without significantly spiraling around it. Such properties are fully consistent with the putative role of an organelle transport motor, present in small numbers to maintain movement over long ranges relative to cellular size scales. The contrast between myosin II and myosin V resembles that between a human running on the moon and one walking on earth, where the former allows for faster motion when in larger ensembles but for less

  8. Fluorescence Images of DNA-Bound YOYO between Coupled Silver Particles


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


    Oligonucleotide-bound silver particles were coupled through hybridization with target complementary oligonucleotides. YOYO molecules were intercalated into DNA duplexes bound between the coupled metal particles. Fluorescence images of YOYO molecules were monitored by scanning confocal microscopy. Relative to the free single YOYO, the emission brightness of the image was enhanced 80-fold after intercalating the fluorophores into the DNA duplexes between the coupled silver particles. Some image...

  9. Bound state in positron scattering by allene (United States)

    Barbosa, Alessandra Souza; Sanchez, Sergio d'Almeida; Bettega, Márcio H. F.


    We report integral and differential cross sections for positron collisions with allene, calculated with the Schwinger multichannel method. The cross sections were computed in the static-polarization approximation for energies up to 7 eV. We have tested a series of single-particle basis sets and different polarization schemes to improve the description of low-energy positron scattering by the allene molecule. We have found that the use of extra centers with no net charge with additional single-particle s - and p -type functions centered at them are essential in order to accurately reproduce the polarization potential and, hence, obtain proper scattering cross sections. The choice of the allene molecule was due to the fact that it is a highly symmetric molecule with no permanent dipole moment and would allow several different calculations. Our cross sections are compared to the available experimental data for the total cross section with a reasonable agreement after correcting their results due to the low angular discrimination of their apparatus. Also, a virtual state was observed in the integral cross section that became a bound state when the description of the polarization potential is improved. We also observed a Ramsauer-Townsend minimum in the cross section whose location varies from 2.7 to 3.4 eV, depending on the polarization scheme used in the calculations.

  10. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M


    We study the photo-association of an ultracold cloud of magnetically trapped helium atoms: pairs of colliding atoms interact with one or two laser fields to produce a purely long range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}P{sub 0}) molecule, or a {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) long range molecule. Light shifts in one photon photo-association spectra are measured and studied as a function of the laser polarization and intensity, and the vibrational state of the excited molecule. They result from the light-induced coupling between the excited molecule, and bound and scattering states of the interaction between two metastable atoms. Their analysis leads to the determination of the scattering length a = (7.2 {+-} 0.6) ruling collisions between spin polarized atoms. The two photon photo-association spectra show evidence of the production of polarized, long-range {sup 4}He{sub 2}(2{sup 3}S{sub 1}-2{sup 3}S{sub 1}) molecules. They are said to be exotic as they are made of two metastable atoms, each one carrying a enough energy to ionize the other. The corresponding lineshapes are calculated and decomposed in sums and products of Breit-Wigner and Fano profiles associated to one and two photon processes. The experimental spectra are fit, and an intrinsic lifetime {tau} = (1.4 {+-} 0.3) {mu}s is deduced. It is checked whether this lifetime could be limited by spin-dipole induced Penning autoionization. This interpretation requires that there is a quasi-bound state close to the dissociation threshold in the singlet interaction potential between metastable helium atoms for the theory to match the experiment. (author)

  11. Ultracold molecule assembly with photonic crystals (United States)

    Pérez-Ríos, Jesús; Kim, May E.; Hung, Chen-Lung


    Photoassociation (PA) is a powerful technique to synthesize molecules directly and continuously from cold and ultracold atoms into deeply bound molecular states. In freespace, however, PA efficiency is constrained by the number of spontaneous decay channels linking the initial excited molecular state to a sea of final (meta)stable rovibronic levels. Here, we propose a novel scheme based on molecules strongly coupled to a guided photonic mode in a photonic crystal waveguide that turns PA into a powerful tool for near deterministic formation of ultracold molecules in their ground rovibrational level. Our example shows a potential ground state molecule production efficiency > 90 % , and a saturation rate > {10}6 molecules per second. By combining state-of-the-art cold atomic and molecular physics with nanophotonic engineering, our scheme presents a novel experimental package for trapping, cooling, and optically manipulating ultracold molecules, thus opening up new possibilities in the direction of ultracold chemistry and quantum information.

  12. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze


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

  13. Spectroscopic characterizations of non-amphiphilic 2-(4-biphenylyl)-6-phenyl benzoxazole molecules at the air-water interface and in Langmuir-Blodgett films

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, S.A. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India); Deb, S. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India); Bhattacharjee, D. [Department of Physics, Tripura University, Suryamaninagar, Agartala: 799130 Tripura (India)]. E-mail:


    This communication reports about the successful incorporation of a well-known non-amphiphilic derivative of oxazole chromophore 2-(4-biphenylyl)-6-phenyl benzoxazole abbreviated as PBBO, in Langmuir-Blodgett films when mixed with stearic acid (SA) as well as also an inert polymer matrix polymethylmethacrylate (PMMA). The surface pressure versus area per molecule isotherms of the Langmuir films of PBBO mixed with PMMA or SA at different mole fractions reveal that the area per molecule decreases consistently with increasing mole fractions of PBBO. Area per molecule versus mole fraction curve shows that the experimental data points coincide with the ideality curve predicted by the additivity rule, which leads to the conclusion of either ideal mixing or complete demixing of the binary components. The UV-vis absorption and fluorescence spectroscopic studies of mixed LB films of PBBO reveal the nature of complete demixing of the binary components of the sample molecules (PBBO) and PMMA or SA molecules. This complete demixing leads to the formation of clusters and aggregates of PBBO molecules in Langmuir and Langmuir-Blodgett films. J-type aggregates of PBBO molecules in LB films have been confirmed by UV-vis absorption spectroscopic study. Aggregation of PBBO molecules in LB films giving rise to excimeric emission has been demonstrated by fluorescence spectroscopic study. Excitation spectroscopic study clearly confirmed the presence of excimeric sites.

  14. Cardiorenal syndrome: role of protein-bound uremic toxins. (United States)

    Lekawanvijit, Suree; Krum, Henry


    Renal impairment is a strong independent risk factor associated with poor prognosis in cardiovascular disease patients. Renal dysfunction is likely contributed by progressive renal structural damage. Accurate detection of kidney injury in a timely manner as well as increased knowledge of the pathophysiology and mechanisms underlying this injury is of great importance in developing therapeutic interventions for combating renal complications at an early stage. Regarding the role of uremic solutes in the pathophysiology of cardiorenal syndrome, a number of further studies are warranted. There may be uremic solutes discovered from proteomics not yet chemically identified or tested for biological activity. Beyond Protein-bound uremic toxins, uremic solutes in other classes (according to the European Uraemic Toxin Work Group classification) may have adverse cardiorenal effects. Although most small water-soluble solutes and middle molecules can be satisfactorily removed by either conventional or newly developed dialysis strategies, targeting uremic toxins with cardiorenal toxicity at predialysis stage of chronic kidney disease may retard or prevent incident dialysis as well as the initiation/progression of cardiorenal syndrome. Copyright © 2015 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  15. 1H NMR study of the magnetic properties and electronic structure of the hydroxide complex of substrate-bound heme oxygenase from Neisseria meningitidis: influence of the axial water deprotonation on the distal H-bond network. (United States)

    Ma, Li-Hua; Liu, Yangzhong; Zhang, Xuhang; Yoshida, Tadashi; La Mar, Gerd N


    The substrate and active site residues of the low-spin hydroxide complex of the protohemin complex of Neisseria meningitidis heme oxygenase (NmHO) have been assigned by saturation transfer between the hydroxide and previously characterized aquo complex. The available dipolar shifts allowed the quantitation of both the orientation and anisotropy of the paramagnetic susceptibility tensor. The resulting positive sign, and reduced magnitude of the axial anisotropy relative to the cyanide complex, dictate that the orbital ground state is the conventional "d(pi)" (d(2)(xy)(d(xz), d(yz))(3)); and not the unusual "d(xy)" (d(2)(xz)d(2)(yz)d(xy)) orbital ground state reported for the hydroxide complex of the homologous heme oxygenase (HO) from Pseudomonas aeruginosa (Caignan, G.; Deshmukh, R.; Zeng, Y.; Wilks, A.; Bunce, R. A.; Rivera, M. J. Am. Chem. Soc. 2003, 125, 11842-11852) and proposed as a signature of the HO distal cavity. The conservation of slow labile proton exchange with solvent from pH 7.0 to 10.8 confirms the extraordinary dynamic stability of NmHO complexes. Comparison of the diamagnetic contribution to the labile proton chemical shifts in the aquo and hydroxide complexes reveals strongly conserved bond strengths in the distal H-bond network, with the exception of the distal His53 N(epsilon)(1)H. The iron-ligated water is linked to His53 primarily by a pair of nonligated, ordered water molecules that transmit the conversion of the ligated H-bond donor (H(2)O) to a H-bond acceptor (OH(-)), thereby increasing the H-bond donor strength of the His53 side chain.

  16. Computational Lower Bounds Using Diagonalization

    Indian Academy of Sciences (India)

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

  17. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg


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

  18. Facile synthesis of highly water-soluble fullerenes more than half-covered by hydroxyl groups. (United States)

    Kokubo, Ken; Matsubayashi, Kenji; Tategaki, Hiroshi; Takada, Hiroya; Oshima, Takumi


    Using a novel hydrogen peroxide heating method, we synthesized milky white, water-soluble polyhydroxylated fullerenes (fullerenols) with 36-40 hydroxyl groups (estimated average) along with 8-9 secondary bound water molecules. The fullerenols exhibited high water solubility up to 58.9 mg/mL in a neutral (pH = 7) condition. Dynamic light scattering analysis showed a high dispersion property, to give a narrow particle size distribution within 0.7-2.0 nm.

  19. Flow enhancement of water flow through silica slit pores with graphene-coated walls

    DEFF Research Database (Denmark)

    Walther, J. H.; Popadic, A.; Koumoutsakos, P.

    We present continuum simulations of water flow past fullerene molecules. The governing Navier-Stokes equations are complemented with the Navier slip bound-ary condition with a slip length that is extracted from related molecular dynamics simulations. We find that several quantities of interest...

  20. Probing the Role of Active Site Water in the Sesquiterpene Cyclization Reaction Catalyzed by Aristolochene Synthase. (United States)

    Chen, Mengbin; Chou, Wayne K W; Al-Lami, Naeemah; Faraldos, Juan A; Allemann, Rudolf K; Cane, David E; Christianson, David W


    Aristolochene synthase (ATAS) is a high-fidelity terpenoid cyclase that converts farnesyl diphosphate exclusively into the bicyclic hydrocarbon aristolochene. Previously determined crystal structures of ATAS complexes revealed trapped active site water molecules that could potentially interact with catalytic intermediates: water "w" hydrogen bonds with S303 and N299, water molecules "w1" and "w2" hydrogen bond with Q151, and a fourth water molecule coordinates to the Mg(2+)C ion. There is no obvious role for water in the ATAS mechanism because the enzyme exclusively generates a hydrocarbon product. Thus, these water molecules are tightly controlled so that they cannot react with carbocation intermediates. Steady-state kinetics and product distribution analyses of eight ATAS mutants designed to perturb interactions with active site water molecules (S303A, S303H, S303D, N299A, N299L, N299A/S303A, Q151H, and Q151E) indicate relatively modest effects on catalysis but significant effects on sesquiterpene product distributions. X-ray crystal structures of S303A, N299A, N299A/S303A, and Q151H mutants reveal minimal perturbation of active site solvent structure. Seven of the eight mutants generate farnesol and nerolidol, possibly resulting from addition of the Mg(2+)C-bound water molecule to the initially formed farnesyl cation, but no products are generated that would suggest enhanced reactivity of other active site water molecules. However, intermediate germacrene A tends to accumulate in these mutants. Thus, apart from the possible reactivity of Mg(2+)C-bound water, active site water molecules in ATAS are not directly involved in the chemistry of catalysis but instead contribute to the template that governs the conformation of the flexible substrate and carbocation intermediates.

  1. [Adhesion molecules and cancer]. (United States)

    Pierres, A; Benoliel, A M; Bongrand, P


    This review was aimed at summarizing recent advances in the understanding of cell adhesion in order to discuss the possible relevance of new knowledge to the exploration of cancer patients and elaboration of therapeutic strategies. During the last 10 years, many adhesion molecules were identified, thus allowing to determine their tissue distribution and functional regulation. The concept of adhesiveness was refined. It is now well known that adhesive rate (i.e., the minimal contact time required for bond formation) and binding strength (i.e., the minimal force required to detach bound cells) are distinct parameters. They may be regulated independently, and influence the cell behavior in different ways. It is now possible to achieve accurate control of tumor cell adhesiveness, either by inhibiting an adhesive mechanism (through monoclonal antibodies, competitive ligands, or inhibition of receptor expression with antisense strategy or gene knock-out) or by promoting a binding mechanism (with receptor transfection or pro-inflammatory stimulation). Recent progress opens new possibilities for diagnosis and treatment. First, the interpretation of experimental data may be improved. Cell adhesive behavior is not entirely accounted for by the density of membrane adhesion receptors. Indeed, adhesion is influenced by receptor connection to the cytoskeleton and structure of the cell coat. An adhesion receptor may be anti-metastatic through an increase in tumor cohesion and cell differentiation, or pro-metastatic, through facilitation of cell migration towards a target tissue. New therapeutic strategies may include anti-adhesive procedure aimed at preventing metastasis formation. The potential importance of a better control of inflammatory processes is also emphasized in view of the influence of these processes on the expression of adhesion molecules.

  2. Tunneling Ionization of Diatomic Molecules

    DEFF Research Database (Denmark)

    Svensmark, Jens Søren Sieg


    When a molecule is subject to a strong laser field, there is a probability that an electron can escape, even though the electrons are bound by a large potential barrier. This is possible because electrons are quantum mechanical in nature, and they are therefore able to tunnel through potential...... barriers, an ability classical particles do not possess. Tunnelling is a fundamental quantum mechanical process, a process that is distinctly non-classical, so solving this tunnelling problem is not only relevant for molecular physics, but also for quantum theory in general. In this dissertation the theory...... of tunneling ionizaion of molecules is presented and the results of numerical calculations are shown. One perhaps surprising result is, that the frequently used Born-Oppenheimer approximation breaks down for weak fields when describing tunneling ionization. An analytic theory applicable in the weak-field limit...

  3. Space-bounded communication complexity

    DEFF Research Database (Denmark)

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


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

  4. Quantum effects at low-energy atom–molecule interface

    Indian Academy of Sciences (India)

    The effects of quantum interference in inter-conversion between cold atoms and diatomic molecules are analysed in this study. Within the framework of Fano's theory, continuum bound anisotropic dressed state formalism of atom–molecule quantum dynamics is presented. This formalism is applicable in photo- and ...

  5. Insights into the mechanism of the reaction between tetrachloro-p-benzoquinone and hydrogen peroxide and their implications in the catalytic role of water molecules in producing the hydroxyl radial. (United States)

    Li, Ping; Wang, Weihua; Sun, Qiao; Li, Zhen; Du, Aijun; Bi, Siwei; Zhao, Yan


    Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Molecule Matters van der Waals Molecules

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 7. Molecule Matters van der Waals Molecules - Rg•••HF Complexes are Debye Molecules! E Arunan. Feature Article Volume 15 Issue 7 July 2010 pp 667-674. Fulltext. Click here to view fulltext PDF. Permanent link:

  7. Mobility of molecules and ions solubilized in protein gels: diffusion in the thick fraction of hen egg white. (United States)

    Krise, Keith M; Milosavljevic, Bratoljub H


    The thick fraction of hen egg white is a protein hydrogel with an immeasurably high viscosity composed of ∼90% water that can serve as a model system for mammalian mucous membrane. Measurements of the rate constants of diffusion-controlled reactions occurring within the gel (and corresponding activation energies) and electric conductivity revealed that the thick fraction of egg white can be envisioned as a 3D network comprising hydrated protein molecules (held by intermolecular S-S bridges) surrounded by water pools and channels (of nonuniform diameters) that have a microviscosity that is very similar to that of bulk water. This was corroborated by differential scanning calorimetry measurements that revealed that 16% of water is bound to proteins. The melting kinetics of ice crystallites (produced from the freezable water) indicates nonhomogeneous water pool size.

