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Sample records for bound water molecules

  1. Detection of long-lived bound water molecules in complexes of human dihydrofolate reductase with methotrexate and NADPH.

    Science.gov (United States)

    Meiering, E M; Wagner, G

    1995-03-24

    The locations of long-lived bound water molecules in the binary complex of human dihydrofolate reductase (hDHFR) with methotrexate (MTX) and the ternary complex of hDHFR with MTX and NADPH have been investigated using 15N-resolved, three-dimensional ROESY-HMQC and NOESY-HSQC spectra acquired at 25 degrees C and 8 degrees C. NOEs with NH groups of the protein are detected for five bound water molecules in the binary complex and six bound water molecules in the ternary complex. Inspection of crystal structures of hDHFR reveals that the bound water molecules perform structural and functional roles in the complexes. Two water molecules located outside the active site, WatA and WatB, have similar NOEs in the binary and ternary complexes. These water molecules from multiple hydrogen bonds bridging loops and/or secondary structural elements in crystal structures of hDHFR and so stabilize the tertiary fold of the enzyme. Two water molecules in the active site, WatC and WatD, also have similar NOEs in both complexes. In crystal structures of hDHFR, WatC is involved in MTX binding by forming hydrogen bonds to the ligand and protein, while WatD stabilizes WatC by hydrogen bonding to it and the protein. A third active-site water molecule, WatE, has a markedly stronger NOE in the ternary complex than in the binary complex. Differences in the binding of WatE in the binary and ternary complexes are important for understanding the mechanism of DHFR, since this water molecule is believed to be involved in substrate protonation. Although the increased NOE intensity for WatE could be caused by a change in the position of water molecule, it may also be caused by an increase in its lifetime, since structural fluctuations in the active site are decreased upon cofactor binding. NOEs for one other water molecule, WatF, may be observed in the ternary complex but not the binary complex. WatF forms hydrogen bonds bridging the cofactor and the protein in crystal structures of hDHFR.

  2. 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

    2003-01-01

    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)

  3. Protein-bound water molecule counting by resolution of (1)H spin-lattice relaxation mechanisms.

    OpenAIRE

    Kiihne, S; Bryant, R G

    2000-01-01

    Water proton spin-lattice relaxation is studied in dilute solutions of bovine serum albumin as a function of magnetic field strength, oxygen concentration, and solvent deuteration. In contrast to previous studies conducted at high protein concentrations, the observed relaxation dispersion is accurately Lorentzian with an effective correlation time of 41 +/- 3 ns when measured at low proton and low protein concentrations to minimize protein aggregation. Elimination of oxygen flattens the relax...

  4. Bound-free Spectra for Diatomic Molecules

    Science.gov (United States)

    Schwenke, David W.

    2012-01-01

    It is now recognized that prediction of radiative heating of entering space craft requires explicit treatment of the radiation field from the infrared (IR) to the vacuum ultra violet (VUV). While at low temperatures and longer wavelengths, molecular radiation is well described by bound-bound transitions, in the short wavelength, high temperature regime, bound-free transitions can play an important role. In this work we describe first principles calculations we have carried out for bound-bound and bound-free transitions in N2, O2, C2, CO, CN, NO, and N2+. Compared to bound ]bound transitions, bound-free transitions have several particularities that make them different to deal with. These include more complicated line shapes and a dependence of emission intensity on both bound state diatomic and atomic concentrations. These will be discussed in detail below. The general procedure we used was the same for all species. The first step is to generate potential energy curves, transition moments, and coupling matrix elements by carrying out ab initio electronic structure calculations. These calculations are expensive, and thus approximations need to be made in order to make the calculations tractable. The only practical method we have to carry out these calculations is the internally contracted multi-reference configuration interaction (icMRCI) method as implemented in the program suite Molpro. This is a widely used method for these kinds of calculations, and is capable of generating very accurate results. With this method, we must first of choose which electrons to correlate, the one-electron basis to use, and then how to generate the molecular orbitals.

  5. A possibility of a protein-bound water molecule as the ionizable group responsible for pKe at the alkaline side in human matrix metalloproteinase 7 activity.

    Science.gov (United States)

    Morishima, Aiko; Yasukawa, Kiyoshi; Inouye, Kuniyo

    2012-05-01

    Human matrix metalloproteinase 7 (MMP-7) activity exhibits broad bell-shaped pH profile with the acidic and alkaline pK(a) (pK(e1) and pK(e2)) values of about 4 and 10. The ionizable group for pK(e2) was assigned to Lys or Arg by thermodynamic analysis; however, no such residues are present in the active site. Hence, based on the crystal structure, we hypothesized that a water molecule bound to the main-chain nitrogen of Ala162 (W1) or the main-chain carbonyl oxygen of Pro217 (W2) is a candidate for the ionizable group for pK(e2) [Takeharu, H. et al. (2011) Biochim. Biophys. Acta 1814, 1940-1946]. In this study, we inspected this hypothesis. In the hydrolysis of (7-methoxycoumarin-4-yl)acetyl-L-Pro-L-Leu-Gly-L-Leu-[N(3)-(2,4-dinitrophenyl)-L-2,3-diaminopropionyl]-L-Ala-L-Arg-NH(2), all 19 variants, in which one of all Lys and Arg residues was replaced by Ala, retained activity, indicating that neither Lys nor Arg is the ionizable group. pK(e2) values of A162S, A162V and A162G were 9.6 ± 0.1, 9.5 ± 0.1 and 10.4 ± 0.2, respectively, different from that of wild-type MMP-7 (WT) (9.9 ± 0.1) by 0.3-0.5 pH unit, and those of P217S, P217V and P217G were 10.1 ± 0.1, 9.8 ± 0.1 and 9.7 ± 0.1, respectively, different from that of WT by 0.1-0.2 pH unit. These results suggest a possibility of W1 or W2 as the ionizable group for pK(e2).

  6. The local characteristics of the bound states of muonic molecules

    Energy Technology Data Exchange (ETDEWEB)

    Abramov, D.I. [Sankt Peterburgskij Univ., St. Petersburg (Russian Federation); Bogdanova, L.N. [Institute of Theoretical and Experimental Physics, Moscow (Russian Federation); Gusev, V.V. [Institut Fiziki Vysokikh Ehnergij, Protvino (Russian Federation); Ponomarev, L.I. [Rossijskij Nauchnyj Tsentr ``Kurchatovskij Inst.``, Moscow (Russian Federation)

    1996-10-01

    The sticking probabilities {omega}{sup Jv}, G- and {gamma}-factors for all bound states of mesic molecules HH{mu}, HD{mu}, HT{mu}, DD{mu}, DT{mu}, and TT{mu} with J = 0 and v = 0, 1 have been calculated in the adiabatic hyperspherical approach (AHSA). (orig.). 6 refs.

  7. When water molecules meet air

    OpenAIRE

    Hsie, Cho-Shuen; Campen, R. Kramer; Verde, Ana Vila; Bolhuis, Peter; Nienhuys, Han-Kwang; Bonn, Mischa

    2012-01-01

    About 70% of our planet is covered in water. Most of that water exists as water in the bulk – the neighbors of water molecules are other water molecules – and only a small fraction of molecules are at the air-water interface. Despite the small relative abundance of interfacial water, it is of the utmost importance: it governs the chemistry involving the surface of oceans and seawater aerosols, or the small water droplets forming clouds. Reactions at the air-water interface are directly releva...

  8. 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...... vibrational bands of the cluster molecules in the challenging far-infrared and terahertz spectral regions.A key parameter in the validation of the performance of theoretical predictions for weak non-covalent intermolecular interactions is the dissociation energy D0 that depends heavily on the class of large...

  9. Weakly and strongly associated nonfreezable water bound in bones.

    Science.gov (United States)

    Turov, V V; Gun'ko, V M; Zarko, V I; Leboda, R; Jablonski, M; Gorzelak, M; Jagiello-Wojtowicz, E

    2006-03-15

    Water bound in bone of rat tail vertebrae was investigated by 1H NMR spectroscopy at 210-300 K and by the thermally stimulated depolarization current (TSDC) method at 190-265 K. The 1H NMR spectra of water clusters were calculated by the GIAO method with the B3LYP/6-31G(d,p) basis set, and the solvent effects were analyzed by the HF/SM5.45/6-31G(d) method. The 1H NMR spectra of water in bone tissue include two signals that can be assigned to typical water (chemical shift of proton resonance deltaH=4-5 ppm) and unusual water (deltaH=1.2-1.7 ppm). According to the quantum chemical calculations, the latter can be attributed to water molecules without the hydrogen bonds through the hydrogen atoms, e.g., interacting with hydrophobic environment. An increase in the amount of water in bone leads to an increase in the amount of typical water, which is characterized by higher associativity (i.e., a larger average number of hydrogen bonds per molecule) and fills larger pores, cavities and pockets in bone tissue.

  10. Structure and dynamics of water molecules confined in triglyceride oils.

    Science.gov (United States)

    Groot, Carien C M; Velikov, Krassimir P; Bakker, Huib J

    2016-10-26

    Though it is commonly known that a small amount of water can be present in triglyceride oil, a molecular picture of how water molecules organize in the oil phase is lacking. We investigate the hydrogen-bond configuration and dynamics of water in triacetin, tributyrin and trioctanoin using linear infrared and time-resolved two-dimensional infrared (2DIR) spectroscopy of the water hydroxyl stretch vibration. We identify water molecules with a single strong hydrogen bond to the triglyceride, water molecules with two weaker hydrogen bonds to the triglycerides, and water clusters. These species do not interconvert on the 20 ps timescale of the experiment, as evidenced by the absence of cross-peaks in the 2DIR spectrum. The vibrational response of water molecules with a single strong hydrogen bond to the triglyceride depends strongly on the excitation frequency, revealing the presence of different subspecies of singly-bound water molecules that correspond to different hydrogen-bond locations. In contrast, the water molecules with two weaker hydrogen bonds to the triglyceride correspond to a single, specific hydrogen-bond configuration; these molecules likely bridge the carbonyl groups of adjacent triglyceride molecules, which can have considerable influence on liquid triglyceride properties.

  11. Water molecules orientation in surface layer

    Science.gov (United States)

    Klingo, V. V.

    2000-08-01

    The water molecules orientation has been investigated theoretically in the water surface layer. The surface molecule orientation is determined by the direction of a molecule dipole moment in relation to outward normal to the water surface. Entropy expressions of the superficial molecules in statistical meaning and from thermodynamical approach to a liquid surface tension have been found. The molecules share directed opposite to the outward normal that is hydrogen protons inside is equal 51.6%. 48.4% water molecules are directed along to surface outward normal that is by oxygen inside. A potential jump at the water surface layer amounts about 0.2 volts.

  12. Positron-molecule interactions: resonant attachment, annihilation, and bound states

    CERN Document Server

    Gribakin, G F; Surko, C M; 10.1103/RevModPhys.82.2557

    2010-01-01

    This article presents an overview of current understanding of the interaction of low-energy positrons with molecules with emphasis on resonances, positron attachment and annihilation. Annihilation rates measured as a function of positron energy reveal the presence of vibrational Feshbach resonances (VFR) for many polyatomic molecules. These resonances lead to strong enhancement of the annihilation rates. They also provide evidence that positrons bind to many molecular species. A quantitative theory of VFR-mediated attachment to small molecules is presented. It is tested successfully for selected molecules (e.g., methyl halides and methanol) where all modes couple to the positron continuum. Combination and overtone resonances are observed and their role is elucidated. In larger molecules, annihilation rates from VFR far exceed those explicable on the basis of single-mode resonances. These enhancements increase rapidly with the number of vibrational degrees of freedom. While the details are as yet unclear, intr...

  13. Determination of free and bound water in fine coal filter cake

    Energy Technology Data Exchange (ETDEWEB)

    D.P. Patil; B.K. Parekh [Center for Applied Energy Research, Lexington, KY (US)

    2004-12-01

    The bound water in fine coal filter cake represents the water that cannot be removed using mechanical dewatering techniques. The amount of bound water in a fine coal filter cake, in other words, represents the moisture content achievable by an ideal dewatering technique. In this study the dilatometer technique was used to measure the bound and free water in a fine coal filter cake. Results showed that addition of cationic and non-ionic surfactants reduced the bound water content in the filter cake from 13.73% to 3.72% and 8.28%, respectively. Decrease in bound water content was attributed to the adsorption of surfactants on the coal surface, which increased the coal hydrophobicity. Addition of 10 g/t of cationic and anionic flocculants also reduced the bound water content from 13.73% to 4.58% and 6.63%, respectively, which was attributed to the replacement of surface water molecules with the polymer. Based on the free and bound water data, ideal dewatering curves were developed for both surfactants and flocculants.

  14. Formation of deeply bound LiRb molecules via photoassociation to near asymptotic states

    Science.gov (United States)

    Lorenz, John D.

    We present the results of a spectroscopic study LiRb molecules created via photoassociation (PA) to vibration levels of the 4(1) potential. Atoms are first cooled and trapped in a dual species 7Li/ 85Rb magneto-optical trap (MOT) at temperatures of ≈ 1 mK or less. In a cold sample of sufficient density, PA occurs when a resonant laser field induces a free-bound transition to create molecules in an excited electronic potential. After spontaneous emission the molecules decay to a mixture of free atoms and bound molecules depending on the Franck-Condon factors (FCFs) of the excited and ground state vibrational wavefunctions. While excited LiRb * has been previously detected by trap loss fluorescence detection, ionization spectroscopy is required to determine the population of ground state levels after decay. We detect ground state molecules via resonantly enhanced multiphoton ionization (REMPI) where a two photon ionization transition is enhanced by an intermediate resonance. The intermediate resonances match progressions from the D1pi and possibly B1Π potentials, many of which have known energies obtained from previous heat pipe experiments. This is contrary to the expectation that weakly bound LiRb * should primarily decay to weakly bound levels of the ground state and could point to a possible path for creating molecules in the rovibronic ground state.

  15. Classical interaction model for the water molecule.

    Science.gov (United States)

    Baranyai, András; Bartók, Albert

    2007-05-14

    The authors propose a new classical model for the water molecule. The geometry of the molecule is built on the rigid TIP5P model and has the experimental gas phase dipole moment of water created by four equal point charges. The model preserves its rigidity but the size of the charges increases or decreases following the electric field created by the rest of the molecules. The polarization is expressed by an electric field dependent nonlinear polarization function. The increasing dipole of the molecule slightly increases the size of the water molecule expressed by the oxygen-centered sigma parameter of the Lennard-Jones interaction. After refining the adjustable parameters, the authors performed Monte Carlo simulations to check the ability of the new model in the ice, liquid, and gas phases. They determined the density and internal energy of several ice polymorphs, liquid water, and gaseous water and calculated the heat capacity, the isothermal compressibility, the isobar heat expansion coefficients, and the dielectric constant of ambient water. They also determined the pair-correlation functions of ambient water and calculated the energy of the water dimer. The accuracy of theirs results was satisfactory.

  16. Evidence of water molecules--a statistical evaluation of water molecules based on electron density.

    Science.gov (United States)

    Nittinger, Eva; Schneider, Nadine; Lange, Gudrun; Rarey, Matthias

    2015-04-27

    Water molecules play important roles in many biological processes, especially when mediating protein-ligand interactions. Dehydration and the hydrophobic effect are of central importance for estimating binding affinities. Due to the specific geometric characteristics of hydrogen bond functions of water molecules, meaning two acceptor and two donor functions in a tetrahedral arrangement, they have to be modeled accurately. Despite many attempts in the past years, accurate prediction of water molecules-structurally as well as energetically-remains a grand challenge. One reason is certainly the lack of experimental data, since energetic contributions of water molecules can only be measured indirectly. However, on the structural side, the electron density clearly shows the positions of stable water molecules. This information has the potential to improve models on water structure and energy in proteins and protein interfaces. On the basis of a high-resolution subset of the Protein Data Bank, we have conducted an extensive statistical analysis of 2.3 million water molecules, discriminating those water molecules that are well resolved and those without much evidence of electron density. In order to perform this classification, we introduce a new measurement of electron density around an individual atom enabling the automatic quantification of experimental support. On the basis of this measurement, we present an analysis of water molecules with a detailed profile of geometric and structural features. This data, which is freely available, can be applied to not only modeling and validation of new water models in structural biology but also in molecular design.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-08-15

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

  18. Modelling proton transfer in water molecule chains

    CERN Document Server

    Korzhimanov, Artem; Shutova, Tatiana; Samuelsson, Goran

    2011-01-01

    The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better understood in terms of simplified model problems. Here we have tested, analytically and numerically, a model describing the classical proton hopping process in molecular water chains. In order to capture the main features of the proton hopping process in such molecular chains, we use a simplified model for our analysis. In particular, our discrete model describes a 1D chain of water molecules situated in an external protein channel structure, and each water molecule is allowed to oscillate around its equilibrium point in this system, while the protons are allowed to move along the line of neighboring oxygen atoms. The occurrence and properties of nonlinear solitary transport structures, allowing for much faster proton transport, are discussed, and the possible implications of...

  19. Control of Optical Transitions with Magnetic Fields in Weakly Bound Molecules

    CERN Document Server

    McGuyer, B H; Iwata, G Z; Skomorowski, W; Moszynski, R; Zelevinsky, T

    2015-01-01

    Forbidden optical transitions in weakly bound $^{88}$Sr$_2$ molecules become strongly enabled with moderate applied magnetic fields. We report the control of transition strengths by five orders of magnitude and measurements of highly nonlinear Zeeman shifts, which we explain with an accurate {\\it ab initio} model. Mixed quantization in an optical lattice enables the experimental procedure. Our observation of formerly inaccessible $f$-parity excited states offers a new avenue for improving theoretical models for divalent atom dimers. Furthermore, magnetically enabled transitions may lead to an extremely precise subradiant molecular lattice clock.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  2. Electric dipole moments of nanosolvated acid molecules in water clusters

    CERN Document Server

    Guggemos, Nicholas; Kresin, Vitaly V

    2015-01-01

    The electric dipole moments of $(H_{2}O)_{n}DCl$ ($n=3-9$) clusters have been measured by the beam deflection method. Reflecting the (dynamical) charge distribution within the system, the dipole moment contributes information about the microscopic structure of nanoscale solvation. The addition of a DCl molecule to a water cluster results in a strongly enhanced susceptibility. There is evidence for a noticeable rise in the dipole moment occurring at $n\\approx5-6$. This size is consistent with predictions for the onset of ionic dissociation. Additionally, a molecular dynamics model suggests that even with a nominally bound impurity an enhanced dipole moment can arise due to the thermal and zero point motion of the proton and the water molecules. The experimental measurements and the calculations draw attention to the importance of fluctuations in defining the polarity of water-based nanoclusters, and generally to the essential role played by motional effects in determining the response of fluxional nanoscale sy...

  3. Responses of cultured neural retinal cells to substratum-bound laminin and other extracellular matrix molecules.

    Science.gov (United States)

    Adler, R; Jerdan, J; Hewitt, A T

    1985-11-01

    The responses of cultured chick embryo retinal neurons to several extracellular matrix molecules are described. Retinal cell suspensions in serum-free medium containing the "N1" supplement (J. E. Bottenstein, S. D. Skaper, S. Varon, and J. Sato, 1980, Exp. Cell Res. 125, 183-190) were seeded on tissue culture plastic surfaces pretreated with polyornithine (PORN) and with one of the factors to be tested. Substantial cell survival could be observed after 72 hr in vitro on PORN pretreated with serum or laminin, whereas most cells appeared to be degenerating on untreated PORN, PORN-fibronectin, and PORN-chondronectin. Cell attachment, although quantitatively similar for all these substrata, was temperature-dependent on serum and laminin but not on fibronectin or untreated PORN. In a short-term bioassay, neurite development was abundant on laminin, scarce on serum and fibronectin, and absent on PORN. No positive correlation between cell spreading and neurite production could be seen: cell spreading was more extensive on PORN and fibronectin than on laminin or serum, while on laminin-treated dishes, spreading was similar for neurite-bearing and non-neurite-bearing cells. Laminin effects on retinal neurons were clearly substratum dependent. When bound to tissue culture plastic, laminin showed a dose-dependent inhibitory effect on cell attachment and did not stimulate neurite development. PORN-bound laminin, on the other hand, did not affect cell attachment but caused marked stimulation of neurite development, suggesting that laminin conformation and/or the spatial distribution of active sites play an important role in the neurite-promoting function of this extracellular matrix molecule. Investigation of the embryonic retina with ELISA and immunocytochemical methods showed that laminin is present in this organ during development. Therefore, in vivo and in vitro observations are consistent with the possibility that laminin might influence neuronal development in the retina.

  4. Sequential photochemical and microbial degradation of organic molecules bound to humic Acid.

    Science.gov (United States)

    Amador, J A; Alexander, M; Zika, R G

    1989-11-01

    We studied the effects of photochemical processes on the mineralization by soil microorganisms of [2-C]glycine bound to soil humic acid. Microbial mineralization of these complexes in the dark increased inversely with the molecular weight of the complex molecules. Sunlight irradiation of glycine-humic acid complexes resulted in loss of absorbance in the UV range and an increase in the amount of C-labeled low-molecular-weight photoproducts and the rate and extent of mineralization. More than half of the radioactivity in the low-molecular-weight photoproducts appears to be associated with carboxylic acids. Microbial mineralization of the organic carbon increased with solar flux and was proportional to the loss of A(330). Mineralization was proportional to the percentage of the original complex that was converted to low-molecular-weight photoproducts. Only light at wavelengths below 380 nm had an effect on the molecular weight distribution of the products formed from the glycine-humic acid complexes and on the subsequent microbial mineralization. Our results indicate that photochemical processes generate low-molecular-weight, readily biodegradable molecules from high-molecular-weight complexes of glycine with humic acid.

  5. Enhancement of X-ray-induced breaks in DNA bound to molecules containing platinum: a possible application to hadrontherapy.

    Science.gov (United States)

    Kobayashi, K; Frohlich, H; Usami, N; Takakura, K; Le Sech, C

    2002-01-01

    Complexes made of DNA and chloroterpyridine platinum (PtTC) bound to plasmid DNA were placed in aqueous solution and irradiated with monochromatic X rays tuned to the resonant photoabsorption energy of the L(III) shell of the platinum atom. The number of single- and double-strand breaks (SSBs and DSBs) induced by irradiation on a supercoiled DNA plasmid was measured by the production of the circular-nicked and linear forms. To distinguish the contribution of the direct effects of ionization from the indirect effects due to a free radical attack, experiments were also performed in the presence of a hydroxyl free radical scavenger, dimethyl sulfoxide (DMSO). An enhancement of the number of SSBs and DSBs was observed when the plasmids contained the platinum intercalating molecules. A quantitative analysis was made to evaluate the respective contributions of the direct effects (Auger effect) and the indirect effects (free radical attack) to the number of DNA strand breaks. Even when off-resonant X rays were used, the strand break efficiency remained higher than expected based upon the absorption cross section, suggesting that the platinum bound to DNA might be increasing the yield of strand breaks. A mechanism is suggested that involves photoelectrons generated from the ionization of water which efficiently ionize platinum atoms. If this mechanism is correct, then heavy atoms, with a large cross section for ionization by electrons that are bound to the DNA, should behave as a radiosensitizer. This observation may provide insight into understanding the effects of new radiotherapy protocols, related chemotherapeutic agents such as cisplatin, and conventional radiotherapy for the treatment of tumors. A possible way to deliver the dose selectively in a well-defined volume, which uses the properties of the linear energy transfer of atomic ions interacting with matter, is suggested.

  6. 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.

    1999-06-29

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Gregoire, Genevieve, E-mail: gregoire@cict.fr [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)

    2013-01-01

    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.

  8. 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;

    2016-01-01

    the sensitivity to confirm the diffusion of a small component of water bound to the lipids as found in the simulations. In addition, the orientation of the dipole moment of the water molecules has been determined as a function of their depth in the membrane. Previous indirect estimates of the electrostatic...... 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...... potential within phospholipid membranes imply an enormous electric field of 108-109 V m-1, which is likely to have great significance in controlling the conformation of translocating membrane proteins and in the transfer of ions and molecules across the membrane. We have calculated the membrane potential...

  9. Free enthalpies of replacing water molecules in protein binding pockets

    Science.gov (United States)

    Riniker, Sereina; Barandun, Luzi J.; Diederich, François; Krämer, Oliver; Steffen, Andreas; van Gunsteren, Wilfred F.

    2012-12-01

    Water molecules in the binding pocket of a protein and their role in ligand binding have increasingly raised interest in recent years. Displacement of such water molecules by ligand atoms can be either favourable or unfavourable for ligand binding depending on the change in free enthalpy. In this study, we investigate the displacement of water molecules by an apolar probe in the binding pocket of two proteins, cyclin-dependent kinase 2 and tRNA-guanine transglycosylase, using the method of enveloping distribution sampling (EDS) to obtain free enthalpy differences. In both cases, a ligand core is placed inside the respective pocket and the remaining water molecules are converted to apolar probes, both individually and in pairs. The free enthalpy difference between a water molecule and a CH3 group at the same location in the pocket in comparison to their presence in bulk solution calculated from EDS molecular dynamics simulations corresponds to the binding free enthalpy of CH3 at this location. From the free enthalpy difference and the enthalpy difference, the entropic contribution of the displacement can be obtained too. The overlay of the resulting occupancy volumes of the water molecules with crystal structures of analogous ligands shows qualitative correlation between experimentally measured inhibition constants and the calculated free enthalpy differences. Thus, such an EDS analysis of the water molecules in the binding pocket may give valuable insight for potency optimization in drug design.

  10. Composition of Phoebe and Iapetus: Bound Water and Possible Deuterated Water

    Science.gov (United States)

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

    2016-10-01

    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

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

    DEFF Research Database (Denmark)

    Thomsen, Theresa; Schlosser, Anders; Holmskov, Uffe

    2011-01-01

    as pattern recognition molecules. Ficolins are soluble oligomeric proteins composed of trimeric collagen-like regions linked to fibrinogen-related domains (FReDs) that have the ability to sense molecular patterns on both pathogens and apoptotic cell surfaces and activate the complement system. The ficolins......D-containing molecules, and discusses structural resemblance but also diversity in recognition of acetylated ligands....

  12. Visualization of single receptor molecules bound to human rhinovirus under physiological conditions.

    Science.gov (United States)

    Kienberger, Ferry; Rankl, Christian; Pastushenko, Vassili; Zhu, Rong; Blaas, Dieter; Hinterdorfer, Peter

    2005-09-01

    Dynamic force microscopy (DFM) was used to image human rhinovirus HRV2 alone and complexed with single receptor molecules under near physiological conditions. Specific and site-directed immobilization of HRV2 on a model cell membrane resulted in a crystalline arrangement of virus particles with hexagonal symmetry and 35 nm spacing. High-resolution imaging of the virus capsid revealed about 20 resolvable structural features with 3 nm diameters; this finding is in agreement with protrusions seen by cryo-electron microscopy. Binding of receptor molecules to individual virus particles was observed after injection of soluble receptors into the liquid cell. Virus-receptor complexes with zero, one, two, or three attached receptor molecules were resolved. The number of receptor molecules associated to virions increased over time. Occasionally, dissociation of single receptor molecules from viral particles was also observed.

  13. Quantum control of electron wave packets in bound molecules by trains of half-cycle pulses

    Energy Technology Data Exchange (ETDEWEB)

    Persson, Emil; Pichler, Markus; Wachter, Georg; Hisch, Thomas; Burgdoerfer, Joachim; Graefe, Stefanie [Institute for Theoretical Physics, Vienna University of Technology, Wiedner Hauptstr. 8-10, A-1040 Vienna (Austria); Jakubetz, Werner [Institute for Theoretical Chemistry, University of Vienna, Waehringerstr. 38, A-1090 Vienna (Austria)

    2011-10-15

    We investigate protocols for transient localization of electrons in homodiatomic molecules, as well as permanent localization via population inversion in polar molecules. By examining three different model systems with one electronic and one nuclear degree of freedom, we identify mechanisms leading to control over the localization of the electronic wave packets. We show that electronic states dressed by the quasi-dc component of the train of half-cycle pulses steer the combined electronic and nuclear motion toward the targeted state.

  14. On the Several Molecules and Nanostructures of Water

    OpenAIRE

    Cynthia Kolb Whitney

    2012-01-01

    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 in...

  15. Dielectric relaxation time and structure of bound water in biological materials

    Energy Technology Data Exchange (ETDEWEB)

    Mashimo, S.; Kuwabara, S.; Yagihara, S.; Higasi, K.

    1987-12-03

    The dielectric behavior of living tissues and a number of biological materials was examined by new equipment of the time domain reflectometry method in a wide frequency range of 10/sup 7/-10/sup 10/ Hz. The authors found two peaks of Debye absorption around 100 MHz and 20 GHz for all the materials. The low-frequency absorption is probably due to bound water while the high-frequency absorption to free water. From the observed relaxation times of bound water a hypothesis is ventured on the structure of bound water and its relaxation mechanism.

  16. On the Several Molecules and Nanostructures of Water

    Directory of Open Access Journals (Sweden)

    Cynthia Kolb Whitney

    2012-01-01

    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.

  17. On equilibrium structures of the water molecule

    Science.gov (United States)

    Császár, Attila G.; Czakó, Gábor; Furtenbacher, Tibor; Tennyson, Jonathan; Szalay, Viktor; Shirin, Sergei V.; Zobov, Nikolai F.; Polyansky, Oleg L.

    2005-06-01

    Equilibrium structures are fundamental entities in molecular sciences. They can be inferred from experimental data by complicated inverse procedures which often rely on several assumptions, including the Born-Oppenheimer approximation. Theory provides a direct route to equilibrium geometries. A recent high-quality ab initio semiglobal adiabatic potential-energy surface (PES) of the electronic ground state of water, reported by Polyansky et al. [Polyansky et al.Science 299, 539 (2003)] and called CVRQD here, is analyzed in this respect. The equilibrium geometries resulting from this direct route are deemed to be of higher accuracy than those that can be determined by analyzing experimental data. Detailed investigation of the effect of the breakdown of the Born-Oppenheimer approximation suggests that the concept of an isotope-independent equilibrium structure holds to about 3×10-5Å and 0.02° for water. The mass-independent [Born-Oppenheimer (BO)] equilibrium bond length and bond angle on the ground electronic state PES of water is reBO=0.95782Å and θeBO=104.485°, respectively. The related mass-dependent (adiabatic) equilibrium bond length and bond angle of H2O16 is read=0.95785Å and θead=104.500°, respectively, while those of D2O16 are read=0.95783Å and θead=104.490°. Pure ab initio prediction of J =1 and 2 rotational levels on the vibrational ground state by the CVRQD PESs is accurate to better than 0.002cm-1 for all isotopologs of water considered. Elaborate adjustment of the CVRQD PESs to reproduce all observed rovibrational transitions to better than 0.05cm-1 (or the lower ones to better than 0.0035cm-1) does not result in noticeable changes in the adiabatic equilibrium structure parameters. The expectation values of the ground vibrational state rotational constants of the water isotopologs, computed in the Eckart frame using the CVRQD PESs and atomic masses, deviate from the experimentally measured ones only marginally, especially for A0 and B0. The

  18. Adsorption mechanism of water molecule on goethite (010) surface

    Science.gov (United States)

    Xiu, Fangyuan; Zhou, Long; Xia, Shuwei; Yu, Liangmin

    2016-12-01

    Goethite widely exists among ocean sediments; it plays an important role in fixing heavy metals and adsorbing organic contaminants. So the understanding of the adsorbing process of water molecule on its surface will be very helpful to further reveal such environmental friendly processes. The configuration, electronic properties and interaction energy of water molecules adsorbed on pnma goethite (010) surface were investigated in detail by using density functional theory on 6-31G (d,p) basis set and projector- augment wave (PAW) method. The mechanism of the interaction between goethite surface and H2O was proposed. Despite the differences in total energy, there are four possible types of water molecule adsorption configurations on goethite (010) surface (Aa, Ab, Ba, Bb), forming coordination bond with surface Fe atom. Results of theoretical modeling indicate that the dissociation process of adsorbed water is an endothermic reaction with high activation energy. The dissociation of adsorbed water molecule is a proton transportation process between water's O atoms and surface. PDOS results indicate that the bonding between H2O and (010) surface is due to the overlapping of water's 2p orbitals and Fe's 3d orbitals. These results clarify the mechanism on how adsorbed water is dissociated on the surface of goethite and potentially provide useful information of the surface chemistry of goethite.

  19. The elliptical oscillations of the protons of water molecules

    Directory of Open Access Journals (Sweden)

    Николай Тимофеевич Малафаев

    2017-01-01

    Full Text Available The analysis of elliptical oscillations of the protons of water molecules by means of a dual-frequency pendulum model is carried out. The vibrational mode is determined, for which the average angles of pendulum deviation are consistent with the corners of bends of hydrogen bonds in water. The possibility of occurrence of elliptical and ellipse-like rotation of protons in the liquid water around the axis of molecules bonds in a non-uniform in the angle field of intermolecular forces is proved

  20. A surface-bound molecule that undergoes optically biased Brownian rotation

    Science.gov (United States)

    Hutchison, James A.; Uji-I, Hiroshi; Deres, Ania; Vosch, Tom; Rocha, Susana; Müller, Sibylle; Bastian, Andreas A.; Enderlein, Jörg; Nourouzi, Hassan; Li, Chen; Herrmann, Andreas; Müllen, Klaus; de Schryver, Frans; Hofkens, Johan

    2014-02-01

    Developing molecular systems with functions analogous to those of macroscopic machine components, such as rotors, gyroscopes and valves, is a long-standing goal of nanotechnology. However, macroscopic analogies go only so far in predicting function in nanoscale environments, where friction dominates over inertia. In some instances, ratchet mechanisms have been used to bias the ever-present random, thermally driven (Brownian) motion and drive molecular diffusion in desired directions. Here, we visualize the motions of surface-bound molecular rotors using defocused fluorescence imaging, and observe the transition from hindered to free Brownian rotation by tuning medium viscosity. We show that the otherwise random rotations can be biased by the polarization of the excitation light field, even though the associated optical torque is insufficient to overcome thermal fluctuations. The biased rotation is attributed instead to a fluctuating-friction mechanism in which photoexcitation of the rotor strongly inhibits its diffusion rate.

  1. Transport behavior of water molecules through two-dimensional nanopores

    Energy Technology Data Exchange (ETDEWEB)

    Zhu, Chongqin; Li, Hui; Meng, Sheng, E-mail: smeng@iphy.ac.cn [Beijing National Laboratory for Condensed Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China)

    2014-11-14

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  2. Transport behavior of water molecules through two-dimensional nanopores

    Science.gov (United States)

    Zhu, Chongqin; Li, Hui; Meng, Sheng

    2014-11-01

    Water transport through a two-dimensional nanoporous membrane has attracted increasing attention in recent years thanks to great demands in water purification and desalination applications. However, few studies have been reported on the microscopic mechanisms of water transport through structured nanopores, especially at the atomistic scale. Here we investigate the microstructure of water flow through two-dimensional model graphene membrane containing a variety of nanopores of different size by using molecular dynamics simulations. Our results clearly indicate that the continuum flow transits to discrete molecular flow patterns with decreasing pore sizes. While for pores with a diameter ≥15 Å water flux exhibits a linear dependence on the pore area, a nonlinear relationship between water flux and pore area has been identified for smaller pores. We attribute this deviation from linear behavior to the presence of discrete water flow, which is strongly influenced by the water-membrane interaction and hydrogen bonding between water molecules.

  3. Structures of water molecules in carbon nanotubes under electric fields

    Energy Technology Data Exchange (ETDEWEB)

    Winarto,; Takaiwa, Daisuke; Yamamoto, Eiji; Yasuoka, Kenji, E-mail: yasuoka@mech.keio.ac.jp [Department of Mechanical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522 (Japan)

    2015-03-28

    Carbon nanotubes (CNTs) are promising for water transport through membranes and for use as nano-pumps. The development of CNT-based nanofluidic devices, however, requires a better understanding of the properties of water molecules in CNTs because they can be very different from those in the bulk. Using all-atom molecular dynamics simulations, we investigate the effect of axial electric fields on the structure of water molecules in CNTs having diameters ranging from (7,7) to (10,10). The water dipole moments were aligned parallel to the electric field, which increases the density of water inside the CNTs and forms ordered ice-like structures. The electric field induces the transition from liquid to ice nanotubes in a wide range of CNT diameters. Moreover, we found an increase in the lifetime of hydrogen bonds for water structures in the CNTs. Fast librational motion breaks some hydrogen bonds, but the molecular pairs do not separate and the hydrogen bonds reform. Thus, hydrogen bonds maintain the water structure in the CNTs, and the water molecules move collectively, decreasing the axial diffusion coefficient and permeation rate.

  4. Stalled RNAP-II molecules bound to non-coding rDNA spacers are required for normal nucleolus architecture.

    Science.gov (United States)

    Freire-Picos, M A; Landeira-Ameijeiras, V; Mayán, María D

    2013-07-01

    The correct distribution of nuclear domains is critical for the maintenance of normal cellular processes such as transcription and replication, which are regulated depending on their location and surroundings. The most well-characterized nuclear domain, the nucleolus, is essential for cell survival and metabolism. Alterations in nucleolar structure affect nuclear dynamics; however, how the nucleolus and the rest of the nuclear domains are interconnected is largely unknown. In this report, we demonstrate that RNAP-II is vital for the maintenance of the typical crescent-shaped structure of the nucleolar rDNA repeats and rRNA transcription. When stalled RNAP-II molecules are not bound to the chromatin, the nucleolus loses its typical crescent-shaped structure. However, the RNAP-II interaction with Seh1p, or cryptic transcription by RNAP-II, is not critical for morphological changes.

  5. Recrystallization of freezable bound water in aqueous solutions of medium concentration

    Science.gov (United States)

    Lishan, Zhao; Liqing, Pan; Ailing, Ji; Zexian, Cao; Qiang, Wang

    2016-07-01

    For aqueous solutions with freezable bound water, vitrification and recrystallization are mingled, which brings difficulty to application and misleads the interpretation of relevant experiments. Here, we report a quantification scheme for the freezable bound water based on the water-content dependence of glass transition temperature, by which also the concentration range for the solutions that may undergo recrystallization finds a clear definition. Furthermore, we find that depending on the amount of the freezable bound water, different temperature protocols should be devised to achieve a complete recrystallization. Our results may be helpful for understanding the dynamics of supercooled aqueous solutions and for improving their manipulation in various industries. Project supported by the Knowledge Innovation Project of Chinese Academy of Sciences on Water Science Research (Grant No. KJZD-EW-M03) and the National Natural Science Foundation of China (Grant Nos. 11474325 and 11290161).

  6. Target molecules of food phytochemicals: food science bound for the next dimension.

    Science.gov (United States)

    Murakami, Akira; Ohnishi, Kohta

    2012-05-01

    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.

  7. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

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

    2015-01-01

    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 ...

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

    NARCIS (Netherlands)

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

    2012-01-01

    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 H2O@C

  9. Computational modeling of chemical reactions and interstitial growth and remodeling involving charged solutes and solid-bound molecules.

    Science.gov (United States)

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

    2014-10-01

    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 ( www.febio.org ). The availability of this framework may be particularly beneficial to optimizing tissue engineering culture systems by examining the

  10. Recrystallization of freezable bound water in aqueous solutions of medium concentrations

    Institute of Scientific and Technical Information of China (English)

    赵立山; 潘礼庆; 纪爱玲; 曹则贤; 王强

    2016-01-01

    For aqueous solutions with freezable bound water, vitrification and recrystallization are mingled, which brings diffi-culty to application and misleads the interpretation of relevant experiments. Here, we report a quantification scheme for the freezable bound water based on the water-content dependence of glass transition temperature, by which also the concentra-tion range for the solutions that may undergo recrystallization finds a clear definition. Furthermore, we find that depending on the amount of the freezable bound water, different temperature protocols should be devised to achieve a complete recrys-tallization. Our results may be helpful for understanding the dynamics of supercooled aqueous solutions and for improving their manipulation in various industries.

  11. Variational path integral molecular dynamics study of a water molecule

    Science.gov (United States)

    Miura, Shinichi

    2013-08-01

    In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482, 165 (2009)] is applied to a water molecule on the adiabatic potential energy surface. The method numerically generates an exact wavefunction using a trial wavefunction of the target system. It has been shown that even if a poor trial wavefunction is employed, the exact quantum distribution is numerically extracted, demonstrating the robustness of the variational path integral method.

  12. Dissociative Electron Attachment to Polyatomic Molecules - I : Water

    CERN Document Server

    Ram, N Bhargava; Krishnakumar, E

    2010-01-01

    Using the velocity map imaging technique, we studied and characterized the process of Dissociative Electron Attachment (DEA) in polyatomic molecules like Water, Hydrogen Sulphide, Ammonia, Methane, Formic Acid and Propyl Amine. We present the details of these studies in a series of 5 articles. In the first article here, we discuss the DEA process in gas phase water ($H_{2}O$ and $D_{2}O$) molecules. Electrons of 6.5 eV, 8.5 eV and 12 eV are captured by water molecules in neutral ground state to form $H_{2}O^{-*}$ ($D_{2}O^{-*}$) resonant states which dissociate into an anion fragment and one or more neutrals. Kinetic energy and angular distributions of the fragment anions $H^{-}$($D^{-}$) and $O^{-}$ produced from the three negative ion resonant states in the entire $2\\pi$ scattering range are obtained. Unique angular distribution patterns are observed at the 8.5 eV and 11.8 eV resonances showing dissociation dynamics beyond the axial recoil approximation.

  13. Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of adhesion molecule CD44

    Energy Technology Data Exchange (ETDEWEB)

    Mori, Tomoyuki; Kitano, Ken; Terawaki, Shin-ichi; Maesaki, Ryoko; Hakoshima, Toshio, E-mail: hakosima@bs.naist.jp [Structural Biology Laboratory, Nara Institute of Science and Technology, Keihanna Science City, Nara 630-0192 (Japan)

    2007-10-01

    The radixin FERM domain complexed with the CD44 cytoplasmic tail peptide has been crystallized. A diffraction data set from the complex was collected to 2.1 Å. CD44 is an important adhesion molecule that specifically binds hyaluronic acid and regulates cell–cell and cell–matrix interactions. Increasing evidence has indicated that CD44 is assembled in a regulated manner into the membrane–cytoskeletal junction, a process that is mediated by ERM (ezrin/radixin/moesin) proteins. Crystals of a complex between the radixin FERM domain and the C-terminal cytoplasmic region of CD44 have been obtained. The crystal of the radixin FERM domain bound to the CD44 cytoplasmic tail peptide belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.70, b = 66.18, c = 86.22 Å, and contain one complex in the crystallographic asymmetric unit. An intensity data set was collected to a resolution of 2.1 Å.

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

    Energy Technology Data Exchange (ETDEWEB)

    Goble, J.H. Jr.

    1982-05-01

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

  15. Formation of deeply bound ultracold LiRb molecules via photoassociation near the Li 2 S1 /2+Rb 5 P3 /2 asymptote

    Science.gov (United States)

    Lorenz, John; Altaf, Adeel; Dutta, Sourav; Chen, Yong P.; Elliott, D. S.

    2014-12-01

    We present spectra of ultracold 7Li85Rb molecules in their electronic ground state formed by spontaneous decay of weakly bound photoassociated molecules. Beginning with atoms in a dual-species magneto-optical trap, weakly bound molecules are formed in the 4(1) electronic state, which corresponds to the B1Π state at short range. These molecules spontaneously decay to the electronic ground state and we use resonantly enhanced multiphoton ionization to determine the vibrational population distribution in the electronic ground states after spontaneous emission. Many of the observed lines from the spectra are consistent with transitions from the X1Σ+ ground electronic state to either the B1Π or the D1Π electronic state that has been previously observed, with levels possibly as low as X1Σ+ (v''=2 ) being populated. We do not observe decay to weakly bound vibrational levels of the X1Σ+ or a3Σ+ electronic state in the spectra. We also deduce a lower bound of 3900 cm -1 for the dissociation energy of the LiRb + molecular ion.

  16. 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: david.cappelletti@unipg.it; Pirani, Fernando [Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia (Italy)

    2014-03-28

    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.

  17. Geometry-dependent distributed polarizability models for the water molecule

    Energy Technology Data Exchange (ETDEWEB)

    Loboda, Oleksandr; Ingrosso, Francesca; Ruiz-López, Manuel F.; Millot, Claude [Université de Lorraine, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506 (France); CNRS, SRSMC UMR 7565, Vandoeuvre-les-Nancy F-54506 (France); Szalewicz, Krzysztof [Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716 (United States)

    2016-01-21

    Geometry-dependent distributed polarizability models have been constructed by fits to ab initio calculations at the coupled cluster level of theory with up to noniterative triple excitations in an augmented triple-zeta quality basis set for the water molecule in the field of a point charge. The investigated models include (i) charge-flow polarizabilities between chemically bonded atoms, (ii) isotropic or anisotropic dipolar polarizabilities on oxygen atom or on all atoms, and (iii) combinations of models (i) and (ii). For each model, the polarizability parameters have been optimized to reproduce the induction energy of a water molecule polarized by a point charge successively occupying a grid of points surrounding the molecule. The quality of the models is ascertained by examining their ability to reproduce these induction energies as well as the molecular dipolar and quadrupolar polarizabilities. The geometry dependence of the distributed polarizability models has been explored by changing bond lengths and HOH angle to generate 125 molecular structures (reduced to 75 symmetry-unique ones). For each considered model, the distributed polarizability components have been fitted as a function of the geometry by a Taylor expansion in monomer coordinate displacements up to the sum of powers equal to 4.

  18. Synthesis and properties of water-soluble asterisk molecules.

    Science.gov (United States)

    Menger, Fredric M; Azov, Vladimir A

    2002-09-18

    An asterisk is comprised of six semirigid arms projecting from a benzene nucleus. In the case at hand, asterisks were synthesized with one, two, or three aromatic rings (connected by sulfur atoms) in each of the six arms. A phosphomonoester at the termini of each arm solubilized the asterisks in water. The colloidal properties of these amphiphilic molecules were investigated by UV-vis and fluorescence spectroscopy, calorimetry, light scattering, surface tensiometry, and pulse-gradient spin-echo NMR. Solubility, solubilization, metal binding, and micelle "seeding" experiments were also carried out. Chain-conformation and supramolecular assembly into remarkable molecular "scrolls" were investigated by X-ray analysis and electron microscopy, respectively. One of the more interesting properties of the asterisks is that they remain monomeric in water despite having as many as 19 hydrophobic aromatic rings exposed to the water. The reasons for this behavior, and the possibility of exploiting it for constructing enzyme models free from aggregation equilibria, are discussed.

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

    Directory of Open Access Journals (Sweden)

    Jan Kučera

    2011-07-01

    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.

  20. Continuum simulations of water flow past fullerene molecules

    Science.gov (United States)

    Popadić, A.; Praprotnik, M.; Koumoutsakos, P.; Walther, J. H.

    2015-09-01

    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 solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

  1. Characterizing Structural Stability of Amyloid Motif Fibrils Mediated by Water Molecules.

    Science.gov (United States)

    Choi, Hyunsung; Chang, Hyun Joon; Lee, Myeongsang; Na, Sungsoo

    2017-02-04

    In biological systems, structural confinements of amyloid fibrils can be mediated by the role of water molecules. However, the underlying effect of the dynamic behavior of water molecules on structural stabilities of amyloid fibrils is still unclear. By performing molecular dynamics simulations, we investigate the dynamic features and the effect of interior water molecules on conformations and mechanical characteristics of various amyloid fibrils. We find that a specific mechanism induced by the dynamic properties of interior water molecules can affect diffusion of water molecules inside amyloid fibrils, inducing their different structural stabilities. The conformation of amyloid fibrils induced by interior water molecules show the fibrils' different mechanical features. We elucidate the role of confined and movable interior water molecules in structural stabilities of various amyloid fibrils. Our results offer insights not only in further understanding of mechanical features of amyloids as mediated by water molecules, but also in the fine-tuning of the functional abilities of amyloid fibrils for applications.

  2. Glutamate Water Gates in the Ion Binding Pocket of Na+ Bound Na+, K+-ATPase

    Science.gov (United States)

    Han, Minwoo; Kopec, Wojciech; Solov’yov, Ilia A.; Khandelia, Himanshu

    2017-01-01

    The dynamically changing protonation states of the six acidic amino acid residues in the ion binding pocket of the Na+, K+ -ATPase (NKA) during the ion transport cycle are proposed to drive ion binding, release and possibly determine Na+ or K+ selectivity. We use molecular dynamics (MD) and density functional theory (DFT) simulations to determine the protonation scheme of the Na+ bound conformation of NKA. MD simulations of all possible protonation schemes show that the bound Na+ ions are most stably bound when three or four protons reside in the binding sites, and that Glu954 in site III is always protonated. Glutamic acid residues in the three binding sites act as water gates, and their deprotonation triggers water entry to the binding sites. From DFT calculations of Na+ binding energies, we conclude that three protons in the binding site are needed to effectively bind Na+ from water and four are needed to release them in the next step. Protonation of Asp926 in site III will induce Na+ release, and Glu327, Glu954 and Glu779 are all likely to be protonated in the Na+ bound occluded conformation. Our data provides key insights into the role of protons in the Na+ binding and release mechanism of NKA. PMID:28084301

  3. Formation of deeply bound ultracold LiRb molecules via photoassociation near the Li 2S$_{1/2}$ + Rb 5P$_{3/2}$ asymptote

    CERN Document Server

    Lorenz, John; Dutta, Sourav; Chen, Yong P; Elliott, D S

    2014-01-01

    We present spectra of ultracold $^7$Li$^{85}$Rb molecules in their electronic ground state formed by spontaneous decay of weakly bound photoassociated molecules. Beginning with atoms in a dual species magneto-optical trap (MOT), weakly bound molecules are formed in the 4(1) electronic state, which corresponds to the B$^1\\Pi$ state at short range. These molecules spontaneously decay to the electronic ground state and we use resonantly enhanced multiphoton ionization (REMPI) to determine the vibrational population distribution in the electronic ground states after spontaneous emission. Many of the observed lines from the spectra are consistent with transitions from the X$^1\\Sigma^+$ ground electronic state to either the B$^1\\Pi$ or D$^1\\Pi$ electronic states that have been previously observed, with levels possibly as low as X$^1\\Sigma^+$ $(v'' = 2)$ being populated. We do not observe decay to weakly bound vibrational levels of the X$^1\\Sigma^+$ or a$^3\\Sigma^+$ electronic states in the spectra. We also deduce a...

  4. The role of free and bound water in irradiation preservation: Free radical damage as a function of the physical state of water

    Science.gov (United States)

    Wedemeyer, Gary; Dollar, A.M.

    1964-01-01

    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.

  5. An upper-bound assessment of the benefits of reducing perchlorate in drinking water.

    Science.gov (United States)

    Lutter, Randall

    2014-10-01

    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.

  6. Sticking of molecules on non-porous amorphous water ice

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    Accurate modeling of physical and chemical processes in the interstellar medium requires detailed knowledge of how atoms and molecule adsorb on dust grains. However, the sticking coefficient, a number between 0 and 1 that measures the first step in the interaction of a particle with a surface, is usually assumed in simulations of ISM environments to be either 0.5 or 1. Here we report on the determination of the sticking coefficient of H$_2$, D$_2$, N$_2$, O$_2$, CO, CH$_4$, and CO$_2$ on non-porous amorphous solid water (np-ASW). The sticking coefficient was measured over a wide range of surface temperatures using a highly collimated molecular beam. We showed that the standard way of measuring the sticking coefficient --- the King-Wells method --- leads to the underestimation of trapping events in which there is incomplete energy accommodation of the molecule on the surface. Surface scattering experiments with the use of a pulsed molecular beam are used instead to measure the sticking coefficient. Based on th...

  7. A study of the structural and spectral characteristics of free and bound water in kaolinite

    Science.gov (United States)

    Kasprzhitskii, A. S.; Lazorenko, G. I.; Sulavko, S. N.; Yavna, V. A.; Kochur, A. G.

    2016-09-01

    The dependence of the Si-O stretching vibration line intensity in the IR spectrum of kaolinite on the humidity of this mineral has been experimentally investigated. The experimental data were interpreted on the basis of density functional theory (DFT) calculations with allowance for the real crystallographic features of the kaolinite sample, determined by structural analysis. Some specific features of the intensity behavior in the plastic state are revealed, which can be used to develop techniques for determining its limits. The differences in the O-H bond lengths and H-O-H angles for the H2O molecules adsorbed by basal surfaces and located in the porous space of the mineral are determined. Based on the DFT data, it was found that bond lengths and bond angles for a water molecule adsorbed on the siloxane surface are systematically smaller than for a water molecule adsorbed on the hydroxyl surface.

  8. Hydrogen production by a hyperthermophilic membrane-bound hydrogenase in water-soluble nanolipoprotein particles.

    Science.gov (United States)

    Baker, Sarah E; Hopkins, Robert C; Blanchette, Craig D; Walsworth, Vicki L; Sumbad, Rhoda; Fischer, Nicholas O; Kuhn, Edward A; Coleman, Matt; Chromy, Brett A; Létant, Sonia E; Hoeprich, Paul D; Adams, Michael W W; Henderson, Paul T

    2009-06-10

    Hydrogenases constitute a promising class of enzymes for ex vivo hydrogen production. Implementation of such applications is currently hindered by oxygen sensitivity and, in the case of membrane-bound hydrogenases (MBHs), poor water solubility. Nanolipoprotein particles (NLPs) formed from apolipoproteins and phospholipids offer a novel means of incorporating MBHs into a well-defined water-soluble matrix that maintains the enzymatic activity and is amenable to incorporation into more complex architectures. We report the synthesis, hydrogen-evolving activity, and physical characterization of the first MBH-NLP assembly. This may ultimately lead to the development of biomimetic hydrogen-production devices.

  9. Mineral and Protein-Bound Water and Latching Action Control Mechanical Behavior at Protein-Mineral Interfaces in Biological Nanocomposites

    Directory of Open Access Journals (Sweden)

    Pijush Ghosh

    2008-01-01

    Full Text Available The nacre structure consists of laminated interlocked mineral platelets separated by nanoscale organic layers. Here, the role of close proximity of mineral to the proteins on mechanical behavior of the protein is investigated through steered molecular dynamics simulations. Our simulations indicate that energy required for unfolding protein in the proximity of mineral aragonite is several times higher than that for isolated protein in the absence of the mineral. Here, we present details of specific mechanisms which result in higher energy for protein unfolding in the proximity of mineral. At the early stage of pulling, peaks in the load-displacement (LD plot at mineral proximity are quantitatively correlated to the interaction energy between atoms involved in the latching phenomenon of amino acid side chain to aragonite surface. Water plays an important role during mineral and protein interaction and water molecules closer to the mineral surface are highly oriented and remain rigidly attached as the protein strand is pulled. Also, the high magnitude of load for a given displacement originates from attractive interactions between the protein, protein-bound water, and mineral. This study provides an insight into mineral-protein interactions that are predominant in biological nanocomposites and also provides guidelines towards design of biomimetic nanocomposites.

  10. 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

    2008-01-01

    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.

  11. Concentration of nitrogen molecules needed by nitrogen nanobubbles existing in bulk water

    Institute of Scientific and Technical Information of China (English)

    张萌; 涂育松; 方海平

    2013-01-01

    This paper investigates the stability of nitrogen nanobubbles under dif-ferent concentrations of nitrogen molecules by molecular dynamics simulations. It is found that the stability of nanobubbles is very sensitive to the concentration of nitrogen molecules in water. A sharp transition between disperse states and assemble states of nitrogen molecules is observed when the concentration of nitrogen molecules is changed. The relevant critical concentration of nitrogen molecules needed by the existing nitrogen nanobubbles is analyzed.

  12. Quantum Tunneling of Water in Beryl: A New State of the Water Molecule.

    Science.gov (United States)

    Kolesnikov, Alexander I; Reiter, George F; Choudhury, Narayani; Prisk, Timothy R; Mamontov, Eugene; Podlesnyak, Andrey; Ehlers, George; Seel, Andrew G; Wesolowski, David J; Anovitz, Lawrence M

    2016-04-22

    Using neutron scattering and ab initio simulations, we document the discovery of a new "quantum tunneling state" of the water molecule confined in 5 Å channels in the mineral beryl, characterized by extended proton and electron delocalization. We observed a number of peaks in the inelastic neutron scattering spectra that were uniquely assigned to water quantum tunneling. In addition, the water proton momentum distribution was measured with deep inelastic neutron scattering, which directly revealed coherent delocalization of the protons in the ground state.

  13. The equivalent potential of water molecules for electronic structure of lysine

    Institute of Scientific and Technical Information of China (English)

    LI ChunJie; ZHENG HaoPing; WANG XueMei

    2007-01-01

    In order to get more reliable electronic structures of proteins in aqueous solution,it is necessary to construct a potential of water molecules for protein's electronic structure calculation.The lysine is a hydrophilic amino acid.It is positively charged (Lys+) in neutral water solution.The first-principles,all-electron,ab initio calculations,based on the density functional theory,have been performed to construct such an equivalent potential of water molecules for lysine (Lys+).The process consists of three parts.First,the electronic structure of the cluster containing Lys+ and water molecules is calculated.By adjusting the positions of water molecules,the geometric structure of the cluster having minimum total energy is determined.Then,based on the structure,the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method.Finally,the electronic structure of Lys+ with the potential of dipoles is calculated.The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules.Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained.The major effect of water molecules on lysine's electronic structure is raising the occupied eigenvalues about 0.5032 eV,and broadening energy gap 89%.The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.

  14. The equivalent potential of water molecules for electronic structure of lysine

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    In order to get more reliable electronic structures of proteins in aqueous solution, it is necessary to construct a potential of water molecules for protein’s electronic structure calculation. The lysine is a hydrophilic amino acid. It is positively charged (Lys+) in neutral water solution. The first-principles, all-electron, ab initio calcula-tions, based on the density functional theory, have been performed to construct such an equivalent potential of water molecules for lysine (Lys+). The process consists of three parts. First, the electronic structure of the cluster containing Lys+ and water molecules is calculated. By adjusting the positions of water molecules, the geometric structure of the cluster having minimum total energy is determined. Then, based on the structure, the electronic structure of Lys+ with the potential of water molecules is calculated using the self-consistent cluster-embedding (SCCE) method. Finally, the electronic structure of Lys+ with the potential of dipoles is calculated. The dipoles are adjusted so that the electronic structure of Lys+ with the potential of dipoles is close to that of water molecules. Thus the equivalent potential of water molecules for the electronic structure of lysine is obtained. The major effect of water molecules on lysine’s electronic structure is raising the occupied eigenvalues about 0.5032 eV, and broadening energy gap 89%. The effect of water molecules on the electronic structure of lysine can be simulated by dipoles potential.

  15. Electron capture by bare ions on water molecules

    Science.gov (United States)

    Rivarola, Roberto; Montenegro, Pablo; Monti, Juan; Fojón, Omar

    2016-05-01

    Single electron capture from water molecules by impact of bare ions is theoretically investigated at intermediate and high collision energies. This reaction is of fundamental importance to determine the deposition of energy in biological matter irradiated with ion beams (hadrontherapy), dominating other ionizing processes of the target at low-intermediate impact velocities and giving principal contributions to the energetic region where electronic stopping power maximizes. The dynamics of the interaction between the aggregates is described within the one active-electron continuum distorted wave-eikonal initial state theory. The orbitals of the target in the ground state are represented using the approximate self-consistent complete neglect of differential orbitals (SC-CNDO) model. The contribution of different molecular orbitals on the partial cross sections to selected n-principal quantum number projectile states is discriminated as well as the collaboration of these n-states on total cross sections. The latter ones are dominated by capture to n=1 states at high enough energies decreasing their contribution as n increases.

  16. Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation.

    Science.gov (United States)

    Quick, Matthias; Winther, Anne-Marie Lund; Shi, Lei; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A

    2009-04-07

    The first crystal structure of the neurotransmitter/sodium symporter homolog LeuT revealed an occluded binding pocket containing leucine and 2 Na(+); later structures showed tricyclic antidepressants (TCAs) in an extracellular vestibule approximately 11 A above the bound leucine and 2 Na(+). We recently found this region to be a second binding (S2) site and that binding of substrate to this site triggers Na(+)-coupled substrate symport. Here, we show a profound inhibitory effect of n-octyl-beta-d-glucopyranoside (OG), the detergent used for LeuT crystallization, on substrate binding to the S2 site. In parallel, we determined at 2.8 A the structure of LeuT-E290S, a mutant that, like LeuT-WT, binds 2 substrate molecules. This structure was similar to that of WT and clearly revealed an OG molecule in the S2 site. We also observed electron density at the S2 site in LeuT-WT crystals, and this also was accounted for by an OG molecule in that site. Computational analyses, based on the available crystal structures of LeuT, indicated the nature of structural arrangements in the extracellular region of LeuT that differentiate the actions of substrates from inhibitors bound in the S2 site. We conclude that the current LeuT crystal structures, all of which have been solved in OG, represent functionally blocked forms of the transporter, whereas a substrate bound in the S2 site will promote a different state that is essential for Na(+)-coupled symport.

  17. Small molecule, big difference: the role of water in the crystallization of paclitaxel.

    Science.gov (United States)

    Vella-Zarb, Liana; Baisch, Ulrich; Dinnebier, Robert E

    2013-02-01

    Paclitaxel is an important antineoplastic drug, which is used widely in the treatment of many forms of cancer. The crystal structures of the anhydrous form and the hemihydrate were determined from laboratory X-ray powder diffraction data, whereas the dihydrate was solved from single-crystal synchrotron diffraction data. Intermolecular spaces allow for the inclusion of loosely bound water molecules, which are then lost easily upon heating. All three forms were found to crystallize in the orthorhombic spacegroup P2(1)2(1)2(1), with Z' = 2. The unit cell parameters were found to be a = 9.6530(3) Å, b = 28.1196(8) Å, c = 33.5378(14) Å, and V = 9103.5(5) Å for the anhydrous form (363 K); a = 9.6890(2) Å, b = 28.0760(4) Å, c = 33.6166(8) Å, and V = 9144.7(3) Å(3) for the hemihydrate (333 K); and a = 9.512(6) Å, b = 28.064(16) Å, c = 33.08(2) Å, and V = 8829.0(9) Å(3) for the dihydrate (120 K). Water loss occurs in two steps between 120 K ≤ t ≤ 363 K. The thermal stability of the hydrates and accompanying unit cell changes were observed in situ via temperature-resolved X-ray powder diffraction and thermogravimetric analysis.

  18. X-Ray Structural Study of Amyloid-Like Fibrils of Tau Peptides Bound to Small-Molecule Ligands.

    Science.gov (United States)

    Tayeb-Fligelman, Einav; Landau, Meytal

    2017-01-01

    Atomic structures of Tau involved in Alzheimer's disease complexed with small molecule binders are the first step to define the Tau pharmacophore, leading the way to a structure-based design of improved diagnostics and therapeutics. Yet the partially disordered and polymorphic nature of Tau hinders structural analyses. Fortunately, short segments from amyloid proteins, which exhibit similar biophysical properties to the full-length proteins, also form fibrils and oligomers, and their atomic structures can be determined using X-ray microcrystallography. Such structures were successfully used to design amyloid inhibitors. This chapter describes experimental procedures used to determine crystal structures of Tau peptide segments in complex with small-molecule binders.

  19. Upper Bound Solution for the Face Stability of Shield Tunnel below the Water Table

    Directory of Open Access Journals (Sweden)

    Xilin Lu

    2014-01-01

    Full Text Available By FE simulation with Mohr-Coulomb perfect elastoplasticity model, the relationship between the support pressure and displacement of the shield tunnel face was obtained. According to the plastic strain distribution at collapse state, an appropriate failure mechanism was proposed for upper bound limit analysis, and the formula to calculate the limit support pressure was deduced. The limit support pressure was rearranged to be the summation of soil cohesion c, surcharge load q, and soil gravity γ multiplied by their corresponding coefficients Nc, Nq, and Nγ, and parametric studies were carried out on these coefficients. In order to consider the influence of seepage on the face stability, the pore water pressure distribution and the seepage force on the tunnel face were obtained by FE simulation. After adding the power of seepage force into the equation of the upper bound limit analysis, the total limit support pressure for stabilizing the tunnel face under seepage condition was obtained. The total limit support pressure was shown to increase almost linearly with the water table.

  20. Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: application to liquid argon and water.

    Science.gov (United States)

    White, Ronald P; Meirovitch, Hagai

    2004-12-08

    The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy S and free energy F by analyzing Boltzmann samples obtained by Monte Carlo or molecular dynamics techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). At each step of the process the system is divided into two parts, the already treated molecules (the "past"), which are fixed, and the as yet unspecified (mobile) "future" molecules. Obtaining the TP exactly requires calculating partition functions over all positions of the future molecules in the presence of the frozen past, thus it is customary to invoke various approximations to best represent these quantities. In a recent publication [Proc. Natl. Acad. Sci. USA 101, 9235 (2004)] we developed a version of HS called complete HSMC, where each TP is calculated from an MC simulation involving all of the future molecules (the complete future); the method was applied very successfully to Lennard-Jones systems (liquid argon) and a box of TIP3P water molecules. In its basic implementation the method provides lower and upper bounds for F, where the latter can be evaluated only for relatively small systems. Here we introduce a new expression for an upper bound, which can be evaluated for larger systems. We also propose a new exact expression for F and verify its effectiveness. These free energy functionals lead to significantly improved accuracy (as applied to the liquid systems above) which is comparable to our thermodynamic integration results. We formalize and discuss theoretical aspects of HSMC that have not been addressed in previous studies. Additionally, several functionals are developed and shown to provide the free energy through the analysis of a single configuration.

  1. Synthesis and electrocatalytic water oxidation by electrode-bound helical peptide chromophore-catalyst assemblies.

    Science.gov (United States)

    Ryan, Derek M; Coggins, Michael K; Concepcion, Javier J; Ashford, Dennis L; Fang, Zhen; Alibabaei, Leila; Ma, Da; Meyer, Thomas J; Waters, Marcey L

    2014-08-01

    Artificial photosynthesis based on dye-sensitized photoelectrosynthesis cells requires the assembly of a chromophore and catalyst in close proximity on the surface of a transparent, high band gap oxide semiconductor for integrated light absorption and catalysis. While there are a number of approaches to assemble mixtures of chromophores and catalysts on a surface for use in artificial photosynthesis based on dye-sensitized photoelectrosynthesis cells, the synthesis of discrete surface-bound chromophore-catalyst conjugates is a challenging task with few examples to date. Herein, a versatile synthetic approach and electrochemical characterization of a series of oligoproline-based light-harvesting chromophore-water-oxidation catalyst assemblies is described. This approach combines solid-phase peptide synthesis for systematic variation of the backbone, copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) as an orthogonal approach to install the chromophore, and assembly of the water-oxidation catalyst in the final step. Importantly, the catalyst was found to be incompatible with the conditions both for amide bond formation and for the CuAAC reaction. The modular nature of the synthesis with late-stage assembly of the catalyst allows for systematic variation in the spatial arrangement of light-harvesting chromophore and water-oxidation catalyst and the role of intrastrand distance on chromophore-catalyst assembly properties. Controlled potential electrolysis experiments verified that the surface-bound assemblies function as water-oxidation electrocatalysts, and electrochemical kinetics data demonstrate that the assemblies exhibit greater than 10-fold rate enhancements compared to the homogeneous catalyst alone.

  2. Uncoupling between soil and xylem water isotopic composition: how to discriminate mobile and tightly-bound water?

    Science.gov (United States)

    Martín Gómez, Paula; Aguilera, Mònica; Pemán, Jesús; Gil Pelegrín, Eustaquio; Ferrio, Juan Pedro

    2014-05-01

    As a general rule, no isotopic fractionation occurs during water uptake and water transport, thus, xylem water reflects source water. However, this correspondence does not always happen. Isotopic enrichment of xylem water has been found in several cases and has been either associated to 'stem processes' like cuticular evaporation 1 and xylem-phloem communication under water stress 2,3 or to 'soil processes' such as species-specific use of contrasting water sources retained at different water potential forces in soil. In this regard, it has been demonstrated that mobile and tightly-bound water may show different isotopic signature 4,5. However, standard cryogenic distillation does not allow to separate different water pools within soil samples. Here, we carried out a study in a mixed adult forest (Pinus sylvestris, Quercus subpyrenaica and Buxus sempervirens) growing in a relatively deep loamy soil in the Pre-Pyrenees. During one year, we sampled xylem from twigs and soil at different depths (10, 30 and 50 cm). We also sampled xylem from trunk and bigger branches to assess whether xylem water was enriched in the distal parts of the tree. We found average deviations in the isotopic signature from xylem to soil of 4o 2o and 2.4o in δ18O and 18.3o 7.3o and 8.9o in δ2H, for P.sylvestris, Q.subpyrenaica and B.sempervirens respectively. Xylem water was always enriched compared to soil. In contrast, we did not find clear differences in isotopic composition between xylem samples along the tree. Declining the hypothesis that 'stem processes' would cause these uncoupling between soil and xylem isotopic values, we tested the possibility to separate mobile and tightly-bound water by centrifugation. Even though we could separate two water fractions in soils close to saturation, we could not recover a mobile fraction in drier soils. In this regard, we welcome suggestions on alternatives to separate different soil fractions in order to find the correspondence between soil and

  3. Nuclear magnetic relaxation studies of water in frozen biological tissues. Cross-relaxation effects between protein and bound water protons

    Science.gov (United States)

    Escanyé, J. M.; Canet, D.; Robert, J.

    Water proton longitudinal relaxation has been investigated in frozen mouse tissues including tumors. The nonfreezable water which gives rise to a relatively sharp NMR signal at this temperature (263 K) is identified as water bound to macromolecules. Measurements have been carried out by the nonselective inversion-recovery method at 90 and 6 MHz. Partially selective inversion has been achieved at 90 MHz by the DANTE sequence. The experimental data are analyzed by means of Solomon-type equations. This analysis provides the cross-relaxation term from which the dipolar contribution to water relaxation rate, arising from interactions with macromolecular protons, is calculated. This contribution seems to be dominant. The number of water protons interacting with a given macromolecular proton is found to be of the order of 10. The data at both frequencies can be consistently interpreted in terms of water diffusion, with a characteristic time of about 10 -9 sec. These conclusions are valid for all the tissues investigated here, their relaxation parameters exhibiting only slight differences.

  4. Cramér-Rao Lower Bound for Point Based Image Registration With Heteroscedastic Error Model for Application in Single Molecule Microscopy.

    Science.gov (United States)

    Cohen, E A K; Kim, D; Ober, R J

    2015-12-01

    The Cramér-Rao lower bound for the estimation of the affine transformation parameters in a multivariate heteroscedastic errors-in-variables model is derived. The model is suitable for feature-based image registration in which both sets of control points are localized with errors whose covariance matrices vary from point to point. With focus given to the registration of fluorescence microscopy images, the Cramér-Rao lower bound for the estimation of a feature's position (e.g., of a single molecule) in a registered image is also derived. In the particular case where all covariance matrices for the localization errors are scalar multiples of a common positive definite matrix (e.g., the identity matrix), as can be assumed in fluorescence microscopy, then simplified expressions for the Cramér-Rao lower bound are given. Under certain simplifying assumptions these expressions are shown to match asymptotic distributions for a previously presented set of estimators. Theoretical results are verified with simulations and experimental data.

  5. Ultracold atom-molecule collisions and bound states in magnetic fields: tuning zero-energy Feshbach resonances in He-NH (3Sigma-)

    CERN Document Server

    Gonzalez-Martinez, M L; Gonzalez-Martinez, Maykel Leonardo; Hutson, Jeremy M.

    2006-01-01

    We have generalized the BOUND and MOLSCAT packages to allow calculations in basis sets where the monomer Hamiltonians are off-diagonal and used the new capability to carry out bound-state and scattering calculations on 3He-NH and 4He-NH as a function of magnetic field. Following the bound-state energies to the point where they cross thresholds gives very precise predictions of the magnetic fields at which zero-energy Feshbach resonances occur. We have used this to locate and characterize two very narrow Feshbach resonances in 3He-NH. Such resonances can be used to tune elastic and inelastic collision cross sections, and sweeping the magnetic field across them will allow a form of quantum control in which separated atoms and molecules are associated to form complexes. For the first resonance, where only elastic scattering is possible, the scattering length shows a pole as a function of magnetic field and there is a very large peak in the elastic cross section. For the second resonance, however, inelastic scatt...

  6. Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: induced fit and bound water.

    Science.gov (United States)

    Tanious, Farial A; Laine, William; Peixoto, Paul; Bailly, Christian; Goodwin, Kristie D; Lewis, Mark A; Long, Eric C; Georgiadis, Millie M; Tidwell, Richard R; Wilson, W David

    2007-06-12

    RT29 is a dicationic diamidine derivative that does not obey the classical "rules" for shape and functional group placement that are expected to result in strong binding and specific recognition of the DNA minor groove. The compound contains a benzimidazole diphenyl ether core that is flanked by the amidine cations. The diphenyl ether is highly twisted and gives the entire compound too much curvature to fit well to the shape of the minor groove. DNase I footprinting, fluorescence intercalator displacement studies, and circular dichroism spectra, however, indicate that the compound is an AT specific minor groove binding agent. Even more surprisingly, quantitative biosensor-surface plasmon resonance and isothermal titration calorimetric results indicate that the compound binds with exceptional strength to certain AT sequences in DNA with a large negative enthalpy of binding. Crystallographic results for the DNA complex of RT29 compared to calculated results for the free compound show that the compound undergoes significant conformational changes to enhance its minor groove interactions. In addition, a water molecule is incorporated directly into the complex to complete the compound-DNA interface, and it forms an essential link between the compound and base pair edges at the floor of the minor groove. The calculated DeltaCp value for complex formation is substantially less than the experimentally observed value, which supports the idea of water being an intrinsic part of the complex with a major contribution to the DeltaCp value. Both the induced fit conformational changes of the compound and the bound water are essential for strong binding to DNA by RT29.

  7. Competitive Adsorption of Naphthenic Acids and Polyaromatic Molecules at a Toluene-Water Interface.

    Science.gov (United States)

    Teklebrhan, Robel B; Jian, Cuiying; Choi, Phillip; Xu, Zhenghe; Sjöblom, Johan

    2016-12-22

    The early-stage competitive co-adsorption of interfacially active naphthenic acids (NAs) and polyaromatic (PA) molecules to a toluene-water interface from the bulk toluene phase was studied using molecular dynamics (MD) simulation. The NA molecules studied had the same polar functional group but different cycloaliphatic nonpolar tails, and a perylene bisimide (PBI)-based molecule was used as a representative PA compound. The results from our simulations suggest that the size and structural features of NA molecules greatly influence the interfacial activity of PA molecules and partitioning of NA molecules at the toluene-water interface. At low concentrations of PA (∼2.3 wt %) and NA (∼0.4 wt %) molecules, NA molecules containing large cycloaliphatic rings (e.g., four rings) or with a very long aliphatic tail (e.g., carbon chain length of 14) were observed to impede the migration of PA molecules to the interface, whereas small NA molecules containing two cycloaliphatic rings had little effect on the adsorption of PA molecules at the toluene-water interface. At high NA concentrations, the adsorption of PA molecules (∼5.75-17.25 wt %) was greatly hindered by the presence of small NA molecules (∼1.6-4.8 wt %) due to the solvation of PA nanoaggregates in the bulk. Adsorption mechanisms of PA and NA molecules at toluene-water interfaces were clarified through a detailed analysis on the interactions among different species in the system. The results obtained from this work provide insights into designing appropriate chemical demulsifiers or co-demulsifiers for breaking water-in-oil emulsions of great industrial applications.

  8. Subdivision of phase space for anisotropically interacting water molecules

    Science.gov (United States)

    Epifanov, S. Yu.; Vigasin, A. A.

    An efficient numerical algorithm is employed which enables one to perform multidimensional integrations of complicated integrands. Temperature dependence of the second virial coefficient for water is reproduced using the Matsuoka Clementi Yoshimine intermolecular water water potential. Metastable states are shown to occupy significant domain in the water dimer phase space.

  9. Experimental Study of Water Cluster Molecules with Relevance to Mesospheric Clouds

    Science.gov (United States)

    Robertson, Scott; Sternovsky, Zoltan; Horanyi, Mihaly

    2000-10-01

    We have begun an experimental investigation of the properties of the water cluster molecules responsible for clouds occurring in the polar mesopause. These clusters disturb the charge balance in the ionosphere by attaching electrons which then creates localized reductions in the electron density. A supersonic nozzle sprays a mixture of water vapor and argon into vacuum and the expansion leads to condensation of clusters with 4 to 11 water molecules. Initial measurements are of the collision cross section of these molecules with neutral gas. The cross sections have a minimum at six waters consistent with the tighter molecular arrangement predicted for this cluster number. Additional measurements are underway for charging processes.

  10. Encapsulation and characterization of proton-bound amine homodimers in a water-soluble, self-assembled supramolecular host

    OpenAIRE

    Pluth, Michael D.; Fiedler, Dorothea; Mugridge, Jeffrey S.; Bergman, Robert G.; Raymond, Kenneth N.

    2009-01-01

    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 that 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 formatio...

  11. Super resolution microscopy of lipid bilayer phases and single molecule kinetic studies on merocyanine 540 bound lipid vesicles

    Science.gov (United States)

    Kuo, Chin-Kuei

    Recently, observing biological process and structural details in live cell became feasible after the introduction of super-resolution microscopy. Super-resolution microscopy by single molecule localization is the method that has commonly been used for such purpose. There are mainly three approaches to it: stochastic optical reconstruction microscopy (STORM), photoactivated localization microscopy (PALM), and point accumulation in nanoscale topology (PAINT). STORM and PALM rely on external laser control and use of photoactivable fluorescent protein or photoswitchable dyes and are technically challenging. The PAINT method relies on the control of thermal reaction rates to enable the switching between bright and dark states. Therefore, many conventional fluorescent probes can be applied in PAINT method and the images denote different information composed of interactions between the probe and its immediate environment by variations of probe parameters. The existence of lipid rafts has been under debates for decades due to the lack of a tool to directly visualize them in live cells. In the thesis, we combine PAINT with a phase sensitive dye, Merocyanine 540, to enable nanoscale observation of phase separation on supported lipid bilayers of mixed liquid/gel phases. The imaging results are presented in the chapter 3. Given that this is the first example of visualization of nanoscale phase separation of lipid bilayers using an optical microscope, we further looked into the kinetics of MC540 monomer dimer equilibrium in lipid bilayers using single molecule intensity time trajectory analysis and polarization dependent imaging. Our finding confirms that perpendicular monomeric MC540 (to the membrance surface) is the emitting speices in our system and it stays fluorescent for roughly 3 ms before it switches off to dark states. This part of analysis is presented in the chapter 4. All the materials, procedures to carry out experiments and data analysis, methods involved in our

  12. Application of a convergent, composite coupled cluster approach to bound state, adiabatic electron affinities in atoms and small molecules

    Science.gov (United States)

    Feller, David

    2016-01-01

    Benchmark quality adiabatic electron affinities for a collection of atoms and small molecules were obtained with the Feller-Peterson-Dixon composite coupled cluster theory method. Prior applications of this method demonstrated its ability to accurately predict atomization energies/heats of formation for more than 170 molecules. In the current work, the 1-particle expansion involved very large correlation consistent basis sets, ranging up to aug-cc-pV9Z (aug-cc-pV10Z for H and H2), with the goal of minimizing the residual basis set truncation error that must otherwise be approximated with extrapolation formulas. The n-particle expansion begins with coupled cluster calculations through iterative single and double excitations plus a quasiperturbative treatment of "connected" triple excitations (CCSD(T)) pushed to the complete basis set limit followed by CCSDT, CCSDTQ, or CCSDTQ5 corrections. Due to the small size of the systems examined here, it was possible in many cases to extend the n-particle expansion to the full configuration interaction wave function limit. Additional, smaller corrections associated with core/valence correlation, scalar relativity, anharmonic zero point vibrational energies, and non-adiabatic effects were also included. The overall root mean square (RMS) deviation was 0.005 eV (0.12 kcal/mol). This level of agreement was comparable to what was found with molecular heats of formation. A 95% confidence level corresponds to roughly twice the RMS value or 0.01 eV. While the atomic electron affinities are known experimentally to high accuracy, the molecular values are less certain. This contributes to the difficulty of gauging the accuracy of the theoretical results. A limited number of electron affinities were determined with the explicitly correlated CCSD(T)-F12b method. After extending the VnZ-F12 orbital basis sets with additional diffuse functions, the F12b method was found to accurately reproduce the best F/F- value obtained with standard

  13. Implication of Crystal Water Molecules in Inhibitor Binding at ALR2 Active Site

    Directory of Open Access Journals (Sweden)

    Hymavati

    2012-01-01

    Full Text Available Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecule. The solvent environment around such biomolecule controls their structure and plays important role in protein-ligand interactions. An understanding of the nature and role of these water molecules in the active site of a protein could greatly increase the efficiency of rational drug design approaches. We have performed the comparative crystal structure analysis of aldose reductase to understand the role of crystal water in protein-ligand interaction. Molecular dynamics simulation has shown the versatile nature of water molecules in bridge H bonding during interaction. Occupancy and life time of water molecules depend on the type of cocrystallized ligand present in the structure. The information may be useful in rational approach to customize the ligand, and thereby longer occupancy and life time for bridge H-bonding.

  14. Quasi-bound complexes in collisions of different linear molecules: Classical trajectory study of their manifestations in rotational relaxation and spectral line broadening

    Science.gov (United States)

    Ivanov, Sergey V.

    2016-07-01

    Stable bimolecular complexes (tightly bound dimers) in the gas phase are usually created during third body stabilization of their unstable precursors-quasi-bound complexes (QCs). The latter can arise under the condition that at least one of the colliding partners has an internal degree of freedom. In this article, the principal difference between "orbitings" and QCs is demonstrated in the classical nonreactive scattering picture. Additionally, fractions of QCs in binary collisions of different linear molecules are compared. Also in the article the influence of QCs on rotational R-T relaxation and on vibration-rotational spectral line broadening is discussed. Explicit formulae shedding light on the QCs contribution to the R-T relaxation cross section and the line width and shift are presented. The obtained results emphasize the need for including QCs in every theoretical modeling of spectroscopic manifestation of intermolecular interactions. Besides the topics above, the possible manifestation of non-impact effects in the central regions of spectral lines due to QCs is stated. And finally, special consideration is given to the problem of adequate simulation of QCs formation at different pressures.

  15. Bacterial Surface-Displayed GII.4 Human Norovirus Capsid Proteins Bound to HBGA-Like Molecules in Romaine Lettuce.

    Science.gov (United States)

    Wang, Ming; Rong, Shaofeng; Tian, Peng; Zhou, Yue; Guan, Shimin; Li, Qianqian; Wang, Dapeng

    2017-01-01

    Human Noroviruses (HuNoVs) are the main cause of non-bacterial gastroenteritis. Contaminated produce is a main vehicle for dissemination of HuNoVs. In this study, we used an ice nucleation protein mediated surface display system to present the protruding domain of GII.4 HuNoV capsid protein on bacterial surface and used it as a new strategy to explore interaction between HuNoV protein and receptor candidates from romaine lettuce. The surface-displayed HuNoV proteins were confirmed on the surface of the transformed bacteria by an immunofluorescence assay. The distribution patterns of the surface-displayed HuNoV proteins in romaine lettuce were identified through a confocal immunofluorescence assay. The surface-displayed HuNoV proteins could be found in the stomata, and the surfaces of vein and leaf of romaine lettuce. The surface-displayed HuNoV proteins could be captured by an ELISA assay utilizing extract from leaf (LE) or vein (VE). The binding of the surface-displayed HuNoV proteins to LE or VE could be competitively blocked by histo-blood group antigens from human saliva. In addition, the binding of the surface-displayed HuNoV proteins to LE or VE could also be attenuated by heat denaturation of lettuce proteins, and abolished by oxidation of lettuce carbohydrates. The results indicated that histo-blood group antigen-like molecules in LE or VE were involved in the binding of the surface-displayed HuNoV proteins to romaine lettuce. All data demonstrated that the surface-displayed HuNoV proteins could be utilized in a new and simple system for investigation of the interaction between the HuNoVs and their candidate ligands.

  16. Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

    NARCIS (Netherlands)

    Y.L.A. Rezus; H.J. Bakker

    2008-01-01

    We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at

  17. Unraveling the Sc(3+) Hydration Geometry: The Strange Case of the Far-Coordinated Water Molecule.

    Science.gov (United States)

    Migliorati, Valentina; D'Angelo, Paola

    2016-07-05

    The hydration structure and dynamics of Sc(3+) in aqueous solution have been investigated using a combined approach based on quantum mechanical (QM) calculations, molecular dynamics (MD) simulations, and extended X-ray absorption fine structure (EXAFS) spectroscopy. An effective Sc-water two-body potential has been generated from QM calculations and then used in the MD simulation of Sc(3+) in water, and the reliability of the entire procedure has been assessed by comparing the theoretical structural results with the EXAFS experimental data. The outstanding outcome of this work is that the Sc(3+) ion forms a well-defined capped square antiprism (SAP) complex in aqueous solution, where the eight water molecules closest to the ion are located at the vertexes of a SAP polyhedron, while the ninth water molecule occupying the capping position is unusually found at a very long distance from the ion. This far-coordinated water molecule possesses a degree of structure comparable with the other first shell molecules surrounding the ion at much shorter distances, and its presence gave us the unique opportunity to easily identify the geometry of the Sc(3+) coordination polyhedron. Despite very strong ion-water interactions, the Sc(3+) hydration shell is very labile, as the far-coordinated ligand allows first shell water molecules to easily exchange their positions both inside the solvation shell and with the rest of the solvent molecules.

  18. 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.

    Science.gov (United States)

    Yin, Liusong; Stern, Lawrence J

    2014-04-01

    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.

  19. Investigation of the structure and stability of SnO2 nanocrystal and its surface-bound water

    Science.gov (United States)

    Wang, H.; Wesolowski, D. J.; Proffen, T. E.; Kolesnikov, A. I.; Vlcek, L.; Wang, W.; Feygenson, M.; Sofo, J. O.; Anovitz, L.

    2012-12-01

    Driven partly by a myriad use of engineered metal oxide nanoparticles, understanding their stabilities and interactions with environmental matrix during and after applications are desired. SnO2 (cassiterite) is one of the frequently used oxides in solid-state gas sensors and oxidation catalysts. A close relationship between the gas sensitivity and catalysis of oxides with their surface chemistry ensures continuous interests in the study of SnO2-water interfacial complexity (unavoidable "contamination" in which water can potentially participate in reactions and change SnO2 conductivity). Such information is important, as the existence of hydration layers on the surface of SnO2 nanoparticles not only play a critical role in stabilizing the nanoparticle but also affect its selectivity/sensitivity, as a nanosensor. SnO2 nanoparticles (2-5 nm) synthesized by a wet chemical route are dominated by {110} faces and are capped with H2O or D2O water molecules (after purification), depending on isotopic composition of water used for syntheses. When water is in direct contact with terminal Sn and O atoms, there is a controversial argument as to whether or not dissociative adsorption occurs (i.e., formation of hydroxyl groups). Although theoretical studies point toward a tendency for dissociative configuration in the direct contact layer, experimental studies have not unambiguously confirmed this conclusion. We present combined investigations using neutron total scattering (NPDF at the NOMAD beamline, SNS) and inelastic neutron scattering (INS at the SEQUOIA beamline, SNS) techniques as static and dynamic probes to reveal structure and dynamics of water and SnO2 nanocrystalline stability upon dehydration. The NPDF results (measured with deuterated samples) suggest layered water configurations with G(r) signals dominated by O-D bonds at 0.98 Å, and the second hydration layer that gives a broad peak at 2.5-4 Å. There is no evidence of a third hydration layer at 5-7 Å as shown

  20. Bound on the Slope of Steady Water Waves with Favorable Vorticity

    Science.gov (United States)

    Strauss, Walter A.; Wheeler, Miles H.

    2016-12-01

    We consider the angle {θ} of inclination (with respect to the horizontal) of the profile of a steady two dimensional inviscid symmetric periodic or solitary water wave subject to gravity. Although {θ} may surpass 30° for some irrotational waves close to the extreme wave, Amick (Arch Ration Mech Anal 99(2):91-114, 1987) proved that for any irrotational wave the angle must be less than 31.15°. Is the situation similar for periodic or solitary waves that are not irrotational? The extreme Gerstner wave has infinite depth, adverse vorticity and vertical cusps ( θ = 90°). Moreover, numerical calculations show that even waves of finite depth can overturn if the vorticity is adverse. In this paper, on the other hand, we prove an upper bound of 45° on {θ} for a large class of waves with favorable vorticity and finite depth. In particular, the vorticity can be any constant with the favorable sign. We also prove a series of general inequalities on the pressure within the fluid, including the fact that any overturning wave must have a pressure sink.