  8. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.


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

  9. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

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

  10. Distance bounds on quantum dynamics (United States)

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


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

  11. Moderate deviations for bounded subsequences

    Directory of Open Access Journals (Sweden)

    George Stoica


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

  12. Spin Labeling ESR Investigation of Covalently Bound Residues in Soil (United States)

    Aleksandrova, Olga; Steinhoff, Heinz-Juergen; Klasmeier, Joerg; Schulz, Marcus; Matthies, Michael


    Organic xenobiotic chemicals, such as pesticides, biocides and veterinary pharmaceuticals, interact with soil, which results in the simultaneous formations of metabolites, mineralization products, and bound or non-extractable residues (NER). Substances or metabolites with reactive functional groups, such as aniline or phenol, have a tendency to give a larger proportion of NER. Despite numerous studies on NER, the majority of their chemical structures is still unknown. Reversible sequestration and irreversible formation of NER were also observed for veterinary antibiotic pharmaceuticals, after their application to soil with and without manure. For this purpose, we hypothesized a key role of specific functional groups of soil contaminants, via which contaminants are covalently bound to soil constituents, and advance a method of spin labeling ESR investigation of reaction products using a membrane method. Spin labels (SL) represent chemically stable paramagnetic molecules used as molecular labels and molecular probes for testing the covalent binding, structural properties, and molecular mobility of different physical, chemical, and biological systems. In the case of covalent binding of SL, their ESR spectra become broadened. We used stable nitroxide radicals (NR) as SL. These radicals modeled organic chemical contaminants and differed only in one functional group. The paramagnetic SL 4-Amino Tempo (4-amino-2,2,6,6-tetramethyl-1-piperidinylox) differed from Tempo (2,2,6,6-Tetramethylpiperidinooxy) in a substituent at the para-position of the piperidine ring, whereas Aniline Tempo (1-Piperidinyloxy, 2,2,6,-tetramethyl, 6-Aniline) differed from Tempo in an Aniline substituting one CH3 functional group. Before experimental analysis, we tested temporal changes in the concentration of both NR incubated with soil and found that the life-times of them in soil exceeded 3 days. We contaminated and labeled soil samples with NR, adding to soil the aqueous solution, which already

  13. Formation and dynamics of van der Waals molecules in buffer-gas traps


    Brahms, Nathan; Tscherbul, Timur V.; Zhang, Peng; Kłos, Jacek; Forrey, Robert C.; Au, Yat Shan; Sadeghpour, H. R.; Dalgarno, A.; Doyle, John M.; Walker, Thad G.


    We show that weakly bound He-containing van der Waals molecules can be produced and magnetically trapped in buffer-gas cooling experiments, and provide a general model for the formation and dynamics of these molecules. Our analysis shows that, at typical experimental parameters, thermodynamics favors the formation of van der Waals complexes composed of a helium atom bound to most open-shell atoms and molecules, and that complex formation occurs quickly enough to ensure chemical equilibrium. F...

  14. Water (United States)

    ... Home Nutrition Nutrition basics Water Water Did you know that water makes up more ... to drink more water Other drinks How much water do you need? top Water is very important, ...

  15. Radiolysis of water molecules adsorbed on Al/sub 2/O/sub 3/, La/sub 2/O/sub 3/, Er/sub 2/O/sub 3/, BeO. [Gamma radiation

    Energy Technology Data Exchange (ETDEWEB)

    Garibov, A.A.; Melikzade, M.M.; Bakirov, M.Ya.; Ramazanova, M.Kh. (AN Azerbajdzhanskoj SSR, Baku. Sektor Radiatsionnykh Issledovanij)

    A study was made on kinetics of processes of hydrogen formation during gamma radiolysis of water in adsorbed state on the surface of Al/sub 2/O/sub 3/, La/sub 2/O/sub 3/, Er/sub 2/O/sub 3/ and BeO samples. It was revealed, that the presence of oxides causes the increase of the process rate and the yield of hydrogen during the heterogeneous radiolysis of water. It was established that beryllium oxide posseses the greatest catalytic activity among oxides investigated. In the presence of beryllium oxide the total yield of hydrogen molecules per 100 eV of absorbed energy attaines 4.4. Taking into consideration the energy absorbed by adsorbed water the yield is 210.

  16. Lower bounds in differential privacy


    De, Anindya


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

  17. Geometry of Homogeneous Bounded Domains

    CERN Document Server

    Vesentini, E


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

  18. Wronskian method for bound states

    Energy Technology Data Exchange (ETDEWEB)

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


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

  19. Physical state of poorly water soluble therapeutic molecules loaded into SBA-15 ordered mesoporous silica carriers: a case study with itraconazole and ibuprofen. (United States)

    Mellaerts, Randy; Jammaer, Jasper A G; Van Speybroeck, Michiel; Chen, Hong; Van Humbeeck, Jan; Augustijns, Patrick; Van den Mooter, Guy; Martens, Johan A


    The ordered mesoporous silica material SBA-15 was loaded with the model drugs itraconazole and ibuprofen using three different procedures: (i) adsorption from solution, (ii) incipient wetness impregnation, and (iii) heating of a mixture of drug and SBA-15 powder. The location of the drug molecules in the SBA-15 particles and molecular interactions were investigated using nitrogen adsorption, TGA, DSC, DRS UV-vis, and XPS. The in vitro release of hydrophobic model drugs was evaluated in an aqueous environment simulating gastric fluid. The effectiveness of the loading method was found to be strongly compound dependent. Incipient wetness impregnation using a concentrated itraconazole solution in dichloromethane followed by solvent evaporation was most efficient for dispersing itraconazole in SBA-15. The itraconazole molecules were located on the mesopore walls and inside micropores of the mesopore walls. When SBA-15 was loaded by slurrying it in a diluted itraconazole solution from which the solvent was evaporated, the itraconazole molecules ended up in the mesopores that they plugged locally. At a loading of 30 wt %, itraconazole exhibited intermolecular interactions inside the mesopores revealed by UV spectroscopy and endothermic events traced with DSC. The physical mixing of itraconazole and SBA-15 powder followed by heating above the itraconazole melting temperature resulted in formulations in which glassy itraconazole particles were deposited externally on the SBA-15 particles. Loading with ibuprofen was successful with each of the three loading procedures. Ibuprofen preferably is positioned inside the micropores. In vitro release experiments showed fast release kinetics provided the drug molecules were evenly deposited over the mesoporous surface.

  20. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins

    Directory of Open Access Journals (Sweden)

    Hagai Meirovitch


    Full Text Available A mobile loop changes its conformation from “open” (free enzyme to “closed” upon ligand binding. The difference in the Helmholtz free energy, ΔFloop between these states sheds light on the mechanism of binding. With our “hypothetical scanning molecular dynamics” (HSMD-TI method ΔFloop = Ffree − Fbound where Ffree and Fbound are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI procedure. In previous work the free and bound loop structures were both attached to the same “template” which was “cut” from the crystal structure of the free protein. Our results for loop 287−290 of AcetylCholineEsterase agree with the experiment, ΔFloop~ −4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., Nwater = 140 − 180 waters in a sphere of a 18 Å radius. Here we calculate ΔFloop for the more realistic case, where two templates are “cut” from the crystal structures, 2dfp.pdb (bound and 2ace.pdb (free, where Nwater = 40 − 160; this requires adding a computationally more demanding (second TI procedure. While the results for Nwater ≤ 140 are computationally sound, ΔFloop is always positive (18 ± 2 kcal/mol for Nwater = 140. These (disagreeing results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å2 for 2ace. While this conformational uncertainty is an inherent difficulty, the (unstable results for Nwater = 160 suggest that it might be alleviated by applying different (initial structural optimizations to each template.

  1. Cyclotron transitions of bound ions (United States)

    Bezchastnov, Victor G.; Pavlov, George G.


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

  2. Hadronic molecules with hidden charm and bottom

    Directory of Open Access Journals (Sweden)

    Guo Feng-Kun


    Full Text Available Many of the new structures observed since 2003 in experiments in the heavy quarkonium mass region, such as the X(3872 and Zc (3900, are rather close to certain thresholds, and thus can be good candidates of hadronic molecules, which are loose bound systems of hadrons. We will discuss the consequences of heavy quark symmetry for hadronic molecules with heavy quarks. We will also emphasize that the hadronic molecular component of a given structure can be directly probed in long-distance processes, while the short-distance processes are not sensitive to it.

  3. Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling (United States)


    Small molecules that increase the oxygen affinity of human hemoglobin may reduce sickling of red blood cells in patients with sickle cell disease. We screened 38 700 compounds using small molecule microarrays and identified 427 molecules that bind to hemoglobin. We developed a high-throughput assay for evaluating the ability of the 427 small molecules to modulate the oxygen affinity of hemoglobin. We identified a novel allosteric effector of hemoglobin, di(5-(2,3-dihydro-1,4-benzodioxin-2-yl)-4H-1,2,4-triazol-3-yl)disulfide (TD-1). TD-1 induced a greater increase in oxygen affinity of human hemoglobin in solution and in red blood cells than did 5-hydroxymethyl-2-furfural (5-HMF), N-ethylmaleimide (NEM), or diformamidine disulfide. The three-dimensional structure of hemoglobin complexed with TD-1 revealed that monomeric units of TD-1 bound covalently to β-Cys93 and β-Cys112, as well as noncovalently to the central water cavity of the hemoglobin tetramer. The binding of TD-1 to hemoglobin stabilized the relaxed state (R3-state) of hemoglobin. TD-1 increased the oxygen affinity of sickle hemoglobin and inhibited in vitro hypoxia-induced sickling of red blood cells in patients with sickle cell disease without causing hemolysis. Our study indicates that TD-1 represents a novel lead molecule for the treatment of patients with sickle cell disease. PMID:25061917

  4. Universal quantum dot-based sandwich-like immunoassay strategy for rapid and ultrasensitive detection of small molecules using portable and reusable optofluidic nano-biosensing platform

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Liping; Zhu, Anna; Lou, Xuening; Song, Dan; Yang, Rong [School of Environment and Natural Resources, Renmin University of China, Beijing (China); Shi, Hanchang [School of Environment, Tsinghua University, Beijing (China); Long, Feng, E-mail: [School of Environment and Natural Resources, Renmin University of China, Beijing (China)


    A universal sandwich-like immunoassay strategy based on quantum-dots immunoprobe (QD-labeled anti-mouse IgG antibody) was developed for rapid and ultrasensitive detection of small molecules. A portable and reusable optofluidic nano-biosensing platform was applied to investigate the sandwich-like immunoassay mechanism and format of small molecules, as well as the binding kinetics between QD immunoprobe and anti-small molecule antibody. A two-step immunoassay method that involves pre-incubation mixture of different concentration of small molecule and anti-small molecule antibody, and subsequent introduction of QD immunoprobe into the optofluidic cell was conducted for small molecule determination. Compared with the one-step immunoassay method, the two-step immunoassay method can obtain higher fluorescence signal and higher sensitivity index, thus improving the nano-biosensing performance. Based on the proposed strategy, two mode targets, namely, microcystin-LR (MC-LR) and Bisphenol A (BPA) were tested with high sensitivity, rapidity, and ease of use. A higher concentration of small molecules in the sample led to less anti-small molecule antibody bound with antigen-carrier protein conjugate immobilized onto the sensor surface, and less QD immunoprobes bound with anti-small molecule antibody. This phenomenon lowered the fluorescence signal detected by nano-biosensing platform. Under optimal operating conditions, MC-LR and BPA exhibited a limit of detection of 0.003 and 0.04 μg/L, respectively. The LODs were better than those of the indirect competitive immunoassay method for small molecules via Cy5.5-labeled anti-small molecule antibody. The proposed QD-based sandwich-like immunoassay strategy was evaluated in spiked water samples, and showed good recovery, precision and accuracy without complicated sample pretreatments. All these results demonstrate that the new detection strategy could be readily applied to the other trace small molecules in real water samples

  5. Lower bounds for randomized Exclusive Write PRAMs

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, P.D.


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

  6. Water-soluble small-molecule probes for RNA based on a two-photon fluorescence "off-on" process: systematic analysis in live cell imaging and understanding of structure-activity relationships. (United States)

    Li, Hong; Li, Yuncang; Zhang, Huihui; Xu, Guoyong; Zhang, Yuliang; Liu, Xiaohu; Zhou, Hongping; Yang, Xingyuan; Zhang, Xuanjun; Tian, Yupeng


    The conveniently obtained water-soluble small-molecule L1-5 were selective for RNA with remarkable "off-on" two-photon fluorescence responses in vitro and in vivo, showing that L1-5 can surprisingly stain mitochondria or nucleoli individually with orange fluorescence under different focal lengths. Compounds L6-8 were prepared, for comparison, to further explore the mechanism of the binding of L1-5 with RNA, which revealed that the synergistic effect of the amino group and the pyridinium cation played a significant role in distinct cell imaging.

  7. Entrapment of a neutral Tm(III)-based complex with two inner-sphere coordinated water molecules into PEG-stabilized vesicles: towards an alternative strategy to develop high-performance LipoCEST contrast agents for MR imaging. (United States)

    Chahid, Bochra; Vander Elst, Luce; Flament, Julien; Boumezbeur, Fawzi; Medina, Christelle; Port, Marc; Muller, Robert N; Lesieur, Sylviane


    Chemical exchange saturation transfer (CEST) probes issued from the encapsulation of a water proton paramagnetic shift reagent into the inner aqueous volume of lipid vesicles provide an emerging class of frequency-selective contrast agents with huge potential in the field of molecular magnetic resonance imaging (MRI). This work deals with the generation of such LipoCEST agents properly designed to optimize, under isotonic conditions, the chemical shift offset of the intra-liposomal water protons as well as the number of exchangeable protons under reasonably low radiofrequency (RF) fields of saturation. The strategy lies in the loading of poly(ethylene glycol)-stabilized nanosized liposomes with uncharged lanthanide chelates, binding more than one water molecule in the first hydration sphere, exemplified here by [Tm(III)-DO3A (H2 O)2 ] complex. The key properties of the probes are demonstrated by complementary NMR investigations. The residence lifetime of the water molecules coordinated to the lanthanide center was outstandingly short (9.5 ± 0.2 ns from (17) O NMR), and indeed relevant for effective LipoCEST responsiveness. The (1) H NMR CEST spectra (7.01 T magnetic field) prove that the theoretically expected optimal sensitivity can be approximated in the nanomolar concentration range, at reasonably low RF presaturation pulses (6.7-12 μT) and saturation frequency offsets of the intra-liposomal water protons beyond 10 ppm, making possible selective irradiation in biological environment. CEST-MRI images (7.01 T magnetic field and 10-12 μT RF pulse) explicitly confirm the interest of these newly conceived LipoCEST agents, indeed among the most efficient ones developed so far under isosmotic conditions. Copyright © 2014 John Wiley & Sons, Ltd.

  8. Volume Stability of Bitumen Bound Building Blocks

    Directory of Open Access Journals (Sweden)

    Thanaya I.N.A.


    Full Text Available This paper covers results of laboratory investigations on the volume stability of masonry units incorporating waste materials bound with bitumen (Bitublocks, due to moisture adsorption, thermal exposure and vacuum saturation. The materials used were steel slag, crushed glass, coal fly ash, and 50 pen bitumen. The samples were produced in hot mix method, compacted, then exposed to moist and temperature. It was found that moisture adsorption from the environment caused the Bitublock to expand. The samples with less intense curing regime experienced lower expansion and became stable faster, and vice versa. Under thermal condition (at 70°C, the samples with less intense curing regime underwent higher expansion, and vice versa. They were also highly reversible. Their volume stability was found unique under water exposure. The expansion on first vacuum saturation cycle was irreversible, then largely reversible on the following cycles.

  9. {1H}/{2H} and {1H}/{17O} nuclear quadrupole double-resonance study of several hydroxide compounds. II. The water molecule (United States)

    Poplett, Ian J. F.

    Using the technique of double resonance with coupled multiplets at 77 K and room temperature, 17O double-resonance signals were detected from the H 2O molecules in a number of hydrates of the alkali metal and alkaline earth metal hydroxides at natural abundance. The deuteron double-resonance signals were measured in deuterated samples at 77 K using double resonance by level crossing. The correlations between the 17O and 2H quadrupole coupling constants and the hydrogen bond strength are discussed. The 17O DRCM results for BeSO 4 · 4H 2O are included.

  10. Heavy exotic molecules with charm and bottom (United States)

    Liu, Yizhuang; Zahed, Ismail


    We revisit the formation of pion-mediated heavy-light exotic molecules with both charm and bottom and their chiral partners under the general strictures of both heavy-quark and chiral symmetry. The chiral exotic partners with good parity formed using the (0+ ,1+) multiplet are about twice more bound than their primary exotic partners formed using the (0- ,1-) multiplet. The chiral couplings across the multiplets (0± ,1±) cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for J ≤ 1. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with JPC =1++ bind, which we identify as the reported neutral X (3872). Also, the bottom isotriplet exotic with JPC =1+- binds, which we identify as a mixture of the reported charged exotics Zb+ (10610) and Zb+ (10650). The bound isosinglet with JPC =1++ is suggested as a possible neutral Xb (10532) not yet reported.

  11. Tritiated Water Interaction with Stainless Steel

    Energy Technology Data Exchange (ETDEWEB)

    Glen R. Longhurst


    Experiments conducted to study tritium permeation of stainless steel at ambient and elevated temperatures revealed that HT converts relatively quickly to HTO. Further, the HTO partial pressure contributes essentially equally with elemental tritium gas in driving permeation through the stainless steel. Such permeation appears to be due to dissociation of the water molecule on the hot stainless steel surface. There is an equilibrium concentration of HTO vapor above adsorbed gas on the walls of the experimental apparatus evident from freezing transients. The uptake process of tritium from the carrier gas involves both surface adsorption and isotopic exchange with surface bound water.

  12. IM-CRDS for the analysis of matrix-bound water isotopes: a streamlined (and updated) tool for ecohydrologists to probe small-scale variability in plants Yasuhara, S. (,Carter, J.A. (, Dennis, K.J. ( 1Picarro Inc., 3105 Patrick Henry Drive, Santa Clara, CA 95054 (United States)

    Yasuhara, S.


    The ability to measure the isotopic composition of matrix-bound water is valuable to many facets of earth and environmental sciences. For example, ecohydrologists use stable isotopes of oxygen and hydrogen in plant and soil water, in combination with measurements of atmospheric water vapor, surface water and precipitation, to estimate budgets of evapotranspiration. Likewise, water isotopes of oceanic water, brines and other waters with high total dissolved solids (TDS, e.g., juices) are relevant to studying large-scale oceanic circulation, small-scale mixing, groundwater contamination, the balance of evaporation to precipitation, and the provenance of food. Conventionally matrix-bound water has been extracted using cryogenic distillation, whereby water is distilled from the material in question (e.g., a leaf sample) by heating under vacuum and collecting the resultant water vapor using liquid nitrogen. The water can then be analyzed for its stable isotopic composition by a variety of methods, including isotope ratio mass spectrometry and laser techniques, such as Cavity Ring-Down Spectroscopy (CRDS). Here we present recent improvements in an alternative, and stream-lined, solution for integrated sample extraction and isotopic measurement using a Picarro Induction Module (IM) coupled to commercially-available CRDS analyzer from Picarro. This technique is also valuable for waters with high TDS, which can have detrimental effects on flash vaporization process, typically used for the introduction of water to Picarro CRDS water isotope analyzers. The IM works by inductively heating a sample held within a metal sample holder in a glass vial flushed with dry air. Tested samples include leaves, stems, twigs, calibration water, juices, and salt water. The heating process evolves water vapor which is then swept through the system at approximately 150 standard cubic centimeters per minute. The evolved water vapor passes through an activated charcoal cartridge for removal of

  13. Control of the selectivity of the aquaporin water channel family by global orientational tuning

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Tajkhorshid, E.; Nollert, P.


    and orientation of a single file of seven to nine water molecules inside the channel. Two conserved asparagines force a central water molecule to serve strictly as a hydrogen bond donor to its neighboring water molecules. Assisted by the electrostatic potential generated by two half-membrane spanning loops......Aquaporins are transmembrane channels found in cell membranes of all life forms. We examine their apparently paradoxical property, facilitation of efficient permeation of water while excluding protons, which is of critical importance to preserving the electrochemical potential across the cell...... membrane. We have determined the structure of the Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T mutant (2.1 angstroms) forms, and carried out 12-nanosecond molecular dynamics simulations that define the spatial and temporal probability distribution...

  14. Towards Automatic Resource Bound Analysis for OCaml


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


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

  15. Distance hijacking attacks on distance bounding protocols


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


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

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

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


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

  17. Broadband Microwave Spectroscopy as a Tool to Study Intermolecular Interactions in the Diphenyl Ether - Water System (United States)

    Fatima, Mariyam; Perez, Cristobal; Schnell, Melanie


    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.

  18. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    Massaro, D.


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

  19. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil


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

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

    Li, Zhuo; Xing, Li-Juan


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

  1. [Biophysics of single molecules]. (United States)

    Serdiuk, I N; Deriusheva, E I


    The modern methods of research of biological molecules whose application led to the development of a new field of science, biophysics of single molecules, are reviewed. The measurement of the characteristics of single molecules enables one to reveal their individual features, and it is just for this reason that much more information can be obtained from one molecule than from the entire ensample of molecules. The high sensitivity of the methods considered in detail makes it possible to come close to the solution of the basic problem of practical importance, namely, the determination of the nucleotide sequence of a single DNA molecule.

  2. Impact of Water-Dilution on the Solvation Properties of the Ionic Liquid 1-Methyltriethoxy-3-ethylimidazolium Acetate for Model Biomass Molecules. (United States)

    Schutt, Timothy C; Hegde, Govind A; Bharadwaj, Vivek S; Johns, Adam J; Maupin, C Mark


    Many studies have suggested that the processing of lignocellulosic biomass could provide a renewable feedstock to supplant much of the current demand on petroleum sources. Currently, alkyl imidazolium-based ionic liquids (ILs) have shown considerable promise in the pretreatment, solvation, and hydrolysis of lignocellulosic materials although their high cost and unfavorable viscosity has limited their widespread use. Functionalizing these ILs with an oligo(ethoxy) tail has previously been shown through experiment to decrease the IL's viscosity resulting in enhanced mass transport characteristics, in addition to other favorable traits including decreased inhibition of some enzymes. Additionally, the use of cosolvents to mitigate the cost and unfavorable traits of ILs is an area of growing interest with particular attention on water as the presence of water in biomass processes is inevitable. Through the use of biased and unbiased molecular dynamics (MD) simulations, this study provides a molecular-level perspective of the various solvent-solvent and solvent-solute interactions in binary mixtures of water and 1-methyltriethoxy-3-ethylimidazolium acetate ([Me-(OEt) 3 -Et-IM + ] [OAc - ]) in the presence of model cellulose compounds (i.e., glucose and cellobiose). It is observed that at ∼75% w/w IL and water a transition in the nanostructure of the solvent occurs between water-like and IL-like solvation characteristics. It is shown that H-bonding interactions between the anion and water are a major driving force that significantly impacts the solvent properties of the IL as well as conformational preferences of the cellulosic model compound. In addition, it is found that the oligo(ethoxy) cation tail is responsible for the reduction in the propensity for tail aggregation as compared to alkyl tails of similar length, which, combined with increased ionic shielding, results in increased diffusion and enhanced water-like solvation characteristics.

  3. Structures of the Substrate-free and Product-bound Forms of HmuO, a Heme Oxygenase from Corynebacterium diphtheriae (United States)

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


    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

  4. One novel 1D coordination polymer with parallel dinuclear copper(II) macrocyclic platforms bridged by trans dimeric half-water molecules and two dinuclear copper(II) macrocyclic complexes with different coordination geometry obtained from different solvents (United States)

    Chu, Zhaolian; You, Wei; Huang, Wei


    Three dinuclear copper(II) macrocyclic complexes, formulated as [Cu 2L(N 3) 2(0.5H 2O) 2] n ( 1), [Cu 2L(ClO 4) 2(CH 3CH 2OH)] ( 2) and [Cu 2L(CH 3OH) 2](ClO 4) 2 ( 3) (LH 2 = [2+2] Schiff base macrocyclic ligand condensed from 4-chloro-2,6-diformylphenol and 1,3-diaminopropane), have been prepared and determined by X-ray single-crystal diffraction. Complex 1 shows two six-coordinate Cu(II) centers in which two monodentate N3- anions and two half-water molecules are bonded at the apical positions in the trans configuration. Furthermore, the dimeric half-water molecules serve as a μ2-bridge linking adjacent macrocyclic units together with the multiple O sbnd H…N hydrogen bonds with azide anions, forming a novel 1D chain-like coordination polymer. Complexes 2 and 3 are obtained from different solvents (ethanol and methanol) and they can be converted into each other. The molecular structures and packing mode of 2 and 3 are different where six-coordinate and five-coordinate copper(II) centers are present, respectively.

  5. CD molecules 2005: human cell differentiation molecules

    Czech Academy of Sciences Publication Activity Database

    Zola, H.; Swart, B.; Nicholson, I.; Aasted, B.; Bensussan, A.; Boumsell, L.; Buckley, C.; Clark, G.; Drbal, Karel; Engel, P.; Hart, D.; Hořejší, Václav; Isacke, C.; Macardle, P.; Malavasi, F.; Mason, D.; Olive, D.; Saalmüller, A.; Schlossman, S.F.; Schwartz-Albiez, R.; Simmons, P.; Tedder, T.F.; Uguccioni, M.; Warren, H.


    Roč. 106, č. 9 (2005), s. 3123-3126 ISSN 0006-4971 Institutional research plan: CEZ:AV0Z5052915 Keywords : CD molecules * leukocyte antigen Subject RIV: EC - Immunology Impact factor: 10.131, year: 2005

  6. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas


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

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

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


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

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

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


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

  9. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan


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

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

    African Journals Online (AJOL)

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


    Nitroaromatic compounds including synthetic nitro musks are important raw materials and intermediates in the synthesis of explosives, dyes, and pesticides, pharmaceutical and personal care-products (PPCPs). The nitro musks such as musk xylene (MX) and musk ketone (MK) are extensively used as fragrance ingredients in PPCPs and other commercial toiletries. Identification and quantification of a bound 4-amino-MX (4-AMX) metabolite as well as a 2- amino-MK (2-AMK) metabolite were carried out by gas chromatography-mass spectrometry' (GC/MS), with selected ion monitoring (SIM) in both the electron ionization (ElMS) and electron capture (EC) negative ion chemical ionization (NICIMS) modes. Detection of 4-AMX and 2-AMK occurred after the cysteine adducts in carp hemoglobin, derived from the nitroso metabolites, were released by alkaline hydrolysis. The released metabolites were extracted into n-hexane. The extract was preconcentrated by evaporation, and analyzed by GC-SIM-MS. A comparison between the El and EC approaches was made. EC NICIMS detected both metabolites whereas only 4-AMX was detected by ElMS. The EC NICIMS approach exhibited fewer matrix responses and provided a lower detection limit. Quantitation in both approaches was based on internal standard and a calibration plot. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Q

  12. Application of MRIL-WD (Magnetic Resonance Imaging Logging While Drilling) for irreducible water saturation, total reservoir, free-fluid, bound-fluid porosity measurements and its value for the petrophysical analysis of RT/RM data from the Shah Deniz well (United States)

    Amirov, Elnur


    Sperry-Sun (Sperry Drilling Services) is the leader in MWD/LWD reliability, has developed the industry's first LWD NMR/MRIL-WD (nuclear magnetic resonance) tool. The MRIL-WD (magnetic resonance imaging logging-while-drilling) service directly measures the T1 component of hydrogen in subsurface rock units while drilling to obtain total reservoir porosity and to dissect the observed total porosity into its respective components of free fluid and bound fluid porosity. These T1 data are used to secure accurate total, free-fluid, capillary-bound water, and clay-bound water porosity of the reservoir sections which can be drilled in the several Runs. Over the last decade, results from Magnetic Resonance Imaging logs (NMR) have added significant value to petrophysical analysis and understanding by providing total, free-fluid and bound-fluid porosities, combined with fluid typing capabilities. With MRIL-WD very valuable Real-Time or Recorded Memory data/information is now available during or shortly after the drilling operation (formation properties measurement can be taken right after a drill bit penetration), while trip in and trip out as well. A key point in utilizing MRIL in an LWD environment is motion-tolerant measurements. Recent MRIL-WD logging runs from the Shah Deniz wells located in the Khazarian-Caspian Sea of the Azerbaijan Republic helped to delineate and assess hydrocarbon bearing zones. Acquired results demonstrate how MRIL data can be acquired while-drilling and provide reliable/high quality measurements. Magnetic Resonance Imaging logs at some developments wells have become a cornerstone in formation evaluation and petrophysical understanding. By providing total, free-fluid, and bound-fluid porosities together with fluid typing, MRIL results have significantly added to the assessment of reservoirs. In order to reduce NPT (Non-Productive Time) and save the rig operations time, there is always the desire to obtain logging results as soon as possible

  13. Is JPC = 3-+ molecule possible? (United States)

    Zhu, Wei; Liu, Yan-Rui; Yao, Tao


    The confirmation of charged charmonium-like states indicates that heavy quark molecules should exist. Here we discuss the possibility of a molecule state with JPC = 3-+. In a one-boson-exchange model investigation for the S wave C = + D*D¯2* states, one finds that the strongest attraction is in the case J = 3 and I = 0 for both π and σ exchanges. Numerical analysis indicates that this hadronic bound state might exist if a phenomenological cutoff parameter around 2.3 GeV (1.5 GeV) is reasonable with a dipole (monopole) type form factor in the one-pion-exchange model. The cutoff for binding solutions may be reduced to a smaller value once the σ exchange contribution is included. If a state around the D*D¯2* threshold (≈4472 MeV) in the channel J/ψω (P wave) is observed, the heavy quark spin symmetry implies that it is not a cc¯ meson and the JPC are likely to be 3-+. Supported by National Natural Science Foundation of China (11275115), Shandong Province Natural Science Foundation (ZR2010AM023), SRF for ROCS, SEM, and Independent Innovation Foundation of Shandong University

  14. Solvatochromic shifts of polar and non-polar molecules in ambient and supercritical water: a sequential quantum mechanics/molecular mechanics study including solute-solvent electron exchange-correlation. (United States)