  1. Affinity transformation from hydrophilicity to hydrophobicity of water molecules on the basis of adsorption of water in graphitic nanopores.

    Science.gov (United States)

    Ohba, Tomonori; Kanoh, Hirofumi; Kaneko, Katsumi

    2004-02-11

    The interaction of water with hydrophobic surfaces is quite important in a variety of chemical and biochemical phenomena. The coexistence of water and oil can be realized by introduction of surfactants. In the case of water vapor adsorption on graphitic nanopores, plenty of water can be adsorbed in graphitic nanopores without surfactants, although the graphitic surface is not hydrophilic. Why are water molecules adsorbed in hydrophobic nanopores remarkably? This work can give an explicit insight to water adsorption in hydrophobic graphite nanopores using experimental and theoretical approaches. Water molecules are associated with each other to form the cluster of 1 nm in size, leading to a significant stabilization of the cluster in the graphitic nanopores. This mechanism can be widely applied to interfacial phenomena relating to coexistence of water and nanostructural materials of hydrophobicity.

  2. Frictional energy barrier and blocking temperature in water molecules and carbon nanotubes system

    Science.gov (United States)

    Zhang, Jianwei; Li, Jiaxi; Li, Wenfeng

    2015-03-01

    Water transport through hydrophobic channels of single-walled carbon nanotubes has attracted a lot interests, especially, various potential applications of SWCNTs have been proposed for designing novel nanofluidic devices. By adopting Molecular dynamics method, we investigated mechanics and statistics properties of water molecules escaping from a confined single-walled carbon nanotube. From our numerical MD simulations and statistical model, we determined the friction energy barrier of water molecules in (10.10) SWCNT is 9.88 kcal/mol, and which is the minimal energy for flowing a water molecules in CNT. By only using friction energy barrier and relaxation time parameter, our model can fit all different situations MD simulation results. In order to describing the frictional lock behavior of water molecules, we introduced a new blocking temperature, below this temperature (391K for our system), water is locked in CNT due to friction energy barrier. We found that the blocking temperature is closely related to system response time, and it also shows a linear behavior to frictional energy barrier. Furthermore, we found several other interesting statistics results when a water molecules leaving SWCNTs. This work was supported by NSFC No. 11274240 and NO. 51471119.

  3. Heterogeneity of the state and functionality of water molecules sorbed in an amorphous sugar matrix.

    Science.gov (United States)

    Imamura, Koreyoshi; Kagotani, Ryo; Nomura, Mayo; Kinugawa, Kohshi; Nakanishi, Kazuhiro

    2012-04-01

    An amorphous matrix, comprised of sugar molecules, is frequently used in the pharmaceutical industry. An amorphous sugar matrix exhibits high hygroscopicity, and it has been established that the sorbed water lowers the glass transition temperature T(g) of the amorphous sugar matrix. It is naturally expected that the random allocation and configuration of sugar molecules would result in heterogeneity of states for sorbed water. However, most analyses of the behavior of water, when sorbed to an amorphous sugar matrix, have implicitly assumed that all of the sorbed water molecules are in a single state. In this study, the states of water molecules sorbed in an amorphous sugar matrix were analyzed by Fourier-transform IR spectroscopy and a Fourier self-deconvolution technique. When sorbed water molecules were classified into five states, according to the extent to which they are restricted, three of the states resulted in a lowering of T(g) of an amorphous sugar matrix, while the other two were independent of the plasticization of the matrix. This finding provides an explanation for the paradoxical fact that compression at several hundreds of MPa significantly decreases the equilibrium water content at a given RH, while the T(g) remains unchanged.

  4. Branch-and-Bound algorithm applied to uncertainty quantification of a Boiling Water Reactor Station Blackout

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Joseph, E-mail: joseph.nielsen@inl.gov [Idaho National Laboratory, 1955 N. Fremont Avenue, P.O. Box 1625, Idaho Falls, ID 83402 (United States); University of Idaho, Department of Mechanical Engineering and Nuclear Engineering Program, 1776 Science Center Drive, Idaho Falls, ID 83402-1575 (United States); Tokuhiro, Akira [University of Idaho, Department of Mechanical Engineering and Nuclear Engineering Program, 1776 Science Center Drive, Idaho Falls, ID 83402-1575 (United States); Hiromoto, Robert [University of Idaho, Department of Computer Science, 1776 Science Center Drive, Idaho Falls, ID 83402-1575 (United States); Tu, Lei [University of Idaho, Department of Mechanical Engineering and Nuclear Engineering Program, 1776 Science Center Drive, Idaho Falls, ID 83402-1575 (United States)

    2015-12-15

    state. Dynamic PRA (DPRA) methods provide a more rigorous analysis of complex dynamic systems. Unfortunately DPRA methods introduce issues associated with combinatorial explosion of states. This paper presents a methodology to address combinatorial explosion using a Branch-and-Bound algorithm applied to Dynamic Event Trees (DET), which utilize LENDIT (L – Length, E – Energy, N – Number, D – Distribution, I – Information, and T – Time) as well as a set theory to describe system, state, resource, and response (S2R2) sets to create bounding functions for the DET. The optimization of the DET in identifying high probability failure branches is extended to create a Phenomenological Identification and Ranking Table (PIRT) methodology to evaluate modeling parameters important to safety of those failure branches that have a high probability of failure. The PIRT can then be used as a tool to identify and evaluate the need for experimental validation of models that have the potential to reduce risk. In order to demonstrate this methodology, a Boiling Water Reactor (BWR) Station Blackout (SBO) case study is presented.

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

    Science.gov (United States)

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

    2015-01-22

    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.

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

    Science.gov (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

    2016-09-30

    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.

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

    DEFF Research Database (Denmark)

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

    2007-01-01

    have quite big cavities, with 41 water molecules on average in 2C8 and 54-58 in 2C9 and 3A4, giving a water volume of 1500-2100 A3. The two crystal structures of 2C9 differ quite appreciably, whereas those of 3A4 are quite similar. The active-site cavity is connected to the surroundings by three to six......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...

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

    Science.gov (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.

    2016-09-01

    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.

  9. Auger spectrum of a water molecule after single and double core ionization.

    Science.gov (United States)

    Inhester, L; Burmeister, C F; Groenhof, G; Grubmüller, H

    2012-04-14

    The high intensity of free electron lasers opens up the possibility to perform single-shot molecule scattering experiments. However, even for small molecules, radiation damage induced by absorption of high intense x-ray radiation is not yet fully understood. One of the striking effects which occurs under intense x-ray illumination is the creation of double core ionized molecules in considerable quantity. To provide insight into this process, we have studied the dynamics of water molecules in single and double core ionized states by means of electronic transition rate calculations and ab initio molecular dynamics (MD) simulations. From the MD trajectories, photoionization and Auger transition rates were computed based on electronic continuum wavefunctions obtained by explicit integration of the coupled radial Schrödinger equations. These rates served to solve the master equations for the populations of the relevant electronic states. To account for the nuclear dynamics during the core hole lifetime, the calculated electron emission spectra for different molecular geometries were incoherently accumulated according to the obtained time-dependent populations, thus neglecting possible interference effects between different decay pathways. We find that, in contrast to the single core ionized water molecule, the nuclear dynamics for the double core ionized water molecule during the core hole lifetime leaves a clear fingerprint in the resulting electron emission spectra. The lifetime of the double core ionized water was found to be significantly shorter than half of the single core hole lifetime.

  10. Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice.

    Science.gov (United States)

    Zhukova, Elena S; Torgashev, Victor I; Gorshunov, Boris P; Lebedev, Vladimir V; Shakurov, Gil'man S; Kremer, Reinhard K; Pestrjakov, Efim V; Thomas, Victor G; Fursenko, Dimitry A; Prokhorov, Anatoly S; Dressel, Martin

    2014-06-14

    Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be3Al2Si6O18, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ɛ'(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from several wavenumbers up to ν = 7000 cm(-1), at temperatures 5-300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ɛ'(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν1, ν2, and ν3 of the H2O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm(-1) reveal a rich set of highly anisotropic features in the low-energy response of H2O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ~90 cm(-1) and ~160 cm(-1), several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400-500 cm(-1)) and translational (150-200 cm(-1)) vibrations of water-I molecule that is weakly coupled to the nano-cavity "walls." A model is presented that explains the "fine structure" of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six-well potential relief felt by a molecule within the cavity.

  11. Vibrational states of a water molecule in a nano-cavity of beryl crystal lattice

    Energy Technology Data Exchange (ETDEWEB)

    Zhukova, Elena S., E-mail: zhukovaelenka@gmail.com; Gorshunov, Boris P. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); 1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany); A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Vavilova Street 38, 119991 Moscow (Russian Federation); Torgashev, Victor I. [Faculty of Physics, Southern Federal University, 5 Zorge St., 344090 Rostov-on-Don (Russian Federation); Lebedev, Vladimir V. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); Landau Institute for Theoretical Physics, Russian Academy of Sciences, Akademika Semenova av., 1-A, 142432 Chernogolovka, Moscow Region (Russian Federation); Shakurov, Gil' man S. [Kazan Physical-Technical Institute, Russian Academy of Sciences, 10/7 Sibirsky Trakt, 420029 Kazan (Russian Federation); Kremer, Reinhard K. [Max-Planck-Institut für Festkörperforschung, Heisenbergstrasse 1, 70569 Stuttgart (Germany); Pestrjakov, Efim V. [Institute of Laser Physics, Russian Academy of Sciences, 13/3 Ac. Lavrentyev' s Prosp., 630090 Novosibirsk (Russian Federation); Thomas, Victor G.; Fursenko, Dimitry A. [Institute of Geology and Mineralogy, Russian Academy of Sciences, 3 Ac. Koptyug' s Prosp., 630090 Novosibirsk (Russian Federation); Prokhorov, Anatoly S. [Moscow Institute of Physics and Technology, 9 Institutskiy per., 141700 Dolgoprudny, Moscow Region (Russian Federation); A.M. Prokhorov General Physics Institute, Russian Academy of Sciences, Vavilova Street 38, 119991 Moscow (Russian Federation); Dressel, Martin [1. Physikalisches Institut, Universität Stuttgart, Pfaffenwaldring 57, 70550 Stuttgart (Germany)

    2014-06-14

    Low-energy excitations of a single water molecule are studied when confined within a nano-size cavity formed by the ionic crystal lattice. Optical spectra are measured of manganese doped beryl single crystal Mn:Be{sub 3}Al{sub 2}Si{sub 6}O{sub 18}, that contains water molecules individually isolated in 0.51 nm diameter voids within the crystal lattice. Two types of orientation are distinguished: water-I molecules have their dipole moments aligned perpendicular to the c axis and dipole moments of water-II molecules are parallel to the c-axis. The optical conductivity σ(ν) and permittivity ε{sup ′}(ν) spectra are recorded in terahertz and infrared ranges, at frequencies from several wavenumbers up to ν = 7000 cm{sup −1}, at temperatures 5–300 K and for two polarizations, when the electric vector E of the radiation is parallel and perpendicular to the c-axis. Comparative experiments on as-grown and on dehydrated samples allow to identify the spectra of σ(ν) and ε{sup ′}(ν) caused exclusively by water molecules. In the infrared range, well-known internal modes ν{sub 1}, ν{sub 2}, and ν{sub 3} of the H{sub 2}O molecule are observed for both polarizations, indicating the presence of water-I and water-II molecules in the crystal. Spectra recorded below 1000 cm{sup −1} reveal a rich set of highly anisotropic features in the low-energy response of H{sub 2}O molecule in a crystalline nano-cavity. While for E∥c only two absorption peaks are detected, at ∼90 cm{sup −1} and ∼160 cm{sup −1}, several absorption bands are discovered for E⊥c, each consisting of narrower resonances. The bands are assigned to librational (400–500 cm{sup −1}) and translational (150–200 cm{sup −1}) vibrations of water-I molecule that is weakly coupled to the nano-cavity “walls.” A model is presented that explains the “fine structure” of the bands by a splitting of the energy levels due to quantum tunneling between the minima in a six-well potential

  12. 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.

    2014-04-01

    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).

  13. Sustainable Innovation in Network-Bound Systems: Implications for the Consumption of Water, Waste Water and Electricity Services

    NARCIS (Netherlands)

    Vliet, van B.J.M.

    2012-01-01

    Network-bound systems are crucial in environmental governance as the usage of their services embody significant environmental impacts. Conditions for network-bound systems providing services to consumers have altered dramatically over the last decades. Liberalization and privatization have led to a

  14. 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)

    1994-12-31

    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.

  15. Water molecules inside protein structure affect binding of monosaccharides with HIV-1 antibody 2G12.

    Science.gov (United States)

    Ueno-Noto, Kaori; Takano, Keiko

    2016-10-05

    Water molecules inside biomolecules constitute integral parts of their structure and participate in the functions of the proteins. Some of the X-ray crystallographic data are insufficient for analyzing a series of ligand-protein complexes in the same condition. We theoretically investigated antibody binding abilities of saccharide ligands and the effects of the inner water molecules of ligand-antibody complexes. Classical molecular dynamics and quantum chemical simulations using a model with possible water molecules inside the protein were performed with saccharide ligands and Human Immunodeficiency Virus 1 neutralizing antibody 2G12 complexes to estimate how inner water molecules of the protein affect the dynamics of the complexes as well as the ligand-antibody interaction. Our results indicate the fact that d-fructose's strong affinity to the antibody was partly due to the good retentiveness of solvent water molecules of the ligand and its stability of the ligand's conformation and relative position in the active site. © 2016 Wiley Periodicals, Inc.

  16. Quasielastic neutron scattering investigation of motion of water molecules in n-propyl alcohol-water mixture

    OpenAIRE

    Nakada, Masaru; Maruyama, Kenji; Yamamuro, Osamu; MISAWA, Masakatsu

    2009-01-01

    The dynamics of water molecules in the n-propyl alcohol-water mixtures is investigated by using quasielastic neutron scattering measurements. The dynamic structure factor S(Q,E) obtained from incoherent scattering of hydrogen atoms of water is fitted with jump diffusion and relaxing cage models. The diffusion constant obtained from the relaxing cage model, which gives better fitting with S(Q,E), shows better agreement to the experimental value than that of jump diffusion model. The dependence...

  17. Interaction of water molecules with hexagonal 2D systems. A DFT study

    Science.gov (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.

  18. Derivative fluorimetry analysis of new cluster structures formed by ethanol and Water molecules

    Institute of Scientific and Technical Information of China (English)

    Bin Wu; Ying Liu; Caiqin Han; Xiaosen Luo; Jian Lu; Xiaowu Ni

    2009-01-01

    The ultraviolet (UV) light excited fluorescence spectra of ethanol-water mixture with different concentra-tions are investigated by derivative fluorimetry. It is found that there are 8 types of luminescent cluster molecules, formed by ethanol and water molecules in different ways, existing in the solution. The peak wavelengths of all these clusters' fluorescence spectra are measured and their contents are obtained by measuring the peak values in the second derivative fluorescence spectra. The spectra corresponding to the 8 types of clusters are obtained by Gaussian decomposition. It is found that two kinds of cluster molecules whose peak wavelengths are 330 and 345 nm have an optimal excitation wavelength located at (236±3) nm. This research contributes to the study of ethanol-water cluster structures and their physical and chemical characteristics.

  19. Changes in content of free, conjugated and bound polyamines and osmotic adjustment in adaptation of vetiver grass to water deficit.

    Science.gov (United States)

    Zhou, Qiang; Yu, Bingjun

    2010-06-01

    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.

  20. Local lateral environment of the molecules at the surface of DMSO-water mixtures

    Science.gov (United States)

    Fábián, Balázs; Idrissi, Abdenacer; Marekha, Bogdan; Jedlovszky, Pál

    2016-10-01

    Molecular dynamics simulations of the liquid-vapour interface of dimethyl sulphoxide (DMSO)-water mixtures of 11 different compositions, including two neat systems are performed on the canonical (N, V, T) ensemble at 298 K. The molecules constituting the surface layer of these systems are selected by means of the identification of the truly interfacial molecules (ITIM) method, and their local lateral environment at the liquid surface is investigated by performing Voronoi analysis. The obtained results reveal that both molecules prefer to be in a mixed local environment, consisting of both kinds of molecules, at the liquid surface, and this preference is even stronger here than in the bulk liquid phase. Neat-like patches, in which a molecule is surrounded by like neighbours, are not found. However, vacancies that are surrounded solely by water molecules are observed at the liquid surface. Our results show that strongly hydrogen bonded DMSO·H2O complexes, known to exist in the bulk phase of these mixtures, are absent from the liquid surface.

  1. Proton transfer in hydrogen-bonded network of phenol molecules: intracluster formation of water.

    Science.gov (United States)

    Lengyel, Jozef; Gorejová, Radka; Herman, Zdeněk; Fárník, Michal

    2013-11-07

    Electron ionization and time-of-flight mass spectrometry was used to investigate the phenol clusters (PhOH)n of different size from single molecule to large clusters: in coexpansion with He, the dimers n = 2 are mostly generated; in Ar, large species of n ≥ 10 also occur. Besides [(PhOH)n](+•) cluster ion series, hydrated phenol cluster ions [(PhOH)n·xH2O](+•) with up to x = 3 water molecules and dehydrated phenol clusters [(PhOH)n-H2O](+•) were observed. The hydrated phenol series exhibits minima and maxima that are interpreted as evidence for proton transfer between the hydrogen bonded cluster ions of cyclic structures. The proton transfer leads to a water generation within the clusters, and subsequent elimination of the diphenyl ether molecule(s) from the cluster yields the hydrated phenol cluster ions. Alternatively, a water molecule release yields a series of dehydrated phenols, among which the diphenyl ether ion [PhOPh](+•) (n = 2) constitutes the maximum.

  2. Collision Dynamics and Solvation of Water Molecules in a Liquid Methanol Film

    CERN Document Server

    Thomson, Erik S; Andersson, Patrik U; Marković, Nikola; Pettersson, Jan B C; 10.1021/jz200929y

    2011-01-01

    Environmental molecular beam experiments are used to examine water interactions with liquid methanol films at temperatures from 170 K to 190 K. We find that water molecules with 0.32 eV incident kinetic energy are efficiently trapped by the liquid methanol. The scattering process is characterized by an efficient loss of energy to surface modes with a minor component of the incident beam that is inelastically scattered. Thermal desorption of water molecules has a well characterized Arrhenius form with an activation energy of 0.47{\\pm}0.11 eV and pre-exponential factor of 4.6 {\\times} 10^(15{\\pm}3) s^(-1). We also observe a temperature dependent incorporation of incident water into the methanol layer. The implication for fundamental studies and environmental applications is that even an alcohol as simple as methanol can exhibit complex and temperature dependent surfactant behavior.

  3. Molecular Water Lilies: Orienting Single Molecules in a Polymer Film by Solvent Vapor Annealing

    CERN Document Server

    Wuersch, Dominik; Eder, Theresa; Aggarwal, A Vikas; Idelson, Alissa; Hoeger, Sigurd; Lupton, John M; Vogelsang, Jan

    2016-01-01

    The microscopic orientation and position of photoactive molecules is crucial to the operation of optoelectronic devices such as OLEDs and solar cells. Here, we introduce a shape-persistent macrocyclic molecule as an excellent fluorescent probe to simply measure (i) its orientation by rotating the excitation polarization and recording the strength of modulation in photoluminescence (PL), and (ii) its position in a film by analyzing the overall PL brightness at the molecular level. The unique shape, the absorption and the fluorescence properties of this probe yields information on molecular orientation and position. We control orientation and positioning of the probe in a polymer film by solvent vapor annealing (SVA). During the SVA process the molecules accumulate at the polymer/air interface, where they adopt a flat conformation, much like water lilies on the surface of a pond. The results are significant for OLED fabrication and single-molecule spectroscopy (SMS) in general.

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

    KAUST Repository

    Shinagawa, Tatsuya

    2015-01-01

    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. An interpretation of the enhancement of the water dipole moment due to the presence of other water molecules.

    Science.gov (United States)

    Kemp, Daniel D; Gordon, Mark S

    2008-06-05

    The dipole moment of the gas phase water monomer is 1.85 D. When solvated in bulk water, the dipole moment of an individual water molecule is observed to be enhanced to the much larger value of 2.9 +/- 0.6 D. To understand the origin of this dipole moment enhancement, the effective fragment potential (EFP) method is used to solvate an ab initio water molecule to predict the dipole moments for various cluster sizes. The dipole moment as a function of cluster size, nH 2O, is investigated [for n = 6-20 (even n), 26, 32, 41, and 50]. Localized charge distributions are used in conjunction with localized molecular orbitals to interpret the dipole moment enhancement. These calculations suggest that the enhancement of the dipole moment originates from the decrease of the angle between the dipole vectors of the lone pairs on oxygen as the number of hydrogen bonds to that oxygen increases. Thus, the decreased angle, and the consequent increase in water dipole moment, is most likely to occur in environments with a larger number of hydrogen bonds, such as the center of a cluster of water molecules.

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

    DEFF Research Database (Denmark)

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

    1992-01-01

    , 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...

  7. 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 ...

  8. Calculating pure rotational transitions of water molecule with a simple Lanczos method

    Indian Academy of Sciences (India)

    Pranab Sarkar

    2001-04-01

    We have calculated pure rotational transitions of water molecule from a kinetic energy operator (KEO) with the -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 agree well with the observed values.

  9. Proton Migration in Clusters Consisting of Protonated Pyridine Solvated by Water Molecules.

    Science.gov (United States)

    Berthias, Francis; Feketeová, Linda; Chermette, Henry; Forquet, Valérian; Morell, Christophe; Abdoul-Carime, Hassan; Farizon, Bernadette; Farizon, Michel; Märk, Tilmann D

    2015-10-26

    Proton transfer (PT) from protonated pyridine to water molecules is observed after excitation of microhydrated protonated pyridine (Py) clusters PyH(+) (H2 O)n (n=0-5) is induced by a single collision with an Ar atom at high incident velocity (95×10(3)  m s(-1) ). Besides the fragmentation channel associated with the evaporation of water molecules, the charged-fragment mass spectrum shows competition between the production of the PyH(+) ion (or its corresponding charged fragments) and the production of H(+) (H2 O) or H(+) (H2 O)2 ions. The increase in the production of protonated water fragments as a function of the number of H2 O molecules in the parent cluster ion as well sd the observation of a stable H(+) (H2 O)2 fragment, even in the case of the dissociation of PyH(+) (H2 O)2 , are evidence of the crucial role of PT in the relaxation process, even for a small number of solvating water molecules.

  10. 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.

    2011-01-01

    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...

  11. Structures of the Ca2+-regulated photoprotein obelin Y138F mutant before and after bioluminescence support the catalytic function of a water molecule in the reaction.

    Science.gov (United States)

    Natashin, Pavel V; Ding, Wei; Eremeeva, Elena V; Markova, Svetlana V; Lee, John; Vysotski, Eugene S; Liu, Zhi-Jie

    2014-03-01

    Ca(2+)-regulated photoproteins, which are responsible for light emission in a variety of marine coelenterates, are a highly valuable tool for measuring Ca(2+) inside living cells. All of the photoproteins are a single-chain polypeptide to which a 2-hydroperoxycoelenterazine molecule is tightly but noncovalently bound. Bioluminescence results from the oxidative decarboxylation of 2-hydroperoxycoelenterazine, generating protein-bound coelenteramide in an excited state. Here, the crystal structures of the Y138F obelin mutant before and after bioluminescence are reported at 1.72 and 1.30 Å resolution, respectively. The comparison of the spatial structures of the conformational states of Y138F obelin with those of wild-type obelin gives clear evidence that the substitution of Tyr by Phe does not affect the overall structure of both Y138F obelin and its product following Ca(2+) discharge compared with the corresponding conformational states of wild-type obelin. Despite the similarity of the overall structures and internal cavities of Y138F and wild-type obelins, there is a substantial difference: in the cavity of Y138F obelin a water molecule corresponding to W2 in wild-type obelin is not found. However, in Ca(2+)-discharged Y138F obelin this water molecule now appears in the same location. This finding, together with the observed much slower kinetics of Y138F obelin, clearly supports the hypothesis that the function of a water molecule in this location is to catalyze the 2-hydroperoxycoelenterazine decarboxylation reaction by protonation of a dioxetanone anion before its decomposition into the excited-state product. Although obelin differs from other hydromedusan Ca(2+)-regulated photoproteins in some of its properties, they are believed to share a common mechanism.

  12. Conserved water molecules in family 1 glycosidases: a DXMS and molecular dynamics study.

    Science.gov (United States)

    Teze, David; Hendrickx, Johann; Dion, Michel; Tellier, Charles; Woods, Virgil L; Tran, Vinh; Sanejouand, Yves-Henri

    2013-08-27

    By taking advantage of the wealth of structural data available for family 1 glycoside hydrolases, a study of the conservation of internal water molecules found in this ubiquitous family of enzymes was undertaken. Strikingly, seven water molecules are observed in more than 90% of the known structures. To gain insight into their possible function, the water dynamics inside Thermus thermophilus β-glycosidase was probed using deuterium exchange mass spectroscopy, allowing the pinpointing of peptide L117-A125, which exchanges most of its amide hydrogens quickly in spite of the fact that it is for the most part buried in the crystal structure. To help interpret this result, a molecular dynamics simulation was performed whose analysis suggests that two water channels are involved in the process. The longest one (∼16 Å) extends between the protein surface and W120, whose side chain interacts with E164 (the acid-base residue involved in the catalytic mechanism), whereas the other channel allows for the exchange with the bulk of the highly conserved water molecules belonging to the hydration shell of D121, a deeply buried residue. Our simulation also shows that another chain of highly conserved water molecules, going from the protein surface to the bottom of the active site cleft close to the nucleophile residue involved in the catalytic mechanism, is able to exchange with the bulk on the nanosecond time scale. It is tempting to speculate that at least one of these three water channels could be involved in the function of family 1 glycoside hydrolases.

  13. Understanding the role of ions and water molecules in the NaCl dissolution process

    CERN Document Server

    Klimeš, Jiří; Michaelides, Angelos

    2013-01-01

    The dissolution of NaCl in water is one of the most common everyday processes, yet it remains poorly understood at the molecular level. Here we report the results of an extensive density functional theory study in which the initial stages of NaCl dissolution have been examined at low water coverages. Our specific approach is to study how the energetic cost of moving an ion or a pair of ions to a less coordinated site at the surface of various NaCl crystals varies with the number of water molecules adsorbed on the surface. This "microsolvation" approach allows us to study the dependence of the defect energies on the number of water molecules in the cluster and thus to establish when and where dissolution becomes favorable. Moreover, this approach allows us to understand the roles of the individual ions and water molecules in the dissolution process. Consistent with previous work we identify a clear preference for dissolution of Cl ions over Na ions. However, the detailed information obtained here leads to the ...

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

    Science.gov (United States)

    Das Arulsamy, Andrew; Kregar, Zlatko; Eleršič, Kristina; Modic, Martina; Subramani, Uma Shankar

    2011-09-01

    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 the 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 the 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 first-order electronic-phase transition temperature.

  15. 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

    2011-01-01

    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...

  16. Neuroscience of water molecules: a salute to professor Linus Carl Pauling.

    Science.gov (United States)

    Nakada, Tsutomu

    2009-04-01

    More than 35 years ago double Nobel laureate Linus Carl Pauling published a powerful model of the molecular mechanism of general anesthesia, generally referred to as the hydrate-microcrystal (aqueous-phase) theory. This hypothesis, based on the molecular behavior of water molecules, did not receive serious attention during Pauling's life time, when scientific tools for examining complex systems such as the brain were still in their infancy. The situation has since drastically changed, and, now, in the twenty first century, many scientific tools are available for examining different types of complex systems. The discovery of aquaporin-4, a subtype of water channel abundantly expressed in glial systems, further highlighted the concept that the dynamics of water molecules in the cerebral cortex play an important role in important physiological brain functions including consciousness and information processing.

  17. Formation of prebiotic molecules in liquid water environments on the surface of Titan

    Science.gov (United States)

    Neish, Catherine Dorothy

    Saturn's moon Titan represents a unique locale for studying prebiotic chemistry. Reactions occurring in its thick nitrogen-methane atmosphere produce a wide variety of carbon, hydrogen, and nitrogen containing organic molecules. If these molecules are exposed to liquid water, they may react further to produce oxygen-containing species, a key step in the formation of terrestrial biomolecules. On average, Titan's surface is too cold for liquid water. However, models indicate that melting caused by impacts and/or cryovolcanism may lead to its episodic availability. One possible cryovolcanic dome, Ganesa Macula, was identified in early observations by the Cassini spacecraft. In this work, I estimate the height and morphology of this feature using a synthetic aperture radar (SAR) image. I then use a thermal conduction code to calculate the freezing timescale for an initially liquid dome, yielding freezing timescales of ~10^2 - 10^5 years. To determine how far aqueous organic chemistry can proceed in liquid water environments on Titan, I measure the rate coefficients of Titan analogue organic molecules ("tholins") with low temperature aqueous solutions to produce oxygenated species. These reactions display first-order kinetics with half- lives between 0.4 and 7 days at 273 K (in water) and between 0.3 and 14 days at 253 K (in 13 wt. % ammonia-water). Tholin hydrolysis in aqueous solutions is thus very fast compared to the freezing timescales of impact melts and volcanic sites on Titan, which take hundreds to thousands of years to freeze. The fast incorporation of oxygen, along with new chemistry made available by the introduction of ammonia, may lead to the formation of molecules of prebiotic interest in these transient liquid water environments. This chemistry makes impact craters and cryovolcanoes important targets for future missions to Titan.

  18. Rotational excitation of water by hydrogen molecules: comparison of results from classical and quantum mechanics.

    Science.gov (United States)

    Faure, Alexandre; Wiesenfeld, Laurent; Wernli, Michael; Valiron, Pierre

    2006-06-07

    Quasiclassical trajectory calculations are carried out for rotational excitation of water by hydrogen molecules. State-to-state rate coefficients are determined at 100 K and are compared to available quantum results. A good agreement between classical and quantum rates is observed for downward transitions, with an average accuracy of classical results better than a factor of 2. It is thus found that the ambiguities described by Faure and Wiesenfeld [J. Chem. Phys. 121, 6771 (2004)] can be solved in the particular case of waterlike asymmetric-top molecules.

  19. Monte Carlo simulation of several biologically relevant molecules and zwitterions in water

    Science.gov (United States)

    Patuwo, Michael Y.; Bettens, Ryan P. A.

    2012-02-01

    In this work, we study the hydration free energies of butane, zwitterionic alanine, valine, serine, threonine, and asparagine, and two neuraminidase inhibitors by means of Monte Carlo (MC) simulation. The solute molecule, represented in the form of distributed multipoles and modified 6-12 potential, was varied from a non-interacting 'ghost' molecule to its full potential functions in TIP4P water. Intermediate systems with soft-core solute-solvent interaction potentials are simulated separately and then subjected to Bennett's Acceptance ratio (BAR) for the free energy calculation. Hydration shells surrounding the solute particles were used to assess the quality of potential functions.

  20. Fourier transform infrared spectroscopic studies of proton transfer processes and the dissociation of Zn2+-bound water in alcohol dehydrogenases.

    Science.gov (United States)

    Nadolny, C; Zundel, G

    1997-08-01

    The following complexes were investigated by Fourier transform difference spectroscopy: binary complexes of alcohol dehydrogenases from yeast (YADH) and horse liver (LADH) with nicotinamide adenine dinucleotide (NAD+) and adenosine (5')-diphospho(5)-beta-D-ribose (ADP-Rib); the binary complex of Zn2+-free YADH with NAD+, the ternary complex of LADH with NAD+ and 2,2,2-trifluoroethanol. After addition of NAD+ to YADH and LADH, protonation of the N1 atom of the adenine ring of NAD+ is observed. It is shown that this proton arises from the dissociation of the Zn2+-bound water. The interaction of the Zn2+ ion with water is very strong, since this interaction is not just an electrostatic interaction. If the Zn2+ ions are in a tetrahedral environment, a large covalent contribution also occurs. If ADP-Rib is present instead of NAD+, no protonation of the N1 atom of the adenine ring of ADP-Rib is found, which demonstrates that the positively charged nicotinamide ring favors the conduction of the positive charge. All these results confirm the mechanism of Brändén et al. (1975): the Zn2+-bound water is split and the arising (OH)- deprotonates the alcohol. In the case of the ternary complex of LADH with NAD+ and 2,2,2-trifluoroethanol, we demonstrate that the alcohol is deprotonated and the alcoholate ion is bound directly to the Zn2+ ion. The conduction of the proton from the active site to the N1 atom of adenine occurs via a hydrogen-bonded chain with large proton polarizability due to collective proton motion. The nature and mechanism of this pathway are discussed on the basis of data from previous studies.

  1. Parameterization of ammonia and water content of atmospheric droplets with fixed number of sulfuric acid molecules

    Science.gov (United States)

    Napari, I.; Makkonen, R.; Kulmala, M.; Vehkamäki, H.

    2006-12-01

    We present a parameterization for numbers of water and ammonia molecules in an equilibrium droplet with fixed number of sulfuric acid molecules at known relative humidity, ammonia mixing ratio and temperature. The radius of the droplet is also parameterized. The parameterizations are based on macroscopic model of solution droplets and up-to-date thermodynamics. The binary parameterizations are valid for temperatures 190-330 K and relative humidities 1-99%. The ternary parameterization can be used at temperatures 240-300 K, relative humidities 5-95%, and ammonia mixing ratios 10 - 4 -100 ppt. In both cases the parameterizations are valid for droplets containing up to 10 11 sulfuric acid molecules. The droplet composition is always between the limits of pure ammonium bisulfate and pure ammonium sulfate.

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

    KAUST Repository

    Yoon, Seyoon

    2013-01-01

    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.

  3. Temperature dependence of local solubility of hydrophobic molecules in the liquid-vapor interface of water.

    Science.gov (United States)

    Abe, Kiharu; Sumi, Tomonari; Koga, Kenichiro

    2014-11-14

    One important aspect of the hydrophobic effect is that solubility of small, nonpolar molecules in liquid water decreases with increasing temperature. We investigate here how the characteristic temperature dependence in liquid water persists or changes in the vicinity of the liquid-vapor interface. From the molecular dynamics simulation and the test-particle insertion method, the local solubility Σ of methane in the liquid-vapor interface of water as well as Σ of nonpolar solutes in the interface of simple liquids are calculated as a function of the distance z from the interface. We then examine the temperature dependence of Σ under two conditions: variation of Σ at fixed position z and that at fixed local solvent density around the solute molecule. It is found that the temperature dependence of Σ at fixed z depends on the position z and the system, whereas Σ at fixed local density decreases with increasing temperature for all the model solutions at any fixed density between vapor and liquid phases. The monotonic decrease of Σ under the fixed-density condition in the liquid-vapor interface is in accord with what we know for the solubility of nonpolar molecules in bulk liquid water under the fixed-volume condition but it is much robust since the solvent density to be fixed can be anything between the coexisting vapor and liquid phases. A unique feature found in the water interface is that there is a minimum in the local solubility profile Σ(z) on the liquid side of the interface. We find that with decreasing temperature the minimum of Σ grows and at the same time the first peak in the oscillatory density profile of water develops. It is likely that the minimum of Σ is due to the layering structure of the free interface of water.

  4. 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.

    1998-02-01

    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.

  5. Analysis of the ecological problems bound with algae biomass harvesting in lagoon waters

    Energy Technology Data Exchange (ETDEWEB)

    Chassany de Casabianca, M.

    1984-12-01

    The aim of this work was to analyse the growth of algae in two lagoon ecosystems: a natural open lagoon water plan and a semi-artificial eutrophicated pool. The growth conditions are optimized as a function of ecological parameters, harvesting cycle and harvest load. The organic matter required and the water purification effect are also studied.

  6. [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].

    Science.gov (United States)

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

    2014-09-01

    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.

  7. Efficient floating diffuse functions for accurate characterization of the surface-bound excess electrons in water cluster anions.

    Science.gov (United States)

    Zhang, Changzhe; Bu, Yuxiang

    2017-01-25

    In this work, the effect of diffuse function types (atom-centered diffuse functions versus floating functions and s-type versus p-type diffuse functions) on the structures and properties of three representative water cluster anions featuring a surface-bound excess electron is studied and we find that an effective combination of such two kinds of diffuse functions can not only reduce the computational cost but also, most importantly, considerably improve the accuracy of results and even avoid incorrect predictions of spectra and the EE shape. Our results indicate that (a) simple augmentation of atom-centered diffuse functions is beneficial for the vertical detachment energy convergence, but it leads to very poor descriptions for the singly occupied molecular orbital (SOMO) and lowest unoccupied molecular orbital (LUMO) distributions of the water cluster anions featuring a surface-bound excess electron and thus a significant ultraviolet spectrum redshift; (b) the ghost-atom-based floating diffuse functions can not only contribute to accurate electronic calculations of the ground state but also avoid poor and even incorrect descriptions of the SOMO and the LUMO induced by excessive augmentation of atom-centered diffuse functions; (c) the floating functions can be realized by ghost atoms and their positions could be determined through an optimization routine along the dipole moment vector direction. In addition, both the s- and p-type floating functions are necessary to supplement in the basis set which are responsible for the ground (s-type character) and excited (p-type character) states of the surface-bound excess electron, respectively. The exponents of the diffuse functions should also be determined to make the diffuse functions cover the main region of the excess electron distribution. Note that excessive augmentation of such diffuse functions is redundant and even can lead to unreasonable LUMO characteristics.

  8. Local thermodynamics of the water molecules around single- and double-stranded DNA studied by grid inhomogeneous solvation theory

    Science.gov (United States)

    Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

    2016-09-01

    Thermodynamic properties of water molecules around single- and double-stranded DNAs (ssDNAs and dsDNAs) with different sequences were investigated using grid inhomogeneous solvation theory. Free energies of water molecules solvating the minor groove of dsDNAs are lower than those near ssDNAs, while water molecules should be released during the formation of dsDNA. Free energies of water molecules around dsDNA are lower than those around ssDNA even in the second and third hydration shells. Our findings will help to clarify the role of water molecules in the formation of dsDNA from ssDNAs, thus facilitating the designs of drugs or nanomaterials using DNA.

  9. 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.;

    2004-01-01

    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...... of PTP1B and form a novel basis for structure-based inhibitor design....

  10. Diagrammatic perturbation theory applied to the ground state of the water molecule

    Science.gov (United States)

    Silver, D. M.; Wilson, S.

    1977-01-01

    The diagrammatic many-body perturbation theory is applied to the ground state of the water molecule within the algebraic approximation. Using four different basis sets, the total energy, the equilibrium OH bond length, and the equilibrium HOH bond angle are examined. The latter is found to be a particularly sensitive test of the convergence of perturbation expansions. Certain third-order results, which incorporate all two-, three-, and four-body effects, show evidence of good convergence properties.

  11. PERMEABILITY OF STERLET SPERM MEMBRANES (ACIPENSER RUTHENUS L., 1758 FOR WATER MOLECULES

    Directory of Open Access Journals (Sweden)

    A. Puhovkin

    2016-03-01

    Full Text Available Purpose. The literature analysis of the results cryopreservation of different fish species highlights a variation of many parameters, in particular the sperm survival rate during the freezing and unfreezing process. The survival capability of spermatozoa may be called the main parameter, which indentifies the efficiency of the entire process of low temperature freezing of reproductive products. Therefore, the goal of this work was to investigate and find the causes of different degrees of fish sperm cryoimmunity, in particular that of starlet, which is a valuable of sturgeon (Acipenser species. We also studies the possibility to find the optimum ways to improve the efficiency of the survival rate of the defrosted spermatozoa of different fish species for their further use to produce viable offspring. Methodology. The determination of sterlet sperm membrane permeability was performed after carrying out all necessary manipulations with brood males which included: prespawning incubation, hormonal stimulation, determination of sperm maturity degree, obtaining the sperm by stripping. The measurement of sperm membrane permeability for water molecules was performed based on the technique, which had been used earlier to measure carp sperm permeability, but taking account the specific peculiarities inherent to sterlet sperm. Findings. Based on the performed measurements, we determined the sterlet sperm membrane permeability for water molecules with the use of photometric method. The received experimental data show the highest degree of sterlet sperm membrane permeability for water molecules as compared to carp sperm membrane permeability. Originality. As a result of this experiment, we determined for the first time the absolute value of sterlet sperm membrane permeability for water molecules with the use of photometric method as well as compared the results with those obtained during our work with the carp sperm. Practical value. The data obtained during

  12. Calculation of FDCS for the low and intermediate energy ionization of water molecules

    Science.gov (United States)

    Purohit, G.; Singh, P.; Dom, A.; Patidar, V.

    2015-09-01

    Triply differential cross sections for the electron induced ionization of the 3a1 and 1b1 orbitals of the water molecule are calculated within the distorted wave Born approximation. The distorted wave functions are numerically calculated by modelling both the initial and the final channels whereas single-center Slater type wave functions are used for describing the molecular target. A good agreement with the existing experimental data is obtained.

  13. Mathematical Modeling to Study the Dynamics of A Diatomic Molecule N2 in Water

    CERN Document Server

    Sharma, Nitin

    2010-01-01

    In the present work an attempt has been made to study the dynamics of a diatomic molecule N2 in water. The proposed model consists of Langevin stochastic differential equation whose solution is obtained through Euler's method. The proposed work has been concluded by studying the behavior of statistical parameters like variance in position, variance in velocity and covariance between position and velocity. This model incorporates the important parameters like acceleration, intermolecular force, frictional force and random force.

  14. Contributions of tryptophan 24 and glutamate 30 to binding long-lived water molecules in the ternary complex of human dihydrofolate reductase with methotrexate and NADPH studied by site-directed mutagenesis and nuclear magnetic resonance spectroscopy.

    Science.gov (United States)

    Meiering, E M; Li, H; Delcamp, T J; Freisheim, J H; Wagner, G

    1995-03-24

    Previous NMR studies on the ternary complex of human dihydrofolate reductase (hDHFR) with methotrexate (MTX) and NADPH detected six long-lived bound water molecules. Two of the water molecules, WatA and WatB, stabilize the structure of the protein while the other four, WatC, WatD, WatE and WatF, are involved in substrate binding and specificity. WatE may also act as a proton shuttle during catalysis. Here, the contributions of individual residues to the binding of these water molecules are investigated by performing NMR experiments on ternary complexes of mutant enzymes, W24F, E30A and E30Q. W24 and E30 are conserved residues that form hydrogen bonds with WatE in crystal structures of DHFR. Nuclear Overhauser effects (NOEs) are detected between WatE and the protein in all the mutant complexes, hence WatE still has a long lifetime bound to the complex when one of its hydrogen-bonding partners is deleted or altered by mutagenesis. The NOEs for WatE are much weaker, however, in the mutants than in wild-type. The NOEs for the other water molecules in and near the active site, WatA, WatC, WatD and WatF, also tend to be weaker in the mutant complexes. Little or no change is apparent in the NOEs for WatB, which is located outside the active site, farthest from the mutated residues. The decreased NOE intensities for the bound water molecules could be caused by changes in the positions and/or lifetimes of the water molecules. Chemical shift and NOE data indicate that the mutants have structures very similar to that of wild-type hDHFR, with possible conformational changes occurring only near the mutated residues. Based on the lack of structural change in the protein and evidence for increased structural fluctuations in the active sites of the mutant enzymes, it is likely that the NOE changes are caused, at least in part, by decreases in the lifetimes of the bound water molecules.

  15. Effects of water molecules of Ar-Cs MHD disk generator operated with strong MHD interaction

    Energy Technology Data Exchange (ETDEWEB)

    Ishikawa, M.; Kosugi, A.; Inui, Y.; Kabashima, S.