    Ma, Haibo; Ma, Yingjin


    Polar and non-polar solutes (acetone and benzene) dissolved in ambient water and supercritical water are investigated theoretically using a sequential quantum mechanics (QM)/molecular mechanics (MM) method which combines classical molecular dynamics simulations and QM/MM calculations. From the detailed analysis of the dependence of the QM region size and point charge background region size as well as the different functionals, it is found that the inclusion of the solvent molecules within the first solvation shell into the QM region to account for the exchange-correlation between a solute and neighboring solvent molecules is important for the highly accurate spectral shift calculations, especially vital for the non-polar solutes whose interactions with the solvents are dominated by the quantum dispersions. At the same time, sufficiently large surrounding partial charge region (r(cutoff) ≥15 Å) as well as the functional corrections to describe the long-range dispersion-corrections are also essential for the study of the electronic excited states in condensed phase. Our calculated solvatochromic shift values and their density dependencies at ambient and high temperature conditions are found to be in good agreements with experimental observations. This indicates that sound theoretical studies of solvatochromic shift can be achieved provided that a reasonable computational scheme with sufficiently large N(water) (QM) and r(cutoff) values is implemented. We also find both of aqueous acetone and aqueous benzene under high temperatures present three distinctive regions: low-density gas-like region, supercritical region, and high-density liquid-like region. The plateau behavior of solvatochromic shift in the supercritical region can be ascribed to the solvent clustering around the solute, which is a fundamental phenomenon of supercritical fluids (SCFs). The density dependence of our calculated coordination number of the first solvation shell nicely reproduces the trend

  15. Influence of Adsorbed Water on the Oxygen Evolution Reaction on Oxides

    DEFF Research Database (Denmark)

    Siahrostami, Samira; Vojvodic, Aleksandra


    We study the interface between adsorbed water and stoichiometric, defect-free (110) rutile oxide surfaces of TiO2, RuO2, and IrO2 in order to understand how water influences the stabilities of the intermediates of the oxygen evolution reaction (OER). In our model the water is treated as explicitly...... molecules binding to bridging oxygens. The third chain interacts weakly and predominantly with the H2O molecules of the second layer, resembling bulk water. We find that the stability of the water layer close to the oxide surface is almost the same as the one found on flat metal surfaces, such as the Pt(111...... adsorbed H2O molecules, which are found to form two-dimensional water chains (layers) on all investigated oxide surfaces. The first chain formed by the most strongly bound H2O molecules is adsorbed on the 5-fold coordinated surface metal atoms. The second chain is composed of less strongly bound H2O...

  16. Intermolecular potential functions from spectroscopic properties of weakly bound complexes. Third progress report, July 1, 1991--June 30, 1992

    Energy Technology Data Exchange (ETDEWEB)

    Muenter, J.S.


    Goal is to consolidate the information from high resolution spectroscopy of weakly bound cluster molecules through a theoretical model of intermolecular potential energy surfaces. The ability to construct analytic intermolecular potential functions that accurately predict the interaction energy between small molecules will have a major impact in chemistry, biochemistry, and biology. This document presents the evolution and capabilities of a potential function model developed here, and then describes plans for future developments and applications. This potential energy surface (PES) model was first used on (HCCH){sub 2}, (CO{sub 2}){sub 2}, HCCH - CO{sub 2}; it had to be modified to work with HX dimers and CO{sub 2}-HX complexes. Potential functions have been calculated for 15 different molecular complexes containing 7 different monomer molecules. Current questions, logical extensions and new applications of the model are discussed. The questions are those raised by changing the repulsion and dispersion terms. A major extension of the PES model will be the inclusion of induction effects. Projects in progress include PES calculations on (HCCH){sub 3}, CO{sub 2} containing complexes, (HX){sub 2}, HX - CO{sub 2}, CO{sub 2} - CO, (CO{sub 2}){sub 3}, and (OCS){sub 2}. The first PES calculation for a nonlinear molecule will be for water and ammonia complexes. Possible long-term applications for biological molecules are discussed. Differences between computer programs used for molecular mechanics and dynamics in biological systems are discussed, as is the problem of errors. 12 figs, 74 refs. (DLC)

  17. Nonvalence Correlation-Bound Anion States of Polycyclic Aromatic Hydrocarbons. (United States)

    Voora, Vamsee K; Jordan, Kenneth D


    In this work, we characterize the nonvalence correlation-bound anion states of several polycyclic aromatic hydrocarbon (PAH) molecules. Unlike the analogous image potential states of graphene that localize the charge density of the excess electron above and below the plane of the sheet, we find that for PAHs, much of the charge distribution of the excess electron is localized around the periphery of the molecule. This is a consequence of the electrostatic interaction of the electron with the polar CH groups. By replacing the H atoms by F atoms or the CH groups by N atoms, the charge density of the excess electron shifts from the periphery to above and below the plane of the ring systems.

  18. Two applications of the thermogram of the alcohol/water binary system with compositions of cryobiological interests. (United States)

    Weng, Lindong; Li, Weizhong; Zuo, Jianguo


    Quantitative analyses of the bound water content in the alcohol aqueous solution and its osmotic behavior should be cryobiologically significant. This paper has presented two applications of the thermogram of the alcohol/water system recorded by differential scanning calorimeter (DSC). Both applications are: (1) generating the quantitative relationship between the bound water content and the solution composition; (2) calculating the osmotic virial coefficients for alcohols. Five alcohols including methanol, ethanol, ethylene glycol, propylene glycol and glycerol are investigated. In the present study, partial binary phase diagrams of these five alcohol solutions are determined in the first place. The bound water contents in these solutions are quantitatively evaluated by three criteria afterwards. In the end, the osmotic virial coefficients for these alcohols are calculated according to the osmotic virial equation. It is turned out that the bound water fraction out of the total water content increases with a rising molality. The ability of the solute to restrict water molecules can be weakened when the solution becomes more concentrated. The results also indicate that propylene glycol should be the strongest "water-blocker" while methanol the weakest one. These findings can deepen our understanding of the cryoprotective properties of the alcohols from the perspectives of their roles in binding free water and promoting the osmotic efflux of cell water. Copyright © 2011 Elsevier Inc. All rights reserved.

  19. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.


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

  20. Nuclear magnetic resonance relaxometry as a spectroscopic probe of the coordination sphere of a paramagnetic metal bound to a humic acid mixture

    Energy Technology Data Exchange (ETDEWEB)

    Melton, Joe R.; Kantzas, Apostolos [Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB (Canada); Langford, Cooper H. [Department of Chemistry, University of Calgary, 2500 University Drive NW, Calgary, AB (Canada)], E-mail:


    Protons on water molecules are strongly affected by paramagnetic ions. Since the acid-base properties of water facilitate rapid proton exchange, a single proton nuclear magnetic resonance (NMR) signal is seen in aqueous solutions of paramagnetic ions. Proton relaxation times are significantly affected by paramagnetic species and the readily detectable single signal serves as a powerful amplifier of the information contained concerning the protons in the paramagnetic environment. Where water molecules coordinated to free paramagnetic ions and to metal complexes of ligands that form non-labile (on the NMR time scale) complexes, the effects on water in the two environments can be distinguished. This can provide information on the nature of the ligand binding sites. The example of Cu{sup 2+} bound to the Laurentian humic acid mixture reported here using convenient low field NMR relaxometers shows that the information can enrich our understanding of complexation and speciation in the presence of complex mixture ligands characteristic of natural water systems. In this case, the data underline the role of aggregation and conformation in defining the complexation sites.

  1. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)


    Advances in our ability to slow down and cool atoms and molecules to ultracold temperatures have paved the way to a revolution in basic research on molecules. Ultracold molecules are sensitive of very weak interactions, even when separated by large distances, which allow studies of the effect of those interactions on the behavior of molecules. In this program, we have explored ways to form ultracold molecules starting from pairs of atoms that have already reached the ultracold regime. We devised methods that enhance the efficiency of ultracold molecule production, for example by tuning external magnetic fields and using appropriate laser excitations. We also investigates the properties of those ultracold molecules, especially their de-excitation into stable molecules. We studied the possibility of creating new classes of ultra-long range molecules, named macrodimers, thousand times more extended than regular molecules. Again, such objects are possible because ultra low temperatures prevent their breakup by collision. Finally, we carried out calculations on how chemical reactions are affected and modified at ultracold temperatures. Normally, reactions become less effective as the temperature decreases, but at ultracold temperatures, they can become very effective. We studied this counter-intuitive behavior for benchmark chemical reactions involving molecular hydrogen.

  2. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics


    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  3. Distance hijacking attacks on distance bounding protocols


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


    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define a fourth main type of attacks on distance bounding protocols, called Distance Hijacking attacks. We show that many proposed distance bounding protocols are vulnerable to these attacks, and we propose solutions to make these protocols resilient to Distance Hijacking. Additionally, we generalize Distance Hijacking to Location Hijacking, to which ...

  4. Boundedly UC spaces: characterisations and preservation | Jain ...

    African Journals Online (AJOL)

    A metric space (X, d) is called a boundedly UC space if every closed and bounded subset of X is a UC space. A metric space (X, d) is called a UC space if each real-valued continuous function on (X, d) is uniformly continuous. In this paper, we study twenty-two equivalent conditions for a metric space to be a boundedly UC ...

  5. Bounded cohomology of discrete groups

    CERN Document Server

    Frigerio, Roberto


    The author manages a near perfect equilibrium between necessary technicalities (always well motivated) and geometric intuition, leading the readers from the first simple definition to the most striking applications of the theory in 13 very pleasant chapters. This book can serve as an ideal textbook for a graduate topics course on the subject and become the much-needed standard reference on Gromov's beautiful theory. -Michelle Bucher The theory of bounded cohomology, introduced by Gromov in the late 1980s, has had powerful applications in geometric group theory and the geometry and topology of manifolds, and has been the topic of active research continuing to this day. This monograph provides a unified, self-contained introduction to the theory and its applications, making it accessible to a student who has completed a first course in algebraic topology and manifold theory. The book can be used as a source for research projects for master's students, as a thorough introduction to the field for graduate student...

  6. Water (United States)

    ... environment and your health: Green living Sun Water Health effects of water pollution How to protect yourself from water pollution Air Chemicals Noise Quizzes Links to more information girlshealth glossary girlshealth. ...

  7. Peptide specific expansion of CD8(+) T cells by recombinant plate bound MHC/peptide complexes

    DEFF Research Database (Denmark)

    Schmidt, Esben G W; Buus, Soren; Thorn, Mette


    to in vitro T cell stimulation was investigated. By use of an antigenic peptide derived from the cytomegalovirus (CMVp) we tested the stimulatory efficacy of recombinant plate bound MHC molecules (PB-MHC), being immobilized in culture plates. A single stimulation of non-adherent peripheral blood mononuclear...

  8. Bounded sets in fast complete inductive limits

    Directory of Open Access Journals (Sweden)

    Jan Kucera


    Full Text Available Let E1⊂E2⊂… be a sequence of locally convex spaces with all identity maps: En→En+1 continuous and E=indlim En fast complete. Then each set bounded in E is also bounded in some En iff for any Banach disk B bounded in E and n∈N, the closure of B⋂En in B is bounded in some Em. This holds, in particular, if all spaces En are webbed.

  9. Valuation models and Simon's bounded rationality

    National Research Council Canada - National Science Library

    Alexandra Strommer de Farias Godoi


    This paper aims at reconciling the evidence that sophisticated valuation models are increasingly used by companies in their investment appraisal with the literature of bounded rationality, according...

  10. Some Improved Nonperturbative Bounds for Fermionic Expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Martin, E-mail: [Universita di Roma Tre, Dipartimento di Matematica (Italy)


    We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

  11. A strongly quasiconvex PAC-Bayesian bound

    DEFF Research Database (Denmark)

    Thiemann, Niklas; Igel, Christian; Wintenberger, Olivier

    We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured by the Ku......We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured...

  12. Protein packing defects "heat up" interfacial water. (United States)

    Sierra, María Belén; Accordino, Sebastián R; Rodriguez-Fris, J Ariel; Morini, Marcela A; Appignanesi, Gustavo A; Fernández Stigliano, Ariel


    Ligands must displace water molecules from their corresponding protein surface binding site during association. Thus, protein binding sites are expected to be surrounded by non-tightly-bound, easily removable water molecules. In turn, the existence of packing defects at protein binding sites has been also established. At such structural motifs, named dehydrons, the protein backbone is exposed to the solvent since the intramolecular interactions are incompletely wrapped by non-polar groups. Hence, dehydrons are sticky since they depend on additional intermolecular wrapping in order to properly protect the structure from water attack. Thus, a picture of protein binding is emerging wherein binding sites should be both dehydrons rich and surrounded by easily removable water. In this work we shall indeed confirm such a link between structure and dynamics by showing the existence of a firm correlation between the degree of underwrapping of the protein chain and the mobility of the corresponding hydration water molecules. In other words, we shall show that protein packing defects promote their local dehydration, thus producing a region of "hot" interfacial water which might be easily removed by a ligand upon association.

  13. Quantum and classical dynamics of water dissociation on Ni(111): A test of the site-averaging model in dissociative chemisorption of polyatomic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Bin [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Department of Chemical Physics, University of Science and Technology of China, Hefei 230026 (China); Guo, Hua, E-mail: [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)


    Recently, we reported the first highly accurate nine-dimensional global potential energy surface (PES) for water interacting with a rigid Ni(111) surface, built on a large number of density functional theory points [B. Jiang and H. Guo, Phys. Rev. Lett. 114, 166101 (2015)]. Here, we investigate site-specific reaction probabilities on this PES using a quasi-seven-dimensional quantum dynamical model. It is shown that the site-specific reactivity is largely controlled by the topography of the PES instead of the barrier height alone, underscoring the importance of multidimensional dynamics. In addition, the full-dimensional dissociation probability is estimated by averaging fixed-site reaction probabilities with appropriate weights. To validate this model and gain insights into the dynamics, additional quasi-classical trajectory calculations in both full and reduced dimensions have also been performed and important dynamical factors such as the steering effect are discussed.

  14. How is the water molecule activated on metalloporphyrins? Oxygenation of substrates induced through one-photon/two-electron conversion in artificial photosynthesis by visible light. (United States)

    Shimada, Tetsuya; Kumagai, Akihiro; Funyu, Shigeaki; Takagi, Shinsuke; Masui, Dai; Nabetani, Yu; Tachibana, Hiroshi; Tryk, Donald A; Inoue, Haruo


    The reaction mechanism of the highly efficient (phi = 0.60), selective photochemical epoxidation of alkenes sensitized by CO-coordinated tetra(2,4,6-trimethyl)phenylporphyrinatoruthenium(II) (Ru(II)TMP(CO)), with water acting both as an electron and oxygen atom donor, was investigated. The steady-state light irradiation of the reaction mixture indicated the formation of the Ru(II)TMP (CO) cation radical under neutral conditions, which was effectively trapped by an hydroxide ion to regenerate the starting sensitizer. By means of a laser flash photolysis experiment, the formation of the cation radical as the primary process from the triplet excited state of Ru(II)TMP(CO) was clearly observed. Four kinds of transients were detected in completely different ranges of the delay time: the excited triplet state of Ru(II)TMP(CO) [delay time region artificial photosynthesis.