    1998-07-01

    Effects of water molecule impurity are studied on performance of a disk type MHD generator operated with Ar-Cs weakly ionized plasma. To reveal phenomena for a wide range of operation conditions, time-dependent one-dimensional analyses are carried out, where an up-wind, second order Chakravarthy TVD scheme is applied for the gasdynamics, while a Galerkin FEM is used for the electrodynamics. A simplified model is used for the water molecule impurity, where total effects of nonelastic collision between electrons and water molecules are estimated by the collision loss factor of electrons and also the electron momentum-transfer collision frequency is taken into account. The collision loss factor of electrons and the electron momentum-transfer collision frequency are taken from references, and the loss factor is assumed to be 700 independently of the electron temperature. On the Fuji-1 facilities at Tokyo Institute Technology, Japan, series of experiment A4105 were carried out with the Disk F-4 generator. Ar was heated with the heat-exchanger heated by the natural gas-air combustion and the metal cesium was used as the seeding material, while SCM maintained the magnetic field of 4.7 T at the center of disk and the very strong MHD interaction was realized. The thermal input was about 3 MW, the electrical output was about 500 kW with the enthalpy extraction ratio of about 17%. The numerical analyses have shown that the water molecule enhances the ionization instability at the low voltage loading because of insufficient Joule heating for electrons. The generator performance is degraded and the strong MHD interaction between the unstable plasma and the flow field induces slow and fast moving shock waves, leading to the very complicated flow field. The fast and slow moving shocks collide with each other, merge into a sharp shock moving downward, and then the shock front moves back slightly to maintain the pressure balance, collides again with another weak moving shock, and

  16. Toward an improved control of the fixed-node error in quantum Monte Carlo: The case of the water molecule

    CERN Document Server

    Caffarel, Michel; Giner, Emmanuel; Scemama, Anthony

    2016-01-01

    All-electron Fixed-node Diffusion Monte Carlo (FN-DMC) calculations for the nonrelativistic ground-state energy of the water molecule at equilibrium geometry are presented. The determinantal part of the trial wavefunction is obtained from a perturbatively selected Configuration Interaction calculation (CIPSI method) including up to about 1.4 million of determinants. Calculations are made using the cc-pCV$n$Z family of basis sets, with $n$=2 to 5. In contrast with most QMC works no re-optimization of the determinantal part in presence of a Jastrow is performed. For the largest cc-pCV5Z basis set the lowest upper bound for the ground-state energy reported so far of -76.43744(18) is obtained. The fixed-node energy is found to decrease regularly as a function of the cardinal number $n$ and the Complete Basis Set limit (CBS) associated with {\\it exact nodes} is easily extracted. The resulting energy of -76.43894(12) -in perfect agreement with the best experimentally derived value- is the most accurate theoretical ...

  17. The rare crystallographic structure of d(CGCGCG)(2): the natural spermidine molecule bound to the minor groove of left-handed Z-DNA d(CGCGCG)(2) at 10 degrees C.

    Science.gov (United States)

    Ohishi, Hirofumi; Tozuka, Yoshitaka; Da-Yang, Zhou; Ishida, Toshimasa; Nakatani, Kazuhiko

    2007-06-22

    Several crystal structure analyses of complexes of synthetic polyamine compounds, including N(1)-(2-(2-aminoethylamino))ethyl)ethane-1,2-diamine PA(222) and N(1)-(2-(2-(2-aminoethylamino)ethylamino)ethyl)ethane-1,2-diamine PA(2222), and left-handed Z-DNA d(CGCGCG)(2) have been reported. However, until now, there have been no examples of naturally occurring polyamines bound to the minor groove of the left-handed Z-DNA of d(CGCGCG)(2) molecule. We have found that spermidine, a natural polyamine, is connected to the minor groove of left-handed Z-DNA of d(CGCGCG)(2) molecule in a crystalline complex grown at 10 degrees C. The electron density of the DNA molecule was clear enough to determine that the spermidine was connected in the minor groove of two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2). This is the first example that a spermidine molecule can form a bridge conformation between two symmetry related molecules of left-handed Z-DNA d(CGCGCG)(2) in the minor groove.

  18. Are there Helium-like Protonic States of Individual Water Molecules in Liquid H2O?

    CERN Document Server

    Mueller-Herold, Ulrich

    2015-01-01

    Are there indications that individual H2O molecules in liquid water can loose their bent structure, i.e. that the protons give up their rigid angular correlation and behave largely uncorrelated, similar to electrons in the ground-state of helium? In agreement with the two-state picture of liquid water this would allow for the thermal coexistence of tetraedrically coordinated and spherical water molecules in the liquid. In the Hooke-Calogero model of a confined triatomic of XY2-type it is shown that energetically low-lying zero orbital-momentum states, which are bent if unconfined can change to helium-like shape under increasing confinement strength f. For the respective states this occurs at different values for f. It turns out that at f = 2.79 a bent and a helium-like state can thermally coexist. In order to characterize more precisely 'helium-like' angular correlation a maximum entropy estimate for the marginal correlation of electrons in the helium ground state is given. KEY WORDS: Liquid water, molecular ...

  19. 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)

    2005-01-01

    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.

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

    Directory of Open Access Journals (Sweden)

    Stephan Loew

    2011-01-01

    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.

  1. 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

    2013-01-01

    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.

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

    DEFF Research Database (Denmark)

    Malmstrøm, Torsten; Andersson, Carlaxel; Hjortkjær, Jes

    1999-01-01

    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....

  3. Interstellar ices as witnesses of star formation: selective deuteration of water and organic molecules unveiled

    CERN Document Server

    Cazaux, S; Spaans, M

    2011-01-01

    The environments where stars are born contain gas and dust grains covered by icy mantles. As the star forms and heats up its surroundings, the ices evaporate which leads to a very complex chemistry with high abundances of deuterated molecules. While formaldehyde and water are both ice constituents, deuterated formaldehyde is very abundant in comets and star forming regions, while deuterated water rarely is. Here, we explain this selective deuteration by following the formation and evolution of the ices as a cloud collapses to form a star. We show that the deuteration of formaldehyde is sensitive to the gas D/H ratio as the cloud undergoes gravitational collapse, while the deuteration of water strongly depends on the dust temperature at the time of ice formation.

  4. Calculations for ion-impact induced ionization and fragmentation of water molecules

    Science.gov (United States)

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

    2012-10-01

    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)

  5. Influence of the water molecules near surface of viral protein on virus activation process

    Energy Technology Data Exchange (ETDEWEB)

    O, Shepelenko S; S, Salnikov A; V, Rak S; P, Goncharova E; B, Ryzhikov A, E-mail: shep@vector.nsc.r, E-mail: shep@ngs.r [Federal State Research Institution State Research Center of Virology and Biotechnology VECTOR of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being (FSRI SRC VB VECTOR) Koltsovo, Novosibirsk Region (Russian Federation)

    2009-06-01

    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

  6. The Effect of Water Molecules on Mechanical Properties of Bamboo Microfibrils

    Science.gov (United States)

    Rahbar, Nima

    Bamboo fibers have higher strength-to-weight ratios than steel and concrete. The unique properties of bamboo fibers come from their natural composite structures that comprise mainly cellulose nanofibrils in a matrix of intertwined hemicellulose and lignin called lignin-carbohydrate complex (LCC). Here, we have utilized atomistic simulations to investigate the mechanical properties and mechanisms of interactions between these materials, in the presence of water molecules. Our results suggest that hemicellulose exhibits better mechanical properties and lignin shows greater tendency to adhere to cellulose nanofibrils. Consequently, the role of hemicellulose found to be enhancing the mechanical properties and lignin found to be providing the strength of bamboo fibers. The abundance of Hbonds in hemicellulose chains is responsible for improving the mechanical behavior of LCC. The strong van der Waals forces between lignin molecules and cellulose nanofibrils is responsible for higher adhesion energy between LCC/cellulose nanofibrils. We also found out that the amorphous regions of cellulose nanofibrils is the weakest interface in bamboo Microfibrils. In presence of water, the elastic modulus of lignin increases at low water content (less than 10 NSF CAREER Grant No. 1261284.

  7. Intramolecular cyclization of aspartic acid residues assisted by three water molecules: a density functional theory study

    Science.gov (United States)

    Takahashi, Ohgi; Kirikoshi, Ryota

    2014-01-01

    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.

  8. Detection of water molecules in inert gas based plasma by the ratios of atomic spectral lines

    Science.gov (United States)

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

    2017-01-01

    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%.

  9. Behavior of freezable bound water in the bacterial cellulose produced by Acetobacter xylinum: an approach using thermoporosimetry.

    Science.gov (United States)

    Kaewnopparat, Sanae; Sansernluk, Kamonlawat; Faroongsarng, Damrongsak

    2008-01-01

    The aim of the study is to examine thermal behavior of water within reticulated structure of bacterial cellulose (BC) films by sub-ambient differential scanning calorimetry (DSC). BC films with different carbon source, either manitol (BC (a)) or glycerol (BC (b)), were produced by Acetobacter xylinum using Hestrin and Shramm culture medium under static condition at 30 +/- 0.2 degrees C for 3 days. BC samples were characterized by electron scanning microscopy and X-ray diffraction spectroscopy. The pore analysis was done by B.H.J. nitrogen adsorption. The pre-treated with 100% relative humidity, at 30.0 +/- 0.2 degrees C for 7 days samples were subjected to a between 25 and -150 degrees C-cooling-heating cycle of DSC at 5.00 degrees C/min rate. The pre-treated samples were also hydrated by adding 1 mul of water and thermally run with identical conditions. It is observed that cellulose fibrils of BC (a) were thinner and reticulated to form slightly smaller porosity than those of BC (b). They exhibited slightly but non-significantly different crystalline features. The freezable bound water behaved as a water confinement within pores rather than a solvent of polymer which is possible to use thermoporosimetry based on Gibb-Thomson equation to approach pore structure of BC. In comparison with nitrogen adsorption, it was found that thermoporosimetry underestimated the BC porosity, i.e., the mean diameters of 23.0 nm vs. 27.8 nm and 27.9 nm vs. 33.9 nm for BC (a) and BC (b), respectively, by thermoporosimetry vs. B.H.J. nitrogen adsorption. It may be due to large non-freezable water fraction interacting with cellulose, and the validity of pore range based on thermodynamic assumptions of Gibb-Thomson theory.

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

    Science.gov (United States)

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

    2015-11-01

    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 by continuum flow solvers, allowing for investigations into spatiotemporal scales inaccessible to atomistic simulations.

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

    DEFF Research Database (Denmark)

    Hermenau, Martin; Riede, Moritz; Leo, Karl

    2011-01-01

    Small molecule organic solar cells were studied with respect to water and oxygen induced degradation by mapping the spatial distribution of reaction products in order to elucidate the degradation patterns and failure mechanisms. The active layers consist of a 30 nm bulk heterojunction formed...... with isotopic labeling using H218O and 18O2 provided information on where and to what extent the atmosphere had reacted with the device. A comparison was made between the use of a humid (oxygen free) atmosphere, a dry oxygen atmosphere, and a dry (oxygen free) nitrogen atmosphere during testing of devices...

  12. 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

    2016-01-01

    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.

  13. Proton transfer from the bulk to the bound ubiquinone QB of the reaction center in chromatophores of Rhodobacter sphaeroides: Retarded conveyance by neutral water

    Science.gov (United States)

    Gopta, Oksana A.; Cherepanov, Dmitry A.; Junge, Wolfgang; Mulkidjanian, Armen Y.

    1999-01-01

    The mechanism of proton transfer from the bulk into the membrane protein interior was studied. The light-induced reduction of a bound ubiquinone molecule QB by the photosynthetic reaction center is accompanied by proton trapping. We used kinetic spectroscopy to measure (i) the electron transfer to QB (at 450 nm), (ii) the electrogenic proton delivery from the surface to the QB site (by electrochromic carotenoid response at 524 nm), and (iii) the disappearance of protons from the bulk solution (by pH indicators). The electron transfer to QB− and the proton-related electrogenesis proceeded with the same time constant of ≈100 μs (at pH 6.2), whereas the alkalinization in the bulk was distinctly delayed (τ ≈ 400 μs). We investigated the latter reaction as a function of the pH indicator concentration, the added pH buffers, and the temperature. The results led us to the following conclusions: (i) proton transfer from the surface-located acidic groups into the QB site followed the reduction of QB without measurable delay; (ii) the reprotonation of these surface groups by pH indicators and hydronium ions was impeded, supposedly, because of their slow diffusion in the surface water layer; and (iii) as a result, the protons were slowly donated by neutral water to refill the proton vacancies at the surface. It is conceivable that the same mechanism accounts for the delayed relaxation of the surface pH changes into the bulk observed previously with bacteriorhodopsin membranes and thylakoids. Concerning the coupling between proton pumps in bioenergetic membranes, our results imply a tendency for the transient confinement of protons at the membrane surface. PMID:10557290

  14. Explicit Consideration of Water Molecules to Study Vibrational Circular DICHROÎSM of Monosaccharide's

    Science.gov (United States)

    Moussi, Sofiane; Ouamerali, Ourida

    2014-06-01

    Carbohydrates have multiples roles in biological systems. It has been found that the glycoside bond is fundamentally important in many aspects of chemistry and biology and forms the basis of carbohydrate chemistry. That means the stereochemical information, namely, glycosidic linkages α or β, gives an significant features of the carbohydrate glycosidation position of the glycosylic acceptor. For these reasons, much effort was made for the synthesis and analysis of the glycoside bond. Vibrational circular dichroism VCD has some advantages over conventional electronic circular dichroism (ECD) due to the applicability to all organic molecules and the reliability of ab initio quantum calculation. However, for a molecule with many chiral centers such as carbohydrates, determination of the absolute configuration tends to be difficult because the information from each stereochemical center is mixed and averaged over the spectrum. In the CH stretching region, only two VCD studies on carbohydrates have been reported and spectra--structure correlation, as determined for the glycoside band, remains to be investigated. T. Taniguchi and collaborators report that methyl glycosides exhibit a characteristic VCD peak, the sign of which solely reflects the C-1 absolute configuration. This work is a theoretical contribution to study the behaviour of VCD spectrum's of the monosaccharides when the water molecules are taken explicitly. This study is focused on six different monosaccharides in theirs absolute configuration R and S. We used the method of density functional theory DFT by means of the B3LYP hybrid functional and 6-31G * basis set.

  15. Effects of a Single Water Molecule on the Reaction Barrier of Interstellar CO2 Formation Reaction.

    Science.gov (United States)

    Tachikawa, Hiroto; Kawabata, Hiroshi

    2016-08-25

    The mechanism by which CO2 is formed in the interstellar space remains a mystery. The most likely reaction is collision between CO and OH; however, previous theoretical works have shown that the activation barrier for CO2 formation is high enough to prevent the reaction at the low thermal conditions of space (∼10 K). The effects of single water molecule on the reaction barrier of CO2 formation from reaction between CO and OH have been investigated here by means of ab initio calculation. The barrier height along the lowest-energy pathway in the reaction between CO and OH in the absence of the H2O molecule was calculated to be 2.3 kcal/mol when CCSD(T) energy corrections are combined with the MP2 basis set limit. In the case of the hydrated (H2O-CO-OH) system, the inclusion of a single H2O molecule into the system significantly decreased the barrier height to 0.2 kcal/mol. This suggests that CO2 can be formed when CO and OH react in the presence of H2O, even under thermal conditions as low as 10 K.

  16. Structure and stability of SnO2 nanocrystals and surface-bound water species.

    Science.gov (United States)

    Wang, Hsiu-Wen; Wesolowski, David J; Proffen, Thomas E; Vlcek, Lukas; Wang, Wei; Allard, Lawrence F; Kolesnikov, Alexander I; Feygenson, Mikhail; Anovitz, Lawrence M; Paul, Rick L

    2013-05-08

    The structure of SnO2 nanoparticles (avg. 5 nm) with a few layers of water on the surface has been elucidated by atomic pair distribution function (PDF) methods using in situ neutron total scattering data and molecular dynamics (MD) simulations. Analysis of PDF, neutron prompt gamma, and thermogravimetric data, coupled with MD-generated surface D2O/OD configurations demonstrates that the minimum concentration of OD groups required to prevent rapid growth of nanoparticles during thermal dehydration corresponds to ~0.7 monolayer coverage. Surface hydration layers not only stabilize the SnO2 nanoparticles but also induce particle-size-dependent structural modifications and are likely to promote interfacial reactions through hydrogen bonds between adjacent particles. Upon heating/dehydration under vacuum above 250 °C, nanoparticles start to grow with low activation energies, rapid increase of nanoparticle size, and a reduction in the a lattice dimension. This study underscores the value of neutron diffraction and prompt-gamma analysis, coupled with molecular modeling, in elucidating the influence of surface hydration on the structure and metastable persistence of oxide nanomaterials.

  17. Bound entanglement and entanglement bounds

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, Simeon [Physikalisch-Astronomische Fakultaet, Friedrich-Schiller-Univesitaet Jena (Germany)]|[Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany); Melo, Fernando de; Mintert, Florian; Buchleitner, Andreas [Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany)]|[Max-Planck-Institut fuer Physik komplexer Systeme, Noethnitzer Str.38, D-01187 Dresden (Germany); Bae, Joonwoo [School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-012 (Korea); Hiesmayr, Beatrix [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria)

    2008-07-01

    We investigate the separability of Bell-diagonal states of two qutrits. By using lower bounds to algebraically estimate concurrence, we find convex regions of bound entangled states. Some of these regions exactly coincide with the obtained results when employing optimal entanglement witnesses, what shows that the lower bound can serve as a precise detector of entanglement. Some hitherto unknown regions of bound entangled states were discovered with this approach, and delimited efficiently.

  18. 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)

    2012-12-19

    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.

  19. Binding of an octylglucoside detergent molecule in the second substrate (S2) site of LeuT establishes an inhibitor-bound conformation

    OpenAIRE

    Quick, Matthias; Winther, Anne-Marie Lund; Shi, Lei; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A.

    2009-01-01

    The first crystal structure of the neurotransmitter/sodium symporter homolog LeuT revealed an occluded binding pocket containing leucine and 2 Na+; later structures showed tricyclic antidepressants (TCAs) in an extracellular vestibule ≈11 Å above the bound leucine and 2 Na+. We recently found this region to be a second binding (S2) site and that binding of substrate to this site triggers Na+-coupled substrate symport. Here, we show a profound inhibitory effect of n-octyl-β-d-glucopyranoside (...

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

    KAUST Repository

    Rungger, Ivan

    2010-06-04

    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.

  1. [Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data].

    Science.gov (United States)

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

    2013-01-01

    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.

  2. A microfluidics-based turning assay reveals complex growth cone responses to integrated gradients of substrate-bound ECM molecules and diffusible guidance cues.

    Science.gov (United States)

    Joanne Wang, C; Li, Xiong; Lin, Benjamin; Shim, Sangwoo; Ming, Guo-Li; Levchenko, Andre

    2008-02-01

    Neuronal growth cones contain sophisticated molecular machinery precisely regulating their migration in response to complex combinatorial gradients of diverse external cues. The details of this regulation are still largely unknown, in part due to limitations of the currently available experimental techniques. Microfluidic devices have been shown to be capable of generating complex, stable and precisely controlled chemical gradients, but their use in studying growth cone migration has been limited in part due to the effects of shear stress. Here we describe a microfluidics-based turning-assay chip designed to overcome this issue. In addition to generating precise gradients of soluble guidance cues, the chip can also fabricate complex composite gradients of diffusible and surface-bound guidance cues that mimic the conditions the growth cones realistically counter in vivo. Applying this assay to Xenopus embryonic spinal neurons, we demonstrate that the presence of a surface-bound laminin gradient can finely tune the polarity of growth cone responses (repulsion or attraction) to gradients of brain-derived neurotrophic factor (BDNF), with the guidance outcome dependent on the mean BDNF concentration. The flexibility inherent in this assay holds significant potential for refinement of our understanding of nervous system development and regeneration, and can be extended to elucidate other cellular processes involving chemotaxis of shear sensitive cells.

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

    Science.gov (United States)

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

    2013-07-03

    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.

  4. Water solvent effects using continuum and discrete models: The nitromethane molecule, CH3NO2.

    Science.gov (United States)

    Modesto-Costa, Lucas; Uhl, Elmar; Borges, Itamar

    2015-11-15

    The first three valence transitions of the two nitromethane conformers (CH3NO2) are two dark n → π* transitions and a very intense π → π* transition. In this work, these transitions in gas-phase and solvated in water of both conformers were investigated theoretically. The polarizable continuum model (PCM), two conductor-like screening (COSMO) models, and the discrete sequential quantum mechanics/molecular mechanics (S-QM/MM) method were used to describe the solvation effect on the electronic spectra. Time dependent density functional theory (TDDFT), configuration interaction including all single substitutions and perturbed double excitations (CIS(D)), the symmetry-adapted-cluster CI (SAC-CI), the multistate complete active space second order perturbation theory (CASPT2), and the algebraic-diagrammatic construction (ADC(2)) electronic structure methods were used. Gas-phase CASPT2, SAC-CI, and ADC(2) results are in very good agreement with published experimental and theoretical spectra. Among the continuum models, PCM combined either with CASPT2, SAC-CI, or B3LYP provided good agreement with available experimental data. COSMO combined with ADC(2) described the overall trends of the transition energy shifts. The effect of increasing the number of explicit water molecules in the S-QM/MM approach was discussed and the formation of hydrogen bonds was clearly established. By including explicitly 24 water molecules corresponding to the complete first solvation shell in the S-QM/MM approach, the ADC(2) method gives more accurate results as compared to the TDDFT approach and with similar computational demands. The ADC(2) with S-QM/MM model is, therefore, the best compromise for accurate solvent calculations in a polar environment.

  5. Experimental measurements of water molecule binding energies for the second and third solvation shells of [Ca(H2O)n]2+ complexes

    Science.gov (United States)

    Bruzzi, E.; Stace, A. J.

    2017-01-01

    Further understanding of the biological role of the Ca2+ ion in an aqueous environment requires quantitative measurements of both the short- and long-range interactions experienced by the ion in an aqueous medium. Here, we present experimental measurements of binding energies for water molecules occupying the second and, quite possibly, the third solvation shell surrounding a central Ca2+ ion in [Ca(H2O)n]2+ complexes. Results for these large, previously inaccessible, complexes have come from the application of finite heat bath theory to kinetic energy measurements following unimolecular decay. Even at n = 20, the results show water molecules to be more strongly bound to Ca2+ than would be expected just from the presence of an extended network of hydrogen bonds. For n > 10, there is very good agreement between the experimental binding energies and recently published density functional theory calculations. Comparisons are made with similar data recorded for [Ca(NH3)n]2+ and [Ca(CH3OH)n]2+ complexes.

  6. Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell.

    Science.gov (United States)

    Choi, Youngjin; Cho, Kum Won; Jeong, Karpjoo; Jung, Seunho

    2006-06-12

    Systematic computational work for a series of 13 disaccharides was performed to provide an atomic-level insight of unique biochemical role of the alpha,alpha-(1-->1)-linked glucopyranoside dimer over the other glycosidically linked sugars. Superior osmotic and cryoprotective abilities of trehalose were explained on the basis of conformational and hydration characteristics of the trehalose molecule. Analyses of the hydration number and radial distribution function of solvent water molecules showed that there was very little hydration adjacent to the glycosidic oxygen of trehalose and that the dynamic conformation of trehalose was less flexible than any of the other sugars due to this anisotropic hydration. The remarkable conformational rigidity that allowed trehalose to act as a sugar template was required for stable interactions with hydrogen-bonded water molecules. Trehalose made an average of 2.8 long-lived hydrogen bonds per each MD step, which was much larger than the average of 2.1 for the other sugars. The stable hydrogen-bond network is derived from the formation of long-lived water bridges at the expense of decreasing the dynamics of the water molecules. Evidence for this dynamic reduction of water by trehalose was also established based on each of the lowest translational diffusion coefficients and the lowest intermolecular coulombic energy of the water molecules around trehalose. Overall results indicate that trehalose functions as a 'dynamic reducer' for solvent water molecules based on its anisotropic hydration and conformational rigidity, suggesting that macroscopic solvent properties could be modulated by changes in the type of glycosidic linkages in sugar molecules.

  7. 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;

    2015-01-01

    in a variety of cellular processes in which it has been linked to a number of disorders such as schizophrenia and autism. Despite extensive studies on the Ca(2+)-activated state of NCS proteins, little is known about the conformational dynamics of the Mg(2+)-bound and apo states, both of which are populated...... by populating one intermediate state consisting of a folded C-domain and an unfolded N-domain. The interconversion at equilibrium between the different molecular states populated by NCS-1 was monitored in real time through constant-force measurements and the energy landscapes underlying the observed transitions......Neuronal calcium sensor-1 (NCS-1) is the primordial member of a family of proteins responsible primarily for sensing changes in neuronal Ca(2+) concentration. NCS-1 is a multispecific protein interacting with a number of binding partners in both calcium-dependent and independent manners, and acting...

  8. Rotations and vibrations of water molecule inside the fullerene cage: infrared study of H2O@C60

    Science.gov (United States)

    Room, Toomas; Shugai, A.; Nagel, U.; Mamone, S.; Krachmalnicoff, A.; Whitby, R. J.; Levitt, M. H.; Nishida, T.; Murata, Y.; Lei, Xuegong; Li, Yongjun; Turro, N. J.

    2015-03-01

    Water is the second molecule after hydrogen what has been trapped inside the cage of a C60 molecule by the molucular surgery method. We studied isolated water molecule isotopologs H2O, D2O, and HDO in the solid phase at cryogenic temperatures using IR spectroscopy. The water molecule rotation transitions were observed in the THz and vibration-rotation transitions in the mid-IR range. The slow conversion between para and ortho water allowed us to record the time evolution of spectra and to separate ortho and para absorption lines of water. The similarity of the rotation spectrum of caged water to water in the gas phase indicates that water is free to rotate in the C60 cage even at temperature as low as 3 K. However, spectral lines show a splitting of about 0.5 meV what is not compatible with the icosahedral symmetry of C60. Different models (e.g. crystal field effects in solid C60, C60 cage distortions) will be discussed. This work was supported by institutional research funding IUT23-3 of the Estonian Ministry of Education and Research.

  9. Electron impact ionization of water molecules in ice and liquid phases

    Energy Technology Data Exchange (ETDEWEB)

    Joshipura, K N [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120 (India); Gangopadhyay, Sumona [Department of Physics, Sardar Patel University, Vallabh Vidyanagar-388120 (India); Limbachiya, C G [P S Science College, Kadi (N.G.) 382 715 (India); Vinodkumar, Minaxi [V P and R P T P Science College, Vallabh Vidyanagar-388 120 (India)

    2007-09-15

    Electron scattering processes in ice or water are known to occur in natural as well as man-made systems. But the processes are difficult to investigate in theory or in laboratory. We present our calculations on total ionization cross section (Q{sub ion}) for collisions of electrons with H{sub 2}O molecules in condensed matter (ice and liquid) forms, at impact energies from ionization threshold to 1000 eV, extendable to about 1 MeV. Our theoretical method determines the total inelastic cross section (Q{sub inel}) of electron impact on H{sub 2}O (ice), by starting with the complex scattering potential partial wave formalism. Reasonable approximations are invoked to project out the ionization cross section of H{sub 2}O molecule in ice (or liquid) form by using the Q{sub inel} as an input. Properties of the condensed phase H{sub 2}O are incorporated together with bulk screening effects in the scattering echanism. Due to medium effects, the present Q{sub ion} are found to be lower than the corresponding values for H{sub 2}O in free or gaseous state. Macroscopic cross sections and electron mean free paths for the bulk medium are also calculated. This study has potential applications in radiation biology as well as chemistry and in planetary science and astrophysics.

  10. Rate-Enhancing Roles of Water Molecules in Methyltrioxorhenium-Catalyzed Olefin Epoxidation by Hydrogen Peroxide.

    Science.gov (United States)

    Goldsmith, Bryan R; Hwang, Taeho; Seritan, Stefan; Peters, Baron; Scott, Susannah L

    2015-08-01

    Olefin epoxidation catalyzed by methyltrioxorhenium (MTO, CH3ReO3) is strongly accelerated in the presence of H2O. The participation of H2O in each of the elementary steps of the catalytic cycle, involving the formation of the peroxo complexes (CH3ReO2(η(2)-O2), A, and CH3ReO(η(2)-O2)2(H2O), B), as well as in their subsequent epoxidation of cyclohexene, was examined in aqueous acetonitrile. Experimental measurements demonstrate that the epoxidation steps exhibit only weak [H2O] dependence, attributed by DFT calculations to hydrogen bonding between uncoordinated H2O and a peroxo ligand. The primary cause of the observed H2O acceleration is the strong co-catalytic effect of water on the rates at which A and B are regenerated and consequently on the relative abundances of the three interconverting Re-containing species at steady state. Proton transfer from weakly coordinated H2O2 to the oxo ligands of MTO and A, resulting in peroxo complex formation, is directly mediated by solvent H2O molecules. Computed activation parameters and kinetic isotope effects, in combination with proton-inventory experiments, suggest a proton shuttle involving one or (most favorably) two H2O molecules in the key ligand-exchange steps to form A and B from MTO and A, respectively.

  11. Structure of a SARS coronavirus-derived peptide bound to the human major histocompatibility complex class I molecule HLA-B*1501

    DEFF Research Database (Denmark)

    Røder, Gustav; Kristensen, Ole; Kastrup, Jette S;

    2008-01-01

    , the crystal structure of HLA-B*1501 in complex with a SARS coronavirus-derived nonapeptide (VQQESSFVM) has been determined at high resolution (1.87 A). The peptide is deeply anchored in the B and F pockets, but with the Glu4 residue pointing away from the floor in the peptide-binding groove, making......The human leukocyte antigen (HLA) class I system comprises a highly polymorphic set of molecules that specifically bind and present peptides to cytotoxic T cells. HLA-B*1501 is a prototypical member of the HLA-B62 supertype and only two peptide-HLA-B*1501 structures have been determined. Here...

  12. Switching of the magnetocaloric effect of Mn(II) glycolate by water molecules.

    Science.gov (United States)

    Chen, Yan-Cong; Guo, Fu-Sheng; Liu, Jun-Liang; Leng, Ji-Dong; Vrábel, Peter; Orendáč, Martin; Prokleška, Jan; Sechovský, Vladimír; Tong, Ming-Liang

    2014-03-10

    The transformation of Mn(II) glycolates (glc) between the three-dimensional coordination polymer [Mn(glc)2]n (1) and discrete mononuclear phase [Mn(glc)2 (H2O)2] (2) can be reversibly switched by water molecules, which dramatically change the magnetocaloric effect (MCE) of Mn(II) glycolates from the maximum of 6.9 J kg(-1)  K(-1) in 1 to 60.3 J kg(-1)  K(-1) in 2. This case example reveals that the effect of magnetic coupling on MCE plays a dominant role over that of other factors such as magnetic density for 3d-type magnetic refrigerants.

  13. Molecular theories and simulation of ions and polar molecules in water

    CERN Document Server

    Hummer, G; García, A; Hummer, Gerhard; Pratt, Lawrence R.; Garcia, Angel E.

    1998-01-01

    Recent developments in molecular theories and simulation of ions and polar molecules in water are reviewed. The hydration of imidazole and imidazolium solutes is used to exemplify the theoretical issues. The treatment of long-ranged electrostatic interactions in simulations is discussed extensively. It is argued that the Ewald approach is an easy way to get correct hydration free energies in the thermodynamic limit from molecular calculations; and that molecular simulations with Ewald interactions and periodic boundary conditions can also be more efficient than many common alternatives. The Ewald treatment permits a conclusive extrapolation to infinite system size. The picture that emerges from testing of simple models is that the most prominent failings of the simplest theories are associated with solvent proton conformations that lead to non-gaussian fluctuations of electrostatic potentials. Thus, the most favorable cases for the second-order perturbation theories are monoatomic positive ions. For polar and...

  14. Hydration of gelatin molecules in glycerol-water solvent and phase diagram of gelatin organogels.

    Science.gov (United States)

    Sanwlani, Shilpa; Kumar, Pradip; Bohidar, H B

    2011-06-09

    We present a systematic investigation of hydration and gelation of the polypeptide gelatin in water-glycerol mixed solvent (glycerol solutions). Raman spectroscopy results indicated enhancement in water structure in glycerol solutions and the depletion of glycerol density close to hydration sheath of the protein molecule. Gelation concentration (c(g)) was observed to decrease from 1.92 to 1.15% (w/v) while the gelation temperature (T(g)) was observed to increase from 31.4 to 40.7 °C with increase in glycerol concentration. Data on hand established the formation of organogels having interconnected networks, and the universal gelation mechanism could be described through an anomalous percolation model. The viscosity of sol diverged as η ∼ (1 - c(g)/c)(-k) as c(g) was approached from below (c c(g)). It is important to note that values determined for critical exponents k and t were universal; that is, they did not depend on the microscopic details. The measured values were k = 0.38 ± 0.10 and t = 0.92 ± 0.17 whereas the percolation model predicts k = 0.7-1.3 and t = 1.9. Isothermal frequency sweep studies showed power-law dependence of gel storage modulus (G') and loss modulus (G'') on oscillation frequency ω given as G'(ω) ∼ ω(n') and G''(ω) ∼ ω(n''), and consistent with percolation model prediction it was found that n' ≈ n'' ≈ δ ≈ 0.73 close to gelation concentration. We propose a unique 3D phase diagram for the gelatin organogels. Circular dichroism data revealed that the gelatin molecules retained their biological activity in these solvents. Thus, it is shown that the thermomechanical properties of these organogels could be systematically tuned and customized as per application requirement.

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

    Science.gov (United States)

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

    2015-06-01

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

  16. 油纸复合介质中水分子扩散行为的分子动力学模拟%Molecular Dynamics Simulation of the Diffusion Behavior of Water Molecules in Oil and Cellulose Composite Media

    Institute of Scientific and Technical Information of China (English)

    廖瑞金; 朱孟兆; 周欣; 杨丽君; 严家明; 孙才新

    2011-01-01

    The diffusion behaviors of water molecules in oil-cellulose composite media were studied at different temperatures using a molecular dynamics simulation. By analyzing the formation of hydrogen bonds between the water molecules and cellulose we found that the water molecules that were initially present in the oil gradually spread to the cellulose, and hydrogen bonds were formed between them. The water molecules that were present in the cellulose initially also formed hydrogen bonds and were bound to cellulose molecules. By analyzing the diffusion coefficients of the water molecules at different temperatures we found that the diffusion behaviors of the water molecules in the two single-media,namely oil and cellulose, were very different because of their different polarities. The diffusion coefficients of the water molecules in the composite media were influenced greatly by the ratio of water molecules present in the oil and cellulose and a strong correlation was apparent between them. The water molecule-oil interaction energy and the water molecule-cellulose interaction energy were also strongly related to the polarities of the oil and the cellulose. The interaction energies also exhibited a strong correlation to the distribution of water molecules at different temperatures. This was the reason for the weakened influence of temperature on the diffusion coefficient of the water molecules, which was due to the different distributions of water molecules at different temperatures.%对不同温度下水分子在油纸复合介质中的扩散行为进行了分子动力学模拟研究.通过分析水分子与纤维素形成的氢键发现,油中的水分子在模拟过程中会逐渐扩散到纤维素内并与之形成氢键,而纤维素内的水分子则与纤维素形成氢键后被束缚于纤维素中.通过分析水分子的扩散系数发现,由于油和纤维素的极性不同,使得水分子在油和纤维素两种单介质中的扩散行为有较大差别,而在

  17. A proactive role of water molecules in acceptor recognition by Protein-O-fucosyltransferase 2

    Science.gov (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

    2016-01-01

    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

  18. Lattice water molecules tuned spin-crossover for an iron(II) complex with thermal hysteresis.

    Science.gov (United States)

    Luo, Yang-Hui; Yang, Li-Jing; Liu, Qing-Ling; Ling, Yang; Wang, Wei; Sun, Bai-Wang

    2014-11-28

    A new iron(II) complex based on the 4,4'-dimethyl-2,2'-bipyridine ligand [Fe(4,4'-dmbpy)3(ClO4)(SCN)·3H2O (1·3H2O)] has been prepared and characterized. Structural studies and Hirshfeld surface analysis for complex 1·3H2O at three different temperatures (300, 240 and 130 K) are described. The UV-vis absorption spectrum of a water-free sample (1) in methanol solution and magnetic susceptibility measurements for solid-state samples 1·3H2O and 1 revealed that the removal of lattice water molecules from complex 1·3H2O changed the magnetic properties from the low-spin state (1·3H2O) to the complete spin-crossover (1) between 350-220 K with a thermal hysteresis of 7 K, and was accompanied by a colour change from brown to red.

  19. Application of inhomogeneous fluid solvation theory to model the distribution and thermodynamics of water molecules around biomolecules.

    Science.gov (United States)

    Huggins, David J

    2012-11-21

    The structures of biomolecules and the strengths of association between them depend critically on interactions with water molecules. Thus, understanding these interactions is a prerequisite for understanding the structure and function of all biomolecules. Inhomogeneous fluid solvation theory provides a framework to derive thermodynamic properties of individual water molecules from a statistical mechanical analysis. In this work, two biomolecules are analysed to probe the distribution and thermodynamics of surrounding water molecules. The great majority of hydration sites are predicted to contribute favourably to the total free energy with respect to bulk water, though hydration sites close to non-polar regions of the solute do not contribute significantly. Analysis of a biomolecule with a positively and negatively charged functional group predicts that a charged species perturbs the free energy of water molecules to a distance of approximately 6.0 Å. Interestingly, short simulations are found to provide converged predictions if samples are taken with sufficient frequency, a finding that has the potential to significantly reduce the required computational cost of such analysis. In addition, the predicted thermodynamic properties of hydration sites with the potential for direct hydrogen bonding interactions are found to disagree significantly for two different water models. This study provides important information on how inhomogeneous fluid solvation theory can be employed to understand the structures and intermolecular interactions of biomolecules.

  20. Thermodynamic properties of water in the lattice gas model with consideration of the vibrational motions of molecules

    Science.gov (United States)

    Titov, S. V.; Tovbin, Yu. K.

    2016-11-01

    A molecular model developed earlier for a polar fluid within the lattice gas model is supplemented by considering the vibrational motions of molecules using water as an example. A combination of point dipole and Lennard-Jones potentials from SPC parametrization is chosen as the force field model for the molecule. The main thermodynamic properties of liquid water (density, internal energy, and entropy) are studied as functions of temperature. There is qualitative agreement between the calculation results and the experimental data. Ways of refining the molecular theory are discussed.

  1. Correlation of monocyte-monolayer assay results, number of erythrocyte-bound IgG molecules, and IgG subclass composition in the study of red cell alloantibodies other than D.

    Science.gov (United States)

    Zupańska, B; Brojer, E; McIntosh, J; Seyfried, H; Howell, P

    1990-01-01

    Comparisons have been made between the serological and immunological characteristics of 42 blood group alloantibodies (other than D) covering twelve systems using a monocyte-monolayer assay (MMA), a radiometric antiglobulin test for antibody binding and IgG subclass determinations. The results of the MMA correlated well with the level of IgG molecules bound on incompatible cells, and the highest levels in both cases were associated with the presence of the IgG3 subclass. However, limited clinical data shows that, while in general the MMA clearly identifies the clinically significant antibodies, the correlation with the degree of clinical outcome is less well defined, and in some instances other factors may be operating to ameliorate the in vivo effect of the antibody.

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

    Science.gov (United States)

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

    2012-03-01

    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.

  3. Association of Catechin Molecules in Water: Quantitative Binding Study and Complex Structure Analysis.

    Science.gov (United States)

    Ujihara, Tomomi; Hayashi, Nobuyuki

    2016-01-22

    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.

  4. NO Exchange for a Water Molecule Favorably Changes Iontophoretic Release of Ruthenium Complexes to the Skin

    Directory of Open Access Journals (Sweden)

    Danielle C. A. S. de Santana

    2017-01-01

    Full Text Available Ruthenium (Ru complexes have been studied as promising anticancer agents. Ru nitrosyl complex (Ru-NO is one which acts as a pro-drug for the release of nitric oxide (NO. The Ru-aqueous complex formed by the exchange of NO for a water molecule after NO release could also possess therapeutic effects. This study evaluates the influence of iontophoresis on enhancing the skin penetration of Ru-NO and Ru-aqueous and assesses its applicability as a tool in treating diverse skin diseases. Passive and iontophoretic (0.5 mA·cm−2 skin permeation of the complexes were performed for 4 h. The amount of Ru and NO in the stratum corneum (SC, viable epidermis (VE, and receptor solution was quantified while the influence of iontophoresis and irradiation on NO release from Ru-NO complex was also evaluated. Iontophoresis increased the amount of Ru-NO and Ru-aqueous recovered from the receptor solution by 15 and 400 times, respectively, as compared to passive permeation. Iontophoresis produced a higher accumulation of Ru-aqueous in the skin layers as compared to Ru-NO. At least 50% of Ru-NO penetrated the SC was stable after 4 h. The presence of Ru-NO in this skin layer suggests that further controlled release of NO can be achieved by photo-stimulation after iontophoresis.

  5. Fast volumetric imaging of bound and pore water in cortical bone using three-dimensional ultrashort-TE (UTE) and inversion recovery UTE sequences.

    Science.gov (United States)

    Chen, Jun; Carl, Michael; Ma, Yajun; Shao, Hongda; Lu, Xing; Chen, Bimin; Chang, Eric Y; Wu, Zhihong; Du, Jiang

    2016-10-01

    We report the three-dimensional ultrashort-TE (3D UTE) and adiabatic inversion recovery UTE (IR-UTE) sequences employing a radial trajectory with conical view ordering for bi-component T2 * analysis of bound water (T2 *(BW) ) and pore water (T2 *(PW) ) in cortical bone. An interleaved dual-echo 3D UTE acquisition scheme was developed for fast bi-component analysis of bound and pore water in cortical bone. A 3D IR-UTE acquisition scheme employing multiple spokes per IR was developed for bound water imaging. Two-dimensional UTE (2D UTE) and IR-UTE sequences were employed for comparison. The sequences were applied to bovine bone samples (n = 6) and volunteers (n = 6) using a 3-T scanner. Bi-component fitting of 3D UTE images of bovine samples showed a mean T2 *(BW) of 0.26 ± 0.04 ms and T2 *(PW) of 4.16 ± 0.35 ms, with fractions of 21.5 ± 3.6% and 78.5 ± 3.6%, respectively. The 3D IR-UTE signal showed a single-component decay with a mean T2 *(BW) of 0.29 ± 0.05 ms, suggesting selective imaging of bound water. Similar results were achieved with the 2D UTE and IR-UTE sequences. Bi-component fitting of 3D UTE images of the tibial midshafts of healthy volunteers showed a mean T2 *(BW) of 0.32 ± 0.08 ms and T2 *(PW) of 5.78 ± 1.24 ms, with fractions of 34.2 ± 7.4% and 65.8 ± 7.4%, respectively. Single-component fitting of 3D IR-UTE images showed a mean T2 *(BW) of 0.35 ± 0.09 ms. The 3D UTE and 3D IR-UTE techniques allow fast volumetric mapping of bound and pore water in cortical bone. Copyright © 2016 John Wiley & Sons, Ltd.

  6. 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.

    Science.gov (United States)

    Pedersen, Lasse Eggers; Rasmussen, Michael; Harndahl, Mikkel; Nielsen, Morten; Buus, Søren; Jungersen, Gregers

    2016-02-01

    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 (PSCPL) approach. Here, we report the peptide binding motif of SLA-3*04:01 and combine two prediction methods and analysis of both peptide binding affinity and stability of peptide-MHC complexes to improve rational peptide selection. Using a peptide prediction strategy combining PSCPL binding matrices and in silico prediction algorithms (NetMHCpan), peptide ligands from a repository of 8900 peptides were predicted for binding to SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01 and validated by affinity and stability assays. From the pool of predicted peptides for SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01, a total of 71, 28, and 38% were binders with affinities below 500 nM, respectively. Comparison of peptide-SLA binding affinity and complex stability showed that peptides of high affinity generally, but not always, produce complexes of high stability. In conclusion, we demonstrate how state-of-the-art prediction and in vitro immunology tools in combination can be used for accurate selection of peptides for MHC class I binding, hence providing an expansion of the field of peptide-MHC analysis also to include pigs as a livestock experimental model.

  7. (e,3e) and (e,3-1e) differential cross sections for the double ionization of water molecule

    Energy Technology Data Exchange (ETDEWEB)

    Mansouri, A. [Laboratoire de Physique quantique et systemes dynamiques, Departement de Physique, Faculte des Sciences Universite Ferhat Abbas, Setif 19000 (Algeria); Dal Cappello, C., E-mail: cappello@univ-metz.f [Universite Paul Verlaine-Metz, Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR 2843), Institut de Physique, 1 rue Arago, 57078 Metz Cedex 3 (France); Kada, I. [Laboratoire de Physique quantique et systemes dynamiques, Departement de Physique, Faculte des Sciences Universite Ferhat Abbas, Setif 19000 (Algeria); Champion, C. [Universite Paul Verlaine-Metz, Laboratoire de Physique Moleculaire et des Collisions, ICPMB (FR 2843), Institut de Physique, 1 rue Arago, 57078 Metz Cedex 3 (France); Roy, A.C. [School of Mathematical Sciences, Ramakrishna Mission Vivekananda University, Belur Math 711202, West Bengal (India)

    2009-08-24

    We report new results for differential cross sections for the double ionization of water molecule by 1 keV electron impact. The present calculation is based on the first Born approximation. We describe the water molecule by a single centre wave function of Moccia. For the final state, an approximation of the well-known 3C wave function is used. An extensive study has been made by varying the angles of detection and the energies of each ejected electron. We have investigated the double ionization of each molecular state (1b{sub 1}, 3a{sub 1}, 1b{sub 2} and 2a{sub 1}) and identified the mechanisms of this process.

  8. Self-assembly of neuroprotective carbazolium based small molecules at octane/water interface: A simulation investigation

    Science.gov (United States)

    Zolghadr, Amin Reza; Heydari Dokoohaki, Maryam

    2016-11-01

    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.

  9. Structural Analysis of Iac Repressor Bound to Allosteric Effectors

    Energy Technology Data Exchange (ETDEWEB)

    Daber,R.; Stayrook, S.; Rosenberg, A.; Lewis, M.

    2007-01-01

    The lac operon is a model system for understanding how effector molecules regulate transcription and are necessary for allosteric transitions. The crystal structures of the lac repressor bound to inducer and anti-inducer molecules provide a model for how these small molecules can modulate repressor function. The structures of the apo repressor and the repressor bound to effector molecules are compared in atomic detail. All effectors examined here bind to the repressor in the same location and are anchored to the repressor through hydrogen bonds to several hydroxyl groups of the sugar ring. Inducer molecules form a more extensive hydrogen-bonding network compared to anti-inducers and neutral effector molecules. The structures of these effector molecules suggest that the O6 hydroxyl on the galactoside is essential for establishing a water-mediated hydrogen bonding network that bridges the N-terminal and C-terminal sub-domains. The altered hydrogen bonding can account in part for the different structural conformations of the repressor, and is vital for the allosteric transition.

  10. Proton-bound cluster ions in ion mobility spectrometry.

    Science.gov (United States)

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

    1999-10-28

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

  11. Water-COOH Composite Structure with Enhanced Hydrophobicity Formed by Water Molecules Embedded into Carboxyl-Terminated Self-Assembled Monolayers.

    Science.gov (United States)

    Guo, Pan; Tu, Yusong; Yang, Jinrong; Wang, Chunlei; Sheng, Nan; Fang, Haiping

    2015-10-30

    By combining molecular dynamics simulations and quantum mechanics calculations, we show the formation of a composite structure composed of embedded water molecules and the COOH matrix on carboxyl-terminated self-assembled monolayers (COOH SAMs) with appropriate packing densities. This composite structure with an integrated hydrogen bond network inside reduces the hydrogen bonds with the water above. This explains the seeming contradiction on the stability of the surface water on COOH SAMs observed in experiments. The existence of the composite structure at appropriate packing densities results in the two-step distribution of contact angles of water droplets on COOH SAMs, around 0° and 35°, which compares favorably to the experimental measurements of contact angles collected from forty research articles over the past 25 years. These findings provide a molecular-level understanding of water on surfaces (including surfaces on biomolecules) with hydrophilic functional groups.

  12. Effects of water molecules on the chemical stability of MAGeI3 perovskite explored from a theoretical viewpoint.

    Science.gov (United States)

    Sun, Ping-Ping; Chi, Wei-Jie; Li, Ze-Sheng

    2016-09-21

    The stability of perovskite in humid environments is one of the biggest obstacles for its potential applications in light harvesting and electroluminescent displays. Understanding the detailed degradation mechanism of MAGeI3 in moisture is a critical way to explore the practicability of MAGeI3 perovskite. In this study, we report a quantitative and systematic investigation of MAGeI3 degradation processes by exploring the effects of H2O molecules on the structural and electronic properties of the most stable MAGeI3(101) surface under various simulated environmental conditions with different water coverage based on first-principles calculations. The results show that H2O molecules can easily diffuse into the inner side of the perovskite and gradually corrode the structure as the number of H2O molecules increases. As a result of the interactions between perovskite and H2O molecules, a hydrated intermediate will be generated as the first step in the degradation mechanism; the perovskite will further decompose to HI and GeI2. In terms of one MAGeI3 molecule, it will be dissociated completely to GeI2 as a result of hydrolysis reactions with a minimum of 4H2O molecules. In addition, the degradation of the perovskite will also affect the electronic structure, causing a decrease in optical absorption across the visible region of the spectrum and a distinct deformation change in the crystal structure of the material. These findings further illustrate the degradation of the hydrolysis process of MAGeI3 perovskite in humid environments, which should be helpful to inspire experimentalists to take action to prolong the lifetimes of perovskite solar cells to achieve high conversion efficiency in their applications.

  13. Dissociation of water molecules upon keV H+- and Heq+-induced ionization

    NARCIS (Netherlands)

    Alvarado, F; Hoekstra, R; Schlatholter, T

    2005-01-01

    The interaction of keV H+, He+ and He2+, ions with gas-phase H2O molecules leads to formation of H2Oq+ ions which subsequently can undergo dissociation into various fragment species. From coincident determination of the fragmention kinetic energies, kinetic energy releases (KER) for the different di

  14. Femtosecond Hydrogen Bond Dynamics of Bulk-like and Bound Water at Positively and Negatively Charged Lipid Interfaces Revealed by 2D HD-VSFG Spectroscopy.

    Science.gov (United States)

    Singh, Prashant Chandra; Inoue, Ken-Ichi; Nihonyanagi, Satoshi; Yamaguchi, Shoichi; Tahara, Tahei

    2016-08-26

    Interfacial water in the vicinity of lipids plays an important role in many biological processes, such as drug delivery, ion transportation, and lipid fusion. Hence, molecular-level elucidation of the properties of water at lipid interfaces is of the utmost importance. We report the two-dimensional heterodyne-detected vibrational sum frequency generation (2D HD-VSFG) study of the OH stretch of HOD at charged lipid interfaces, which shows that the hydrogen bond dynamics of interfacial water differ drastically, depending on the lipids. The data indicate that the spectral diffusion of the OH stretch at a positively charged lipid interface is dominated by the ultrafast (dynamics, while the dynamics at a negatively charged lipid interface exhibit sub-picosecond dynamics almost exclusively, implying that fast hydrogen bond fluctuation is prohibited. These results reveal that the ultrafast hydrogen bond dynamics at the positively charged lipid-water interface are attributable to the bulk-like property of interfacial water, whereas the slow dynamics at the negatively charged lipid interface are due to bound water, which is hydrogen-bonded to the hydrophilic head group.

  15. Charge-specific size-dependent separation of water-soluble organic molecules by fluorinated nanoporous networks

    Science.gov (United States)

    Byun, Jeehye; Patel, Hasmukh A.; Thirion, Damien; Yavuz, Cafer T.

    2016-11-01

    Molecular architecture in nanoscale spaces can lead to selective chemical interactions and separation of species with similar sizes and functionality. Substrate specific sorbent chemistry is well known through highly crystalline ordered structures such as zeolites, metal organic frameworks and widely available nanoporous carbons. Size and charge-dependent separation of aqueous molecular contaminants, on the contrary, have not been adequately developed. Here we report a charge-specific size-dependent separation of water-soluble molecules through an ultra-microporous polymeric network that features fluorines as the predominant surface functional groups. Treatment of similarly sized organic molecules with and without charges shows that fluorine interacts with charges favourably. Control experiments using similarly constructed frameworks with or without fluorines verify the fluorine-cation interactions. Lack of a σ-hole for fluorine atoms is suggested to be responsible for this distinct property, and future applications of this discovery, such as desalination and mixed matrix membranes, may be expected to follow.

  16. Spatio-temporal distribution of cell-bound and dissolved geosmin in Wahnbach Reservoir: Causes and potential odour nuisances in raw water.

    Science.gov (United States)

    Jähnichen, Sabine; Jäschke, Kathrin; Wieland, Falk; Packroff, Gabriele; Benndorf, Jürgen

    2011-10-15

    In many lakes and reservoirs, problems caused by off-flavours are known to be particularly associated with the occurrence of planktonic and benthic cyanobacteria. Frequently observed objectionable taste and odorous products of cyanobacteria are geosmin and 2-methylisoborneol. Investigations focused on the littoral zone of Wahnbach Reservoir (Germany) revealed that benthic cyanobacteria were present in this oligotrophic drinking water reservoir. Benthic cyanobacteria were found in the depth horizon between 1.75 m and 11 m, particularly on south-exposed slopes. This spatial distribution indicates a possible key role of the underwater light climate. Moreover, cell-bound and dissolved geosmin were detected in corresponding littoral samples. Both fractions were subjected to spatial and primarily temporal variations with maximum concentrations at the end of summer. However, a substantial lowering of the water level caused a diminution of cyanobacterial growth. Due to the drawdown of the water level concentrations of cell-bound geosmin and pigments (as a proxy of cyanobacterial biomass) were remarkably reduced, and dissolved geosmin was never detected during this phase. Except for the influence of water level fluctuation no other abiotic variables had a significant influence on pigment and geosmin concentrations. From geosmin concentrations detected in the littoral zone, the probability of serious episodes of odour events in the raw water of the Wahnbach Reservoir was estimated. Hence, the probability that the raw water was affected by geosmin was minor, which was supported by routine flavour profiles. Nevertheless, the study shows that odorous episodes caused by benthic cyanobacteria are likely to develop even in an oligotrophic lake or reservoir when these cyanobacteria, and consequently odorous production, proliferate. In principle, such a proliferation cannot be excluded as nutrients are available from the sediment pore water, and underwater light at the sediment

  17. Quantum path-integral molecular dynamics calculations of the dipole-bound state of the water dimer anion

    Science.gov (United States)

    Shiga, Motoyuki; Takayanagi, Toshiyuki

    2003-09-01

    The equilibrium structure of the negatively charged water dimer (H 2O) 2- has been studied using the path-integral molecular dynamics simulation. All the atomic motions as well as the excess electron were treated quantum mechanically, employing a semi-empirical model combining a water-water interatomic potential with an electron-water pseudopotential. It is demonstrated that the molecular structure of (H 2O) 2- is more flexible than that of (H 2O) 2; both the donor switching and donor-acceptor interchange can more effectively occur in (H 2O) 2- than in (H 2O) 2. We conclude that this floppy character is a result of the breakdown of the adiabatic Born-Oppenheimer picture.

  18. Hydrogen bonding of single acetic acid with water molecules in dilute aqueous solutions

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In separation processes,hydrogen bonding has a very significant effect on the efficiency of isolation of acetic acid (HOAc) from HOAc/H2O mixtures. This intermolecular interaction on aggregates composed of a single HOAc molecule and varying numbers of H2O molecules has been examined by using ab initio molecular dynamics simulations (AIMD) and quantum chemical calculations (QCC). Thermodynamic data in aqueous solution were obtained through the self-consistent reaction field calculations and the polarizable continuum model. The aggregation free energy of the aggregates in gas phase as well as in aqueous system shows that the 6-membered ring is the most favorable structure in both states. The relative stability of the ring structures inferred from the thermodynamic properties of the QCC is consistent with the ring distributions of the AIMD simulation. The study shows that in dilute aqueous solution of HOAc the more favorable molecular interaction is the hydrogen bonding between HOAc and H2O molecules,resulting in the separation of acetic acid from the HOAc/H2O mixtures with more difficulty than usual.

  19. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

    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.

  20. An aspartate and a water molecule mediate efficient acid-base catalysis in a tailored antibody pocket.

    Science.gov (United States)

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

    2009-11-03

    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 Asp(H35) and Glu(L34) 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 Glu(L34) to alanine mutant, leads to an impressive 10(9)-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.

  1. Partial oxidation of step-bound water leads to anomalous pH effects on metal electrode step-edges.

    Science.gov (United States)

    Schwarz, Kathleen; Xu, Bingjun; Yan, Yushan; Sundararaman, Ravishankar

    2016-06-28

    The design of better heterogeneous catalysts for applications such as fuel cells and electrolyzers requires a mechanistic understanding of electrocatalytic reactions and the dependence of their activity on operating conditions such as pH. A satisfactory explanation for the unexpected pH dependence of electrochemical properties of platinum surfaces has so far remained elusive, with previous explanations resorting to complex co-adsorption of multiple species and resulting in limited predictive power. This knowledge gap suggests that the fundamental properties of these catalysts are not yet understood, limiting systematic improvement. Here, we analyze the change in charge and free energies upon adsorption using density-functional theory (DFT) to establish that water adsorbs on platinum step edges across a wide voltage range, including the double-layer region, with a loss of approximately 0.2 electrons upon adsorption. We show how this as-yet unreported change in net surface charge due to this water explains the anomalous pH variations of the hydrogen underpotential deposition (Hupd) and the potentials of zero total charge (PZTC) observed in published experimental data. This partial oxidation of water is not limited to platinum metal step edges, and we report the charge of the water on metal step edges of commonly used catalytic metals, including copper, silver, iridium, and palladium, illustrating that this partial oxidation of water broadly influences the reactivity of metal electrodes.

  2. Computational study of the interaction of indole-like molecules with water and hydrogen sulfide.

    Science.gov (United States)

    Cabaleiro-Lago, Enrique M; Rodríguez-Otero, Jesús; Peña-Gallego, Ángeles

    2011-10-01

    The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H···π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH(2) ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

  3. Computational study of the interaction of indole-like molecules with water and hydrogen sulfide

    Science.gov (United States)

    Cabaleiro-Lago, Enrique M.; Rodríguez-Otero, Jesús; Peña-Gallego, Ángeles

    2011-10-01

    The characteristics of the interaction between water and hydrogen sulfide with indole and a series of analogs obtained by substituting the NH group of indole by different heteroatoms have been studied by means of ab initio calculations. In all cases, minima were found corresponding to structures where water and hydrogen sulfide interact by means of X-H...π contacts. The interaction energies for all these π complexes are quite similar, spanning from -13.5 to -18.8 kJ/mol, and exhibiting the stability sequence NH > CH2 ≈ PH > Se ≈ S > O, for both water and hydrogen sulfide. Though interaction energies are similar, hydrogen sulfide complexes are slightly favored over their water counterparts when interacting with the π cloud. σ-Type complexes were also considered for the systems studied, but only in the case of water complexes this kind of complexes is relevant. Only for complexes formed by water and indole, a significantly more stable σ-type complex was found with an interaction energy amounting to -23.6 kJ/mol. Oxygen and phosphorous derivatives also form σ-type complexes of similar stability as that observed for π ones. Despite the similar interaction energies exhibited by complexes with water and hydrogen sulfide, the nature of the interaction is very different. For π complexes with water the main contributions to the interaction energy are electrostatic and dispersive contributing with similar amounts, though slightly more from electrostatics. On the contrary, in hydrogen sulfide complexes dispersion is by far the main stabilizing contribution. For the σ-type complexes, the interaction is clearly dominated by the electrostatic contribution, especially in the indole-water complex.

  4. DFT studies of carbohydrate solvation: II. MD-DFTr of a super-molecule complex of glucose, explicit waters, and an implicit solvent (COSMO)

    Science.gov (United States)

    MD-DFTr studies are carried out on the super-molecule solvated complexes of glucose described in paper I. Included were ten explicit water molecules and an implicit solvation model, COSMO, superimposed upon the complex. Starting configurations were taken from DFTr optimized complexes resulting from ...

  5. Coordination geometries of Zn(II) and Cd(II) in phosphotriesterase: Influence of water molecules in the active site

    DEFF Research Database (Denmark)

    Krauss, M; Olsen, Lars; Antony, J;

    2002-01-01

    to the Od1 of the carboxylate of the first-shell aspartate designated M 1, but the energy difference between Cd1Zn2 and the lowest energy Zn1Cd2 structure is only about 2 kcal/mol and decreasing with the addition of water molecules. The Zn1Cd2 arrangement is found experimentally....... performed to analyze the experimentally determined chemical shifts at 212 and 116 ppm, respectively, for the CdCd enzyme. The calculated isotropic shieldings correlate with the coordination number of the metal ions, indicating that the CdCd enzyme has one more ligand at the high shift site than at the low...

  6. Electron- and positron-induced ionization of water molecules: Theory versus experiment at the triply differential scale

    Science.gov (United States)

    Singh, P.; Purohit, G.; Champion, C.; Patidar, V.

    2014-03-01

    Triply differential cross sections for electron- and positron-induced ionization of the 3a1 orbital of the water molecule are calculated within the second-order distorted-wave Born approximation. In this context, distorted-wave functions are numerically calculated by modeling both the initial and the final channels whereas single-center Slater-type wave functions are used for describing the molecular target. A good agreement with the existing experimental data is observed. Differences in the trends of differential cross sections are observed for the electron- and positron-impact ionization.

  7. 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)

    1991-03-01

    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.

  8. GYY4137, a novel water-soluble, H2S-releasing molecule.

    Science.gov (United States)

    Rose, Peter; Dymock, Brian W; Moore, Philip K

    2015-01-01

    Hydrogen sulfide (H2S) is now recognized as the so called "third gasotransmitter" taking its place alongside nitric oxide and carbon monoxide. In recent years, H2S has been reported to exhibit a diverse range of pharmacological effects in biological systems. Much of this evidence is derived from a combination of conventional pharmacological and genetic approaches coupled with the use of chemical compounds such as sodium hydrosulfide, a rapid H2S releasing donor. Developments in the design of new drug entities which attempt to take into account physicochemical properties, targeting to specific cellular organelles, triggering of H2S release upon specific chemical reactions in the cell, and controlling the release of H2S over extended periods of time have been described. For most of these molecules, little or no work has been conducted to determine their biological activity or possible therapeutic effects. It is therefore not clear whether such molecules have therapeutic potential which highlights the need for further in vivo studies. One exception to the general rule is GYY4137 (morpholin-4-ium 4-methoxyphenyl(morpholino) phosphinodithioate), a slow releasing H2S donor, which has been evaluated for activity in a range of pharmacological models both in vitro and in vivo. GYY4137 was first reported to release H2S and exhibit vasodilator activity over 5 years ago and, to date, GYY4137 is becoming increasingly employed as a pharmacological "tool" to explore the biological functions of H2S.

  9. Bound water measurement methods and moisture distribution within sewage sludge%污泥结合水测量方法和水分分布特性

    Institute of Scientific and Technical Information of China (English)

    谢浩辉; 麻红磊; 池涌; 马增益

    2012-01-01

    为了实现污泥高效脱水,对污泥水分分布特征与脱水性能变化的关系进行研究.分别利用热干燥法、抽滤法、压滤法、水活度法和膨胀计法测定同一市政污泥的结合水相对质量分数,通过分析比较测量数据和应用原理,总结出各种方法的优缺点和适用条件.基于膨胀计法对污泥水分能量状态进行了分析,构建了污泥水分分布特征曲线,并阐明污泥在不同水分质量分数时的机械脱水效果.研究表明:5种方法的结合水质量分数(结合水/干基)测量结果差异明显,其中抽滤法测量值最大为628%,水活度法测量值最小,只有34%;膨胀计法操作快捷、原始数据容易处理,优于其余4种测量方法.当污泥水分相对质量分数(全水分/干基)大于183%时,适当提高设备的脱水强度能够较好地改善脱水效果.%Relationship between sludge moisture distribution and dewatering performance was studied to achieve effective dewatering of sewage sludge. Five measurement methods, including drying test, filtration test, expression test, sorption isotherms test and dilatometric test were applied to determine the bound water content within a typical sewage sludge sample. Features and applicable conditions of each method were obtained via analysis and comparison of their measurement data and theories. A sludge moisture distribution curve was constructed via analysis of the sludge moisture energy status in dilatometric method, which could be utilized to elucidate the sludge dewatering performance at different moisture contents. The experimental results indicate that the sludge bound water measurement results from five methods are different, and the maximum data of 628% mass fraction of the sludge bound water (bound water/ dry water) measurement result is obtained from filtration test whereas the minimum data of 34% from sorption isotherms test. The dilatometric method is preferable to the other methods due to its

  10. 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.

    Science.gov (United States)

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

    2017-04-01

    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.

  11. The key role of meteorites in the formation of relevant prebiotic molecules in a formamide/water environment

    Science.gov (United States)

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

    2016-12-01

    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.

  12. Partial oxidation of Step-Bound Water Leads to Anomalous pH Effects on Metal Electrode Step-Edges

    CERN Document Server

    Schwarz, Kathleen; Yan, Yushan; Sundararaman, Ravishankar

    2016-01-01

    The design of better heterogeneous catalysts for applications such as fuel cells and electrolyzers requires a mechanistic understanding of electrocatalytic reactions and the dependence of their activity on operating conditions such as pH. A satisfactory explanation for the unexpected pH dependence of electrochemical properties of platinum surfaces has so far remained elusive, with previous explanations resorting to complex co-adsorption of multiple species and resulting in limited predictive power. This knowledge gap suggests that the fundamental properties of these catalysts are not yet understood, limiting systematic improvement. Here, we analyze the change in charge and free energies upon adsorption using density-functional theory (DFT) to establish that water adsorbs on platinum step edges across a wide voltage range, including the double-layer region, with a loss of approximately 0.2 electrons upon adsorption. We show how the change in net surface charge due to this water explains the anomalous pH variat...

  13. Effect of anodizing voltage on the sorption of water molecules on porous alumina

    Energy Technology Data Exchange (ETDEWEB)

    Vrublevsky, I., E-mail: vrublevsky@bsuir.edu.by [Belarusian State University of Informatics and Radioelectronics, Department of Micro and Nanoelectronics, 220013 Minsk (Belarus); Chernyakova, K. [Belarusian State University of Informatics and Radioelectronics, Department of Micro and Nanoelectronics, 220013 Minsk (Belarus); Bund, A.; Ispas, A.; Schmidt, U. [Fachgebiet Elektrochemie und Galvanotechnik, Technische Universitaet Ilmenau, 98693 Ilmenau (Germany)

    2012-05-01

    The amount of water adsorbed on different centers on the surface of oxalic acid alumina films is a function of the anodizing voltage. It is decreased with increasing the anodizing voltage from 20 up to 50 V, came up to maximum value at 20-30 V and slightly increased at voltages above 50 V. Water adsorption by oxide films formed at voltages below 50 V can be due to the negative surface charge that is present on the alumina surface. The negative surface charge disappears in the films formed at voltages higher than 50 V, and thus, the water is adsorbed on aluminum ions in a tetrahedral and octahedral environment. The correlation between anodizing conditions of aluminum in oxalic acid and the structure and composition of anodic alumina was established by Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM), thermogravimetric and differential thermal analyses (TG/DTA).

  14. The added value of a water footprint approach: Micro- and macroeconomic analysis of cotton production, processing and export in water bound Uzbekistan

    Science.gov (United States)

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

    2013-11-01

    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.

  15. The effects of metabolite molecules produced by drinking water-isolated bacteria on their single and multispecies biofilms.

    Science.gov (United States)

    Simões, Lúcia Chaves; Simões, Manuel; Vieira, Maria João

    2011-08-01

    The elucidation of the mechanisms by which diverse species survive and interact in drinking water (DW) biofilm communities may allow the identification of new biofilm control strategies. The purpose of the present study was to investigate the effects of metabolite molecules produced by bacteria isolated from DW on biofilm formation. Six opportunistic bacteria, viz. Acinetobacter calcoaceticus, Burkholderia cepacia, Methylobacterium sp., Mycobacterium mucogenicum, Sphingomonas capsulata and Staphylococcus sp. isolated from a drinking water distribution systems (DWDS) were used to form single and multispecies biofilms in the presence and absence of crude cell-free supernatants produced by the partner bacteria. Biofilms were characterized in terms of mass and metabolic activity. Additionally, several physiological aspects regulating interspecies interactions (sessile growth rates, antimicrobial activity of cell-free supernatants, and production of iron chelators) were studied to identify bacterial species with biocontrol potential in DWDS. Biofilms of Methylobacterium sp. had the highest growth rate and M. mucogenicum biofilms the lowest. Only B. cepacia was able to produce extracellular iron-chelating molecules. A. calcoaceticus, B. cepacia, Methylobacterium sp. and M. mucogenicum biofilms were strongly inhibited by crude cell-free supernatants from the other bacteria. The crude cell-free supernatants of M. mucogenicum and S. capsulata demonstrated a high potential for inhibiting the growth of counterpart biofilms. Multispecies biofilm formation was strongly inhibited in the absence of A. calcoaceticus. Only crude cell-free supernatants produced by B. cepacia and A. calcoaceticus had no inhibitory effects on multispecies biofilm formation, while metabolite molecules of M. mucogenicum showed the most significant biocontrol potential.

  16. A strategy for the incorporation of water molecules present in a ligand binding site into a three-dimensional quantitative structure--activity relationship analysis.

    Science.gov (United States)

    Pastor, M; Cruciani, G; Watson, K A

    1997-12-05

    Water present in a ligand binding site of a protein has been recognized to play a major role in ligand-protein interactions. To date, rational drug design techniques do not usually incorporate the effect of these water molecules into the design strategy. This work represents a new strategy for including water molecules into a three-dimensional quantitative structure-activity relationship analysis using a set of glucose analogue inhibitors of glycogen phosphorylase (GP). In this series, the structures of the ligand-enzyme complexes have been solved by X-ray crystallography, and the positions of the ligands and the water molecules at the ligand binding site are known. For the structure-activity analysis, some water molecules adjacent to the ligands were included into an assembly which encompasses both the inhibitor and the water involved in the ligand-enzyme interaction. The mobility of some water molecules at the ligand binding site of GP gives rise to differences in the ligand-water assembly which have been accounted for using a simulation study involving force-field energy calculations. The assembly of ligand plus water was used in a GRID/GOLPE analysis, and the models obtained compare favorably with equivalent models when water was excluded. Both models were analyzed in detail and compared with the crystallographic structures of the ligand-enzyme complexes in order to evaluate their ability to reproduce the experimental observations. The results demonstrate that incorporation of water molecules into the analysis improves the predictive ability of the models and makes them easier to interpret. The information obtained from interpretation of the models is in good agreement with the conclusions derived from the structural analysis of the complexes and offers valuable insights into new characteristics of the ligands which may be exploited for the design of more potent inhibitors.

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

    Science.gov (United States)

    Dutta, Bipan; De, Rina; Chowdhury, Joydeep

    2015-12-01

    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.

  18. Attributes of aerosol bound water soluble ions and carbon, and their relationships with AOD over the Brahmaputra Valley

    Science.gov (United States)

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

    2016-10-01

    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

  19. Behavior of Freezable Bound Water in the Bacterial Cellulose Produced by Acetobacter xylinum: An Approach Using Thermoporosimetry

    OpenAIRE

    Kaewnopparat, Sanae; Sansernluk, Kamonlawat; Faroongsarng, Damrongsak

    2008-01-01

    The aim of the study is to examine thermal behavior of water within reticulated structure of bacterial cellulose (BC) films by sub-ambient differential scanning calorimetry (DSC). BC films with different carbon source, either manitol (BC (a)) or glycerol (BC (b)), were produced by Acetobacter xylinum using Hestrin and Shramm culture medium under static condition at 30 ± 0.2°C for 3 days. BC samples were characterized by electron scanning microscopy and X-ray diffraction spectroscopy. The pore...

  20. Willingness-to-pay for water quality improvements in Chinese rivers: an empirical test on the ordering effects of multiple-bounded discrete choices.

    Science.gov (United States)

    Wang, Hua; He, Jie; Kim, Yoonhee; Kamata, Takuya

    2013-12-15

    This paper presents a study of the willingness-to-pay (WTP) for surface water quality improvement in China. In the Huaping County of Yunnan Province, we found that people are willing to pay 74 Yuan (or US$12.33 in 2012 prices) per household per month (or 5% of household income) continuously for five years to achieve an improvement of water quality in the two major local rivers from the current Grade IV to Grade III, which denotes a level suitable for swimming and fishing and matches the water quality level from 10 years ago. This WTP study is based on an actual investment project that was under serious consideration by the government and is based on the multiple-bounded discrete choice (MBDC) approach, which explicitly recognizes the potential uncertainties involved in the study. The potential ordering effects associated with the MBDC approach are empirically tested, and the results indicate that although the presentation order of the polychotomous likelihood choices may not have a significant impact on the WTP estimation, the presentation order of bid levels may have a significant impact.

  1. Coherent Behavior and the Bound State of Water and K(+) Imply Another Model of Bioenergetics: Negative Entropy Instead of High-energy Bonds.

    Science.gov (United States)

    Jaeken, Laurent; Vasilievich Matveev, Vladimir

    2012-01-01

    Observations of coherent cellular behavior cannot be integrated into widely accepted membrane (pump) theory (MT) and its steady state energetics because of the thermal noise of assumed ordinary cell water and freely soluble cytoplasmic K(+). However, Ling disproved MT and proposed an alternative based on coherence, showing that rest (R) and action (A) are two different phases of protoplasm with different energy levels. The R-state is a coherent metastable low-entropy state as water and K(+) are bound to unfolded proteins. The A-state is the higher-entropy state because water and K(+) are free. The R-to-A phase transition is regarded as a mechanism to release energy for biological work, replacing the classical concept of high-energy bonds. Subsequent inactivation during the endergonic A-to-R phase transition needs an input of metabolic energy to restore the low entropy R-state. Matveev's native aggregation hypothesis allows to integrate the energetic details of globular proteins into this view.

  2. Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1993-01-01

    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.

  3. Isolation of pregnancy-associated glycoproteins (PAG from water buffalo (Bubalus bubalis placenta by use of Vicia villosa bound agarose affinity chromatography

    Directory of Open Access Journals (Sweden)

    J.F. Beckers

    2010-02-01

    Full Text Available The present study describes the isolation and characterisation of new PAG molecules extracted from mid- and late-pregnancy placentas in the water buffalo (Bubalis bubalis. After extraction, acid and ammonium sulphate precipitation and DEAE chromatography water buffalo PAG (wbPAG were enriched by Vicia villosa agarose (VVA affininity chromatography. As determined by Western blotting with anti-PAG-sera, apparent molecular masses of immunoreactive bands from VVA peaks ranged from 59.5 to 75.8 kDa and from 57.8 to 80.9 kDa in the mid- and late- pregnancy placenta respectively. Aminoterminal microsequencing of proteins allowed the identification of three distinct wbPAG sequences wich have ben deposed in the SwissProt database: RGSXLTIHPLRNIRDFFYUG (Acc. n. P85048, RGSXLTILPLRNIID (P85049 and RGSXLTHLPLRNI (P85050. Their comparison to those previously identified revealed that two of them were new since they have not been described yet. Our results confirm the suitability of VVA chromatography in enrichment of multiple PAG molecules expressed in buffalo placenta. Productions of specific antisera can be very useful in immonoistochemical and immunocyitochemical studies of PAG expression in fetomaternal interfaces. Purified native PAG are also required for development on specific immoassays (RIA/ELISA currently used for pregnancy diagnosis and physiological investigation in farm animal.

  4. Organic Molecules and Water in the Inner Disks of T Tauri Stars

    Science.gov (United States)

    2011-05-11

    water emission properties in the full Spitzer spectrum (but see Section 4.2.2). By focusing on this wavelength region we can also optimize the...cores and comets are from references given in the text . (A color version of this figure is available in the online journal.) error bars corresponds to...because comets are made of icy material that was originally present in the Jupiter– Saturn region and in the outer solar nebula (the Kuiper Belt) during

  5. Binding Energy of Molecules on Water Ice: Laboratory Measurements and Modeling

    CERN Document Server

    He, Jiao; Vidali, Gianfranco

    2016-01-01

    We measured the binding energy of N$_2$, CO, O$_2$, CH$_4$, and CO$_2$ on non-porous (compact) amorphous solid water (np-ASW), of N$_2$ and CO on porous amorphous solid water (p-ASW), and of NH$_3$ on crystalline water ice. We were able to measure binding energies down to a fraction of 1\\% of a layer, thus making these measurements more appropriate for astrochemistry than the existing values. We found that CO$_2$ forms clusters on np-ASW surface even at very low coverages. The binding energies of N$_2$, CO, O$_2$, and CH$_4$ decrease with coverage in the submonolayer regime. Their values at the low coverage limit are much higher than what is commonly used in gas-grain models. An empirical formula was used to describe the coverage dependence of the binding energies. We used the newly determined binding energy distributions in a simulation of gas-grain chemistry for cold cloud and hot core models. We found that owing to the higher value of desorption energy in the sub-monlayer regime a fraction of all these ice...

  6. Organic Molecules and Water in the Inner Disks of T Tauri Stars

    CERN Document Server

    Carr, John S

    2011-01-01

    We report high signal-to-noise Spitzer IRS spectra of a sample of eleven classical T Tauri stars. Molecular emission from rotational transitions of H2O and OH and ro-vibrational bands of simple organic molecules (CO2, HCN, C2H2) is common among the sources in the sample. The gas temperatures (200-800 K) and emitting areas we derive are consistent with the emission originating in a warm disk atmosphere in the inner planet formation region at radii < 2 AU. The H2O emission appears to form under a limited range of excitation conditions, as shown by the similarity in relative strengths of H2O features from star to star and the narrow range in derived temperature and column density. Emission from highly excited rotational levels of OH is present in all stars; the OH emission flux increases with the stellar accretion rate, and the OH/H2O flux ratio shows a relatively small scatter. We interpret these results as evidence for OH production via FUV photo-dissociation of H2O in the disk surface layers. No obvious ex...

  7. Confined Water Determines Transport Properties of Guest Molecules in Narrow Pores.

    Science.gov (United States)

    Phan, Anh; Cole, David R; Weiß, R Gregor; Dzubiella, Joachim; Striolo, Alberto

    2016-08-23

    We computed the transport of methane through 1 nm wide slit-shaped pores carved out of solid substrates. Models for silica, magnesium oxide, and alumina were used as solid substrates. The pores were filled with water. The results show that the methane permeability through the hydrated pores is strongly dependent on the solid substrate. Detailed analysis of the simulated systems reveals that local properties of confined water, including its structure, and more importantly, evolution of solvation free energy and hydrogen bond structure are responsible for the pronounced differences observed. The simulations are extended to multicomponent systems representative of natural gas, containing methane, ethane, and H2S. The results show that all pores considered have high affinity for H2S, moderate affinity for methane, and low affinity for ethane. The H2S/methane transport selectivity through the hydrated alumina pore is comparable, or superior, to that reported for existing commercial membranes. A multiscale approach was then implemented to demonstrate that a Smoluchowski one-dimensional model is able to reproduce the molecular-level results for short pores when appropriate values for the local self-diffusion coefficients are used as input parameters. We propose that the model can be extended to predict methane transport through uniform hydrated pores of macroscopic length. When verified by experiments, our simulation results could have important implications in applications such as natural gas sweetening and predictions of methane migration through hydraulically fractured shale formations.

  8. Water as probe molecule for midgap states in nanocrystalline strontium titanate by conventional and synchronous luminescence spectroscopy under ambient conditions

    Science.gov (United States)

    Taylor, Sean; Samokhvalov, Alexander

    2017-03-01

    Alkaline earth metal titanates are broad bandgap semiconductors with applications in electronic devices, as catalysts, photocatalysts, sorbents, and sensors. Strontium titanate SrTiO3 is of interest in electronic devices, sensors, in the photocatalytic hydrogen generation, as catalyst and sorbent. Both photocatalysis and operation of electronic devices rely upon the pathways of relaxation of excited charge in the semiconductor, including relaxation through the midgap states. We report characterization of nanocrystalline SrTiO3 at room temperature by "conventional" vs. synchronous luminescence spectroscopy and complementary methods. We determined energies of radiative transitions in the visible range through the two midgap states in the nanocrystalline SrTiO3. Further, adsorption and desorption of vapor of water as "probe molecule" for midgap states in the nanocrystalline SrTiO3 was studied, for the first time, by luminescence spectroscopy under ambient conditions. Emission of visible light from the nanocrystalline SrTiO3 is significantly increased upon desorption of water and decreased (quenched) upon adsorption of water vapor, due to interactions with the surface midgap states.

  9. Photo-electrochemical Oxidation of Organic C1 Molecules over WO3 Films in Aqueous Electrolyte: Competition Between Water Oxidation and C1 Oxidation.

    Science.gov (United States)

    Reichert, Robert; Zambrzycki, Christian; Jusys, Zenonas; Behm, R Jürgen

    2015-11-01

    To better understand organic-molecule-assisted photo-electrochemical water splitting, photo-electrochemistry and on-line mass spectrometry measurements are used to investigate the photo-electrochemical oxidation of the C1 molecules methanol, formaldehyde, and formic acid over WO3 film anodes in aqueous solution and its competition with O2 evolution from water oxidation O2 (+) and CO2 (+) ion currents show that water oxidation is strongly suppressed by the organic species. Photo-electro-oxidation of formic acid is dominated by formation of CO2 , whereas incomplete oxidation of formaldehyde and methanol prevails, with the selectivity for CO2 formation increasing with increasing potential and light intensity. The mechanistic implications for the photo-electro-oxidation of the organic molecules and its competition with water oxidation, which could be derived from this novel approach, are discussed.

  10. Comparison of the solid-phase extraction efficiency of a bounded and an included cyclodextrin-silica microporous composite for polycyclic aromatic hydrocarbons determination in water samples.

    Science.gov (United States)

    Mauri-Aucejo, Adela; Amorós, Pedro; Moragues, Alaina; Guillem, Carmen; Belenguer-Sapiña, Carolina

    2016-08-15

    Solid-phase extraction is one of the most important techniques for sample purification and concentration. A wide variety of solid phases have been used for sample preparation over time. In this work, the efficiency of a new kind of solid-phase extraction adsorbent, which is a microporous material made from modified cyclodextrin bounded to a silica network, is evaluated through an analytical method which combines solid-phase extraction with high-performance liquid chromatography to determine polycyclic aromatic hydrocarbons in water samples. Several parameters that affected the analytes recovery, such as the amount of solid phase, the nature and volume of the eluent or the sample volume and concentration influence have been evaluated. The experimental results indicate that the material possesses adsorption ability to the tested polycyclic aromatic hydrocarbons. Under the optimum conditions, the quantification limits of the method were in the range of 0.09-2.4μgL(-1) and fine linear correlations between peak height and concentration were found around 1.3-70μgL(-1). The method has good repeatability and reproducibility, with coefficients of variation under 8%. Due to the concentration results, this material may represent an alternative for trace analysis of polycyclic aromatic hydrocarbons in water trough solid-phase extraction.

  11. Small molecule mixture analysis by heteronuclear NMR under spin diffusion conditions in the viscous DMSO-water solvent.

    Science.gov (United States)

    Lameiras, Pedro; Patis, Solène; Jakhlal, Jouda; Castex, Stéphanie; Clivio, Pascale; Nuzillard, Jean-Marc

    2017-02-13

    Spin diffusion in NMR occurs for small and medium-sized molecules when their tumbling rate reduces in solution so that magnetization exchange by longitudinal cross relaxation becomes highly efficient. Composite DMSO-water viscous solvents were used for the first time to access the individual NMR spectra of mixture components in spin diffusion conditions. The easy handling and high dissolution power of [D6]DMSO/H2O offers a wide range of potential applications for polar and apolar mixture analysis. In addition to 2D 1H-1H NOESY and 1H-13C HSQC-NOESY, 1H-15N HSQC-NOESY, 1D and 2D 1H-19F HOESY experiments were set up to offer new ways to individualize molecules within a mixture. This article reports the analysis of a polar mixture of four dipeptides dissolved in [D6]DMSO/H2O (7:3, v/v) and of a low polarity fluorinated dinucleotide dissolved in [D6]DMSO/H2O (8:2, v/v) by means of spin diffusion in NOESY, HOESY, and HSQC-NOESY experiments.

  12. Theoretical investigation of hydrogen bonding between water and platinum(II): an atom in molecule (AIM) study

    Science.gov (United States)

    Li, Yan; Zhang, Guiqiu; Chen, Dezhan

    2012-02-01

    Recently, Rizzato et al. [Angew. Chem. Int. Ed. 49, 7440 (2010)] [1] reported a hydrogen-bonding-like interaction between a water molecule and a d8 metal ion (PtII) based on neutron diffraction, and provided the first crystallographic evidence for this interaction. We studied the hydrogen bonding of the O-H ... Pt interaction theoretically using atoms in molecule (AIM) and natural bond orbital analysis (NBO) in the crystallographic geometries. The method used density functional theory (DFT) with the hybrid B3LYP function. For platinum atoms, we used the Los Alamos National Laboratory 2-Double-Zeta (LANL2DZ) basis set, and for the other atoms we used 6-311++G(d,p) basis sets. Criteria based on a topological analysis of the electron density were used in order to characterize the nature of interactions in the complexes. The main purpose of the present work is to provide an answer to the following questions: Why can a filled d orbital of square-planar d8 metal ions such as platinum(II) also act as hydrogen-bond acceptors? Can a study based on the electron charge density answer this question? A good correlation between the density at the intermolecular bond critical point and the energy interaction was found. The interaction is mainly closed-shell and there is some charge transfer in this system.

  13. Bond-selective fragmentation of water molecules with intense, ultrafast, carrier envelope phase stabilized laser pulses

    CERN Document Server

    Mathur, D; Dharmadhikari, J A; Dharmadhikari, A K

    2013-01-01

    Carrier envelope phase (CEP) stabilized pulses of intense 800 nm light of 5 fs duration are used to probe the dissociation dynamics of dications of isotopically-substituted water, HOD. HOD$^{2+}$ dissociates into either H$^+$ + OD$^+$ or D$^+$ + OH$^+$. The branching ratio for these two channels is CEP-dependent; the OD$^+$/OH$^+$ ratio (relative to that measured with CEP-unstabilized pulses) varies from 150% to over 300% at different CEP values, opening prospects of isotope-dependent control over molecular bond breakage. The kinetic energy released as HOD$^{2+}$ Coulomb explodes is also CEP-dependent. Formidable theoretical challenges are identified for proper insights into the overall dynamics which involve non-adiabatic field ionization from HOD to HOD$^+$ and, thence, to HOD$^{2+}$ via electron rescattering.

  14. Electron impact double ionization of single oriented water molecules: evidence of the role of the two-step mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Dal Cappello, C; Champion, C [Universite Paul Verlaine-Metz, LPMC, Institut de Physique, 1 bd Arago, 57078 Metz Cedex 3 (France); Kada, I; Mansouri, A, E-mail: cappello@univ-metz.fr [Universite Ferhat Abbas, LPQSD, Departement de physique, 19000 Setif (Algeria)

    2011-04-01

    Double ionization of single oriented water molecules is here investigated within a theoretical approach based on the second Born approximation. The initial wave function describing the two active electrons is taken from a single-centre description previously used with success for describing the single ionization process whereas the final state wave function describing the two ejected electrons is the approximate BBK wave function. Secondary electron angular distributions for an incident energy close to 600 eV are then reported for particular kinematical conditions and compared to their first Born homologous. Strong similarities are observed in terms of maxima localization as well as identification of the main mechanisms involved in the double ionization. On the contrary, for particular kinematical conditions we demonstrate that the first-order treatment is unable to explain the observations contrary to the second-order approximation which points out pure TS2 contributions.

  15. 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.

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

    Directory of Open Access Journals (Sweden)

    Stella Kiel

    2012-03-01

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-02-15

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

  18. Binding of Solvent Molecules to a Protein Surface in Binary Mixtures Follows a Competitive Langmuir Model.

    Science.gov (United States)

    Kulschewski, Tobias; Pleiss, Jürgen

    2016-09-06

    The binding of solvent molecules to a protein surface was modeled by molecular dynamics simulations of of Candida antarctica (C. antarctica) lipase B in binary mixtures of water, methanol, and toluene. Two models were analyzed: a competitive Langmuir model which assumes identical solvent binding sites with a different affinity toward water (KWat), methanol (KMet), and toluene (KTol) and a competitive Langmuir model with an additional interaction between free water and already bound water (KWatWat). The numbers of protein-bound molecules of both components of a binary mixture were determined for different compositions as a function of their thermodynamic activities in the bulk phase, and the binding constants were simultaneously fitted to the six binding curves (two components of three different mixtures). For both Langmuir models, the values of KWat, KMet, and KTol were highly correlated. The highest binding affinity was found for methanol, which was almost 4-fold higher than the binding affinities of water and toluene (KMet ≫ KWat ≈ KTol). Binding of water was dominated by the water-water interaction (KWatWat). Even for the three protein surface patches of highest water affinity, the binding affinity of methanol was 2-fold higher than water and 8-fold higher than toluene (KMet > KWat > KTol). The Langmuir model provides insights into the protein destabilizing mechanism of methanol which has a high binding affinity toward the protein surface. Thus, destabilizing solvents compete with intraprotein interactions and disrupt the tertiary structure. In contrast, benign solvents such as water or toluene have a low affinity toward the protein surface. Water is a special solvent: only few water molecules bind directly to the protein; most water molecules bind to already bound water molecules thus forming water patches. A quantitative mechanistic model of protein-solvent interactions that includes competition and miscibility of the components contributes a robust basis

  19. Synthesis and Resonance Energy Transfer in Conjugates of Luminescent Cadmium Selenide Quantum Dots and Chlorin e6 Molecules

    Science.gov (United States)

    Fedosyuk, A. A.; Artemyev, M. V.