  15. catena-Poly[[[(oxamide dioxime-κ2N,N')copper(II)]-μ-L-tartrato-κ4O1,O2:O3,O4] tetrahydrate]: a chiral nanochannel framework hosting solvent water molecules. (United States)

    Bélombé, Michel M; Nenwa, Justin; Kouamo, Jean S T Wankap; Ponou, Siméon; Fischer, Andreas


    The crystal structure of the title compound, {[Cu(C(4)H(4)O(6))(C(2)H(6)N(4)O(2))]·4H(2)O}(n), contains the central Cu(II) cation in a distorted octahedral coordination, symmetrically chelated by the two imine N atoms of a neutral oxamide dioxime (H(2)oxado) ligand [Cu-N = 1.9829 (16) Å] and unsymmetrically bis-chelated by two halves of the L-(+)-tartrate(2-) (tart) ligands, each half being linked to the Cu(II) cation via the deprotonated carboxylate group and protonated hydroxy group [Cu-O = 1.9356 (14) and 2.4674 (13) Å, respectively]. The extended asymmetric unit is defined by twofold axes, one passing through the Cu(II) cation and the centre of the oxamide dioxime (H(2)oxado) ligand and the another two (symmetry related) bisecting the central C-C bonds of the tartrate ions. The structure is chiral, consisting of enantiomeric linear-chain polymers oriented along [001], with virtual monomeric {Cu(tart(0.5))(2)(H(2)oxado)} repeat units and with the chains interleaved face-to-face into `twin pillars'. Nanochannels exist, running parallel to the c axis and bisecting a and b, which host `double strings' of solvent water molecules. Extensive hydrogen bonding (O-H···O and N-H···O) between the chains and solvent water molecules, together with extended π-σ interactions, consolidate the bulk crystal structure.

  16. Ultracold Polar Molecules (United States)


    formation of ultracold 87RbCs molecules in their rovibrational ground state by magnetoassociation followed by STIRAP, resulting in 14 papers acknowledging...produce at high densities. We revealed broad Feshbach resonances that we hope will allow production of higher-density 85Rb clouds. We are now...attempting to achieve the next step, formation of 85RbCs molecules. 15. SUBJECT TERMS EOARD, ultracold polar molecules, Feshbach resonance 16. SECURITY

  17. Picosecond orientational dynamics of water in living cells. (United States)

    Tros, Martijn; Zheng, Linli; Hunger, Johannes; Bonn, Mischa; Bonn, Daniel; Smits, Gertien J; Woutersen, Sander


    Cells are extremely crowded, and a central question in biology is how this affects the intracellular water. Here, we use ultrafast vibrational spectroscopy and dielectric-relaxation spectroscopy to observe the random orientational motion of water molecules inside living cells of three prototypical organisms: Escherichia coli, Saccharomyces cerevisiae (yeast), and spores of Bacillus subtilis. In all three organisms, most of the intracellular water exhibits the same random orientational motion as neat water (characteristic time constants ~9 and ~2 ps for the first-order and second-order orientational correlation functions), whereas a smaller fraction exhibits slower orientational dynamics. The fraction of slow intracellular water varies between organisms, ranging from ~20% in E. coli to ~45% in B. subtilis spores. Comparison with the water dynamics observed in solutions mimicking the chemical composition of (parts of) the cytosol shows that the slow water is bound mostly to proteins, and to a lesser extent to other biomolecules and ions.The cytoplasm's crowdedness leads one to expect that cell water is different from bulk water. By measuring the rotational motion of water molecules in living cells, Tros et al. find that apart from a small fraction of water solvating biomolecules, cell water has the same dynamics as bulk water.

  18. New lower bound for the Capacitated Arc Routing Problem

    DEFF Research Database (Denmark)

    Wøhlk, Sanne


    We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided.......We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided....

  19. Inhibition of surface bound carbonate stabilization of tetragonal zirconia

    DEFF Research Database (Denmark)

    Nielsen, Mette Skovgaard; Almdal, Kristoffer; Lelieveld, A. van


    Water is known to initiate a tetragonal to monoclinic phase transformation in zirconia particles. Carbonates on the zirconia surface react with water molecules and hence reduce the transformation rate. This study investigates the possibility of inhibition of the reaction between surface carbonates...... and water in order to increase the transformation rate in the zirconia crystals. It was found possible to limit the reaction by reacting the surface carbonates with alcohols, a thiol and a primary amide prior to reaction with water. It was also concluded that di- and trialcohols are able to stabilize...

  20. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.; Barkely Rosser Jr, J.


    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  1. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.


    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  2. Spatial coagulation with bounded coagulation rate


    Bailleul, Ismael


    We prove that the spatial coagulation equation with bounded coagulation rate is well-posed for all times in a given class of kernels if the convection term of the underlying particle dynamics has divergence bounded below by a positive constant. Multiple coagulations, fragmentation and scattering are also considered.

  3. Schroedinger upper bounds to semirelativistic eigenvalues

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Richard L [Department of Mathematics and Statistics, Concordia University, 1455 de Maisonneuve Boulevard West, Montreal, Quebec, H3G 1M8 (Canada); Lucha, Wolfgang [Institut fuer Hochenergiephysik, Oesterreichische Akademie der Wissenschaften, Nikolsdorfergasse 18, A-1050 Vienna (Austria)


    Problems posed by semirelativistic Hamiltonians of the form H = {radical}(m{sup 2} + p{sup 2}) + V(r) are studied. It is shown that energy upper bounds can be constructed in terms of certain related Schroedinger operators; these bounds include free parameters which can be chosen optimally.

  4. No-arbitrage bounds for financial scenarios

    DEFF Research Database (Denmark)

    Geyer, Alois; Hanke, Michael; Weissensteiner, Alex


    We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...

  5. Nonatomic dual bakery algorithm with bounded tokens

    NARCIS (Netherlands)

    Aravind, Alex A.; Hesselink, Wim H.

    A simple mutual exclusion algorithm is presented that only uses nonatomic shared variables of bounded size, and that satisfies bounded overtaking. When the shared variables behave atomically, it has the first-come-first-served property (FCFS). Nonatomic access makes information vulnerable. The

  6. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki


    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  7. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter


    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function...

  8. On the range of completely bounded maps

    Directory of Open Access Journals (Sweden)

    Richard I. Loebl


    Full Text Available It is shown that if every bounded linear map from a C*-algebra α to a von Neumann algebra β is completely bounded, then either α is finite-dimensional or β⫅⊗Mn, where is a commutative von Neumann algebra and Mn is the algebra of n×n complex matrices.

  9. A polynomial lower bound for testing monotonicity

    NARCIS (Netherlands)

    A. Belovs (Aleksandr); Blais, E. (Eric)


    textabstractWe show that every algorithm for testing n-variate Boolean functions for monotonicity has query complexity Ω(n1/4). All previous lower bounds for this problem were designed for nonadaptive algorithms and, as a result, the best previous lower bound for general (possibly adaptive)

  10. Sugar Blowing-Induced Porous Cobalt Phosphide/Nitrogen-Doped Carbon Nanostructures with Enhanced Electrochemical Oxidation Performance toward Water and Other Small Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chengzhou [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Fu, Shaofang [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Xu, Bo Z. [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Song, Junhua [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Shi, Qiurong [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Engelhard, Mark H. [Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Li, Xiaolin [Energy and Environmental Directory, Pacific Northwest National Laboratory, Richland WA 99352 USA; Beckman, Scott P. [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Sun, Junming [The Gene and Linda Voiland School of Chemical Engineering and Bioengineering, Washington State University, Pullman WA 99164 USA; Du, Dan [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA; Lin, Yuehe [School of Mechanical and Materials Engineering, Washington State University, Pullman WA 99164 USA


    Finely controlled synthesis of high active and robust nonprecious metal catalysts with excellent catalytic efficiency in oxygen evolution reaction (OER) is extremely vital for making the water splitting process more energy-efficient and economical. Among these noble metal-free catalysts, transition-metal-based nanomaterials are considered as one of the most promising OER catalysts due to their relatively low-cost intrinsic activities, high abundance and diversity in terms of structure and morphology. In this work, we reported a facile sugar-blowing technique and low-temperature phosphorization to generate 3D self-supported metal involved carbon nanostructures, which termed as Co2P@Co/nitrogen-doped carbon (Co2P@Co/N-C). By capitalizing on the 3D porous nanostructures with high surface area, generously dispersed active sites, the intimate interaction between active sites and 3D N-doped carbon, the resultant Co2P@Co/N-C exhibited satisfying OER performance superior to CoO@Co/N-C, delivering 10 mA cm-2 at overpotential of 0.32 V. It is noting that in contrast to the substantial current density loss of RuO2, Co2P@Co/N-C showed much enhanced catalytic activity during the stability test and the 1.8-fold increase in current density was observed after stability test. Furthermore, the obtained Co2P@Co/N-C can also be served as an excellent nonprecious metal catalyst for methanol and glucose electrooxidation in alkaline media, further extending their potential applications.

  11. Molecule of the Month

    Indian Academy of Sciences (India)

    The most logical way to reduce the reactivity of a molecule of 1 would be to put a single molecule of 1 in an unreactive "cage". Chemistry Nobel winner Donald J. Cram (1987) has shown that it is indeed possible (Angew. Chem. Int. Ed. Engl., 30, 1028. 1991)!. Cram and co-workers synthesized a variety of spheroidal molecu-.

  12. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 20; Issue 2. Single-Molecule Spectroscopy: Every Molecule is Different! Kankan Bhattacharyya. General Article Volume 20 Issue 2 February 2015 pp 151-164. Fulltext. Click here to view fulltext PDF. Permanent link:

  13. Algebraic theory of molecules

    CERN Document Server

    Iachello, F


    1. The Wave Mechanics of Diatomic Molecules. 2. Summary of Elements of Algebraic Theory. 3. Mechanics of Molecules. 4. Three-Body Algebraic Theory. 5. Four-Body Algebraic Theory. 6. Classical Limit and Coordinate Representation. 8. Prologue to the Future. Appendices. Properties of Lie Algebras; Coupling of Algebras; Hamiltonian Parameters


    NARCIS (Netherlands)


    In this paper, some results obtained on the formation of isolated molecules of composition SnOx in silver and SnFx in copper-are reviewed. Hyperfine interaction and ion beam interaction techniques were used for the identification of these molecules.

  15. Electrons in Molecules

    Indian Academy of Sciences (India)

    “What are electrons doing in molecules?” This is a deceptively simple question that scientists have been trying to answer for more than eighty years. With the advent of quantum mechanics in 1926, it became clear that we must understand the dynamics of electronic motion in atoms, molecules and solids in order to explain ...

  16. Molecule of the Month

    Indian Academy of Sciences (India)

    Atoms in a molecule generally prefer, particularly among the neighbouring ones, certain optimmn geometrical relationships. These are manifested in specific ranges of bond lengths, bond angles, torsion angles etc. As it always happens, chemists are interested in making molecules where these 'standard relationships' are ...

  17. Single molecule electronic devices. (United States)

    Song, Hyunwook; Reed, Mark A; Lee, Takhee


    Single molecule electronic devices in which individual molecules are utilized as active electronic components constitute a promising approach for the ultimate miniaturization and integration of electronic devices in nanotechnology through the bottom-up strategy. Thus, the ability to understand, control, and exploit charge transport at the level of single molecules has become a long-standing desire of scientists and engineers from different disciplines for various potential device applications. Indeed, a study on charge transport through single molecules attached to metallic electrodes is a very challenging task, but rapid advances have been made in recent years. This review article focuses on experimental aspects of electronic devices made with single molecules, with a primary focus on the characterization and manipulation of charge transport in this regime. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Water (United States)

    Leopold, Luna Bergere; Baldwin, Helene L.


    What do you use water for?If someone asked you this question you would probably think right away of water for drinking. Then you would think of water for bathing, brushing teeth, flushing the toilet. Your list would get longer as you thought of water for cooking, washing the dishes, running the garbage grinder. Water for lawn watering, for play pools, for swimming pools, for washing the car and the dog. Water for washing machines and for air conditioning. You can hardly do without water for fun and pleasure—water for swimming, boating, fishing, water-skiing, and skin diving. In school or the public library, you need water to wash your hands, or to have a drink. If your home or school bursts into flames, quantities of water are needed to put it out.In fact, life to Americans is unthinkable without large supplies of fresh, clean water. If you give the matter a little thought, you will realize that people in many countries, even in our own, may suffer from disease and dirt simply because their homes are not equipped with running water. Imagine your own town if for some reason - an explosion, perhaps - water service were cut off for a week or several weeks. You would have to drive or walk to a neighboring town and bring water back in pails. Certainly if people had to carry water themselves they might not be inclined to bathe very often; washing clothes would be a real chore.Nothing can live without water. The earth is covered by water over three-fourths of its surface - water as a liquid in rivers, lakes and oceans, and water as ice and snow on the tops of high mountains and in the polar regions. Only one-quarter of our bodies is bone and muscle; the other three-fourths is made of water. We need water to live, and so do plants and animals. People and animals can live a long time without food, but without water they die in a few days. Without water, everything would die, and the world would turn into a huge desert.

  19. Chemical equilibrium probed by two-dimensional IR spectroscopy: hydrogen bond dynamics of methyl acetate in water. (United States)

    Candelaresi, Marco; Pagliai, Marco; Lima, Manuela; Righini, Roberto


    The solvation dynamics of methyl acetate in heavy water are analyzed by means of two-dimensional infrared spectroscopy, in conjunction with Car-Parrinello molecular dynamics simulations. The C horizontal lineO stretching infrared band of methyl acetate in water splits into a doublet as a consequence of the hydrogen bond interaction with the solvent, which leads to the equilibrium between two solvated species, consisting of one methyl acetate molecule bonded to one and two water molecules. The structure and dynamics of the water molecules bound to methyl acetate are characterized by means of experiments and simulations, allowing an accurate description of the kinetics of the exchange process and the lifetime of the hydrogen bond.

  20. Single molecule logical devices. (United States)

    Renaud, Nicolas; Hliwa, Mohamed; Joachim, Christian


    After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit.

  1. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)


    Experimental studies have been performed to investigate the collisional energy transfer processes of gas-phase molecules that contain large amounts of internal energy. Such molecules are prototypes for molecules under high temperature conditions relevant in combustion and information about their energy transfer mechanisms is needed for a detailed understanding and modeling of the chemistry. We use high resolution transient IR absorption spectroscopy to measure the full, nascent product distributions for collisions of small bath molecules that relax highly vibrationally excited pyrazine molecules with E=38000 cm-1 of vibrational energy. To perform these studies, we developed new instrumentation based on modern IR light sources to expand our experimental capabilities to investigate new molecules as collision partners. This final report describes our research in four areas: the characterization of a new transient absorption spectrometer and the results of state-resolved collision studies of pyrazine(E) with HCl, methane and ammonia. Through this research we have gained fundamental new insights into the microscopic details of relatively large complex molecules at high energy as they undergo quenching collisions and redistribute their energy.

  2. Water (United States)

    ... the tap as described). 3. In all situations, drink or cook only with water that comes out of the tap cold. Water that comes out of the tap warm or hot can contain much higher levels of lead. Boiling ...

  3. Organically bound sulfur in refractory organic substances. (United States)

    Abbt-Braun, G; Jahnel, J B


    The sulfur compounds of refractory organic substances (ROS) of different origin have been characterized. Total organic sulfur was determined by elemental analysis. Sulfur-containing amino acids methionine and cystine were analyzed chromatographically after hydrolysis with HCl or by proteolytic digestion using enzymes. The results obtained from elemental analysis show that the total amount of sulfur is strongly dependent on the origin of the samples, because of different environmental factors during the formation of ROS. For naturally occurring samples isolated from soil seepage water, bog lake water and ground water the carbon-to-sulfur atomic ratios (C/S) decrease with the stage of humification, because of preferential loss of carbon. In humic acids (HA) isolated from secondary effluent the high value of the nitrogen-to-sulfur ratio (N/S) was indicative of a large amount of protein-derived nitrogen and sulfur compounds. In the solutions from acid hydrolysis the total amount of amino acid carbon related to the dissolved organic carbon (DOC) was generally less than 5%. Percentages of cystine related to all the amino acids detected were in the range 4 to 16%; methionine was below the detection limit for most samples. The results show that cystine is very important among the amino acids released. Enzymatic release generally resulted in smaller amounts of amino acids, indicating that these molecules are not only present in bioavailable protein-like structures. The data were compared with those from other approaches reported in the literature for the speciation of sulfur forms in ROS, including potentiometric titration, differential reduction methods, and spectroscopic investigations.

  4. Match-bounded String Rewriting Systems (United States)

    Geser, Alfons; Hofbauer, Dieter; Waldmann, Johannes


    We introduce a new class of automated proof methods for the termination of rewriting systems on strings. The basis of all these methods is to show that rewriting preserves regular languages. To this end, letters are annotated with natural numbers, called match heights. If the minimal height of all positions in a redex is h+1 then every position in the reduct will get height h+1. In a match-bounded system, match heights are globally bounded. Using recent results on deleting systems, we prove that rewriting by a match-bounded system preserves regular languages. Hence it is decidable whether a given rewriting system has a given match bound. We also provide a sufficient criterion for the abence of a match-bound. The problem of existence of a match-bound is still open. Match-boundedness for all strings can be used as an automated criterion for termination, for match-bounded systems are terminating. This criterion can be strengthened by requiring match-boundedness only for a restricted set of strings, for instance the set of right hand sides of forward closures.

  5. Electron correlation in molecules

    CERN Document Server

    Wilson, S


    Electron correlation effects are of vital significance to the calculation of potential energy curves and surfaces, the study of molecular excitation processes, and in the theory of electron-molecule scattering. This text describes methods for addressing one of theoretical chemistry's central problems, the study of electron correlation effects in molecules.Although the energy associated with electron correlation is a small fraction of the total energy of an atom or molecule, it is of the same order of magnitude as most energies of chemical interest. If the solution of quantum mechanical equatio

  6. Functionalized molecules studied by STM: motion, switching and reactivity

    Energy Technology Data Exchange (ETDEWEB)

    Grill, Leonhard [Institut fuer Experimentalphysik, Freie Universitaet Berlin, Arnimallee 14, 14195 Berlin (Germany)


    Functionalized molecules represent the central issue of molecular nanotechnology. Scanning tunnelling microscopy (STM) is a powerful method to investigate such molecules, because it allows us to image them with sub-molecular resolution when adsorbed on a surface and can be used at the same time as a tool to manipulate single molecules in a controlled way. Such studies permit deep insight into the conformational, mechanical and electronic structure and thus functionalities of the molecules. In this review, recent experiments on specially designed molecules, acting as model systems for molecular nanotechnology, are reviewed. The presented studies focus on key functionalities: lateral rolling and hopping motion on a supporting surface, the switching behaviour of azobenzene derivatives by using the STM tip and the controlled reactivity of molecular side groups, which enable the formation of covalently bound molecular nanoarchitectures. (topical review)

  7. Sound velocity bound and neutron stars. (United States)

    Bedaque, Paulo; Steiner, Andrew W


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

  8. Lability of copper bound to humic acid


    Mao, Lingchen; Young, Scott D.; Bailey, Liz


    Geochemical speciation models generally include the assumption that all metal bound to humic acid and fulvic acid (HA, FA) is labile. However, in the current study, we determined the presence of a soluble ‘non-labile’ Cu fraction bound to HA extracted from grassland and peat soils. This was quantified by determining isotopically-exchangeable Cu (E-value) and EDTA-extraction of HA-bound Cu, separated by size-exclusion chromatography (SEC) and assayed by coupled ICP-MS. Evidence of time-depend...

  9. Positivity bounds on double parton distributions

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, Markus; Kasemets, Tomas


    Double hard scattering in proton-proton collisions is described in terms of double parton distributions. We derive bounds on these distributions that follow from their interpretation as probability densities, taking into account all possible spin correlations between two partons in an unpolarized proton. These bounds constrain the size of the polarized distributions and can for instance be used to set upper limits on the effects of spin correlations in double hard scattering. We show that the bounds are stable under leading-order DGLAP evolution to higher scales.

  10. Lower bound for the nuclear kinetic energy

    Energy Technology Data Exchange (ETDEWEB)

    Dehesa, J.S. (Granada Univ. (Spain). Dept. de Fisica Nuclear); Galvez, F.J. (Granada Univ. (Spain). Dept. de Fisica Teorica)


    We argue that the kinetic energy of a many-fermion system is bounded from below by Kqsup(-2/3)A sup(5/3) / , with K = 0.565 where q is the number of spin states available to each particle and sup(1/2) is the root mean square radius of the single-particle density. A simple lower bound for the nuclear kinetic energy is found. Numerical values of the bound for several nuclei are shown, and a comparison with some self-consistent calculations and some pseudo-empirical values is made.

  11. Continuous bounded cohomology of locally compact groups

    CERN Document Server


    Recent research has repeatedly led to connections between important rigidity questions and bounded cohomology. However, the latter has remained by and large intractable. This monograph introduces the functorial study of the continuous bounded cohomology for topological groups, with coefficients in Banach modules. The powerful techniques of this more general theory have successfully solved a number of the original problems in bounded cohomology. As applications, one obtains, in particular, rigidity results for actions on the circle, for representations on complex hyperbolic spaces and on Teichmüller spaces. A special effort has been made to provide detailed proofs or references in quite some generality.

  12. Single molecules and nanotechnology

    CERN Document Server

    Vogel, Horst


    This book focuses on recent advances in the rapidly evolving field of single molecule research. These advances are of importance for the investigation of biopolymers and cellular biochemical reactions, and are essential to the development of quantitative biology. Written by leading experts in the field, the articles cover a broad range of topics, including: quantum photonics of organic dyes and inorganic nanoparticles their use in detecting properties of single molecules the monitoring of single molecule (enzymatic) reactions single protein (un)folding in nanometer-sized confined volumes the dynamics of molecular interactions in biological cells The book is written for advanced students and scientists who wish to survey the concepts, techniques and results of single molecule research and assess them for their own scientific activities.

  13. Quantum dot molecules

    CERN Document Server

    Wu, Jiang


    This book reviews recent advances in the exciting and rapidly growing field of quantum dot molecules (QDMs). It offers state-of-the-art coverage of novel techniques and connects fundamental physical properties with device design.

  14. Electron-molecule collisions

    CERN Document Server

    Takayanagi, Kazuo


    Scattering phenomena play an important role in modern physics. Many significant discoveries have been made through collision experiments. Amongst diverse kinds of collision systems, this book sheds light on the collision of an electron with a molecule. The electron-molecule collision provides a basic scattering problem. It is scattering by a nonspherical, multicentered composite particle with its centers having degrees of freedom of motion. The molecule can even disintegrate, Le., dissociate or ionize into fragments, some or all of which may also be molecules. Although it is a difficult problem, the recent theoretical, experimental, and computational progress has been so significant as to warrant publication of a book that specializes in this field. The progress owes partly to technical develop­ ments in measurements and computations. No less important has been the great and continuing stimulus from such fields of application as astrophysics, the physics of the earth's upper atmosphere, laser physics, radiat...

  15. Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor (United States)

    Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.; Clayden, Jonathan


    Signal transduction through G-protein-coupled receptors (GPCRs) involves binding to signalling molecules at the cell surface, which leads to global changes in molecular conformation that are communicated through the membrane. Artificial mechanisms for communication involving ligand binding and global conformational switching have been demonstrated so far only in the solution phase. Here, we report a membrane-bound synthetic receptor that responds to binding of a ligand by undergoing a conformational change that is propagated over several nanometres, deep into the phospholipid bilayer. Our design uses a helical foldamer core, with structural features borrowed from a class of membrane-active fungal antibiotics, ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore. Using the fluorophore as a remote reporter of conformational change, we find that binding of specific carboxylate ligands to a Cu(II) cofactor at the binding site perturbs the foldamer's global conformation, mimicking the conformational response of a GPCR to ligand binding.

  16. Redshift-space limits of bound structures

    NARCIS (Netherlands)

    Duenner, Rolando; Reisenegger, Andreas; Meza, Andres; Araya, Pablo A.; Quintana, Hernan


    An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called 'island universes'. This new scenario reformulates the question

  17. New Spectral Features from Bound Dark Matter

    DEFF Research Database (Denmark)

    Catena, Riccardo; Kouvaris, Chris


    We demonstrate that dark matter particles gravitationally bound to the Earth can induce a characteristic nuclear recoil signal at low energies in direct detection experiments. The new spectral feature we predict can provide the ultimate smoking gun for dark matter discovery for experiments...... with positive signal but unclear background. The new feature is universal, in that the ratio of bound over halo dark matter event rates at detectors is independent of the dark matter-nucleon cross section....

  18. On bounds for symmetric divergence measures (United States)

    Furuichi, S.; Yanagi, K.; Kuriyama, K.


    In the paper [1], tight bounds for symmetric divergence measures applying the results established by G.L.Gilardoni. In this article, we report on two kinds of extensions for the Sason's results, namely a classical q-extension and a non-commutative(quantum) extension. Especially, we improve Sason's bound of the summation of the absolute value for the difference between two probability distributions, applying the parameter q of Tsallis entropy, under a certain assumption.

  19. Stable Bound States of Asymmetric Dark Matter


    Wise, Mark B.; Zhang, Yue


    The simplest renormalizable effective field theories with asymmetric dark matter bound states contain two additional gauge singlet fields one being the dark matter and the other a mediator particle that the dark matter annihilates into. We examine the physics of one such model with a Dirac fermion as the dark matter and a real scalar mediator. For a range of parameters the Yukawa coupling of the dark matter to the mediator gives rise to stable asymmetric dark matter bound states. We derive pr...

  20. Malabsorption of protein bound vitamin B12.


    Dawson, D W; Sawers, A H; Sharma, R K


    Patients with subnormal serum vitamin B12 concentrations were tested for absorption of protein bound vitamin B12 and compared with controls. Absorption of the protein bound vitamin appeared to decrease with increasing age in healthy subjects. Differences between the result of this test and the result of the Schilling test in patients who had undergone gastric surgery were confirmed; such differences were also seen in some patients who had iron deficiency anaemia, an excessive alcohol intake, ...

  1. Dynamic optimization problems with bounded terminal conditions (United States)

    Lee, A. Y.


    Bounded terminal conditions of nonlinear optimization problems are converted to equality terminal conditions via Valentine's device. In so doing, additional unknown parameters are introduced into the problem. The transformed problems can still be easily solved using the sequential gradient-restoration algorithm (SGRA) via a simple augmentation of the unknown parameter vector pi. Three example problems with bounded terminal conditions are solved to verify this technique.

  2. Structures of the substrate-free and product-bound forms of HmuO, a heme oxygenase from corynebacterium diphtheriae: x-ray crystallography and molecular dynamics investigation. (United States)

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


    Heme oxygenase catalyzes the degradation of heme to biliverdin, iron, and carbon monoxide. Here, we present crystal structures of the substrate-free, Fe(3+)-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 Fe(3+)-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 Fe(3+)-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 Fe(3+)-biliverdin and biliverdin complexes has been determined at 1.70 Å resolution, implying a possible route for iron exit.

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

    DEFF Research Database (Denmark)

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


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

  4. The Physics of Ultracold Sr2 Molecules: Optical Production and Precision Measurement (United States)


    coherence time, (c) Rabi flopping between the two states, and (d) a plot of the line frequency vs. lattice laser power. It is suspected that method of efficient, all-optical production of ultracold 88Sr2 molecules in an optical lattice , with detection via optical fragmentation. High-Q...88Sr2 molecules in an optical lattice , with detection via optical fragmentation. High-Q spectra of the weakly bound molecules in magnetic fields are

  5. Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates

    DEFF Research Database (Denmark)

    Gal, A.; Hansen, Kristoffer Arnsfelt; Koucky, Michal


    We bound the minimum number w of wires needed to compute any (asymptotically good) error-correcting code C:{0,1}Ω(n)→{0,1}n with minimum distance Ω(n), using unbounded fan-in circuits of depth d with arbitrary gates. Our main results are: 1) if d=2, then w=Θ(n (lgn/lglgn)2); 2) if d=3, then w...... bound gives the largest known lower bound for computing any linear map. The upper bounds imply that a (necessarily dense) generator matrix for our code can be written as the product of two sparse matrices. Using known techniques, we also obtain similar (but not tight) bounds for computing pairwise......-independent hash functions. Our lower bounds are based on a superconcentrator-like condition that the graphs of circuits computing good codes must satisfy. This condition is provably intermediate between superconcentrators and their weakenings considered before...

  6. Dynamics and Interactions of Organic Molecules Bound to the Cu(111) Surface


    Wyrick, Jonathan Eugene


    The progress of modern technology is dominated by shrinking component size (with a goal of reaching angstrom scale resolution), particularly with respect to electronics and optimization of common industrial processes such as heterogeneous catalysis. Understanding of such systems lies at the upper end of applicability for first-principles calculations and existing theoretical models, and a scientific framework is needed to understand, predict, and control these systems at the molecular level. ...

  7. Density functional theory studies on the solvent effects in Al(H2O)63+water-exchange reactions: the number and arrangement of outer-sphere water molecules. (United States)

    Liu, Li; Zhang, Jing; Dong, Shaonan; Zhang, Fuping; Wang, Ye; Bi, Shuping


    Density functional theory (DFT) calculations combined with cluster models are performed at the B3LYP/6-311+G(d,p) level for investigating the solvent effects in Al(H 2 O) 6 3+ water-exchange reactions. A "One-by-one" method is proposed to obtain the most representative number and arrangement of explicit H 2 Os in the second hydration sphere. First, all the possible ways to locate one explicit H 2 O in second sphere (N m ' = 1) based on the gas phase structure (N m ' = 0) are examined, and the optimal pathway (with the lowest energy barrier) for N m ' = 1 is determined. Next, more explicit H 2 Os are added one by one until the inner-sphere is fully hydrogen bonded. Finally, the optimal pathways with N m ' = 0-7 are obtained. The structural and energetic parameters as well as the lifetimes of the transition states are compared with the results obtained with the "Independent-minimum" method and the "Independent-average" method, and all three methods show that the pathway with N m ' = 6 may be representative. Our results give a new idea for finding the representative pathway for water-exchange reactions in other hydrated metal ion systems.

  8. Adsorption of biomedical coating molecules, amino acids, and short peptides on magnetite (110) (United States)

    Aschauer, Ulrich; Selloni, Annabella


    Superparamagnetic iron oxide nanoparticles for biomedical applications are usually coated with organic molecules to form a steric barrier against agglomeration. The stability of these coatings is well established in the synthesis medium but is more difficult to assess in physiological environment. To obtain a first theoretical estimate of their stability in such an environment, we perform density functional theory calculations of the adsorption of water, polyvinyl alcohol (PVA) and polyethylene glycol (PEG) coating molecules, as well as the monomer and dimer of glycine as a prototype short peptide, on the (110) surface of magnetite (Fe3O4) in vacuo. Our results show that PVA binds significantly stronger to the surface than both PEG and glycine, while the difference between the latter two is quite small. Depending on the coverage, the water adsorption strength is intermediate between PVA and glycine. Due to its strongly interacting OH side groups, PVA is likely to remain bound to the surface in the presence of short peptides. This stability will have to be further assessed by molecular dynamics in the solvated state for which the present work forms the basis.