    2013-05-01

    We synthesized a new type of conjugates of highly luminescent water soluble CdSe/ZnS colloidal quantum dots covalently bound to Chlorin e6 dye molecules. We observed a resonance energy transfer from quantum dots emitting at 660 nm to Chlorine e6 molecules in our conjugates which can be utilized for phototherapy. Contrary to that quantum dots emitting at 588 nm show non-resonance quenching of excitonic luminescence without the energy transfer to dye molecules.

  20. Double differential distribution of electron emission in the ionization of water molecules by fast bare oxygen ions

    Science.gov (United States)

    Bhattacharjee, Shamik; Biswas, Shubhadeep; Bagdia, Chandan; Roychowdhury, Madhusree; Nandi, Saikat; Misra, Deepankar; Monti, J. M.; Tachino, C. A.; Rivarola, R. D.; Champion, C.; Tribedi, Lokesh C.

    2016-03-01

    The doubly differential distributions of low-energy electron emission in the ionization of water molecules under the impact of fast bare oxygen ions with energy of 48 MeV are measured. The measured data are compared with two quantum-mechanical models, i.e. the post and prior versions of the continuum distorted wave-eikonal initial state (CDW-EIS) approximation, and the first-order Born approximation with initial and final wavefunctions verifying correct boundary conditions (CB1). An overall excellent qualitative agreement is found between the data and the CDW-EIS models whereas the CB1 model showed substantial deviation. However, the detailed angular distributions display some discrepancies with both CDW-EIS models. The single differential and total cross-sections exhibit good agreement with the CDW-EIS models. The present detailed data set could also be used as an input for modeling highly charged ion induced radiation damage in living tissues, whose most abundant component is water. Similar measurements are also carried out for a projectile energy of 60 MeV. However, since the double differential cross-section data show similar results the details are not provided here, except for the total ionization cross-sections results.

  1. Isolation and structural characterization of two water-borne pheromones from Euplotes crassus, a ciliate commonly known to carry membrane-bound pheromones.

    Science.gov (United States)

    Alimenti, Claudio; Vallesi, Adriana; Federici, Sergio; di Giuseppe, Graziano; Fernando, Dini; Carratore, Vitale; Luporini, Pierangelo

    2011-01-01

    Ciliates comprise species synthesizing water-diffusible mating type factors or pheromones and species synthesizing insoluble, cell membrane-bound pheromones. Euplotes crassus has traditionally been placed in the latter group. In contrast with this notion, we found that E. crassus is a constitutive pheromone-secreting ciliate, like other Euplotes species. From cell-free filtrate preparations of the E. crassus strain L-2D, we isolated two distinct pheromones, designated as Ec-α and Ec-1, and determined their complete amino acid sequences by combined chemical and genetic approaches. The Ec-α pheromone sequence extends for 56 amino acid residues with six cysteines and shows a molecular mass of 6,183 Da, while the Ec-1 pheromone sequence extends for 45 amino acid residues with 10 cysteines and shows a molecular mass of 4,840 Da. Marked structural differences distinguish the full-length Ec-α and Ec-1 coding sequences, which have been cloned and characterized from the transcriptionally active macronuclear genome. They were taken as clear indication that the Ec-α and Ec-1 pheromones are specified by genes that are not allelic, but likely derived from a duplicated genetic locus of the transcriptionally silent micronuclear genome.

  2. Chemical interaction of water molecules with framework Al in acid zeolites: a periodic ab initio study on H-clinoptilolite.

    Science.gov (United States)

    Valdiviés-Cruz, Karell; Lam, Anabel; Zicovich-Wilson, Claudio M

    2015-09-28

    Periodic quantum-chemistry methods as implemented in the CRYSTAL14 code were considered to analyse the interaction of acid clinoptilolite with water. Initially adsorbed molecules hydrolyse the Al-O bonds, giving rise to defective dealuminated materials. A suitable and representative periodic model of the partially disordered hydrated H-zeolite is the primitive cell (18 T sites) of a decahydrated trialuminated structure of HEU topology. The water distribution inside the material cavities was initially investigated. The model considered for further dealumination was the most stable one from those generated through a combined force field Monte Carlo and ab initio optimization strategy. Optimizations and energy estimations were made at the hybrid DFT level of theory (PBE0 functional) with an atomic basis set of VDZP quality. The energetics of the different pathways involved in the dealumination process was addressed by considering the Gibbs free energy with thermal and zero-point corrections through phonon analysis. It arises that hydrated models exhibit protonated water clusters stabilized by different kinds of H-bonds. The first Al extraction is slightly more energetically favourable from T3 than T2 sites, but at the same time the latter is more probable owing to its larger Al population. However, concerning the second dealumination step, it is more favourable removing the Al atom from both remaining sites after a starting abstraction from T2 rather than T3. These facts determine that the most probable overall pathways go through a first Al removal from T2. The agreement with experimental results is discussed.

  3. Dihydrogen phosphate-water tape and layers vs dihydrogen phosphate layers tuned by hydrophobic isomeric pyridine-diamine functionalized molecules

    Science.gov (United States)

    Huang, Jing; Liu, Tong-Peng; Huo, Li-Hua; Deng, Zhao-Peng; Gao, Shan

    2017-01-01

    Assembly of six isomeric pyridine-diamine-based molecules, N,N‧-bis(pyridin-4-ylmethyl)ethane-1,2-diamine (M1), N,N‧-bis(pyridin-3-ylmethyl)ethane-1,2-diamine (M2), N,N‧-bis(pyridin-2-ylmethyl)ethane-1,2-diamine (M3), N,N‧-bis(pyridin-4-ylmethyl)propane-1,3-diamine (M4), N,N‧-bis(pyridin-3-ylmethyl)propane-1,2-diamine (M5), and N,N‧-bis(pyridin-2-ylmethyl)propane-1,3-diamine (M6), with phosphoric acid (H3PO4) in different ratio (1:2 and 1:4), leads to the formation of nine salts, H2M12+·2H2PO4-·4H2O (1), H2M22+·2H2PO4-·2H2O (2), H2M32+·2H2PO4-·2H2O (3), H4M14+·4H2PO4- (4), H4M24+·4H2PO4- (5), H4M34+·4H2PO4- (6), H2M42+·2H2PO4-·3H2O (7), 2H2M52+·4H2PO4-·2H3PO4 (8), and H2M62+·2H2PO4- (9), which have been characterized by elemental analysis, IR, TG, PL, powder and single-crystal X-ray diffraction. Structural analyses indicate that hydrogen-bonding patterns of H2PO4- anions, conformation of protonated cations can effectively influence the supramolecular architectures through diverse non-covalent interactions. Hydrous salts 1-3 and 7 present 2D and 3D host-guest supramolecular networks, in which the connection of H2PO4- anions and water molecules generates diverse tape and layer motifs. H2PO4- anions in anhydrous salts 4-6 interconnect with each other through hydrogen bonds to form two types of layers, which are joined by discrete H4M4+ cations into 3D inorganic-organic hybrid supramolecular networks. Salts 8-9 also present 2D and 3D host-guest supramolecular networks where the interconnection of H2PO4- anions and its combination with H3PO4 molecules leads to diverse layers. Luminescent analyses indicate that salts 1-9 exhibit violet and blue emission maximum in the range of 390-467 nm at room temperature.

  4. Construction of diverse supramolecular assemblies of dimetal subunits differing in coordinated water molecules via strong hydrogen bonding interactions: Synthesis, crystal structures and spectroscopic properties

    Indian Academy of Sciences (India)

    Sadhika Khullar; Sanjay K Mandal

    2014-09-01

    Three new supramolecular assemblies (constructed through strong hydrogen bonding) of [Co2(bpta)2(adc)(H2O)4](ClO4)2.2H2O (1), [Cu2(bpta)2(fum)(H2O)2](ClO4)2 (2) and [Cu2(bpta)2(tdc)(H2O) (ClO4)](ClO4).3H2O (3), which are synthesised by one pot self-assembly of the metal salt, bpta ligand and the corresponding dicarboxylate under the same reaction conditions, are reported (where adc = acetylene dicarboxylate, fum = fumarate, tdc = 2,5-thiophenedicarboxylate and bpta = N,N'-bis(2-pyridylmethyl)-tertbutylamine). These compounds have varying degrees of coordinatedwater molecules per dimetal subunits (four for 1, two for 2 and one for 3, respectively). Furthermore, the orientation of the coordinated water molecules in 1 and 2, with respect to the mono (carboxylato)-bridged dimetal subunit, is different (cis and trans, respectively). On the other hand, there is a coordinated perchlorate ion in 3 making the two metal centers inequivalent. Unlike 1 and 3, there are no lattice water molecules in 2. This difference in the dimetal subunit in 1-3 and the presence or absence of the lattice water molecules are the keys to forming the diverse supramolecular assemblies. In 1 and 3, the involvement of lattice water molecules in the construction of such assemblies is distinctly different. In case of 2, the formation of supramolecular assembly depends on the coordinated water molecule (trans to each other) and thus a ladder shaped supramolecular assembly is the result. The strength of hydrogen bonding observed in the networks of 1-3 is indicated in the O…O distances (2.596 Å to 3.160 Å) and the OH…O angles 124° to 176°. All are characterised by elemental analysis, FTIR spectroscopy and single crystal X-ray diffraction studies.

  5. Heavy Exotic Molecules

    CERN Document Server

    Liu, Yizhuang

    2016-01-01

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

  6. 离子土固化剂对膨胀土结合水影响机制研究%Effect of ionic soil stabilizer on bound water of expansive soils

    Institute of Scientific and Technical Information of China (English)

    刘清秉; 项伟; 崔德山

    2012-01-01

    以河南安阳弱膨胀土为对象,通过"水汽等温吸附–热失重、差热分析"对膨胀土表面吸附结合水类型进行界定,比较分析离子土固化剂(ISS)改性前后,膨胀土结合水分布形态及数量变化,并基于傅里叶红外光谱,从水分子结构振动信息角度对膨胀土吸附结合水类型界定方法进行定性验证;结合ISS改性前后黏土矿物组分、表面理化性质的变化,解释分析了不同水汽湿度区间内,ISS对膨胀土水合行为的作用模型及改性机理。结果表明:达到一定的水汽"特征"湿度段,土表面水合状态和结合水性质将发生转变,根据热曲线的脱失温度区间可将结合水界定划分为三种类型:强结合水,"过渡"结合水和弱结合水。ISS作用后,土吸附强结合水量无明显改变,"过渡"结合水及弱结合水含量显著降低。ISS通过对膨胀性黏土矿物表面及层间的物化作用,弱化黏土矿物部分"水合活性中心"能量,从而抑制了膨胀土水化膨胀势。%The "water vapor adsorption isotherm - TG, DSC" method is proposed to define and investigate the type of bound water of typical Anyang weak expansive soils. A comparative analysis of the distribution characteristics and amount of bound water is made between the original soil and ISS-soil. From the perspective of water molecular structure vibration and based on the theory of Fourier transform infrared spectroscopy, the rationality of the proposed method is also qualitatively validated. Finally, the effect of ISS on the bound water is interpreted in terms of the change of the clay mineral composition and surface physicochemical property. The test results indicate that the distribution state and property of the boundwaer will alter at specific relative humidity interval. According to the TG - DSC curve, the bound water can be divided into three types at different elevated temperature ranges, i.e., strongly bound water

  7. The bound conformation of microtubule-stabilizing agents: NMR insights into the bioactive 3D structure of discodermolide and dictyostatin.

    Science.gov (United States)

    Canales, Angeles; Matesanz, Ruth; Gardner, Nicola M; Andreu, José Manuel; Paterson, Ian; Díaz, J Fernando; Jiménez-Barbero, Jesús

    2008-01-01

    A protocol based on a combination of NMR experimental data with molecular mechanics calculations and docking procedures has been employed to determine the microtubule-bound conformation of two microtubule-stabilizing agents, discodermolide (DDM) and dictyostatin (DCT). The data indicate that tubulin in assembled microtubules recognizes DDM through a conformational selection process, with minor changes in the molecular skeleton between the major conformer in water solution and that bound to assembled microtubules. For DCT, the deduced bound geometry presents some key conformation differences around certain torsion angles, with respect to the major conformer in solution, and still displays mobility even when bound. The bound conformer of DCT resembles that of DDM and provides very similar contacts with the receptor. Competition experiments indicate that both molecules compete with the taxane-binding site. A model of the binding mode of DDM and DCT to tubulin is proposed.

  8. Quasiphase Transition in a Single File of Water Molecules Encapsulated in (6,5) Carbon Nanotubes Observed by Temperature-Dependent Photoluminescence Spectroscopy

    Science.gov (United States)

    Ma, Xuedan; Cambré, Sofie; Wenseleers, Wim; Doorn, Stephen K.; Htoon, Han

    2017-01-01

    Molecules confined inside single-walled carbon nanotubes (SWCNTs) behave quite differently from their bulk analogues. In this Letter we present temperature-dependent (4.2 K up to room temperature) photoluminescence (PL) spectra of water-filled and empty single-chirality (6,5) SWCNTs. Superimposed on a linear temperature-dependent PL spectral shift of the empty SWCNTs, an additional stepwise PL spectral shift of the water-filled SWCNTs is observed at ˜150 K . With the empty SWCNTs serving as an ideal reference system, we assign this shift to temperature-induced changes occurring in the single-file chain of water molecules encapsulated in the tubes. Our molecular dynamics simulations further support the occurrence of a quasiphase transition of the orientational order of the water dipoles in the single-file chain.

  9. Adsorption of insulin peptide on charged single-walled carbon nanotubes: significant role of ordered water molecules.

    Science.gov (United States)

    Shen, Jia-Wei; Wu, Tao; Wang, Qi; Kang, Yu; Chen, Xin

    2009-06-02

    Ordered hydration shells: The more ordered hydration shells outside the charged CNT surfaces prevent more compact adsorption of the peptide in the charged CNT systems [picture: see text], but peptide binding strengths on the charged CNT surfaces are stronger due to the electrostatic interaction.Studies of adsorption dynamics and stability for peptides/proteins on single-walled carbon nanotubes (SWNTs) are of great importance for a better understanding of the properties and nature of nanotube-based biosystems. Herein, the dynamics and mechanism of the adsorption of the insulin chain B peptide on different charged SWNTs are investigated by explicit solvent molecular dynamics simulations. The results show that all types of surfaces effectively attract the model peptide. Water molecules play a significant role in peptide adsorption on the surfaces of charged carbon nanotubes (CNTs). Compared to peptide adsorption on neutral CNT surfaces, the more ordered hydration shells outside the tube prevent more compact adsorption of the peptide in charged CNT systems. This shield effect leads to a smaller conformational change and van der Waals interaction between the peptide and surfaces, but peptide binding strengths on charged CNT surfaces are stronger than those on the neutral CNT surface due to the strong electrostatic interaction. The result of these simulations implies the possibility of improving the binding strength of peptides/proteins on CNT surfaces, as well as keeping the integrity of the peptide/protein conformation in peptide/protein-CNT complexes by charging the CNTs.

  10. Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution.

    Science.gov (United States)

    Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue

    2015-03-14

    The structure and dynamics of the nitromethane-water (NM-WT) binary mixture surrounding single walled carbon nanotubes (SWNTs) have been investigated by molecular dynamics simulations. The simulation trajectories show that the NM molecules can be selectively adsorbed both outside the surface and inside the cavity of SWNTs mainly dominated by van der Waals attractions because SWNTs have a higher binding affinity for NM than WT. The binding energies of SWNTs with NM and WT obtained from electronic structure calculations at the M06-2X/6-31+G* level are 15.31 and 5.51 kcal mol(-1), respectively. Compared with the SWNT exterior, the selective adsorption of NM is preferentially occurred in the SWNT interior due to the hydrophobic interactions and the dipole-dipole interactions, which induces the decrease of the hydrogen-bond number of NM with WT and ordered structures of NM with preferred intermolecular orientation in the SWNT cavity. Furthermore, the selective adsorption dynamics of NM from the aqueous solution is regardless of the chirality and radius of SWNTs. The SWNT radius plays a negligible role in the mass density distributions of NM outside the SWNTs, while the mass density of NM in the SWNT interior decreases gradually as the SWNT radius increases. The structural arrangements and intermolecular orientations of NM in the SWNT cavity are greatly dependent on the SWNT radius due to the size effect.

  11. Diffusion of water and selected atoms in DMPC lipid bilayer membranes

    DEFF Research Database (Denmark)

    Hansen, Flemming Yssing; Peters, Günther H.J.; Taub, H.;

    2012-01-01

    with the diffusion rate of selected atoms in the lipid molecules shows that ∼6 water molecules per lipid molecule move on the same time scale as the lipids and may therefore be considered to be tightly bound to them. The quasielastic neutron scattering functions for water and selected atoms in the lipid molecule......Molecular dynamics simulations have been used to determine the diffusion of water molecules as a function of their position in a fully hydrated freestanding 1,2-dimyristoyl-sn-glycero-3-phosphorylcholine (DMPC) bilayer membrane at 303 K and 1 atm. The diffusion rate of water in a ∼10 Å thick layer...

  12. Predictive relationships for the effects of triglyceride ester concentration and water uptake on solubility and partitioning of small molecules into lipid vehicles.

    Science.gov (United States)

    Cao, Yichen; Marra, Michelle; Anderson, Bradley D

    2004-11-01

    The ability to predict drug solubility and partitioning in triglyceride solvents from the chemical structures of the solute and the triglyceride would be highly useful in drug formulation development and in screening drug candidates for lipid solubility and possibly drug bioavailability. This study explores the role of triglyceride ester concentration on small molecule partitioning between lipid vehicles and water, including the effect of ester concentration on water uptake. The influence of solvated water is further examined in studies of small molecule solubility in dry and water saturated lipid vehicles varying in triglyceride ester concentration. A series of model solutes with varying hydrogen bond donating/accepting abilities was chosen for this study while triglyceride ester concentrations were varied by using squalane/tricaprylin solvent mixtures. General linear free energy solvation relationships having the form utilized previously by Abraham were obtained at each solvent composition. An examination of the solvent descriptors indicated that those descriptors representing the sensitivity of the solvent to the solute dipolarity/polarizability, s, and to the hydrogen bond acidity of the solute, a, vary systematically with the concentration of ester moieties in the solvent mixture. An empirical equation has been derived that offers the potential for predicting triglyceride/water partition coefficients and in certain cases, solubility in hydrated, fully-saturated triglyceride solvents for any small molecule for which Abraham solute descriptors can be obtained. Water uptake in triglyceride vehicles is shown to be approximately linear with water activity and may also be described by the empirical relationship developed for other solutes providing an adjustment is made in the value of its hydrogen bond acidity parameter. Water uptake enhances the solubility of benzamide and N-methylbenzamide and a modest "water-dragging" effect by N-methylbenzamide in the

  13. Functions of bounded variation

    OpenAIRE

    Lind, Martin

    2006-01-01

    The paper begins with a short survey of monotone functions. The functions of bounded variation are introduced and some basic properties of these functions are given. Finally the jump function of a function of bounded variation is defined.

  14. Upward Bound alum honored

    OpenAIRE

    Felker, Susan B.

    2005-01-01

    Robert Cobb Jr., of Greensboro, N.C., a 1986-89 participant in the Virginia Tech Upward Bound program, was recently named Virginia's TRIO Achiever for 2004. Federal TRIO programs include Upward Bound and Educational Talent Search.

  15. Water exchange at a hydrated platinum electrode is rare and collective

    CERN Document Server

    Limmer, David T; Madden, Paul A; Chandler, David

    2015-01-01

    We use molecular dynamics simulations to study the exchange kinetics of water molecules at a model metal electrode surface -- exchange between water molecules in the bulk liquid and water molecules bound to the metal. This process is a rare event, with a mean residence time of a bound water of about 40 ns for the model we consider. With analysis borrowed from the techniques of rare-event sampling, we show how this exchange or desorption is controlled by (1) reorganization of the hydrogen bond network within the adlayer of bound water molecules, and by (2) interfacial density fluctuations of the bulk liquid adjacent to the adlayer. We define collective coordinates that describe the desorption mechanism. Spatial and temporal correlations associated with a single event extend over nanometers and tens of picoseconds.

  16. Suppressing the fragmentation of fragile molecules in helium nanodroplets by co-embedding with water: Possible role of the electric dipole moment

    CERN Document Server

    Ren, Yanfei

    2007-01-01

    When fragile molecules such as glycine, polyglicine, alkanes, and alkanethiols are embedded in liquid helium nanodroplets, electron-impact ionization of the beam leads to fragmentation which is as extensive as that of isolated gas-phase molecules. However, it turns out that if a few molecules of water are co-embedded with the peptide and alkane chains, their fragmentation is drastically reduced or completely eliminated. On the other hand, the fragmentation of alkanethiols remains unaffected. On the basis of these observations, it is proposed that the fragmentation "buffering" effect may correlate with the magnitude of the impurity's electric dipole moment, which steers the migration of the ionizing He^+ hole in the droplet.

  17. A hot water extract of Curcuma longa inhibits adhesion molecule protein expression and monocyte adhesion to TNF-α-stimulated human endothelial cells.

    Science.gov (United States)

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

    2015-01-01

    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.

  18. The Calculation of Lyapunov Exponent of Water Molecules Vibration System%基于水分子振动体系的Lyapunov指数的计算

    Institute of Scientific and Technical Information of China (English)

    刘松红; 庞成群

    2012-01-01

    采用wolf重构法改进了水分子振动体系最大Lyapunov指数的计算,通过对水分子振动体系的最大Lyapunov指数的计算,得到了计算水分子振动体系的最大Lyapunov指数合适的初始长度、延迟时间以及总的演化时间。%By adopting wolf reconstruction method and improving the method, we gained the expression of the maximum Lyapunov exponent of water molecules vibration system o From the results of calculating the maximum Lyapunov exponent of water molecules vibration system, we received the appropriate initial length, duration and the total evolution time.

  19. 不同pH值下胞外聚合物对污泥脱水性能及束缚水含量的影响%Influence of extracellular polymeric substances on sludge dewaterability and bound water content at various pH values

    Institute of Scientific and Technical Information of China (English)

    邢奕; 王志强; 洪晨; 司艳晓; 张坤; 刘敏; 田星强; 李洋

    2015-01-01

    The changes of sludge dewaterability and bound water content at various pH values were investigated in this study. The protein and polysaccharide contents in each layer of extracellular polymeric substances ( S-EPS、LB-EPS and TB-EPS) and the organic acid and organic functional group contents in S-EPS were determined in an attempt to explain the influence of EPS on the sludge dewa-terability and bound water content. The results indicate that the sludge dewaterability under acidic conditions is obviously better than that under neutral conditions, and the water content of dewatered sludge ( WC) and the capillary suction time ( CST) can be decreased to 60. 8% and 25. 4 s at pH 3. 03, respectively. Under alkaline conditions, the bound water content in dewatered sludge, the WC and CST significantly increase, and the sludge dewaterability deteriorates. The addition of acid or alkali reduces TB-EPS, on the contrary, increases LB-EPS and S-EPS. Each layer of extracellular polymeric substances has significant correlation with the WC, CST and the bound water content, and S-EPS has most significant correlation with the sludge dewaterability and bound water content. In the process of acid-alkali conditioning, the amount and type of organic-functional groups improve obviously and hydrolysis of partly EPS generates organic acids and other small molecules.%研究了不同pH值下污泥脱水性能和束缚水含量的变化,通过测定污泥调理过程中各层胞外聚合物( S-EPS、LB-EPS和TB-EPS)中蛋白质和多糖的含量、S-EPS中有机官能团以及有机酸的含量,探讨了胞外聚合物对污泥脱水性能及束缚水含量的影响.酸性条件下,污泥的脱水性能明显好于中性条件,并且pH值为3.03时,污泥滤饼含水率( WC)和毛细吸水时间( CST)均降至最低,分别为60.8%和25.4 s;碱性条件下,污泥中束缚水的含量明显增加,WC和CST均大幅升高,污泥脱水性能恶化.酸碱的加入导致污泥中TB-EPS含量降

  20. Isolating Site-Specific Spectral Signatures of Individual Water Molecules in H-Bonded Networks with Isotopomer-Selective Ir-Ir Double Resonance Vibrational Predissociation Spectroscopy

    Science.gov (United States)

    Wolke, Conrad T.; Johnson, Mark

    2016-06-01

    We will discuss an experimental method that directly yields the embedded correlations between the two OH stretches and the intramolecular bending modes associated with a single H2O water molecule embedded in an otherwise all-D isotopologue. This is accomplished using isotopomer-selective IR-IR hole-burning on the Cs+(D2O)5(H2O) clusters formed by gas-phase exchange of a single, intact H2O molecule for D2O in the Cs+(D2O)6 ion. The OH stretching pattern of the Cs+(H2O)6 isotopologue is accurately recovered by superposition of the isotopomer spectra, thus establishing that the H2O incorporation is random and that the OH stretching manifold is largely due to contributions from decoupled water molecules. This behavior enables a powerful new way to extract structural information from vibrational spectra of size-selected clusters by explicitly identifying the local environments responsible for specific infrared features. Extension of this method to address the degree to which OH stretches are decoupled in the protonated water clusters will also be discussed.

  1. Accounting for target flexibility and water molecules by docking to ensembles of target structures: the HCV NS5B palm site I inhibitors case study.

    Science.gov (United States)

    Barreca, Maria Letizia; Iraci, Nunzio; Manfroni, Giuseppe; Gaetani, Rosy; Guercini, Chiara; Sabatini, Stefano; Tabarrini, Oriana; Cecchetti, Violetta

    2014-02-24

    The introduction of new anti-HCV drugs in therapy is an imperative need and is necessary with a view to develop an interferon-free therapy. Thus, the discovery and development of novel small molecule inhibitors of the viral NS5B polymerase represent an exciting area of research for many pharmaceutical companies and academic groups. This study represents a contribution to this field and relies on the identification of the best NS5B model(s) to be used in structure-based computational approaches aimed at identifying novel non-nucleoside inhibitors of one of the protein allosteric sites, namely, palm site I. First, the NS5B inhibitors at palm site I were classified as water-mediated or nonwater-mediated ligands depending on their ability to interact with or displace a specific water molecule. Then, we took advantage of the available X-ray structures of the NS5B/ligand complexes to build different models of protein/water combinations, which were used to investigate the influence on docking studies of solvent sites as well as of the influence of the protein conformations. As the overall trend, we observed improved performance in the docking results of the water-mediated inhibitors by inclusion of explicit water molecules, with an opposite behavior generally happening for the nonwater-mediated inhibitors. The best performing target structures for the two ligand sets were then used for virtual screening simulations of a library containing the known NS5B inhibitors along with related decoys to assess the best performing targets ensembles on the basis of their ability to discriminate active and inactive compounds as well as to generate the correct binding modes. The parallel use of different protein structures/water sets outperformed the use of a single target structure, with the two-protein 3H98/2W-2FVC/7W and 3HKY/NoW-3SKE/NoW models resulting in the best performing ensembles for water-mediated inhibitors and nonwater-mediated inhibitors, respectively. The information

  2. 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)

    2015-03-19

    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.

  3. Collisional properties of weakly bound heteronuclear dimers

    NARCIS (Netherlands)

    Marcelis, B.; Kokkelmans, S.J.J.M.F.; Shlyapnikov, G.V.; Petrov, D.S.

    2008-01-01

    We consider collisional properties of weakly bound heteronuclear molecules (dimers) formed in a two-species mixture of atoms with a large mass difference. We focus on dimers containing light fermionic atoms as they manifest collisional stability due to an effective dimer-dimer repulsion originating

  4. 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

    2012-06-01

    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

  5. Energy transfer in complexes of water-soluble quantum dots and chlorin e6 molecules in different environments.

    Science.gov (United States)

    Martynenko, Irina V; Orlova, Anna O; Maslov, Vladimir G; Baranov, Alexander V; Fedorov, Anatoly V; Artemyev, Mikhail

    2013-01-01

    The photoexcitation energy transfer is found and investigated in complexes of CdSe/ZnS cationic quantum dots and chlorin e6 molecules formed by covalent bonding and electrostatic interaction in aqueous solution and in porous track membranes. The quantum dots and chlorin e6 molecules form stable complexes that exhibit Förster resonance energy transfer (FRET) from quantum dots to chlorin e6 regardless of complex formation conditions. Competitive channels of photoexcitation energy dissipation in the complexes, which hamper the FRET process, were found and discussed.

  6. Water diffusion behavior in epoxy resins with various fluorine contents.

    Science.gov (United States)

    Li, Liang; Chen, Yin; Li, Shanjun

    2006-04-01

    In this work, novolac resin with perfluorinated side chains was synthesized and cured with o-Cresol novolac epoxy resin to obtain epoxy resins with various fluorine contents. Attenuated total reflection Fourier transform infrared spectroscopy (ATR/FT-IR) was used to monitor the in situ water diffusion process in these systems. The diffusion coefficient of water first increased and then slightly decreased with increasing fluorine content, which could be attributed to two opposite effects induced by perfluorinated side chains: enhanced hydrophobicity and increased free volume. In addition, generalized two-dimensional (2D) correlation analysis was employed to investigate both the sorption and the desorption process of water diffusion, and two kinds of water molecules, named bound and free water, were found. It was interesting to find that in the sorption process, the change in the population of bound water molecules occurs earlier than the change in the population of free water molecules, while in the desorption process, the sequence was reversed.

  7. Excitation of water molecules by electron impact with formation of OH-radicals in the A{sup 2}{Sigma}{sup +} state

    Energy Technology Data Exchange (ETDEWEB)

    Khodorkovskii, M A; Murashov, S V [Saint-Petersburg State Polytechnic University, 195251, Saint-Petersburg (Russian Federation); Artamonova, T O; Rakcheeva, L P; Beliaeva, A A; Shakhmin, A L [Russian Scientific Center ' Applied Chemistry' , 197198, Saint-Petersburg (Russian Federation); Michael, D [General Electric Global Research Center, Niskayuna, NY 12309 (United States); Timofeev, N A; Mel' nikov, A S; Shevkunov, I A [Saint-Petersburg State University, 198904, Petrodvorets (Russian Federation); Zissis, G, E-mail: mkhodorkovskii@rscac.spb.r [Universite Touluse 3-Paul Sabatier, LAPLASE Building 3R2, 118rte de Narbonne, F-31062 Touluse Cedex 9 (France)

    2009-11-14

    The excitation cross-sections of the OH-radical band A{sup 2}{Sigma}{sup +} -> X{sup 2} (v' = 0 -> v'' = 0, v' = 1 -> v'' = 1) were measured. OH-radicals were formed during dissociation of water molecules by electron impact in the conditions of crossing of supersonic molecular and electron beams in the energy range 10-120 eV. Measurements were conducted at temperatures of 50, 80 and 200 K. It was shown that the excitation function had a sharp maximum in the region of low energies (at 16 eV) and an extended plateau up to 120 eV. It is proved that there are two channels of molecule dissociation with formation OH (A{sup 2}{Sigma}{sup +}) through excitation of either the triplet b{sup 3}A{sub 1} or the singlet B{sup 1}A{sub 1} states of H{sub 2}O molecules. The form of the excitation function essentially depends on the temperature of water vapours in the beam. With the decrease of the water molecule temperature the height of the plateau in the region 30-120 eV decreases in comparison with that of the peak at 16 eV. The absolute value of the excitation cross-section of the OH band at the temperature 50 K has been measured. It is equal to (1.6 +- 0.5) x 10{sup -18} cm{sup 2} in the maximum at 16 eV. The ratio of cross-sections of bands 1-1 and 0-0 weakly depends on the energy of the exciting electron in the range 12-120 eV and is equal to 0.28 +- 0.05. The appearance threshold is equal to (9.1 +- 0.5) eV.

  8. Single-molecule tracking in live Vibrio cholerae reveals that ToxR recruits the membrane-bound virulence regulator TcpP to the toxT promoter.

    Science.gov (United States)

    Haas, Beth L; Matson, Jyl S; DiRita, Victor J; Biteen, Julie S

    2015-04-01

    Vibrio cholerae causes the human disease cholera by producing a potent toxin. The V. cholerae virulence pathway involves an unusual transcription step: the bitopic inner-membrane proteins TcpP and ToxR activate toxT transcription. As ToxT is the primary direct transcription activator in V. cholerae pathogenicity, its regulation by membrane-localized activators is key in the disease process. However, the molecular mechanisms by which membrane-localized activators engage the transcription process have yet to be uncovered in live cells. Here we report the use of super-resolution microscopy, single-molecule tracking, and gene knockouts to examine the dynamics of individual TcpP proteins in live V. cholerae cells with cholerae to that in mutant strains lacking either toxR or the toxT promoter, we determine that TcpP mobility is greater in the presence of its interaction partners than in their absence. Our findings support a mechanism in which ToxR recruits TcpP to the toxT promoter for transcription activation.

  9. Bonded hydrogen and hydrogen bonding in reciprocal space. Simulation of diffraction by a water molecule and dimer

    NARCIS (Netherlands)

    Poorthuis, G.H.A.; Feil, D.

    1994-01-01

    There seems to be increasing interest in the electron density distribution in molecules and crystals. In particular, the effect of polarization due to internal fields in condensed matter is studied. X-ray diffraction data can contribute to the knowledge required. As the effects of polarization on di

  10. Molecule nanoweaver

    Science.gov (United States)

    Gerald, II; Rex E.; Klingler, Robert J.; Rathke, Jerome W.; Diaz, Rocio; Vukovic, Lela

    2009-03-10

    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.

  11. Specific Na+ and K+ Cation Effects on the Interfacial Water Molecules at the Air/Aqueous Salt Solution Interfaces Probed with Non-resonant Second Harmonic Generation (SHG)

    CERN Document Server

    Bian, Hong-tao; Guo, Yuan; Wang, Hong-fei

    2008-01-01

    Here we report the polarization dependent non-resonant second harmonic generation (SHG) measurement of the interfacial water molecules at the aqueous solution of the following salts: NaF, NaCl, NaBr, KF, KCl, and KBr. Through quantitative polarization analysis of the SHG data,the orientational parameter D value and the relative surface density of the interfacial water molecules at these aqueous solution surfaces were determined. From these results we found that addition of each of the six salts caused increase of the thickness of the interfacial water layer at the surfaces to a certain extent. Noticeably, both the cations and the anions contributed to the changes, and the abilities to increase the thickness of the interfacial water layer were in the following order: KBr > NaBr > KCl > NaCl ~ NaF > KF. Since these changes can not be factorized into individual anion and cation contributions, there are possible ion pairing or association effects, especially for the NaF case. We also found that the orientational ...

  12. Effect of water molecules on the fluorescence enhancement of Aflatoxin B1 mediated by Aflatoxin B1:beta-cyclodextrin complexes. A theoretical study.

    Science.gov (United States)

    Ramírez-Galicia, Guillermo; Garduño-Juárez, Ramón; Gabriela Vargas, M

    2007-01-01

    In order to explain the observed fluorescence enhancement of Aflatoxin B1 (AFB1) when forming AFB1:beta-cyclodextrin (AFB1:beta-CD) inclusion complexes, we have performed a theoretical (quantum chemistry calculations) study of AFB1 and AFB1:beta-CD in vacuum and in the presence of aqueous solvent. The AM1 method was used to calculate the absorption and emission wavelengths of these molecules. With the help of density functional theory (DFT) and time-dependent DFT (TDDFT) vibrational frequencies and related excitation energies of AFB1 and AFB1.(H2O)m = 4,5,6,11 were calculated. On the basis of these calculations we propose a plausible mechanism for the fluorescence enhancement of AFB1 in the presence of beta-CD: (1) before photoexcitation of AFB1 to its S1 excited state, there is a vibrational coupling between the vibrational modes involving the AFB1 carbonyl groups and the bending modes of the nearby water molecules (CG + WM); (2) these interactions allow a thermal relaxation of the excited AFB1 molecules that results in fluorescence quenching; (3) when the AFB1 molecules form inclusion complexes with beta-CD the CG + WM interaction decreases; and (4) this gives rise to a fluorescence enhancement.

  13. Interactions between Asphaltenes and Water in Solutions in Toluene

    DEFF Research Database (Denmark)

    Khvostichenko, Daria; Andersen, Simon Ivar

    2008-01-01

    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...

  14. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available 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].

  15. Graviton Mass Bounds

    CERN Document Server

    de Rham, Claudia; Tolley, Andrew J; Zhou, Shuang-Yong

    2016-01-01

    Recently, aLIGO has announced the first direct detections of gravitational waves, a direct manifestation of the propagating degrees of freedom of gravity. The detected signals GW150914 and GW151226 have been used to examine the basic properties of these gravitational degrees of freedom, particularly setting an upper bound on their mass. It is timely to review what the mass of these gravitational degrees of freedom means from the theoretical point of view, particularly taking into account the recent developments in constructing consistent massive gravity theories. Apart from the GW150914 mass bound, a few other observational bounds have been established from the effects of the Yukawa potential, modified dispersion relation and fifth force that are all induced when the fundamental gravitational degrees of freedom are massive. We review these different mass bounds and examine how they stand in the wake of recent theoretical developments and how they compare to the bound from GW150914.

  16. The cryo-electron microscopy structure of feline calicivirus bound to junctional adhesion molecule A at 9-angstrom resolution reveals receptor-induced flexibility and two distinct conformational changes in the capsid protein VP1.

    Science.gov (United States)

    Bhella, David; Goodfellow, Ian G

    2011-11-01

    Caliciviridae are small icosahedral positive-sense RNA-containing viruses and include the human noroviruses, a leading cause of infectious acute gastroenteritis and feline calicivirus (FCV), which causes respiratory illness and stomatitis in cats. FCV attachment and entry is mediated by feline junctional adhesion molecule A (fJAM-A), which binds to the outer face of the capsomere, inducing a conformational change in the capsid that may be important for viral uncoating. Here we present the results of our structural investigation of the virus-receptor interaction and ensuing conformational changes. Cryo-electron microscopy and three-dimensional image reconstruction were used to solve the structure of the virus decorated with a soluble fragment of the receptor at subnanometer resolution. In initial reconstructions, the P domains of the capsid protein VP1 and fJAM-A were poorly resolved. Sorting experiments led to improved reconstructions of the FCV-fJAM-A complex both before and after the induced conformational change, as well as in three transition states. These data showed that the P domain becomes flexible following fJAM-A binding, leading to a loss of icosahedral symmetry. Furthermore, two distinct conformational changes were seen; an anticlockwise rotation of up to 15° of the P domain was observed in the AB dimers, while tilting of the P domain away from the icosahedral 2-fold axis was seen in the CC dimers. A list of putative contact residues was calculated by fitting high-resolution coordinates for fJAM-A and VP1 to the reconstructed density maps, highlighting regions in both virus and receptor important for virus attachment and entry.

  17. Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

    Science.gov (United States)

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

    2011-04-01

    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 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) 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±0.13 and 198.7±0.01 mV, 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 for

  18. Dual reorientation relaxation routes of water molecules in oxyanion’s hydration shell: A molecular geometry perspective

    Energy Technology Data Exchange (ETDEWEB)

    Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn [Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering and Biodynamic Optical Imaging Center, Peking University, Beijing 100871 (China)

    2015-12-14

    In this study, we examine how complex ions such as oxyanions influence the dynamic properties of water and whether differences exist between simple halide anions and oxyanions. Nitrate anion is taken as an example to investigate the hydration properties of oxyanions. Reorientation relaxation of its hydration water can occur through two different routes: water can either break its hydrogen bond with the nitrate to form one with another water or switch between two oxygen atoms of the same nitrate. The latter molecular mechanism increases the residence time of oxyanion’s hydration water and thus nitrate anion slows down the translational motion of neighbouring water. But it is also a “structure breaker” in that it accelerates the reorientation relaxation of hydration water. Such a result illustrates that differences do exist between the hydration of oxyanions and simple halide anions as a result of different molecular geometries. Furthermore, the rotation of the nitrate solute is coupled with the hydrogen bond rearrangement of its hydration water. The nitrate anion can either tilt along the axis perpendicularly to the plane or rotate in the plane. We find that the two reorientation relaxation routes of the hydration water lead to different relaxation dynamics in each of the two above movements of the nitrate solute. The current study suggests that molecular geometry could play an important role in solute hydration and dynamics.

  19. Structural Changes of Water Molecules Upon the Reduction of Quinones in The Reaction Center from Rhodobactery Sphaeroides

    Institute of Scientific and Technical Information of China (English)

    T.Iwata; M.L.Paddock; M.Y.Okamura; H.Kandori

    2007-01-01

    1 Results The photosynthetic bacterial reaction center (RC) is a membrane protein complex.The RC is composed of three protein subunits and redox components such as bacteriochlorophylls, bacteriopheophytins,and quinones.The RC performs the photochemical electron transfer from the bacteriochlorophyll dimer through a series of electron donor and acceptor molecules to a secondary quinone,QB.QB accepts electrons from a primary quinone,QA,in two sequential electron transfer reactions.The second electron trans...

  20. Xalpha-DVM investigation of double water molecule interactions with active sites of alpha- and beta-subunits of hemoglobin

    Science.gov (United States)

    Yuryeva, Elmira I.

    In this work, the results of Xalpha-discrete variation method calculations of the electronic structure and interatomic parameters of chemical bonding between iron (II) and oxygen molecule with and without extra electrons and protons in active site (AS) of alpha- and beta-subunits of oxyhemoglobin are presented. The Skulachev model of O2 molecule existing in respiration medium in the 2H2O form was used. The introduction of extra electrons does not change considerably the interaction of the iron atom with the O2 oxygen molecule, but strengthens the repulsion in the Fe bond N bonds. In this case, the estimated effective charge of the iron atom is +1.8/1.5e for AS of alpha-/beta-subunits of oxyhemoglobin, and the magnetic moment of iron atoms becomes zero. The deoxygenation effect of the AS of the alpha- and beta-subunits of oxyhemoglobin is due to the ability of extra protons to break down covalent attraction between the iron atom and the nearest oxygen atom and also to weakening of the repulsive component of the covalent Fe bond N interactions.

  1. An application of the novel quantum mechanical/molecular mechanical method combined with the theory of energy representation: An ionic dissociation of a water molecule in the supercritical water.

    Science.gov (United States)

    Takahashi, Hideaki; Satou, Wataru; Hori, Takumi; Nitta, Tomoshige

    2005-01-22

    A novel quantum chemical approach recently developed has been applied to an ionic dissociation of a water molecule (2H(2)O-->H(3)O(+)+OH(-)) in ambient and supercritical water. The method is based on the quantum mechanical/molecular mechanical (QM/MM) simulations combined with the theory of energy representation (QM/MM-ER), where the energy distribution function of MM solvent molecules around a QM solute serves as a fundamental variable to determine the hydration free energy of the solute according to the rigorous framework of the theory of energy representation. The density dependence of the dissociation free energy in the supercritical water has been investigated for the density range from 0.1 to 0.6 g/cm(3) with the temperature fixed at a constant. It has been found that the product ionic species significantly stabilizes in the high density region as compared with the low density. Consequently, the dissociation free energy decreases monotonically as the density increases. The decomposition of the hydration free energy has revealed that the entropic term (-TDeltaS) strongly depends on the density of the solution and dominates the behavior of the dissociation free energy with respect to the variation of the density. The increase in the entropic term in the low density region can be attributed to the decrease in the translational degrees of freedom brought about by the aggregation of solvent water molecules around the ionic solute.

  2. Water-dispersible nanoparticles via interdigitation of sodium dodecylsulphate molecules in octadecylamine-capped gold nanoparticles at a liquid-liquid interface

    Indian Academy of Sciences (India)

    Anita Swami; Amol Jadhav; Ashavani Kumar; Suguna D Adyanthaya; Murali Sastry

    2003-10-01

    This paper describes the formation of water-dispersible gold nanoparticles capped with a bilayer of sodium dodecylsulphate (SDS) and octadecylamine (ODA) molecules. Vigorous shaking of a biphasic mixture consisting of ODA-capped gold nanoparticles in chloroform and SDS in water results in the rapid phase transfer of ODA-capped gold nanoparticles from the organic to the aqueous phase, the latter acquiring a pink, foam-like appearance in the process. Drying of the coloured aqueous phase results in the formation of a highly stable, reddish powder of gold nanoparticles that may be readily redispersed in water. The water-dispersible gold nanoparticles have been investigated by UV-Vis spectroscopy, differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), and Fourier transform infrared spectroscopy (FTIR). These studies indicate the presence of interdigitated bilayers consisting of an ODA primary monolayer directly coordinated to the gold nanoparticle surface and a secondary monolayer of SDS, this secondary monolayer providing sufficient hydrophilicity to facilitate gold nanoparticle transfer into water and rendering them water-dispersible.

  3. Absolute Orientation of Molecules with Competing Hydrophilic Head Groups at the Air/Water Interface Probed with Sum Frequency Generation Vibrational Spectroscopy

    Institute of Scientific and Technical Information of China (English)

    Feng Wang; Zhi Huang; Zhifeng Cui; Hongfei Wang

    2009-01-01

    The constructive or destructive spectral interference between the molecular groups oriented up and down at the interface in the sum-frequency generation (SFG) spectra provides a direct measurement of the absolute orientation of these molecular groups. This simple approach can be employed to interrogate absolute molecular orientations other than using the complex absolute phase measurement in the SFG studies. We used the -CN group in the p-cyanophenol (PCP) molecule as the internal phase standard, and we measured the phases of the SFG fields of the -CN groups in the 3,5-dimethyl-4-hydroxy-benzonitrile (35DMHBN)and 2,6-dimethyl-4-hydroxy-benzonitrile (26DMHBN) at the air/water interface by measuring the SFG spectra of the aqueous surfaces of the mixtures of the PCP, 35DMHBN, and 26DMHBN solutions. The results showed that the 35DMHBN had its -CN group pointing into the aqueous phase; while the 26DMHBN, similar to the PCP, had its -CN group pointing away from the aqueous phase. The tilt angles of the -CN group for both the 35DMHBN and 26DMHBN molecules at the air/water interface were around 25°-45° from the interface normal. These results provided insights on the understanding of the detailed balance of the competing factors, such as solvation of the polar head groups, hydrogen bonding and hydrophobic effects, etc., on influencing the absolute molecular orientation at the air/water interface.

  4. Hydrophobic Porous Material Adsorbs Small Organic Molecules

    Science.gov (United States)

    Sharma, Pramod K.; Hickey, Gregory S.

    1994-01-01

    Composite molecular-sieve material has pore structure designed specifically for preferential adsorption of organic molecules for sizes ranging from 3 to 6 angstrom. Design based on principle that contaminant molecules become strongly bound to surface of adsorbent when size of contaminant molecules is nearly same as that of pores in adsorbent. Material used to remove small organic contaminant molecules from vacuum systems or from enclosed gaseous environments like closed-loop life-support systems.

  5. [Dynamics of Irreversible Evaporation of a Water-Protein Droplet and a Problem of Structural and Dynamical Experiments with Single Molecules].

    Science.gov (United States)

    Shaitan, K V; Armeev, G A; Shaytan, A K

    2016-01-01

    We discuss the effect of isothermal and adiabatic evaporation of water on the state of a water-protein droplet. The discussed problem is of current importance due to development of techniques to perform single molecule experiments using free electron lasers. In such structure-dynamic experiments the delivery of a sample into the X-ray beam is performed using the microdroplet injector. The time between the injection and delivery is in the order of microseconds. In this paper we developed a specialized variant of all-atom molecular dynamics simulations for the study of irreversible isothermal evaporation of the droplet. Using in silico experiments we determined the parameters of isothermal evaporation of the water-protein droplet with the sodium and chloride ions in the concentration range of 0.3 M at different temperatures. The energy of irreversible evaporation determined from in silico experiments at the initial stages of evaporation virtually coincides with the specific heat of evaporation for water. For the kinetics of irreversible adiabatic evaporation an exact analytical solution was obtained in the limit of high thermal conductivity of the droplet (or up to the droplet size of -100 Å). This analytical solution incorporates parameters that are determined using in silico. experiments on isothermal droplet evaporation. We show that the kinetics of adiabatic evaporation and cooling of the droplet scales with the droplet size. Our estimates of the water-protemi droplet. freezing rate in the adiabatic regime in a vacuum chamber show that additional techniques for stabilizing the temperature inside the droplet should be used in order to study the conformational transitions of the protein in single molecules. Isothermal and quasi-isothermal conditions are most suitable for studying the conformational transitions upon object functioning. However, in this case it is necessary to take into account the effects of dehydration and rapid increase of ionic strength in an

  6. Conversion of core oxos to water molecules by 4e-/4H+ reductive dehydration of the Mn4O2(6+) core in the manganese-oxo cubane complex Mn4O4(Ph2PO2)6: a partial model for photosynthetic water binding and activation.

    Science.gov (United States)

    Ruettinger, W F; Dismukes, G C

    2000-03-06

    Reaction of the Mn4O4(6+) "cubane" core complex, Mn4O4L6 (1) (L = diphenylphosphinate, Ph2PO2-), with a hydrogen atom donor, phenothiazine (pzH), forms the dehydrated cluster Mn4O2L6 (2), which has lost two mu-oxo bridges by reduction to water (H2O). The formation of 2 was established by electrospray mass spectrometry, whereas FTIR spectroscopy confirmed the release of water molecules into solution during the reduction of 1. UV-vis and EPR spectroscopies established the stoichiometry and chemical form of the pzH product by showing the production of 4 equiv of the neutral pz radical. By contrast, the irreversible decomposition of 1 to individual Mn(II) ions occurs if the reduction is performed using electrons provided by various proton-lacking reductants, such as cobaltocene or electrochemical reduction. Thus, cubane 1 undergoes coupled four-electron/four-proton reduction with the release of two water molecules, a reaction formally analogous to the reverse sequence of the steps that occur during photosynthetic water oxidation leading to O2 evolution. 1H NMR of solutions of 2 reveal that all six of the phosphinate ligands exhibit paramagnetic broadening, due to coordination to Mn ions, and are magnetically equivalent. A symmetrical core structure is thus indicated. We hypothesize that this structure is produced by the dynamic averaging of phosphinato ligand coordination or exchange of mu-oxos between vacant mu-oxo sites. The paramagnetic 1H NMR of water molecules in solution shows that they are able to freely exchange with water molecules that are bound to the Mn ion(s) in 2, and this exchange can be inhibited by the addition of coordinating anions, such as chloride. Thus, 2 possesses open or labile coordination sites for water and anions, in contrast to solutions of 1, which reveal no evidence for water coordination. Complex 2 exhibits greater paramagnetism than that of 1, as seen by 1H NMR, and it possesses a broad (440 G wide) EPR absorption, centered at g = 2

  7. Comparative modeling of combined transport of water and graded-size molecules across the glomerular capillary wall.

    Science.gov (United States)

    Abdel-Mageed, Samir M; Mohamed, Ehab I

    2016-04-07

    Chronic kidney disease is a common and growing problem worldwide that necessitates recognition of individual risk and appropriate laboratory testing before its progression to end-stage renal failure, requiring dialysis or transplantation for survival. Clearance studies using various graded-size probe molecules established that the passage of molecules/proteins across the glomerular capillary barrier of mammalian kidneys is increasingly restricted as their size increase. Few mathematical models were developed to describe the dynamics of the size-selective functions of macromolecules across membranes and gelatins. In the present study, we compare the behavior of three mathematical descriptions for the Fiber Matrix theory, an Extended Fiber Matrix theory, and an Alternative Statistical Physics analysis to describe the size-selective function of the glomerular capillary barrier; using mainly its hemodynamic, morphometric and hydrodynamic variables; in two experimental rat models. The glomerular basement membrane was represented as a homogeneous three-dimensional network of fibers of uniform length (Lf), radius (Rf), total fractional solid volume of fibers (Vf) and characteristic Darcy permeability. The models were appropriate for simulating in vivo fractional clearance data of neutral Dextran and Ficoll macromolecules from two experimental rat models. We believe that the Lf, Rf and Vf best-fit numerical values may signify new insights for the diagnosis of human nephropathies.

  8. An Intramolecular Silylene Borane Capable of Facile Activation of Small Molecules, Including Metal-Free Dehydrogenation of Water.

    Science.gov (United States)

    Mo, Zhenbo; Szilvási, Tibor; Zhou, Yu-Peng; Yao, Shenglai; Driess, Matthias

    2017-02-27

    The first single-component N-heterocyclic silylene borane 1 (LSi-R-BMes2 ; L=PhC(N(t) Bu)2 ; R=1,12-xanthendiyl spacer; Mes=2,4,6-Me3 C6 H2 ), acting as a frustrated Lewis pair (FLP) in small-molecule activation, can be synthesized in 65 % yields. Its HOMO is largely localized at the silicon(II) atom and the LUMO has mainly boron 2p character. In small-molecule activation 1 allows access to the intramolecular silanone-borane 3 featuring a Si=O→B interaction through reaction with O2 , N2 O, or CO2 , and formation of silanethione borane 4 from reaction with S8 . The Si(II) center in 1 undergoes immediate hydrogenation if exposed to H2 at 1 atm pressure in benzene, affording the silane borane 5-H2 , L(H2 )Si-R-BMes2 . Remarkably, no H2 activation occurs if the single silylene LSiPh and Mes3 B intermolecularly separated are exposed to dihydrogen. Unexpectedly, the pre-organized Si-B separation in 1 enables a metal-free dehydrogenation of H2 O to give the silanone-borane 3 as reactive intermediate.

  9. Self-assembly of a Co(II) dimer through H-bonding of water molecules to a 3D open-framework structure

    Indian Academy of Sciences (India)

    Sujit K Ghosh; Parimal K Bharadwaj

    2005-01-01

    Reaction of pyridine-2,4,6-tricarboxylic acid (ptcH3) with Co(NO3)2.6H2O in presence of 4,4'-bipyridine (4,4'-bpy) in water at room temperature results in the formation of {[Co2(ptcH)2(4,4'-bpy)(H2O)4].2H2O}, (1). The solid-state structure reveals that the compound is a dimeric Co(II) complex assembled to a 3D architecture via an intricate intra- and inter-molecular hydrogen-bonding interactions involving water molecules and carboxylate oxygens of the ligand ptcH2-. Crystal data: monoclinic, space group 21/, = 11.441(5) Å, = 20.212(2) Å, = 7.020(5) Å, = 103.77(5)°, = 1576.7(1) Å3, = 2, 1 = 0.0363, 2 = 0.0856, = 1.000.

  10. A novel strategy to produce highly stable and transparent aqueous 'nanosolutions' of water-insoluble drug molecules

    Energy Technology Data Exchange (ETDEWEB)

    Wang Jiexin; Zhang Zhibing; Le Yuan; Chen Jianfeng [State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing 100029 (China); Zhao Hong, E-mail: chenjf@mail.buct.edu.cn [Research Center of the Ministry of Education for High Gravity Engineering and Technology, Beijing University of Chemical Technology, Beijing 100029 (China)

    2011-07-29

    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.

  11. Complex of myoglobin with phenol bound in a proximal cavity.

    Science.gov (United States)

    Huang, Xiao; Wang, Chunxue; Celeste, Lesa R; Lovelace, Leslie L; Sun, Shenfang; Dawson, John H; Lebioda, Lukasz

    2012-12-01

    Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with Cβ and Cγ of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It appears that the ligand enters the proximal cavity through a gate formed by the flexible loops 79-86 and 93-103. TCP and 4-IP do not bind to Mb in this manner under similar conditions; however, it appears to be likely that dimethyl sulfoxide (DMSO), which was used at a concentration of 0.8 M to facilitate 4-IP dissolution, binds in the phenol/Xe1 binding site. In this structure, a water molecule coordinated to the heme iron was replaced by an oxygen molecule, reflecting the reduction of the heme. Crystals of Mb and G65T Mb soaked for 5-10 min did not show bound phenol. Kinetic studies of TCP dechlorination showed that phenol has a dual effect: it acts as a competitive inhibitor that is likely to interfere with TCP binding at the heme edge and as a weak activator, likely through binding in the proximal cavity. The lack of phenol bound at the heme edge in the crystal structures suggests that its inhibitory binding only takes place when the heme is activated by hydrogen peroxide.

  12. Just three water molecules can trigger the undesired nonenzymatic reactions of aspartic acid residues: new insight from a quantum-chemical study

    Science.gov (United States)

    Takahashi, O.

    2014-03-01

    Aspartic acid (Asp) residues in peptides and proteins (L-Asp) can undergo spontaneous, nonenzymatic reactions under physiological conditions by which abnormal L-β-Asp, D-Asp, and/or D-β-Asp residues are formed. These altered Asp residues may affect the three-dimensional structures of the peptides and proteins and hence their properties and functions. In fact, the altered Asp residues are relevant to age-related diseases such as cataract and Alzheimer's disease. Most of the above reactions of the L-Asp residue proceed via a cyclic succinimide intermediate. In this paper, I propose a detailed mechanism of cyclization of an Asp residue (forming a precursor of the succinimide) by the B3LYP/6-31+G(d,p) density functional theory calculations carried out for a small Asp-containing model compound complexed with three water molecules which act as general acid-base catalysts in 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. Then, successive reorientation of a water molecule and conformational change occur followed by the nucleophilic attack of the iminol nitrogen atom on the carboxyl carbon atom of the Asp side chain to form a five-membered ring. A satisfactory agreement was obtained between the calculated and experimental energetics.

  13. Bounding species distribution models

    Institute of Scientific and Technical Information of China (English)

    Thomas J. STOHLGREN; Catherine S. JARNEVICH; Wayne E. ESAIAS; Jeffrey T. MORISETTE

    2011-01-01

    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].

  14. Lectures on Bound states

    CERN Document Server

    Hoyer, Paul

    2016-01-01

    Even a first approximation of bound states requires contributions of all powers in the coupling. This means that the concept of "lowest order bound state" needs to be defined. In these lectures I discuss the "Born" (no loop, lowest order in $\\hbar$) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. As a check of the method, Positronium states of any momentum are determined as eigenstates of the QED Hamiltonian, quantized at equal time. Analogously, states bound by a strong external field $A^\\mu(\\xv)$ are found as eigenstates of the Dirac Hamiltonian. Their Fock states have dynamically created $e^+e^-$ pairs, whose distribution is determined by the Dirac wave function. The linear potential of $D=1+1$ dimensions confines electrons but repels positrons. As a result, the mass spectrum is continuous and the wave functions have features of both bound states and plane waves. The classical solutions of Gauss' law are explored for hadrons in QCD. A non-vanishing bo...

  15. Bound Water Content in Saturated Wood Cell Wall Determined by Nuclear Magnetic Resonance Spectroscopy%利用核磁共振测定木材吸着水饱和含量

    Institute of Scientific and Technical Information of China (English)

    高鑫; 庄寿增

    2015-01-01

    1H spin-spin relaxation time (T2) of water in 5 species of wood was measured by nuclear magnetic resonance (NMR) spectroscopy at room temperature and-3℃, which is thought to be related to the anatomical structure of the wood. The bound water content within swollen cell wall was determined by comparison of the inversion peak area before and after frozen treatment:Pinus sylvestris 38.3%,Cunninghamia lanceolata 38.5%, Populus sp. 36.0%,Fraxinus excelsior L. 35.6% andOchroma pyramidale 47.6%. The bound water contents determined by NMR spectroscopy were apparently higher than those obtained by the conventional extrapolation methods, but similar to the results obtained by the solute exclusion method, porous plate method, centrifugal dewatering method. It is concluded that NMR may provide a rapid and non-destructive way to determine bound water content in wood.%利用核磁共振(NMR)技术研究了室温与-3℃条件下5种树种木材内水分质子的自旋-自旋弛豫时间(T2)特性,室温下各树种木材试样T2弛豫时间特性的不同是由木材微观构造导致的.通过对比冷冻前后各树种试样的信号反演峰面积,确定了其吸着水饱和含量,樟子松38.3%,杉木38.5%,杨木36.0%,白蜡木35.6%,轻木47.6%,均高于通过吸湿外推法估算数值,与溶剂排出法、多孔板法、离心法等实测法获得的吸着水饱和含量的结果相近,核磁共振技术可作为木材内吸着水含量快速测定的实验方法.

  16. Information, Utility & Bounded Rationality

    CERN Document Server

    Ortega, Pedro A

    2011-01-01

    Perfectly rational decision-makers maximize expected utility, but crucially ignore the resource costs incurred when determining optimal actions. Here we employ an axiomatic framework for bounded rational decision-making based on a thermodynamic interpretation of resource costs as information costs. This leads to a variational "free utility" principle akin to thermodynamical free energy that trades off utility and information costs. We show that bounded optimal control solutions can be derived from this variational principle, which leads in general to stochastic policies. Furthermore, we show that risk-sensitive and robust (minimax) control schemes fall out naturally from this framework if the environment is considered as a bounded rational and perfectly rational opponent, respectively. When resource costs are ignored, the maximum expected utility principle is recovered.

  17. Bounded Computational Capacity Equilibrium

    CERN Document Server

    Hernandez, Penelope

    2010-01-01

    We study repeated games played by players with bounded computational power, where, in contrast to Abreu and Rubisntein (1988), the memory is costly. We prove a folk theorem: the limit set of equilibrium payoffs in mixed strategies, as the cost of memory goes to 0, includes the set of feasible and individually rational payoffs. This result stands in sharp contrast to Abreu and Rubisntein (1988), who proved that when memory is free, the set of equilibrium payoffs in repeated games played by players with bounded computational power is a strict subset of the set of feasible and individually rational payoffs. Our result emphasizes the role of memory cost and of mixing when players have bounded computational power.

  18. Bounding Noncommutative QCD

    CERN Document Server

    Carlson, C E; Lebed, R F; Carlson, Carl E.; Carone, Christopher D.; Lebed, Richard F.

    2001-01-01

    Jurco, Moller, Schraml, Schupp, and Wess have shown how to construct noncommutative SU(N) gauge theories from a consistency relation. Within this framework, we present the Feynman rules for noncommutative QCD and compute explicitly the most dangerous Lorentz-violating operator generated through radiative corrections. We find that interesting effects appear at the one-loop level, in contrast to conventional noncommutative U(N) gauge theories, leading to a stringent bound. Our results are consistent with others appearing recently in the literature that suggest collider limits are not competitive with low-energy tests of Lorentz violation for bounding the scale of spacetime noncommutativity.

  19. Enumerating molecules.

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-04-01

    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.

  20. EPA, Department of Justice, and Hecla Limited settle Clean Water Act violations, reduce pollution bound for South Fork Coeur dAlene River

    Science.gov (United States)

    (Seattle, WA - June 1, 2015) - The U.S. Environmental Protection Agency, U.S. Department of Justice, and Hecla Limited, owner of the Lucky Friday Mine and Mill, have reached a settlement concerning water pollution violations near the headwaters of the Sout

  1. A comparative study of thermo-sensitive hydrogels with water-insoluble paclitaxel in molecule, nanocrystal and microcrystal dispersions

    Science.gov (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

    2015-09-01

    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.

  2. A comparative study of thermo-sensitive hydrogels with water-insoluble paclitaxel in molecule, nanocrystal and microcrystal dispersions.

    Science.gov (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

    2015-09-28

    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.

  3. The DMM Bound

    DEFF Research Database (Denmark)

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

    2010-01-01

    of variables. One application is to the bitsize of the eigenvalues and eigenvectors of an integer matrix, which also yields a new proof that the problem is polynomial. We also compare against recent lower bounds on the absolute value of the root coordinates by Brownawell and Yap [5], obtained under...

  4. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    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.

  5. Size, shape, and site selectivities in the photochemical reactions of molecules adsorbed on pentasil zeolites. Effects of coadsorbed water

    Energy Technology Data Exchange (ETDEWEB)

    Turro, N.J.; Cheng, C.; Abrams, L.; Corbin, D.R.

    1987-04-15

    The photochemistry of methylbenzyl benzyl ketones (ACOB) in the presence of pentasil zeolites follows strikingly different pathways due to the location of the adsorbed ketone. The product distribution, in terms of the cage effect (efficiency of germinate radical combination), demonstrates the effects of sorption and diffusion on the radical species produced by photolysis. p-ACOB is readily adsorbed within the pentasil framework and produces p-AB as the primary product. In contrast, the photolysis product distributions of o-ACOB can be dramatically varied depending upon the extent of its adsorption into the framework. By addition of a nonreactive titrant, such as water, after the ketone adsorption, the photolysis product distributions can be systematically varied depending upon the aluminum content of the framework. The observed results are completely described by considerations of (a) the size and shape sorption of the pentasil zeolites, (b) the sorption of water by the hydrophilic sites of the pentasil zeolites (which depend upon the framework aluminum content), and (c) the hydrophobic characteristics of the pentasil channels which do not contain framework aluminum.

  6. Formation of the prebiotic molecule NH$_2$CHO on astronomical amorphous solid water surfaces: accurate tunneling rate calculations

    CERN Document Server

    Song, Lei

    2016-01-01

    Investigating how formamide forms in the interstellar medium is a hot topic in astrochemistry, which can contribute to our understanding of the origin of life on Earth. We have constructed a QM/MM model to simulate the hydrogenation of isocyanic acid on amorphous solid water surfaces to form formamide. The binding energy of HNCO on the ASW surface varies significantly between different binding sites, we found values between $\\sim$0 and 100 kJ mol$^{-1}$. The barrier for the hydrogenation reaction is almost independent of the binding energy, though. We calculated tunneling rate constants of H + HNCO $\\rightarrow$ NH$_2$CO at temperatures down to 103 K combining QM/MM with instanton theory. Tunneling dominates the reaction at such low temperatures. The tunneling reaction is hardly accelerated by the amorphous solid water surface compared to the gas phase for this system, even though the activation energy of the surface reaction is lower than the one of the gas-phase reaction. Both the height and width of the ba...

  7. Water dynamics in rigid ionomer networks

    Science.gov (United States)

    Osti, N. C.; Etampawala, T. N.; Shrestha, U. M.; Aryal, D.; Tyagi, M.; Diallo, S. O.; Mamontov, E.; Cornelius, C. J.; Perahia, D.

    2016-12-01

    The dynamics of water within ionic polymer networks formed by sulfonated poly(phenylene) (SPP), as revealed by quasi-elastic neutron scattering (QENS), is presented. These polymers are distinguished from other ionic macromolecules by their rigidity and therefore in their network structure. QENS measurements as a function of temperature as the fraction of ionic groups and humidity were varied have shown that the polymer molecules are immobile while absorbed water molecules remain dynamic. The water molecules occupy multiple sites, either bound or loosely constrained, and bounce between the two. With increasing temperature and hydration levels, the system becomes more dynamic. Water molecules remain mobile even at subzero temperatures, illustrating the applicability of the SPP membrane for selective transport over a broad temperature range.

  8. Phase transition study of confined water molecules inside carbon nanotubes: hierarchical multiscale method from molecular dynamics simulation to ab initio calculation.

    Science.gov (United States)

    Javadian, Soheila; Taghavi, Fariba; Yari, Faramarz; Hashemianzadeh, Seyed Majid

    2012-09-01

    In this study, the mechanism of the temperature-dependent phase transition of confined water inside a (9,9) single-walled carbon nanotube (SWCNT) was studied using the hierarchical multi-scale modeling techniques of molecular dynamics (MD) and density functional theory (DFT). The MD calculations verify the formation of hexagonal ice nanotubes at the phase transition temperature T(c)=275K by a sharp change in the location of the oxygen atoms inside the SWCNT. Natural bond orbital (NBO) analysis provides evidence of considerable intermolecular charge transfer during the phase transition and verifies that the ice nanotube contains two different forms of hydrogen bonding due to confinement. Nuclear quadrupole resonance (NQR) and nuclear magnetic resonance (NMR) analyses were used to demonstrate the fundamental influence of intermolecular hydrogen bonding interactions on the formation and electronic structure of ice nanotubes. In addition, the NQR analysis revealed that the rearrangement of nano-confined water molecules during the phase transition could be detected directly by the orientation of ¹⁷O atom EFG tensor components related to the molecular frame axes. The effects of nanoscale confinements in ice nanotubes and water clusters were analyzed by experimentally observable NMR and NQR parameters. These findings showed a close relationship between the phase behavior and orientation of the electronic structure in nanoscale structures and demonstrate the usefulness of NBO and NQR parameters for detecting phase transition phenomena in nanoscale confining environments.

  9. Protein-bound solute removal during extended multipass versus standard hemodialysis

    DEFF Research Database (Denmark)

    Eloot, Sunny; Van Biesen, Wim; Axelsen, Mette;

    2015-01-01

    BACKGROUND: Multipass hemodialysis (MPHD) is a recently described dialysis modality, involving the use of small volumes of dialysate which are repetitively recycled. Dialysis regimes of 8 hours for six days a week using this device result in an increased removal of small water soluble solutes...... and middle molecules compared to standard hemodialysis (SHD). Since protein-bound solutes (PBS) exert important pathophysiological effects, we investigated whether MPHD results in improved removal of PBS as well. METHODS: A cross-over study (Clinical Trial NCT01267760) was performed in nine stable HD...

  10. Molecular properties by Quantum Monte Carlo: an investigation on the role of the wave function ansatz and the basis set in the water molecule

    CERN Document Server

    Zen, Andrea; Sorella, Sandro; Guidoni, Leonardo

    2013-01-01

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely: the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Throu...

  11. On Entropy Bounds and Holography

    CERN Document Server

    Halyo, Edi

    2009-01-01

    We show that the holographic entropy bound for gravitational systems and the Bekenstein entropy bound for nongravitational systems are holographically related. Using the AdS/CFT correspondence, we find that the Bekenstein bound on the boundary is obtained from the holographic bound in the bulk by minimizing the boundary energy with respect the AdS radius or the cosmological constant. This relation may also ameliorate some problems associated with the Bekenstein bound.

  12. 受限于碳纳米管中水分子微观结构的分子动力学模拟研究%Molecular Dynamics Study on Microscopic Structure of Water Molecules Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    刘华; 李春艳; 陈建超; 杨晓峰

    2011-01-01

    Molecular dynamics simulation were performed to study microscopic structure of water molecules confined in the different diameters of carbon nanotubes. Changing the temperature, the radial distribution function diagram of the water molecules confined in the carbon nanotubes was made. By doing the mean square displacement versus time graph of water molecules in carbon nanotubes, diffusion coefficient of water molecules in different diameters of carbon nanotubes was calculated with Einstein method, and it was compared with the diffusion coefficient of water molecules calculated by Knudsen diffusion.%利用分子动力学模拟研究受限于不同管径中水分子的微观结构,改变温度,做出受限水分子的径向分布函数图,并对比说明。通过做水分子在碳纳米管内的均方位移与时间关系图,利用Einstein法算出不同管径中水分子的扩散系数,与利用Knudsen扩散公式计算出的水分子的扩散系数进行比较。

  13. Molecular Dynamics Simulation of Multivalent-Ion Mediated Attraction between DNA Molecules

    Science.gov (United States)

    Dai, Liang; Mu, Yuguang; Nordenskiöld, Lars; van der Maarel, Johan R. C.

    2008-03-01

    All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.

  14. Atoms, Molecules, and Compounds

    CERN Document Server

    Manning, Phillip

    2007-01-01

    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.

  15. A DFT study of the interaction between large PAHs and atomic chlorine or hydrogen chloride molecule: Toward a modelling of the influence of chlorinated species on the trapping of water by soot

    Science.gov (United States)

    Garcia-Fernandez, C.; Radola, B.; Martin-Gondre, L.; Picaud, S.; Rayez, M. T.; Rayez, J. C.; Ouf, F. X.; Rubayo-Soneira, J.

    2017-02-01

    First-principle calculations have been performed to characterize the interaction of chlorinated species (HCl and Cl) with large polycyclic aromatic hydrocarbon (PAH) molecules and radicals. Whereas the characterization of the interaction process on the face of the PAH molecules requires taking into account long-range dispersion interactions in the calculations, trapping at the edge of PAH radicals involves stronger interactions that lead to the dissociation of the HCl molecule. Then, the first steps of water adsorption on the corresponding chlorinated species has been characterized, showing that chlorine may act as an efficient nucleation center for water molecules on such aromatic systems mimicking part of the carbonaceous surfaces that are likely present in soot. These results represent a first but necessary step for a better understanding of soot behavior in industrial or domestic fire situations.

  16. Bounded Satisfiability for PCTL

    CERN Document Server

    Bertrand, Nathalie; Schewe, Sven

    2012-01-01

    While model checking PCTL for Markov chains is decidable in polynomial-time, the decidability of PCTL satisfiability, as well as its finite model property, are long standing open problems. While general satisfiability is an intriguing challenge from a purely theoretical point of view, we argue that general solutions would not be of interest to practitioners: such solutions could be too big to be implementable or even infinite. Inspired by bounded synthesis techniques, we turn to the more applied problem of seeking models of a bounded size: we restrict our search to implementable -- and therefore reasonably simple -- models. We propose a procedure to decide whether or not a given PCTL formula has an implementable model by reducing it to an SMT problem. We have implemented our techniques and found that they can be applied to the practical problem of sanity checking -- a procedure that allows a system designer to check whether their formula has an unexpectedly small model.

  17. Photochemistry in the inner layers of clumpy circumstellar envelopes: formation of water in C-rich objects and of C-bearing molecules in O-rich objects

    CERN Document Server

    Agundez, Marcelino; Guelin, Michel

    2010-01-01

    A mechanism based on the penetration of interstellar ultraviolet photons into the inner layers of clumpy circumstellar envelopes around AGB stars is proposed to explain the non-equilibrium chemistry observed in such objects. We show through a simple modelling approach that in circumstellar envelopes with a certain degree of clumpiness or with moderately low mass loss rates (a few 10^(-7) solar masses per year) a photochemistry can take place in the warm and dense inner layers inducing important changes in the chemical composition. In carbon-rich objects water vapor and ammonia would be formed with abundances of 10^(-8) - 10(^-6) relative to H2, while in oxygen-rich envelopes ammonia and carbon-bearing molecules such as HCN and CS would form with abundances of 10^(-9) - 10^(-7) relative to H2. The proposed mechanism would explain the recent observation of warm water vapor in the carbon-rich envelope IRC +10216 with the Herschel Space Observatory, and predict that H2O should be detectable in other carbon-rich o...

  18. BOUNDING PYRAMIDS AND BOUNDING CONES FOR TRIANGULAR BEZIER SURFACES

    Institute of Scientific and Technical Information of China (English)

    Jian-song Deng; Fa-lai Chen; Li-li Wang

    2000-01-01

    This paper describes practical approaches on how to construct bounding pyramids and bounding cones for triangular Bézier surfaces. Examples are provided to illustrate the process of construction and comparison is made between various surface bounding volumes. Furthermore, as a starting point for the construction,we provide a way to compute hodographs of triangular Bézier surfaces and improve the algorithm for computing the bounding cone of a set of vectors.

  19. Bound states in the continuum

    Science.gov (United States)

    Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin

    2016-09-01

    Bound states in the continuum (BICs) are waves that remain localized even though they coexist with a continuous spectrum of radiating waves that can carry energy away. Their very existence defies conventional wisdom. Although BICs were first proposed in quantum mechanics, they are a general wave phenomenon and have since been identified in electromagnetic waves, acoustic waves in air, water waves and elastic waves in solids. These states have been studied in a wide range of material systems, such as piezoelectric materials, dielectric photonic crystals, optical waveguides and fibres, quantum dots, graphene and topological insulators. In this Review, we describe recent developments in this field with an emphasis on the physical mechanisms that lead to BICs across seemingly very different materials and types of waves. We also discuss experimental realizations, existing applications and directions for future work.

  20. Photonic Molecule Lasers Revisited

    Science.gov (United States)

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

    2014-05-01

    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.

  1. Protein-bound toxins: added value in their removal with high convective volumes.

    Science.gov (United States)

    Abad, Soraya; Vega, Almudena; Quiroga, Borja; Arroyo, David; Panizo, Nayara; Reque, Javier Eduardo; López-Gómez, Juan Manuel

    Chronic kidney disease is associated with an increased risk of cardiovascular events. In recent years, protein-bound toxins have become more important due to their association with increased morbidity and mortality, characterised by inadequate clearance during dialysis. The purpose of this study is to assess the influence of high convective volumes on postdilution online haemodiafiltration (OL-HDF) on the removal of medium-sized molecules, small molecules and protein-bound molecules.

  2. Critical SQG in bounded domains

    OpenAIRE

    Constantin, Peter; Ignatova, Mihaela

    2016-01-01

    We consider the critical dissipative SQG equation in bounded domains, with the square root of the Dirichlet Laplacian dissipation. We prove global a priori interior $C^{\\alpha}$ and Lipschitz bounds for large data.

  3. Blog life: Entropy Bound

    Science.gov (United States)

    Steinberg, Peter

    2008-06-01

    Who is the blog written by? Peter Steinberg is a nuclear physicist at the Brookhaven National Laboratory in New York, US. He is acting project manager of the PHOBOS experiment, which used Brookhaven's Relativistic Heavy Ion Collider (RHIC) to search for unusual events produced during collisions between gold nuclei. He is also involved with the PHENIX experiment, which seeks to discover a new state of matter known as the quark-gluon plasma. In addition to his own blog Entropy Bound, Steinberg is currently blogging on a website that was set up last year to publicize the involvement of US scientists with the Large Hadron Collider (LHC) at CERN.

  4. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent $\\lambda_L \\le 2 \\pi k_B T/\\hbar$. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  5. Bounded Fixed-Point Iteration

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1992-01-01

    they obtain a quadratic bound. These bounds are shown to be tight. Specializing the case of strict and additive functions to functionals of a form that would correspond to iterative programs they show that a linear bound is tight. This is related to several analyses studied in the literature (including...

  6. Error bounds for set inclusions

    Institute of Scientific and Technical Information of China (English)

    ZHENG; Xiyin(郑喜印)

    2003-01-01

    A variant of Robinson-Ursescu Theorem is given in normed spaces. Several error bound theorems for convex inclusions are proved and in particular a positive answer to Li and Singer's conjecture is given under weaker assumption than the assumption required in their conjecture. Perturbation error bounds are also studied. As applications, we study error bounds for convex inequality systems.

  7. Multifunctions of bounded variation

    Science.gov (United States)

    Vinter, R. B.

    2016-02-01

    Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.

  8. 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)

    1994-12-31

    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.

  9. Capillary rise of water in hydrophilic nanopores

    CERN Document Server

    Gruener, Simon; Wallacher, Dirk; Kityk, Andriy V; Huber, Patrick; 10.1103/PhysRevE.79.067301

    2009-01-01

    We report on the capillary rise of water in three-dimensional networks of hydrophilic silica pores with 3.5nm and 5nm mean radii, respectively (porous Vycor monoliths). We find classical square root of time Lucas-Washburn laws for the imbibition dynamics over the entire capillary rise times of up to 16h investigated. Provided we assume two preadsorbed strongly bound layers of water molecules resting at the silica walls, which corresponds to a negative velocity slip length of -0.5nm for water flow in silica nanopores, we can describe the filling process by a retained fluidity and capillarity of water in the pore center. This anticipated partitioning in two dynamic components reflects the structural-thermodynamic partitioning in strongly silica bound water layers and capillary condensed water in the pore center which is documented by sorption isotherm measurements.

  10. Molecular Properties by Quantum Monte Carlo: An Investigation on the Role of the Wave Function Ansatz and the Basis Set in the Water Molecule.

    Science.gov (United States)

    Zen, Andrea; Luo, Ye; Sorella, Sandro; Guidoni, Leonardo

    2013-10-08

    Quantum Monte Carlo methods are accurate and promising many body techniques for electronic structure calculations which, in the last years, are encountering a growing interest thanks to their favorable scaling with the system size and their efficient parallelization, particularly suited for the modern high performance computing facilities. The ansatz of the wave function and its variational flexibility are crucial points for both the accurate description of molecular properties and the capabilities of the method to tackle large systems. In this paper, we extensively analyze, using different variational ansatzes, several properties of the water molecule, namely, the total energy, the dipole and quadrupole momenta, the ionization and atomization energies, the equilibrium configuration, and the harmonic and fundamental frequencies of vibration. The investigation mainly focuses on variational Monte Carlo calculations, although several lattice regularized diffusion Monte Carlo calculations are also reported. Through a systematic study, we provide a useful guide to the choice of the wave function, the pseudopotential, and the basis set for QMC calculations. We also introduce a new method for the computation of forces with finite variance on open systems and a new strategy for the definition of the atomic orbitals involved in the Jastrow-Antisymmetrised Geminal power wave function, in order to drastically reduce the number of variational parameters. This scheme significantly improves the efficiency of QMC energy minimization in case of large basis sets.

  11. Density functional theory, natural bond orbital and quantum theory of atoms in molecule analyses on the hydrogen bonding interactions in tryptophan-water complexes

    Indian Academy of Sciences (India)

    Xiqian Niu; Zhengguo Huang; Lingling Ma; Tingting Shen; Lingfei Guo

    2013-07-01

    The tryptophan-water (Trp-H2O) complexes formed by hydrogen bonding interactions were investigated at the B97XD/6-311++G(d,p) level. Five Trp-H2O complexes possessing various types of hydrogen bonds (H-bonds) were characterized by geometries, energies, vibrational frequencies. The nature of the H-bonds were characterized by the natural bond orbital (NBO) and the quantum theory of atoms in molecule (QTAIM) analyses as well. The intramolecular H-bond formed between the amino and carboxyl oxygen atom of tryptophan was retained in most of the complexes, and the cooperativity between the intra and intermolecular H-bonds exist in some complexes. The intramolecular H-bond and some intermolecular H-bonds are strong and have partial covalent character. The H-bonds formed between carboxyl and oxygen/nitrogen atoms are stronger than other H-bonds. The H-bonds involving methylene of tryptophan as H-donor are weak H-bonds. For all complexes,ele and ex makes major contributions to the total interaction energy (MP2), while disp is the smallest component of the interaction energy. Both hydrogen bonding interaction and structural deformation play important roles in the relative stabilities of the complexes. Regardless of strong H-bonds, the stabilities of some complexes are weakened by the serious structural deformations.

  12. Slow-rise and fast-drop current feature of ultraviolet response spectra for ZnO-nanowire film modulated by water molecules

    Institute of Scientific and Technical Information of China (English)

    Ren Shou-Tian; Wang Qiang; Zhao Feng; Qu Shi-Liang

    2012-01-01

    This study describes the fabrication of ZnO-nanowire films by electro-chemical anodization of Zn foil.The ZnO films are characterized by field emission scanning electron microscopy,X-ray diffraction patterns,and transmission electron microscopy,respectively.The ultraviolet (UV) photo-response properties of the surface-contacted ZnO film are studied through the current evolution processes under different relative humidities.Unlike the usually observed current spectra of the ZnO films,the drop time is shorter than the rise time.The photo-conductivity gain G and the response time γ are both increased with the increase of the applied bias.The photo-conductivity gain G is lowered with the increase of the environmental humidity,while the response time γ is increased.These results can be explained by considering three different surface processes:1) the electron-hole (e-p) pair generation by the UV light illumination,2)the following surface (O-2) species desorption,and 3) the photo-catalytic hydrolysis of water molecules adsorbed on the ZnO surface.The slow-rise and fast-drop current feature is suggested to originate from the sponge-like structure of the ZnO nanowires.

  13. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-20

    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

  14. Observation of pendular butterfly Rydberg molecules.

    Science.gov (United States)

    Niederprüm, Thomas; Thomas, Oliver; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-10-05

    Engineering molecules with a tunable bond length and defined quantum states lies at the heart of quantum chemistry. The unconventional binding mechanism of Rydberg molecules makes them a promising candidate to implement such tunable molecules. A very peculiar type of Rydberg molecules are the so-called butterfly molecules, which are bound by a shape resonance in the electron-perturber scattering. Here we report the observation of these exotic molecules and employ their exceptional properties to engineer their bond length, vibrational state, angular momentum and orientation in a small electric field. Combining the variable bond length with their giant dipole moment of several hundred Debye, we observe counter-intuitive molecules which locate the average electron position beyond the internuclear distance.

  15. 水稳碎石基层双层连铺技术在某高速中的应用%Application of water-bound foundation double-layer paving technique in Pingyang highway

    Institute of Scientific and Technical Information of China (English)

    武海燕

    2011-01-01

    通过对平阳路面五标水稳碎石基层采用双层连铺的施工工艺,对水稳双层连铺与单层铺筑的工艺进行对比,并对试验段扰动最大部位进行芯样钻取,检测结果表明:双层连铺具有层间粘结良好,整体路用性能好,在保证工程质量的前提下,可以有效缩短工期和提高经济效益。%Through applying double-layer paving technique for standard No. 5 water-bound macadam of Pingyang pavement, it compares waterbound double-laying paving technique to single-layer paving technique, carries on core testing for maximum disturbing part at experimental sec- tion. Testing results show that: double-layer paving has some advantages, such as good layer sticking effect, good road performance, and can ef- fectively shorten construction duration and improve economic benefits in the premise of guaranteeing engineering quality.

  16. Universal quantum dot-based sandwich-like immunoassay strategy for rapid and ultrasensitive detection of small molecules using portable and reusable optofluidic nano-biosensing platform.

    Science.gov (United States)

    Zhou, Liping; Zhu, Anna; Lou, Xuening; Song, Dan; Yang, Rong; Shi, Hanchang; Long, Feng

    2016-01-28

    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.

  17. Photoassociative production of ultracold heteronuclear ytterbium molecules

    Energy Technology Data Exchange (ETDEWEB)

    Borkowski, Mateusz; Ciurylo, Roman [Instytut Fizyki, Uniwersytet Mikolaja Kopernika, ul. Grudziadzka 5/7, PL-87-100 Torun (Poland); Julienne, Paul S. [Joint Quantum Institute, National Institute of Standards and Technology and the University of Maryland, 100 Bureau Drive, Stop 8423, Gaithersburg, Maryland 20899-8423 (United States); Yamazaki, Rekishu; Takahashi, Yoshiro [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); CREST, JST, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 (Japan); Hara, Hideaki; Taie, Shintaro; Sugawa, Seiji; Takasu, Yosuke [Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502 (Japan); Enomoto, Katsunari [Department of Physics, University of Toyama, Toyama 930-8555 (Japan)

    2011-09-15

    We report observations of photoassociation (PA) spectra near the intercombination line in isotopic mixtures of ultracold ytterbium gases. Several heteronuclear bound states have been found for the excited {sup 170}Yb{sup 174}Yb and {sup 174}Yb{sup 176}Yb molecules. We develop a single-channel mass-scaled interaction model for the excited state molecule which well reproduces the measured bound state energies. This is an important step toward optical control of interactions in mixtures of ultracold ytterbium gases using heteronuclear optical Feshbach resonances. The model developed is applicable in collisions of other similar systems, such as cadmium and mercury.

  18. Hadron Molecules

    CERN Document Server

    Gutsche, Thomas; Faessler, Amand; Lee, Ian Woo; Lyubovitskij, Valery E

    2010-01-01

    We discuss a possible interpretation of the open charm mesons $D_{s0}^*(2317)$, $D_{s1}(2460)$ and the hidden charm mesons X(3872), Y(3940) and Y(4140) as hadron molecules. Using a phenomenological Lagrangian approach we review the strong and radiative decays of the $D_{s0}^* (2317)$ and $D_{s1}(2460)$ states. The X(3872) is assumed to consist dominantly of molecular hadronic components with an additional small admixture of a charmonium configuration. Determing the radiative ($\\gamma J/\\psi$ and $\\gamma \\psi(2s)$) and strong ($J/\\psi 2\\pi $ and $ J/\\psi 3\\pi$) decay modes we show that present experimental observation is consistent with the molecular structure assumption of the X(3872). Finally we give evidence for molecular interpretations of the Y(3940) and Y(4140) related to the observed strong decay modes $J/\\psi + \\omega$ or $J/\\psi + \\phi$, respectively.

  19. Metal-ion effects on the polarization of metal-bound water and infrared vibrational modes of the coordinated metal center of Mycobacterium tuberculosis pyrazinamidase via quantum mechanical calculations.