    Energy Technology Data Exchange (ETDEWEB)

    Loinard, Laurent; Menten, Karl M.; Guesten, Rolf [Max-Planck Institut fuer Radioastronomie, Auf dem Huegel 69, 53121 Bonn (Germany); Zapata, Luis A.; Rodriguez, Luis F. [Centro de Radioastronomia y Astrofisica, Universidad Nacional Autonoma de Mexico, Apartado Postal 3-72, 58090 Morelia, Michoacan (Mexico)


    We report the detection toward {eta} Carinae of six new molecules, CO, CN, HCO{sup +}, HCN, HNC, and N{sub 2}H{sup +}, and of two of their less abundant isotopic counterparts, {sup 13}CO and H{sup 13}CN. The line profiles are moderately broad ({approx}100 km s{sup -1}), indicating that the emission originates in the dense, possibly clumpy, central arcsecond of the Homunculus Nebula. Contrary to previous claims, CO and HCO{sup +} do not appear to be underabundant in {eta} Carinae. On the other hand, molecules containing nitrogen or the {sup 13}C isotope of carbon are overabundant by about one order of magnitude. This demonstrates that, together with the dust responsible for the dimming of {eta} Carinae following the Great Eruption, the molecules detected here must have formed in situ out of CNO-processed stellar material.

  10. Biokinetic aspects of tissue-bound tritium in algae. (United States)

    Strack, S; Kistner, G


    For the estimate of the radiation exposure of man and for the calculation of the risk of artificial tritium from nuclear power plants, organic tissue-bound tritium is of decisive importance. In model experiments, a tritium incorporation of 61 to 71% was found from tritiated water (HTO) into organic matter of planctonic algae under under reproducible conditions and this was related to the theoretical value. In further experiments the tritium release from these high tritiated algae was of interest. Kept in darkness in tritium-free, non-sterile river water, so that autolytic processes and bacterial decomposition could occur, the concentration of HTO was measured over a period of three weeks. A relatively long half-life of tissue-bound tritium was found under various temperature conditions. Therefore it must be considered that a significant retention of tritium in biological matter has to be taken into account in a natural ecosystem. In streams into which the cooling water of a nuclear reactor is released all conditions are found already for a long turnover and cycling of artificial tritium in living organisms as well as the conditions for a favourable transport of tritium by food chains to man.

  11. Dynamics of quadratic polynomials: Complex bounds for real maps


    Lyubich, Mikhail; Yampolsky, Michael


    We extend Sullivan's complex a priori bounds to real quadratic polynomials with essentially bounded combinatorics. Combined with the previous results of the first author, this yields complex bounds for all real quadratics. Local connectivity of the corresponding Julia sets follows.

  12. Bounds Estimation Via Regression with Asymmetric Cost Functions (United States)

    DeCoste, D.


    This paper addresses a significant but mostly-neglected class of problems that we call bounds estimation. This includes learning empirical best-case and worst-case algorithmic complexity bounds and red-line bounds on sensor data.

  13. Water

    CSIR Research Space (South Africa)

    Van Wyk, Llewellyn V


    Full Text Available , and of the remaining 2,5 percent, some 70 percent is frozen in the polar caps and around 30 percent is present as soil moisture or in underground aquifers. Less than 1 percent is thus accessible for direct use by humans, animals and plants. Consequently... be serviced with harvested water and/or grey water. Conserve and reuse cooling tower water by using efficient systems and strategies. Avoid ?once-through systems? commonly used for evaporation coolers, ice makers, hydraulic equipment, and air compressors...

  14. Universal bounds in even-spin CFTs

    Energy Technology Data Exchange (ETDEWEB)

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


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

  15. Structural and dynamical insights into the membrane-bound α-synuclein.

    Directory of Open Access Journals (Sweden)

    Neha Jain

    Full Text Available Membrane-induced disorder-to-helix transition of α-synuclein, a presynaptic protein, has been implicated in a number of important neuronal functions as well as in the etiology of Parkinson's disease. In order to obtain structural insights of membrane-bound α-synuclein at the residue-specific resolution, we took advantage of the fact that the protein is devoid of tryptophan and incorporated single tryptophan at various residue positions along the sequence. These tryptophans were used as site-specific markers to characterize the structural and dynamical aspects of α-synuclein on the negatively charged small unilamellar lipid vesicles. An array of site-specific fluorescence readouts, such as the spectral-shift, quenching efficiency and anisotropy, allowed us to discern various features of the conformational rearrangements occurring at different locations of α-synuclein on the lipid membrane. In order to define the spatial localization of various regions of the protein near the membrane surface, we utilized a unique and sensitive indicator, namely, red-edge excitation shift (REES, which originates when a fluorophore is located in a highly ordered micro-environment. The extent of REES observed at different residue positions allowed us to directly identify the residues that are localized at the membrane-water interface comprising a thin (∼ 15 Å layer of motionally restrained water molecules and enabled us to construct a dynamic hydration map of the protein. The combination of site-specific fluorescence readouts allowed us to unravel the intriguing molecular details of α-synuclein on the lipid membrane in a direct model-free fashion. Additionally, the combination of methodologies described here are capable of distinguishing subtle but important structural alterations of α-synuclein bound to different negatively charged lipids with varied head-group chemistry. We believe that the structural modulations of α-synuclein on the membrane could

  16. Water

    Directory of Open Access Journals (Sweden)

    E. Sanmuga Priya


    Full Text Available Phytoremediation through aquatic macrophytes treatment system (AMATS for the removal of pollutants and contaminants from various natural sources is a well established environmental protection technique. Water hyacinth (Eichhornia crassipes, a worst invasive aquatic weed has been utilised for various research activities over the last few decades. The biosorption capacity of the water hyacinth in minimising various contaminants present in the industrial wastewater is well studied. The present review quotes the literatures related to the biosorption capacity of the water hyacinth in reducing the concentration of dyestuffs, heavy metals and minimising certain other physiochemical parameters like TSS (total suspended solids, TDS (total dissolved solids, COD (chemical oxygen demand and BOD (biological oxygen demand in textile wastewater. Sorption kinetics through various models, factors influencing the biosorption capacity, and role of physical and chemical modifications in the water hyacinth are also discussed.

  17. Structure of a bacterial microcompartment shell protein bound to a cobalamin cofactor. (United States)

    Thompson, Michael C; Crowley, Christopher S; Kopstein, Jeffrey; Bobik, Thomas A; Yeates, Todd O


    The EutL shell protein is a key component of the ethanolamine-utilization microcompartment, which serves to compartmentalize ethanolamine degradation in diverse bacteria. The apparent function of this shell protein is to facilitate the selective diffusion of large cofactor molecules between the cytoplasm and the lumen of the microcompartment. While EutL is implicated in molecular-transport phenomena, the details of its function, including the identity of its transport substrate, remain unknown. Here, the 2.1 Å resolution X-ray crystal structure of a EutL shell protein bound to cobalamin (vitamin B12) is presented and the potential relevance of the observed protein-ligand interaction is briefly discussed. This work represents the first structure of a bacterial microcompartment shell protein bound to a potentially relevant cofactor molecule.

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

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


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

  19. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 2. Molecule of the Month Isomers of Benzene - Still Pursuing Dreams. J Chandrasekhar. Feature Article Volume 1 Issue 2 February 1996 pp 80-83. Fulltext. Click here to view fulltext PDF. Permanent link:

  20. Electrons in Molecules

    Indian Academy of Sciences (India)

    etc.) as well as explain the variations in bond lengths, bond angles, conformational angles, barriers to internal rotation! inversion, stretching!bending force constants, etc. However, when a molecule is quite large, with many occupied MOs, it is not advisable to bypass the actual computation of forces. As another application of ...

  1. Molecule-based magnets

    Indian Academy of Sciences (India)

    Keywords. Molecular lattices; spin–spin interaction; photo-induced magnetism; single molecule magnets. ... Since the first successful synthesis of molecular magnets in 1986, a large variety of them have been synthesized, which can be categorized on the basis of the chemical nature of the magnetic units involved: organic-, ...

  2. Quantum Interference of Molecules

    Indian Academy of Sciences (India)

    IAS Admin

    GENERAL │ ARTICLE. Quantum Interference of Molecules. Probing the Wave Nature of Matter. Anu Venugopalan. Keywords. Matter waves, wave-particle du- ality, electron interference, decoherence. Anu Venugopalan is on the faculty of the School of. Basic and Applied. Sciences, GGS. Indraprastha University,. Delhi.

  3. Atoms, Molecules and Radiation

    Indian Academy of Sciences (India)

    IAS Admin

    A Refresher Course in Applications of Quantum Mechanics to 'Atoms, Molecules and Radiation' will be held at the Indian Academy of Sciences, Bangalore from December 8 to 20. 2014. The Course is primarily aimed at teachers teaching quantum mechanics and/ or atomic and molecular physics at the UG / PG level.

  4. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - Molecular-Chameleon: Solvatochromism at its Iridescent Best! Photon Rao. Volume 16 Issue 12 December 2011 pp 1303-1306. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Molecule of the Month

    Indian Academy of Sciences (India)

    attempting to adapt the success of organic chemistry in the study of organosilicon compounds. Nevertheless chemists persisted with a sense of doggedness to try and mimic organic molecules with non- carbon elements. The year 1981 marks a watershed in the efforts to prepare and stabilise multiply-bonded compounds of ...

  6. Atoms, Molecules and Radiation

    Indian Academy of Sciences (India)

    IAS Admin


    Nov 10, 2015 ... Module 3: Interaction of electromagnetic radiation with matter: Quantum theory of radiation, spontaneous, stimulated emission and absorption probabilities, electric dipole selection rules, Einstein A and B coefficients, Rabi coefficients, Thomson Scattering, Jaynes-Cummings Model. Module 4: Molecules ...

  7. Molecule of the Month

    Indian Academy of Sciences (India)

    ethanol, blue in isopropyl alcohol, green in acetone and greenish-yellow in anisole. The electronic absorption spectrum of a molecule often depends on the solvent used. The change in position (and, sometimes, intensity) of the UVNis band accompanying a change in the polarity of the medium is called solvatochromism.

  8. Excitons: Molecules in flatland (United States)

    Yao, Wang


    Forming molecules from atoms is commonplace in dense atomic gases. But it now seems that some two-dimensional materials provide a suitable environment for creating complex molecular states from the hydrogen-like electron-hole pairs that form in semiconductors.

  9. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 9. Molecule of the Month Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Feature Article Volume 1 Issue 9 September 1996 pp 66-71. Fulltext. Click here to view fulltext PDF. Permanent link:

  10. Single-Molecule Spectroscopy

    Indian Academy of Sciences (India)

    IAS Admin

    a heterogeneous medium the local environment of each molecule may be different. This gives rise to large vari- ations of those properties which depend on the medium. (e.g., local polarity or viscosity). For instance, in a bio- logical cell the local environment at the membrane may be drastically different from that in the ...

  11. Molecule of the Month

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 16; Issue 12. Molecule of the Month - Adamantane - A Plastic Piece of Diamond. J Chandrasekhar. Volume 16 Issue 12 December 2011 pp 1232-1237. Fulltext. Click here to view fulltext PDF. Permanent link:

  12. Multipole-bound molecular negative ions

    CERN Document Server

    Abdul-Karim, H; Desfrançois, C


    Within the framework of a simple electrostatic model, as compared to recent experimental results, we here discuss the stability of very weakly bound molecular negative ions. In contrast with the case of conventional valence anions, the excess electron is then located in a very diffuse orbital and is mainly bound by electrostatic dipolar, quadrupolar, and polarization forces, at large distances from the neutral molecular core. By fitting a single repulsion parameter of the model to the available experimental data, it is possible to make quantitative predictions of the excess-electron binding energies in these species. Critical values of the dipole moment, quadrupole moment or polarizability required for the observation of stable multipole-bound negative ions are predicted and compared to available experimental data and ab initio calculations. Refs. 26 (author)

  13. Resistivity bound for hydrodynamic bad metals (United States)

    Lucas, Andrew; Hartnoll, Sean A.


    We obtain a rigorous upper bound on the resistivity ρ of an electron fluid whose electronic mean free path is short compared with the scale of spatial inhomogeneities. When such a hydrodynamic electron fluid supports a nonthermal diffusion process—such as an imbalance mode between different bands—we show that the resistivity bound becomes ρ≲AΓ. The coefficient A is independent of temperature and inhomogeneity lengthscale, and Γ is a microscopic momentum-preserving scattering rate. In this way, we obtain a unified mechanism—without umklapp—for ρ˜T2 in a Fermi liquid and the crossover to ρ˜T in quantum critical regimes. This behavior is widely observed in transition metal oxides, organic metals, pnictides, and heavy fermion compounds and has presented a long-standing challenge to transport theory. Our hydrodynamic bound allows phonon contributions to diffusion constants, including thermal diffusion, to directly affect the electrical resistivity.

  14. Correlation Distance and Bounds for Mutual Information

    Directory of Open Access Journals (Sweden)

    Michael J. W. Hall


    Full Text Available The correlation distance quantifies the statistical independence of two classical or quantum systems, via the distance from their joint state to the product of the marginal states. Tight lower bounds are given for the mutual information between pairs of two-valued classical variables and quantum qubits, in terms of the corresponding classical and quantum correlation distances. These bounds are stronger than the Pinsker inequality (and refinements thereof for relative entropy. The classical lower bound may be used to quantify properties of statistical models that violate Bell inequalities. Partially entangled qubits can have lower mutual information than can any two-valued classical variables having the same correlation distance. The qubit correlation distance also provides a direct entanglement criterion, related to the spin covariance matrix. Connections of results with classically-correlated quantum states are briefly discussed.

  15. Equivalence principle and bound kinetic energy. (United States)

    Hohensee, Michael A; Müller, Holger; Wiringa, R B


    We consider the role of the internal kinetic energy of bound systems of matter in tests of the Einstein equivalence principle. Using the gravitational sector of the standard model extension, we show that stringent limits on equivalence principle violations in antimatter can be indirectly obtained from tests using bound systems of normal matter. We estimate the bound kinetic energy of nucleons in a range of light atomic species using Green's function Monte Carlo calculations, and for heavier species using a Woods-Saxon model. We survey the sensitivities of existing and planned experimental tests of the equivalence principle, and report new constraints at the level of between a few parts in 10(6) and parts in 10(8) on violations of the equivalence principle for matter and antimatter.

  16. Yukawa Bound States and Their LHC Phenomenology

    Directory of Open Access Journals (Sweden)

    Enkhbat Tsedenbaljir


    Full Text Available We present the current status on the possible bound states of extra generation quarks. These include phenomenology and search strategy at the LHC. If chiral fourth-generation quarks do exist their strong Yukawa couplings, implied by current experimental lower bound on their masses, may lead to formation of bound states. Due to nearly degenerate 4G masses suggested by Precision Electroweak Test one can employ “heavy isospin” symmetry to classify possible spectrum. Among these states, the color-octet isosinglet vector ω 8 is the easiest to be produced at the LHC. The discovery potential and corresponding decay channels are covered in this paper. With possible light Higgs at ~125 GeV two-Higgs doublet version is briefly discussed.

  17. Braneworld black holes and entropy bounds

    Directory of Open Access Journals (Sweden)

    Y. Heydarzade


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

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

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


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

  19. Entropy Bounds, Holographic Principle and Uncertainty Relation

    Directory of Open Access Journals (Sweden)

    I. V. Volovich


    Full Text Available Abstract: A simple derivation of the bound on entropy is given and the holographic principle is discussed. We estimate the number of quantum states inside space region on the base of uncertainty relation. The result is compared with the Bekenstein formula for entropy bound, which was initially derived from the generalized second law of thermodynamics for black holes. The holographic principle states that the entropy inside a region is bounded by the area of the boundary of that region. This principle can be called the kinematical holographic principle. We argue that it can be derived from the dynamical holographic principle which states that the dynamics of a system in a region should be described by a system which lives on the boundary of the region. This last principle can be valid in general relativity because the ADM hamiltonian reduces to the surface term.

  20. Probing equilibrium of molecular and deprotonated water on TiO 2 (110)

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhi-Tao; Wang, Yang-Gang; Mu, Rentao; Yoon, Yeohoon; Dahal, Arjun; Schenter, Gregory K.; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Lyubinetsky, Igor; Dohnálek, Zdenek


    Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociation barrier. Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. The techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.

  1. A soluble class I molecule analogous to mouse Q10 in the horse and related species. (United States)

    Lew, A M; Valas, R B; Maloy, W L; Coligan, J E


    Horse serum is shown to contain a soluble class I molecule analogous to the secreted Q10 molecule in the mouse. This molecule has several similarities to the recently described mouse Q10 molecule: it is smaller than membrane-bound equine class I molecules; it occurs in a high molecular mass complex of 200-300 kd in serum; and the serum levels of the equine molecule are similar to that of the Q10 molecule (about 30 micrograms/ml). A soluble molecule is also detected in the sera of species related to the horse; it has in fact been found in all the wild members of the order Perissodactyla so far tested. However, it was not detected in the serum of members of the orders Carnivora, Sirenia, Proboscidea, Artiodactyla, and Primates that were tested, nor in the serum of members of the order Rodentia other than in that of the genus Mus.

  2. OMG: Open Molecule Generator

    Directory of Open Access Journals (Sweden)

    Peironcely Julio E


    Full Text Available Abstract Computer Assisted Structure Elucidation has been used for decades to discover the chemical structure of unknown compounds. In this work we introduce the first open source structure generator, Open Molecule Generator (OMG, which for a given elemental composition produces all non-isomorphic chemical structures that match that elemental composition. Furthermore, this structure generator can accept as additional input one or multiple non-overlapping prescribed substructures to drastically reduce the number of possible chemical structures. Being open source allows for customization and future extension of its functionality. OMG relies on a modified version of the Canonical Augmentation Path, which grows intermediate chemical structures by adding bonds and checks that at each step only unique molecules are produced. In order to benchmark the tool, we generated chemical structures for the elemental formulas and substructures of different metabolites and compared the results with a commercially available structure generator. The results obtained, i.e. the number of molecules generated, were identical for elemental compositions having only C, O and H. For elemental compositions containing C, O, H, N, P and S, OMG produces all the chemically valid molecules while the other generator produces more, yet chemically impossible, molecules. The chemical completeness of the OMG results comes at the expense of being slower than the commercial generator. In addition to being open source, OMG clearly showed the added value of constraining the solution space by using multiple prescribed substructures as input. We expect this structure generator to be useful in many fields, but to be especially of great importance for metabolomics, where identifying unknown metabolites is still a major bottleneck.

  3. Career Development and Personal Functioning Differences between Work-Bound and Non-Work Bound Students (United States)

    Creed, Peter A.; Patton, Wendy; Hood, Michelle


    We surveyed 506 Australian high school students on career development (exploration, planning, job-knowledge, decision-making, indecision), personal functioning (well-being, self-esteem, life satisfaction, school satisfaction) and control variables (parent education, school achievement), and tested differences among work-bound, college-bound and…

  4. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math... (United States)


    ... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... hand delivery. Please note that comments submitted by fax or email and those submitted after the... 1995 (PRA) (44 U.S.C. 3506(c)(2)(A)), provides the general public and Federal agencies with an...

  5. Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates

    DEFF Research Database (Denmark)

    Gál, Anna; Hansen, Kristoffer Arnsfelt; Koucký, Michal


    We bound the minimum number w of wires needed to compute any (asymptotically good) error-correcting code C:01(n)01n with minimum distance (n), using unbounded fan-in circuits of depth d with arbitrary gates. Our main results are: (1) If d=2 then w=(n(lognloglogn)2) . (2) If d=3 then w=(nlglgn). (3......, our (n(lognloglogn)2) lower bound gives the largest known lower bound for computing any linear map, improving on the (nlg32n) bound of Pudlak and Rodl (Discrete Mathematics '94). We find the upper bounds surprising. They imply that a (necessarily dense) generator matrix for the code can be written...... as the product of two sparse matrices. The upper bounds are non-explicit: we show the existence of circuits (consisting of only XOR gates) computing good codes within the stated bounds. Using a result by Ishai, Kushilevitz, Ostrovsky, and Sahai (STOC '08), we also obtain similar bounds for computing pairwise...

  6. Violation of Energy Bounds in Designer Gravity

    CERN Document Server

    Hertog, T


    We continue our study of the stability of designer gravity theories, where one considers anti-de Sitter gravity coupled to certain tachyonic scalars with boundary conditions defined by a smooth function W. It has recently been argued there is a lower bound on the conserved energy in terms of the global minimum of W, if the scalar potential arises from a superpotential P and the scalar reaches an extremum of P at infinity. We show, however, there are superpotentials for which these bounds do not hold.

  7. G-frames with bounded linear operators


    Xiao, Xiang-chun; Zhu, Yu-can; Shu, Zhi-biao; Ding, Ming-ling


    In this paper, we introduce the more general g-frame which is called a $K$-g-frame by combining a g-frame with a bounded linear operator $K$ in a Hilbert space. We give several equivalent characterizations for $K$-g-frames and discuss the stability of perturbation for $K$-g-frames. We also investigate the relationship between a $K$-g-frame and the range of the bounded linear operator $K$. In the end, we give two sufficient conditions for the remainder of a $K$-g-frame after an erasure to stil...

  8. Bounds on fake weighted projective space


    Kasprzyk, Alexander M.


    A fake weighted projective space X is a Q-factorial toric variety with Picard number one. As with weighted projective space, X comes equipped with a set of weights (λ0, ..., λn). We see how the singularities of P (λ0, ..., λn) influence the singularities of X, and how the weights bound the number of possible fake weighted projective spaces for a fixed dimension. Finally, we present an upper bound on the ratios λj/Σλi if we wish X to have only terminal (or canonical) singularities.

  9. Fibered Transverse Knots and the Bennequin Bound


    Etnyre, John B.; Van Horn-Morris, Jeremy


    We prove that a nicely fibered link (by which we mean the binding of an open book) in a tight contact manifold $(M,\\xi)$ with zero Giroux torsion has a transverse representative realizing the Bennequin bound if and only if the contact structure it supports (since it is also the binding of an open book) is $\\xi.$ This gives a geometric reason for the non-sharpness of the Bennequin bound for fibered links. We also note that this allows the classification, up to contactomorphism, of maximal self...

  10. Verifying bound entanglement of dephased Werner states (United States)

    Thomas, P.; Bohmann, M.; Vogel, W.


    The verification of quantum entanglement under the influence of realistic noise and decoherence is crucial for the development of quantum technologies. Unfortunately, a full entanglement characterization is generally not possible with most entanglement criteria such as entanglement witnesses or the partial transposition criterion. In particular, so-called bound entanglement cannot be certified via the partial transposition criterion. Here we present the full entanglement verification of dephased qubit and qutrit Werner states via entanglement quasiprobabilities. Remarkably, we are able to reveal bound entanglement for noisy mixed states in the qutrit case. This example demonstrates the strength of the entanglement quasiprobabilities for verifying the full entanglement of quantum states suffering from noise.

  11. A note on BPS vortex bound states

    Directory of Open Access Journals (Sweden)

    A. Alonso-Izquierdo


    Full Text Available In this note we investigate bound states, where scalar and vector bosons are trapped by BPS vortices in the Abelian Higgs model with a critical ratio of the couplings. A class of internal modes of fluctuation around cylindrically symmetric BPS vortices is characterized mathematically, analyzing the spectrum of the second-order fluctuation operator when the Higgs and vector boson masses are equal. A few of these bound states with low values of quantized magnetic flux are described fully, and their main properties are discussed.

  12. A note on BPS vortex bound states

    Energy Technology Data Exchange (ETDEWEB)

    Alonso-Izquierdo, A., E-mail: [Departamento de Matematica Aplicada, Universidad de Salamanca (Spain); Garcia Fuertes, W., E-mail: [Departamento de Fisica, Universidad de Oviedo (Spain); Mateos Guilarte, J., E-mail: [Departamento de Fisica Fundamental, Universidad de Salamanca (Spain)


    In this note we investigate bound states, where scalar and vector bosons are trapped by BPS vortices in the Abelian Higgs model with a critical ratio of the couplings. A class of internal modes of fluctuation around cylindrically symmetric BPS vortices is characterized mathematically, analyzing the spectrum of the second-order fluctuation operator when the Higgs and vector boson masses are equal. A few of these bound states with low values of quantized magnetic flux are described fully, and their main properties are discussed.

  13. Bounds of the Spectral Radius and the Nordhaus-Gaddum Type of the Graphs

    Directory of Open Access Journals (Sweden)

    Tianfei Wang


    Full Text Available The Laplacian spectra are the eigenvalues of Laplacian matrix L(G=D(G-A(G, where D(G and A(G are the diagonal matrix of vertex degrees and the adjacency matrix of a graph G, respectively, and the spectral radius of a graph G is the largest eigenvalue of A(G. The spectra of the graph and corresponding eigenvalues are closely linked to the molecular stability and related chemical properties. In quantum chemistry, spectral radius of a graph is the maximum energy level of molecules. Therefore, good upper bounds for the spectral radius are conducive to evaluate the energy of molecules. In this paper, we first give several sharp upper bounds on the adjacency spectral radius in terms of some invariants of graphs, such as the vertex degree, the average 2-degree, and the number of the triangles. Then, we give some numerical examples which indicate that the results are better than the mentioned upper bounds in some sense. Finally, an upper bound of the Nordhaus-Gaddum type is obtained for the sum of Laplacian spectral radius of a connected graph and its complement. Moreover, some examples are applied to illustrate that our result is valuable.

  14. Bacterial invasion reconstructed molecule by molecule

    Energy Technology Data Exchange (ETDEWEB)

    Werner, James H [Los Alamos National Laboratory


    We propose to visualize the initial stages of bacterial infection of a human host cell with unmatched spatial and temporal resolution. This work will develop a new capability for the laboratory (super-resolution optical imaging), will test unresolved scientific hypotheses regarding host-pathogen interaction dynamics, and leverages state of the art 3D molecular tracking instrumentation developed recently by our group. There is much to be gained by applying new single molecule tools to the important and familiar problem of pathogen entry into a host cell. For example, conventional fluorescence microscopy has identified key host receptors, such as CD44 and {alpha}5{beta}1 integrin, that aggregate near the site of Salmonella typhimurium infection of human cells. However, due to the small size of the bacteria ({approx} 2 {micro}m) and the diffraction of the emitted light, one just sees a fluorescent 'blob' of host receptors that aggregate at the site of attachment, making it difficult to determine the exact number of receptors present or whether there is any particular spatial arrangement of the receptors that facilitates bacterial adhesion/entry. Using newly developed single molecule based super-resolution imaging methods, we will visualize how host receptors are directed to the site of pathogen adhesion and whether host receptors adopt a specific spatial arrangement for successful infection. Furthermore, we will employ our 3D molecular tracking methods to follow the injection of virulence proteins, or effectors, into the host cell by the pathogen Type III secretion system (TTSS). We expect these studies to provide mechanistic insights into the early events of pathogen infection that have here-to-fore been technically beyond our reach. Our Research Goals are: Goal 1--Construct a super-resolution fluorescence microscope and use this new capability to image the spatial distribution of different host receptors (e.g. CD44, as {alpha}5{beta}1 integrin) at the

  15. The iodine molecule insights into intra- and intermolecular perturbation in diatomic molecules

    CERN Document Server

    Lukashov, Sergey; Pravilov, Anatoly


    This book presents experimental and theoretical spectroscopic studies performed over the last 25 years on the iodine molecule’s excited states and their perturbations. It is going to be of interest to researchers who study intra- and intermolecular perturbations in diatomic molecules and more complex systems. The book offers a detailed treatment of the nonadiabatic perturbations of valence, ion pair and Rydberg states induced by intramolecular as well as intermolecular interactions in collisions or in weakly-bound complexes. It also provides an overview of current instrumentation and techniques as well as theoretical approaches describing intra- and intermolecular perturbations. The authors are experts in the use of spectroscopy for the study of intrinsic and collision-induced perturbations in diatomic iodine. They introduced new methods of two- and three-step optical population of the iodine ion-pair states. The iodine molecule has 23 valence states correlating with three dissociation limits, 20 so-called ...

  16. Modelling the spectroscopic behaviour of hot molecules (United States)

    Tennyson, Jonathan


    At elevated temperatures the molecules absorb and emit light in a very complicated fashion which is hard to characterise on the basis of laboraroty measurement. Computed line lists of molecule transitions therefore provide a vital input for models of hot atmospheres. I will describe the calculation and use of such line lists including the BT2 water line list [1], which contains some 500 million distinct rotation-vibration transitions. This linelist proved crucial in the detection of water in extrasolar planet HD189733b and has been used extensively in atmospheric modelling. Illustrations will be given at the meeting. A new linelist for the ammonia molecule has just been completed [2] which shows that standard compilations for this molecule need to be improved. Progress on a more extensive linelist for hot ammonia and linelists for other molecules will be discussed at the meeting. [1] R.J. Barber, J. Tennyson, G.J. Harris and R.N. Tolchenov, Mon. Not. R. Astr. Soc., 368, 1087-1094 (2006) [2] S.N. Yurchenko, R.J. Barber, A. Yachmenev, W. Theil, P. Jensen and J. Tennyson, J. Phys. Chem. A, 113, 11845-11855 (2009).

  17. Colloid Bound Transport of Contaminats In The Unsaturated Zone (United States)

    Hofmann, T.; Christ, A.

    Colloids can play a major role in the relocation of contaminants in the unsaturated zone. The amount of colloid driven transport is defined by soil chemistry, soil water chemistry and water flow velocity as well as colloid composition and formation. In a current research project we investigate the filtration and mobilization of colloids in unsaturated column studies. We use different soil types, chosen by a wide range of mean grain size and heterogeneity. Particle tracers are polystyrene solids with a de- fined negative surface charge and defined size from 50 nm to 10 µm. In addition, we use natural colloids extracted from a wide range of contaminated and uncontaminated land. Experimental conditions are exactly controlled throughout all the time. We alter mainly flow velocity ionic strength in order to study the filtration behaviour of the soils. In addition, Pyrene and Lead are are used as model contaminants. First results show the colloids are not retarded in many coarse structured soil types. Preferential colloid flow shows a major impact in breakthrough behaviour. Colloid bound lead is relocated significant through the unsaturated zone, whereas non colloid bound lead species are strongly retarded. In the presentation we will show results of contami- nant processes and present new results on the filtration behaviour of colloids in the unsaturated zone depending on flow velocity, soil type and colloid size.

  18. Characterization of plasma membrane bound inorganic ...

    African Journals Online (AJOL)

    Background: Currently, a major problem in the management of visceral leishmaniasis or kala-azar, especially in the Indian subcontinent, is the growing unresponsiveness to conventional antimonial therapy. Membrane bound pyrophophatase (PPases) do not exist in plasma membrane from mammals. Thus, H+-PPases ...

  19. Stacked spheres and lower bound theorem

    Indian Academy of Sciences (India)



    Nov 20, 2011 ... Using Kalai's result, Tay (1995) proved LBT for a bigger class of simplicial complexes (namely, normal pseudomanifolds). In 2008, we (Bagchi & Datta) have presented a self-contained combinatorial proof of LBT for normal pseudomanifolds. Stacked spheres and lower bound theorem. Basudeb Datta.

  20. Computational Lower Bounds Using Diagonalization-II

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 4. Computational Lower Bounds Using Diagonalization - II. M V Panduranga Rao. General Article Volume 15 Issue 4 April 2010 pp 337-346 ... Keywords. Diagonalization; time–hierarchy theorem; relativization; Baker–Gill–Solovay theorem.