    Science.gov (United States)

    Salazar-Salinas, Karim; Baldera-Aguayo, Pedro A; Encomendero-Risco, Jimy J; Orihuela, Melvin; Sheen, Patricia; Seminario, Jorge M; Zimic, Mirko

    2014-08-28

    Mycobacterium tuberculosis pyrazinamidase (PZAse) is a key enzyme to activate the pro-drug pyrazinamide (PZA). PZAse is a metalloenzyme that coordinates in vitro different divalent metal cofactors in the metal coordination site (MCS). Several metals including Co(2+), Mn(2+), and Zn(2+) are able to reactivate the metal-depleted PZAse in vitro. We use quantum mechanical calculations to investigate the Zn(2+), Fe(2+), and Mn(2+) metal cofactor effects on the local MCS structure, metal-ligand or metal-residue binding energy, and charge distribution. Results suggest that the major metal-dependent changes occur in the metal-ligand binding energy and charge distribution. Zn(2+) shows the highest binding energy to the ligands (residues). In addition, Zn(2+) and Mn(2+) within the PZAse MCS highly polarize the O-H bond of coordinated water molecules in comparison with Fe(2+). This suggests that the coordination of Zn(2+) or Mn(2+) to the PZAse protein facilitates the deprotonation of coordinated water to generate a nucleophile for catalysis as in carboxypeptidase A. Because metal ion binding is relevant to enzymatic reaction, identification of the metal binding event is important. The infrared vibrational mode shift of the C═Nε (His) bond from the M. tuberculosis MCS is the best IR probe to metal complexation.

  20. Theoretical spectra of floppy molecules

    Science.gov (United States)

    Chen, Hua

    2000-09-01

    Detailed studies of the vibrational dynamics of floppy molecules are presented. Six-D bound-state calculations of the vibrations of rigid water dimer based on several anisotropic site potentials (ASP) are presented. A new sequential diagonalization truncation approach was used to diagonalize the angular part of the Hamiltonian. Symmetrized angular basis and a potential optimized discrete variable representation for intermonomer distance coordinate were used in the calculations. The converged results differ significantly from the results presented by Leforestier et al. [J. Chem. Phys. 106 , 8527 (1997)]. It was demonstrated that ASP-S potential yields more accurate tunneling splittings than other ASP potentials used. Fully coupled 4D quantum mechanical calculations were performed for carbon dioxide dimer using the potential energy surface given by Bukowski et al [J. Chem. Phys., 110, 3785 (1999)]. The intermolecular vibrational frequencies and symmetry adapted force constants were estimated and compared with experiments. The inter-conversion tunneling dynamics was studied using the calculated virtual tunneling splittings. Symmetrized Radau coordinates and the sequential diagonalization truncation approach were formulated for acetylene. A 6D calculation was performed with 5 DVR points for each stretch coordinate, and an angular basis that is capable of converging the angular part of the Hamiltonian to 30 cm-1 for internal energies up to 14000 cm-1. The probability at vinylidene configuration were evaluated. It was found that the eigenstates begin to extend to vinylidene configuration from about 10000 cm-1, and the ra, coordinate is closely related to the vibrational dynamics at high energy. Finally, a direct product DVR was defined for coupled angular momentum operators, and the SDT approach were formulated. They were applied in solving the angular part of the Hamiltonian for carbon dioxide dimer problem. The results show the method is capable of giving very accurate

  1. Improved Range Searching Lower Bounds

    DEFF Research Database (Denmark)

    Larsen, Kasper Green; Nguyen, Huy L.

    2012-01-01

    and Rosenberg's theorem), are also hard for dynamic range searching in the group model. This theorem allows us to reuse decades of research on range reporting lower bounds to immediately obtain a range of new group model lower bounds. Amongst others, this includes an improved lower bound for the fundamental...... problem of dynamic d-dimensional orthogonal range searching, stating that tqtu = Ω((lg n/lg lg n)d-1). Here tq denotes the query time and tu the update time of the data structure. This is an improvement of a lg1-δn factor over the recent lower bound of Larsen [FOCS'11], where δ>0 is a small constant......Table of Contents -------------------------------------------------------------------------------- In this paper we present a number of improved lower bounds for range searching in the pointer machine and the group model. In the pointer machine, we prove lower bounds for the approximate simplex...

  2. 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: tuphysic@sancharnet.in

    2005-09-15

    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.

  3. On functions of bounded variation

    OpenAIRE

    Aistleitner, Christoph; Pausinger, Florian; Svane, Anne Marie; Tichy, Robert F.

    2015-01-01

    The recently introduced concept of $\\mathcal{D}$-variation unifies previous concepts of variation of multivariate functions. In this paper, we give an affirmative answer to the open question from Pausinger \\& Svane (J. Complexity, 2014) whether every function of bounded Hardy--Krause variation is Borel measurable and has bounded $\\mathcal{D}$-variation. Moreover, we show that the space of functions of bounded $\\mathcal{D}$-variation can be turned into a commutative Banach algebra.

  4. Bounding approaches to system identification

    CERN Document Server

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

    1996-01-01

    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.

  5. Upper bounds for centerlines

    CERN Document Server

    Bukh, Boris

    2011-01-01

    In 2008, Bukh, Matousek, and Nivasch conjectured that for every n-point set S in R^d and every k, 0 <= k <= d-1, there exists a k-flat f in R^d (a "centerflat") that lies at "depth" (k+1) n / (k+d+1) - O(1) in S, in the sense that every halfspace that contains f contains at least that many points of S. This claim is true and tight for k=0 (this is Rado's centerpoint theorem), as well as for k = d-1 (trivial). Bukh et al. showed the existence of a (d-2)-flat at depth (d-1) n / (2d-1) - O(1) (the case k = d-2). In this paper we concentrate on the case k=1 (the case of "centerlines"), in which the conjectured value for the leading constant is 2/(d+2). We prove that 2/(d+2) is an *upper bound* for the leading constant. Specifically, we show that for every fixed d and every n there exists an n-point set in R^d for which no line in R^d lies at depth larger than 2n/(d+2) + o(n). This point set is the "stretched grid"---a set which has been previously used by Bukh et al. for other related purposes.

  6. Strongly bound citrate stabilizes the apatite nanocrystals in bone

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Y.-Y.; Rawal, A.; Schmidt-Rohr, K.

    2010-10-12

    Nanocrystals of apatitic calcium phosphate impart the organic-inorganic nanocomposite in bone with favorable mechanical properties. So far, the factors preventing crystal growth beyond the favorable thickness of ca. 3 nm have not been identified. Here we show that the apatite surfaces are studded with strongly bound citrate molecules, whose signals have been identified unambiguously by multinuclear magnetic resonance (NMR) analysis. NMR reveals that bound citrate accounts for 5.5 wt% of the organic matter in bone and covers apatite at a density of about 1 molecule per (2 nm){sup 2}, with its three carboxylate groups at distances of 0.3 to 0.45 nm from the apatite surface. Bound citrate is highly conserved, being found in fish, avian, and mammalian bone, which indicates its critical role in interfering with crystal thickening and stabilizing the apatite nanocrystals in bone

  7. Exotic helium molecules; Molecules exotiques d'helium

    Energy Technology Data Exchange (ETDEWEB)

    Portier, M

    2007-12-15

    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)

  8. Observation of pendular butterfly Rydberg molecules

    CERN Document Server

    Niederprüm, Thomas; Eichert, Tanita; Lippe, Carsten; Pérez-Ríos, Jesús; Greene, Chris H; Ott, Herwig

    2016-01-01

    Obtaining full control over the internal and external quantum states of molecules is the central goal of ultracold chemistry and allows for the study of coherent molecular dynamics, collisions and tests of fundamental laws of physics. When the molecules additionally have a permanent electric dipole moment, the study of dipolar quantum gases and spin-systems with long-range interactions as well as applications in quantum information processing are possible. Rydberg molecules constitute a class of exotic molecules, which are bound by the interaction between the Rydberg electron and the ground state atom. They exhibit extreme bond lengths of hundreds of Bohr radii and giant permanent dipole moments in the kilo-Debye range. A special type with exceptional properties are the so-called butterfly molecules, whose electron density resembles the shape of a butterfly. Here, we report on the photoassociation of butterfly Rydberg molecules and their orientation in a weak electric field. Starting from a Bose-Einstein cond...

  9. Determination of cutin-bound residues of chlorothalonil by immunoassay.

    Science.gov (United States)

    Jahn, C; Schwack, W

    2001-03-01

    An indirect competitive enzyme-linked immunosorbent assay (ELISA) was used to determine photochemically cutin-bound residues of chlorothalonil in enzymatically isolated tomato and apple fruit cuticles. The samples were spiked, irradiated, exhaustively extracted, and depolymerized with boron trifluoride complex resulting in a soluble depolymerisate. With this procedure, the ELISA could be calibrated with free target molecules for the quantification of originally bound chlorothalonil residues. In fruit cuticles that were irradiated for 8 h by simulated sunlight, 0.030 and 0.068 mg/g photoinduced cutin-bound residues of wax-free cuticles (calculated as chlorothalonil) were determined for tomatoes and apples, respectively. For the used antibody mAb chl. 4/11, cross-reactivities with derivatives of chlorothalonil simulating different types of cuticle-bound residues are given and discussed.

  10. Size exclusion and anion exchange high performance liquid chromatography for characterizing metals bound to marine dissolved organic matter

    Energy Technology Data Exchange (ETDEWEB)

    Garcia-Otero, Natalia; Bermejo-Barrera, Pilar [Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n, 15782 Santiago de Compostela (Spain); Moreda-Pineiro, Antonio, E-mail: antonio.moreda@usc.es [Department of Analytical Chemistry, Nutrition and Bromatology, Faculty of Chemistry, University of Santiago de Compostela, Avenida das Ciencias, s/n, 15782 Santiago de Compostela (Spain)

    2013-01-14

    Highlights: Black-Right-Pointing-Pointer Fractionation methods for assessing metals bound to marine DOM were developed. Black-Right-Pointing-Pointer SEC and AEC with UV detection and hyphenated with inductively coupled plasma-mass spectrometry were used. Black-Right-Pointing-Pointer SEC-UV showed marine DOM of molecular weights from 16 to 1 kDa. Black-Right-Pointing-Pointer Cobalt, manganese, strontium and zinc are bound to marine DOM. - Abstract: Size exclusion chromatography (SEC) followed by anion exchange chromatography (AEC) hyphenated with inductively coupled plasma-mass spectrometry (ICP-MS) was applied for fractionating metals bound to marine dissolved organic matter (DOM). Surface seawater samples (100 L) were subjected to tangential flow ultrafiltration (10,000 Da cut off) for isolating and pre-concentrating dissolved large molecules. The isolated fraction (retentate) consisted of 1 L, which was further freeze-dried and re-dissolved to 250 mL with ultrapure water. After HI Trap desalting of the re-dissolved retentate, SEC with UV detection showed marine DOM ranging from 6.5 kDa (lower than the permeable volume of the SEC column) to 16 kDa. A further characterization of this fraction by AEC with UV detection revealed the existence of four groups of macromolecules exhibiting retention times of 2.3, 2.8, 4.5 and 14.0 min. AEC hyphenated with ICP-MS showed the presence of strontium and zinc in the first AE fraction isolated from the SEC fraction; while manganese was found to be bound to the second AE fraction. Cobalt was found to be bound to molecules comprising the third AE fraction.

  11. Analysis of metal cations and inorganic anions in olive oil mill waste waters by atomic absorption spectroscopy and ion chromatography. Detection of metals bound mainly to the organic polymeric fraction.

    Science.gov (United States)

    Arienzo, M; Capasso, R

    2000-04-01

    Metal cations were quantitatively detected by atomic absorption spectrometry in samples of olive oil mill waste waters obtained by a pressure process (omww(1)) (K, 17.1; Mg, 2.72; Ca, 2.24; Na, 0.40; Fe, 0.123; Zn, 0.0630; Mn, 0.0147; Cu, 0.00860 g L(-)(1)) and a centrifugation process (omww(2)) (K, 9.80; Mg, 1.65; Ca, 1.35; Na, 0. 162; Fe, 0.0330; Zn, 0.0301; Mn, 0.00910; Cu, 0.00980 g L(-)(1)). The inorganic anions, determined in the same samples by ion chromatography, proved to be Cl(-), H(2)PO(4)(-), F(-), SO(4)(2)(-), and NO(3)(-) (1.61, 1.05, 0.66, 0.52, and 0.023 g L(-)(1), respectively, in omww(1) and 0.61, 0.40, 0.25, 0.20, and 0.0090 g L(-)(1), respectively, in omww(2)). Most of the metal cations were revealed to be bound to the omww organic polymeric fraction (opf), composed of polysaccharides, phenol polymers, and proteins. Opf relative molecular weight was substantially estimated in the range between 1000 and 30000 Da for approximately 75% and in the range from 30000 to 100000 Da for approximately 25%. The free residual cations pool proved to be neutralized by the inorganic counteranions. Finally, the possible exploitation of this material in agriculture and in environmental biotechnology processes is also discussed in the light of its chemical and biochemical oxygen demand parameters.

  12. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

    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.

  13. A Lower Bound on Concurrence

    Institute of Scientific and Technical Information of China (English)

    LIU Li-Guo; TIAN Cheng-Lin; CHEN Ping-Xing; YUAN Nai-Chang

    2009-01-01

    We derive an analytical lower bound on the concurrence for bipartite quantum systems with an improved computable cross norm or realignment criterion and an improved positive partial transpose criterion respectively.Furthermore we demonstrate that our bound is better than that obtained from the local uncertainty relations criterion with optimal local orthogonal observables which is known as one of the best estimations of concurrence.

  14. Characteristics and Performance of Novel Water-Absorbent Slow Release Nitrogen Fertilizers

    Institute of Scientific and Technical Information of China (English)

    HE Xu-sheng; LIAO Zong-wen; HUANG Pei-zhao; DUAN Ji-xian; GE Ren-shan; LI Hong-bo; GENG Zeng-chao

    2007-01-01

    In this article, a research on the characteristics and performance of water-absorbent slow release nitrogen fertilizer (WASRNF)using infrared spectroscopy (IR), scanning electronic microscopy (SEM), differential scanning calorimetry (DSC), and thermogravimetry analysis (TGA), was present. The results indicate that the water absorbency and nitrogen analysis of WASRNF is 103 g g-1 and 30%, respectively, and WASRNF exhibits approximately neutral pH and very low salt index.WASRNF is a copolymer of nitrogen fertilizer and super absorbent polymer (SAP) monomers which is formed through hydrogen bond interaction, and the molecule contains hydrophilic groups, which is responsible for the absorption and water retention capacity of the molecule. WASRNF is a gel that exhibits the ability to swell, but does not dissolve in water.WASRNF shows non-homogenous nature as a whole, but in local zone it is homogenous, the copolymer molecule shows chain network that is the physical structure responsible for absorption and retention of water in WASRNF. The water retained in WASRNF exists as free and nonfreezing bound and freezing bound water states, with the free and the nonfreezing water accounting for more than 95% of water retained in WASRNF, and the nonfreezing bound water for less than 5%. WASRNF functions in delaying the release of nitrogen from it, thereby serving a novel slow release nitrogenous fertilizer.

  15. Asynchronous Bounded Expected Delay Networks

    CERN Document Server

    Bakhshi, Rena; Fokkink, Wan; Pang, Jun

    2010-01-01

    The commonly used asynchronous bounded delay (ABD) network models assume a fixed bound on message delay. We propose a probabilistic network model, called asynchronous bounded expected delay (ABE) model. Instead of a strict bound, the ABE model requires only a bound on the expected message delay. While the conditions of ABD networks restrict the set of possible executions, in ABE networks all asynchronous executions are possible, but executions with extremely long delays are less probable. In contrast to ABD networks, ABE networks cannot be synchronised efficiently. At the example of an election algorithm, we show that the minimal assumptions of ABE networks are sufficient for the development of efficient algorithms. For anonymous, unidirectional ABE rings of known size N we devise a probabilistic leader election algorithm having average message and time complexity O(N).

  16. 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...

  17. Bounds on tau neutrino magnetic moment and charge radius from Super-K and SNO observations

    CERN Document Server

    Joshipura, A S; Joshipura, Anjan S.; Mohanty, Subhendra

    2001-01-01

    Neutrinos can scatter electrons in water detectors through their magnetic moments and charge radii in addition to the charged and neutral currents channels. The recent solar neutrino charged current event rates announced by SNO with the earlier solar and atmospheric neutrino observations from Super-Kamiokande allows us to put upper bounds of $\\mu < 10^{-31} cm^2$ on the neutrino charge radii. For the electron and muon neutrinos these bounds are comparable with existing bounds but for tau neutrinos these bounds are three orders of magnitude more stringent than earlier terrestrial bounds. These bounds are independent of any specific model of neutrino oscillations.

  18. The Out-bound and In-bound Travelling Market

    Institute of Scientific and Technical Information of China (English)

    Emily Yu

    2009-01-01

    @@ As the Spring Festival of China with a long vocation of seven days nationally is approaching,more and more attention is paid to the out-bound and inn-bound trayeling market.Will people hold their pockets firmly in the"cold winter"of world-wide financial crisis,or will they grab the great discount of traveling and take a good relax?

  19. Geometrical structures, vibrational frequencies, force constants and dissociation energies of isotopic water molecules (H2O, HDO, D2O, HTO, DTO, and T2O) under dipole electric field

    Institute of Scientific and Technical Information of China (English)

    Shi Shun-Ping; Zhang Quan; Zhang Li; Wang Rong; Zhu Zheng-He; Jiang Gang; Fu Yi-Bei

    2011-01-01

    The dissociation limits of isotopic water molecules are derived for the ground state. The equilibrium geometries,the vibrational frequencies, the force constants and the dissociation energies for the ground states of all isotopic water molecules under the dipole electric fields from -0.05 a.u. to 0.05 a.u. are calculated using B3P86/6-311++G(3df,3pf).The results show that when the dipole electric fields change from -0.05 a.u. to 0.05 a.u., the bond length of H-O increases whereas the bond angle of H-O-H decreases because of the charge transfer induced by the applied dipole electric field. The vibrational frequencies and the force constants of isotopic water molecules change under the influence of the strong external torque. The dissociation energies increase when the dipole electric fields change from -0.05 a.u.to 0.05 a.u. and the increased dissociation energies are in the order of H2O, HDO, HTO, D2O, DTO, and T2O under the same external electric fields.

  20. 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.

    Science.gov (United States)

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

    2013-08-26

    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.

  1. Bounds for Certain Character Sums

    Institute of Scientific and Technical Information of China (English)

    杨锦; 郑志勇

    2003-01-01

    This paper shows a connection between exponential sums and character sums. In particular, we introduce a character sum that is an analog of the classical Kloosterman sums and establish the analogous Weil-Estermann's upper bound for it. The paper also analyzes a generalized Hardy-Littlewood example for character sums, which shows that the upper bounds given here are the best possible. The analysis makes use of local bounds for the exponential sums and character sums. The basic theorems have been previously established.

  2. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    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.

  3. Bounded Model Checking of CTL

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Tao; Cong-Hua Zhou; Zhong Chen; Li-Fu Wang

    2007-01-01

    Bounded Model Checking has been recently introduced as an efficient verification method for reactive systems.This technique reduces model checking of linear temporal logic to propositional satisfiability.In this paper we first present how quantified Boolean decision procedures can replace BDDs.We introduce a bounded model checking procedure for temporal logic CTL* which reduces model checking to the satisfiability of quantified Boolean formulas.Our new technique avoids the space blow up of BDDs, and extends the concept of bounded model checking.

  4. Hydration index--a better parameter for explaining small molecule hydration in inhibition of ice recrystallization.

    Science.gov (United States)

    Tam, Roger Y; Ferreira, Sandra S; Czechura, Pawel; Chaytor, Jennifer L; Ben, Robert N

    2008-12-24

    Several simple mono- and disaccharides have been assessed for their ability to inhibit ice recrystallization. Two carbohydrates were found to be effective recrystallization inhibitors. D-galactose (1) was the best monosaccharide and D-melibiose (5) was the most active disaccharide. The ability of each carbohydrate to inhibit ice growth was correlated to its respective hydration number reported in the literature. A hydration number reflects the number of tightly bound water molecules to the carbohydrate and is a function of carbohydrate stereochemistry. It was discovered that using the absolute hydration number of a carbohydrate does not allow one to accurately predict its ability to inhibit ice recrystallization. Consequently, we have defined a hydration index in which the hydration number is divided by the molar volume of the carbohydrate. This new parameter not only takes into account the number of water molecules tightly bound to a carbohydrate but also the size or volume of a particular solute and ultimately the concentration of hydrated water molecules. The hydration index of both mono- and disaccharides correlates well with experimentally measured RI activity. C-Linked derivatives of the monosaccharides appear to have RI activity comparable to that of their O-linked saccharides but a more thorough investigation is required. The relationship between carbohydrate concentration and RI activity was shown to be noncolligative and a 0.022 M solution of D-galactose (1) and C-linked galactose derivative (10) inhibited recrystallization as well as a 3% DMSO solution. The carbohydrates examined in this study did not possess any thermal hysteresis activity (selective depression of freezing point relative to melting point) or dynamic ice shaping. As such, we propose that they are inhibiting recrystallization at the interface between bulk water and the quasi liquid layer (a semiordered interface between ice and bulk water) by disrupting the preordering of water.

  5. Water

    Science.gov (United States)

    ... www.girlshealth.gov/ 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, ...

  6. Computing Constrained Cramer Rao Bounds

    CERN Document Server

    Tune, Paul

    2012-01-01

    We revisit the problem of computing submatrices of the Cram\\'er-Rao bound (CRB), which lower bounds the variance of any unbiased estimator of a vector parameter $\\vth$. We explore iterative methods that avoid direct inversion of the Fisher information matrix, which can be computationally expensive when the dimension of $\\vth$ is large. The computation of the bound is related to the quadratic matrix program, where there are highly efficient methods for solving it. We present several methods, and show that algorithms in prior work are special instances of existing optimization algorithms. Some of these methods converge to the bound monotonically, but in particular, algorithms converging non-monotonically are much faster. We then extend the work to encompass the computation of the CRB when the Fisher information matrix is singular and when the parameter $\\vth$ is subject to constraints. As an application, we consider the design of a data streaming algorithm for network measurement.

  7. Bound states in string nets

    Science.gov (United States)

    Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien

    2016-11-01

    We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

  8. Some bounds for quantum copying

    CERN Document Server

    Rastegin, A E

    2001-01-01

    We derive lower bounds on the absolute error and the relative error of an abstract copying of two-state set. We do not specify a copying transformation and a dimension of state space. Only the unitarity of quantum mechanical transformations is used. Our approach is based on the notion of angle between two states. We first prove several useful statements, simply expressed in terms of angles. We then examine a lower bound on the absolute error, that was first considered by Hillery and Buzek. Our reasonings supplement and reinforce the results, obtained by them. So, we derive more strong bounds on the absolute error, and we also consider a tradeoff between size of error and corresponding probability distributions. After that we examine a lower bound on the relative error.

  9. Bound states in string nets

    CERN Document Server

    Schulz, M D; Vidal, J

    2016-01-01

    We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

  10. Characterization of the fine specificity of peptide antibodies to HLA-DQ beta-chain molecules

    DEFF Research Database (Denmark)

    Petersen, J S; Atar, D; Karlsen, Alan E

    1990-01-01

    specifically recognized DQw7 beta peptides and two antisera bound only to DQw8 beta peptides from the region containing the amino acid in position 57. To analyze whether the antisera bound to native HLA-DQ beta-chain molecules, FACS analysis was carried out. Seven of the 20 antisera bound to intact EBV...

  11. Interaction of C4-binding protein with cell-bound C4b. A quantitative analysis of binding and the role of C4-binding protein in proteolysis of cell-bound C4b

    OpenAIRE

    1983-01-01

    Purified C4-binding protein (C4-bp) was shown to bind to cell-bound C4b by radioactive tracer techniques. With EAC4 bearing greater than 3,000 C4b-molecules/cell, the number of C4-bp molecules bound was directly proportional to the number of C4b molecule on the cell surface; EAC4 bearing less than 3,000 C4b-molecules/cell bound a very small amount of C4-bp. Scatchard analysis of binding of C4-bp indicated an equilibrium constant of 4.6 X 10(8) L/M and a maximum of 0.43 C4-bp molecules bound p...

  12. Microcanonical distribution for one-electron triatomic molecules

    CERN Document Server

    Lazarou, C; Emmanouilidou, A

    2015-01-01

    We formulate a microcanonical distribution for an arbitrary one-electron triatomic molecule. This distribution can be used to describe the initial state in strongly-driven two-electron triatomic molecules. Namely, in many semiclassical models that describe ionization of two-electron molecules driven by intense infrared laser fields in the tunneling regime initially one electron tunnels while the other electron is bound. The microcanonical distribution presented in this work can be used to describe the initial state of this bound electron.

  13. Flux controllable pumping of water molecules in a double-walled carb on nanotub e%通量可控的双壁碳纳米管水分子泵∗

    Institute of Scientific and Technical Information of China (English)

    曹平; 罗成林; 陈贵虎; 韩典荣; 朱兴凤; 戴亚飞

    2015-01-01

    A water pumping system model has been designed based on the double-walled carbon nanotube. In this system, the inner tube is fixed as the water channel, while the exterior one can move, similar to the piston motion along the axial direction, to create a pumping force. Molecular dynamics simulations confirm that both the water flux and the water dipole orientation are sensitive to the velocity of motions of the outer tube so that a controllable unidirectional water flow can be achieved in this system by varying the velocity. Its pumping ability comes mainly from the carbon–water van der Waals driving forces of the exterior tube. The piston motion of the outer tube changes the position of the vdW balance point, which not only leads to the increase of vdW force on the water molecules already residing in the inner tube, but also enlarges their accelerated distance. Meanwhile, the orientation of water molecules inside the inner tube is strongly coupled to the water flux, the probability of +dipole states attains unity at v=0.05 Å/ps, where the water flux reaches its maximum value (2.02 ns−1). Compared to the pump which is controlled by uniform electric field, the transmission efficiency of our mechanical pump is higher. This design may open a new way for water pumping in the field of nanodevices.%以双壁碳纳米管作为基本单元设计了一种新型纳米机械水泵,其内管固定作为水分子通道,外管做活塞式轴向运动。分子动力学计算表明,水分子净通量及管内水分子电偶极矩分布均与外管运动速率有强烈耦合效应。该设计可以实现水分子的高效单向运输,且输运效率可以通过外管活塞运动的速率进行调控。这些发现可为未来实用纳米分子泵器件的设计提供新的思路。

  14. Classification of billiard motions in domains bounded by confocal parabolas

    Energy Technology Data Exchange (ETDEWEB)

    Fokicheva, V V [M. V. Lomonosov Moscow State University, Faculty of Mechanics and Mathematics, Moscow (Russian Federation)

    2014-08-01

    We consider the billiard dynamical system in a domain bounded by confocal parabolas. We describe such domains in which the billiard problem can be correctly stated. In each such domain we prove the integrability for the system, analyse the arising Liouville foliation, and calculate the invariant of Liouville equivalence--the so-called marked molecule. It turns out that billiard systems in certain parabolic domains have the same closures of solutions (integral trajectories) as the systems of Goryachev-Chaplygin-Sretenskii and Joukowski at suitable energy levels. We also describe the billiard motion in noncompact domains bounded by confocal parabolas, namely, we describe the topology of the Liouville foliation in terms of rough molecules. Bibliography: 16 titles.

  15. A bio-inspired, small molecule electron-coupled-proton buffer for decoupling the half-reactions of electrolytic water splitting.

    Science.gov (United States)

    Rausch, Benjamin; Symes, Mark D; Cronin, Leroy

    2013-09-18

    Electron-coupled-proton buffers (ECPBs) allow H2 and O2 evolution to be separated from each other in time during the electrolysis of water. Natural photosynthetic systems achieve an analogous feat during water splitting and employ a range of intermediate redox mediators such as quinone derivatives to aid this process. Drawing on this natural example, we show that a low molecular weight quinone derivative is capable of decoupling H2 evolution from O2 evolution at scale during electrochemical water splitting. This work could significantly lower the cost of ECPBs, paving the way for their more widespread adoption in water splitting.

  16. Physical state of poorly water soluble therapeutic molecules loaded into SBA-15 ordered mesoporous silica carriers: a case study with itraconazole and ibuprofen.

    Science.gov (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

    2008-08-19

    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.

  17. Solar energy driven photocatalytic membrane modules for water reuse in agricultural and food industries. Pre-industrial experience using s-triazines as model molecules

    OpenAIRE

    Ignazio Renato Bellobono; Franca Morazzoni; Riccardo Bianchi; Emilia Simona Mangone; Rodica Stanescu; Cristina Costache; Paola Maria Tozzi

    2005-01-01

    A membrane module, utilizing photocatalytic membranes, has been employed in a pilot plant, in conditions of solar irradiation, to investigate photomineralisation of atrazine, propazine, terbutylazine, symazine, prometryn, and ametryn, as model molecules of s-triazine herbicides, at a standard concentration (1.0 ppm) simulating those of contaminated aquifers, by using ozone as oxygen supplier. Photocatalytic composite membranes immobilised 30±3 wt.% of TiO2 and 6 wt.% of a synergic mixture of ...

  18. Universal bound on the efficiency of molecular motors

    Science.gov (United States)

    Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

    2016-12-01

    The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a molecular motor running against an external force or torque, we show that the thermodynamic efficiency of such motors is universally bounded by an expression involving only experimentally accessible quantities. For motors pulling cargo through a viscous fluid, a universal bound for the corresponding Stokes efficiency follows as a variant. A similar result holds if mechanical force is used to synthesize molecules of high chemical potential. Crucially, no knowledge of the detailed underlying mechano-chemical mechanism is required for applying these bounds.

  19. Experimental activation of bound entanglement.

    Science.gov (United States)

    Kaneda, Fumihiro; Shimizu, Ryosuke; Ishizaka, Satoshi; Mitsumori, Yasuyoshi; Kosaka, Hideo; Edamatsu, Keiichi

    2012-07-27

    Entanglement is one of the essential resources in quantum information and communication technology (QICT). The entanglement thus far explored and applied to QICT has been pure and distillable entanglement. Yet, there is another type of entanglement, called "bound entanglement," which is not distillable by local operations and classical communication. We demonstrate the experimental "activation" of the bound entanglement held in the four-qubit Smolin state, unleashing its immanent entanglement in distillable form, with the help of auxiliary two-qubit entanglement and local operations and classical communication. We anticipate that it opens the way to a new class of QICT applications that utilize more general classes of entanglement than ever, including bound entanglement.

  20. Eta nuclear bound states revisited

    CERN Document Server

    Friedman, E; Mareš, J

    2013-01-01

    The strong energy dependence of the s-wave eta-N scattering amplitude at and below threshold, as evident in coupled-channels K-matrix fits and chiral models that incorporate the S11 N*(1535) resonance, is included self consistently in eta-nuclear bound state calculations. This approach, applied recently in calculations of kaonic atoms and Kbar-nuclear bound states, is found to impose stronger constraints than ever on the onset of eta-nuclear binding, with a minimum value of Re a_{eta N} approximately 0.9 fm required to accommodate an eta-4He bound state. Binding energies and widths of eta-nuclear states are calculated within several underlying eta-N models for nuclei across the periodic table, including eta-25Mg for which some evidence was proposed in a recent COSY experiment.

  1. 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

    Science.gov (United States)

    Amirov, Elnur

    2016-04-01

    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

  2. 高密度CO2处理虾仁营养组成和水分子状态的变化规律%Changes in nutritious component and water molecule of peeled shrimp during dense phase carbon dioxide treatment

    Institute of Scientific and Technical Information of China (English)

    陈亚励; 屈小娟; 刘书成; 吉宏武; 郝记明; 黄万有; 郭明慧

    2014-01-01

    and small molecular compounds containing nitrogen (e.g. free amino acids) were carried out with CO2 in the unloading process. While using the untreated peeled shrimp, the contents of myofibrillar and sarcoplasmic protein decreased significantly (P<0.05) and the content of insoluble protein increased significantly (P<0.05) with exposure to time, temperature, and pressure when DPCD was increasing. The reason for that was myofibrillar and sarcoplasmic protein were denatured and transformed to insoluble protein by DPCD. The results of low field nuclear magnetic resonance (LF-NMR) showed that peeled shrimp contained four kinds of water molecules with different mobility. With exposure to time, temperature, and pressure when DPCD was increasing, the degree of freedom of bound water increased while the degree of freedom of immobilized water and free water decreased. Nonetheless, the content of bound water and free water increased significantly (P<0.05) while the content of immobilized water decreased significantly (P<0.05), when the peeled shrimp was treated for 30 min at 15 MPa and 55℃ of DPCD. Microorganism and PPO from Litopenaeus vannamei were inactivated, but the content of moisture, crude protein, crude fat, and ash decreased by 7%、3%、25%, and 11%, respectively. Sarcoplasmic and myofibrillar protein were denatured, and the free water ratio increased significantly (P<0.05). The research results will provide a reference for the application of DPCD in shrimp processing.%为了探讨高密度CO2(dense phase carbon dioxide,DPCD)处理对虾仁肌肉品质的影响,以未处理的新鲜虾仁为对照,研究了DPCD处理过程中虾仁营养组成和水分子状态的变化规律。结果表明:在温度35~55℃和压力5~25 MPa的条件下处理10~50 min,与未处理虾仁相比,虾仁的水分、粗蛋白、粗脂肪和灰分含量均显著下降(P<0.05),尤其是脂肪含量下降幅度最大;随着DPCD处理强度增加,虾仁肌

  3. Lower Bounds for Sparse Recovery

    CERN Document Server

    Ba, Khanh Do; Price, Eric; Woodruff, David P

    2011-01-01

    We consider the following k-sparse recovery problem: design an m x n matrix A, such that for any signal x, given Ax we can efficiently recover x' satisfying ||x-x'||_1 <= C min_{k-sparse} x"} ||x-x"||_1. It is known that there exist matrices A with this property that have only O(k log (n/k)) rows. In this paper we show that this bound is tight. Our bound holds even for the more general /randomized/ version of the problem, where A is a random variable and the recovery algorithm is required to work for any fixed x with constant probability (over A).

  4. Variables Bounding Based Retiming Algorithm

    Institute of Scientific and Technical Information of China (English)

    宫宗伟; 林争辉; 陈后鹏

    2002-01-01

    Retiming is a technique for optimizing sequential circuits. In this paper, wediscuss this problem and propose an improved retiming algorithm based on variables bounding.Through the computation of the lower and upper bounds on variables, the algorithm can signi-ficantly reduce the number of constraints and speed up the execution of retiming. Furthermore,the elements of matrixes D and W are computed in a demand-driven way, which can reducethe capacity of memory. It is shown through the experimental results on ISCAS89 benchmarksthat our algorithm is very effective for large-scale sequential circuits.

  5. Bounds for Completely Decomposable Jacobians

    CERN Document Server

    Duursma, Iwan

    2010-01-01

    A curve over the field of two elements with completely decomposable Jacobian is shown to have at most six rational points and genus at most 26. The bounds are sharp. The previous upper bound for the genus was 145. We also show that a curve over the field of $q$ elements with more than $q^{m/2}+1$ rational points has at least one Frobenius angle in the open interval $(\\pi/m,3\\pi/m)$. The proofs make use of the explicit formula method.

  6. Variational Bounds for Creeping Composites

    Science.gov (United States)

    Procházka, Petr

    2010-05-01

    In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.

  7. Pieter Paul Rubens, "Prometheus Bound."

    Science.gov (United States)

    Shoemaker, Marla K.

    1986-01-01

    Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)

  8. Market access through bound tariffs

    DEFF Research Database (Denmark)

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

    2010-01-01

    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 on t...

  9. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

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

    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 on t...

  10. CD(4) has bounded width

    CERN Document Server

    Carvalho, Catarina; Marković, Petar; Maróti, Miklós

    2007-01-01

    We prove that the constraint languages invariant under a short sequence of J\\'onsson terms (containing at most three non-trivial ternary terms) are tractable by showing that they have bounded width. This improves the previous result by Kiss and Valeriote and presents some evidence that the Larose-Zadori conjecture holds in the congruence-distributive case.

  11. A Functional Calculus for Quotient Bounded Operators

    Directory of Open Access Journals (Sweden)

    Sorin Mirel Stoian

    2006-12-01

    Full Text Available If (X, P is a sequentially locally convex space, then a quotient bounded operator T beloging to QP is regular (in the sense of Waelbroeck if and only if it is a bounded element (in the sense of Allan of algebra QP. The classic functional calculus for bounded operators on Banach space is generalized for bounded elements of algebra QP.

  12. Hadronic molecules with hidden charm and bottom

    Directory of Open Access Journals (Sweden)

    Guo Feng-Kun

    2016-01-01

    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.

  13. Mesoscopic Simulation of Aggregates in Surfactant/Oil/Water Systems

    Institute of Scientific and Technical Information of China (English)

    苑世领; 蔡政亭; 徐桂英

    2003-01-01

    The aggregates in sodium dedecylsulphate(SDS)/dimethylbenzene/water systems have been investigated using dissipative particles dynamic(DPD) simulation method.Through analyzing three-dimensional structures of aggregates,three simulated results are found.One is the phase separation,which is clearly observed by water density and the aggregates in the simulated cell;another is the water morphology in reverse micelle,which can be found through the isodensity slice of water including bound water,trapped water and bulky water;the third is about the water/oil interface,i.e.,ionic surfactant molecules,SDS,prefer to exist in the interface between water and oil phase at the low concentraion.

  14. 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: longf04@ruc.edu.cn [School of Environment and Natural Resources, Renmin University of China, Beijing (China)

    2016-01-28

    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

  15. 磷脂分子在水中形成不同聚集体的机制探讨%Discussion on mechanism of the formation of different phospholipid molecules aggregates in water

    Institute of Scientific and Technical Information of China (English)

    薛士兴; 王向涛; 李永吉

    2012-01-01

    Phospholipid molecules are the basic composition of life, which possesses amphiphilic molecular structure and biological homology. The self-assembly aggregates of liposomes is widely used in drug delivery systems. However, the structure of the phospholipid molecule aggregates in water were diverse, including not only spherical liposomes, but also tubular structures (such as microtubules) . By studying related literature, the mechanism of the formation of different phospholipid molecule aggregates was analyzed and summarized, with focus on the effects of the amphiphilic structure and molecular morphology of the phospholipid molecules on the formation of different self-assembly aggregates. This discussion may have important theoretical significance for the preparation of phospholipid molecular aggregates.%磷脂分子作为生命体的基本组成物质,既具有两亲性的分子结构,又具有生物同源性,因此,其自组装聚集体-脂质体在药物载体方面得到广泛应用.但磷脂分子在水中形成的聚集体结构多样,不仅有球状的脂质体,还有管状结构(如微管).本文通过研究国内外相关文献,分析、整理和归纳了磷脂分子在水中形成不同聚集体的机制,主要讲述了磷脂分子的两亲性结构、分子形态对形成不同自组装聚集体的影响,对于磷脂分子聚集体的制备具有重要的理论指导意义.

  16. Ab initio study of the chemical states of water on Cr 2O 3(0 0 0 1): From the isolated molecule to saturation coverage

    Science.gov (United States)

    Costa, Dominique; Sharkas, Kamal; Islam, Mazharul M.; Marcus, Philippe

    2009-08-01

    The reactivity of the (0 0 0 1)-Cr-Cr 2O 3 surface towards water was studied by means of periodic DFT + U. Several water coverages were studied, from 1.2H 2O/nm 2 to 14.1H 2O/nm 2, corresponding to ¼, 1, 2 and 3 water/Cr at the (0 0 0 1)-Cr 2O 3 surface, respectively. With increasing coverage, water gradually completes the coordination sphere of the surface Cr atoms from 3 (dry surface) to 4 (1.2 and 4.7H 2O/nm 2), 5 (9.4H 2O/nm 2) and 6 (14.1H 2O/nm 2). For all studied coverages, water replaces an O atom from the missing above plane. At coverages 1.2 and 4.7H 2O/nm 2, the Cr-O s (surface oxygen) acid-base character and bond directionality govern the water adsorption. The adsorption is molecular at the lowest coverage. At 4.7H 2O/nm 2, molecular and dissociative states are isoenergetic. The activation energy barrier between the two states being as low as 12 kJ/mol, allowing protons exchanges between the OH groups, as evidenced by ab inito molecular dynamics at room temperature. At coverages of 9.4 and 14.1H 2O/nm 2, 1D- (respectively, 2D-) water networks are formed. The resulting surface terminations are -Cr(OH) 2 and -Cr(OH) 3- like, respectively. The increased stability of those terminations as compared to the previous ones are due to the stabilization of the adsorbed phase through a H-bond network and to the increase in the Cr coordination number, stabilizing the Cr ( t2g) orbitals in the valence band. An atomistic thermodynamic approach allows us to specify the temperature and water pressure domains of prevalence for each surface termination. It is found that the -Cr(OH) 3-like, -Cr(OH) 2 and anhydrous surfaces may be stabilized depending on ( T, P) conditions. Calculated energies of adsorption and OH frequencies are in good agreement with published experimental data and support the full hydroxylation model, where the Cr achieves a 6-fold coordination, at saturation.

  17. Heavy Exotic Molecules with Charm and Bottom

    CERN Document Server

    Liu, Yizhuang

    2016-01-01

    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 $(0^\\pm, 1^\\pm)$ cause the chiral exotic partners to unbind, and the primary exotic molecules to be about twice more bound, for $J\\leq 1$. Our multi-channel coupling results show that only the charm isosinglet exotic molecules with $J^{PC}=1^{++}$ binds, which we identify as the reported neutral $X(3872)$. Also, the bottom isotriplet exotic with $J^{PC}=1^{+-}$ binds, which we identify as a mixture of the reported charged exotics $Z^+_b(10610)$ and $Z^+_b(10650)$. The bound isosinglet with $J^{PC}=1^{++}$ is suggested as a possible neutral $X_b(10532)$ not yet reported.

  18. Heavy exotic molecules with charm and bottom

    Science.gov (United States)

    Liu, Yizhuang; Zahed, Ismail

    2016-11-01

    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.

  19. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    Chhanda Samanta

    2001-08-01

    The essential aspect of contemporary physics is to understand properties of nucleonic matter that constitutes the world around us. Over the years research in nuclear physics has provided strong guidance in understanding the basic principles of nuclear interactions. But, the scenario of 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 nuclei are posing new challenges to both theory and experiments. Fortunately, nature has provided a few loosely bound stable nuclei that have been studied thoroughly for decades. Attempts are being made to find a consistent picture for the unstable nuclei starting from their stable counterparts. Some significant differences in the structure and reaction mechanisms are found.

  20. 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. (syasuhara@picarro.com)1,Carter, J.A. (jcarter@picarro.com)1, Dennis, K.J. (kdennis@picarro.com)1 1Picarro Inc., 3105 Patrick Henry Drive, Santa Clara, CA 95054

    Science.gov (United States)

    Yasuhara, S.

    2013-12-01

    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

  1. Lower Bounds on Paraclique Density.

    Science.gov (United States)

    Hagan, Ronald D; Langston, Michael A; Wang, Kai

    2016-05-11

    The scientific literature teems with clique-centric clustering strategies. In this paper we analyze one such method, the paraclique algorithm. Paraclique has found practical utility in a variety of application domains, and has been successfully employed to reduce the effects of noise. Nevertheless, its formal analysis and worst-case guarantees have remained elusive. We address this issue by deriving a series of lower bounds on paraclique densities.

  2. Bound Modes in Dielectric Microcavities

    CERN Document Server

    Visser, P M; Lenstra, D

    2002-01-01

    We demonstrate how exactly bound cavity modes can be realized in dielectric structures other than 3d photonic crystals. For a microcavity consisting of crossed anisotropic layers, we derive the cavity resonance frequencies, and spontaneous emission rates. For a dielectric structure with dissipative loss and central layer with gain, the beta factor of direct spontaneous emission into a cavity mode and the laser threshold is calculated.

  3. Entropy Bounds in Spherical Space

    CERN Document Server

    Brevik, I; Odintsov, S D; Brevik, Iver; Milton, Kimball A.; Odintsov, Sergei D.

    2002-01-01

    Exact calculations are given for the Casimir energy for various fields in $R\\times S^3$ geometry. The Green's function method naturally gives a result in a form convenient in the high-temperature limit, while the statistical mechanical approach gives a form appropriate for low temperatures. The equivalence of these two representations is demonstrated. Some discrepancies with previous work are noted. In no case, even for ${\\cal N}=4$ SUSY, is the ratio of entropy to energy found to be bounded.

  4. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math...

    Science.gov (United States)

    2013-03-26

    ... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... Upward Bound Math Science Annual Performance Report. OMB Control Number: 1840-NEW. Type of Review: New... under the regular Upward Bound (UB) and Upward Bound Math and Science (UBMS) Programs. The Department...

  5. Trapping and manipulating single molecules of DNA

    Science.gov (United States)

    Shon, Min Ju

    This thesis presents the development and application of nanoscale techniques to trap and manipulate biomolecules, with a focus on DNA. These methods combine single-molecule microscopy and nano- and micro-fabrication to study biophysical properties of DNA and proteins. The Dimple Machine is a lab-on-a-chip device that can isolate and confine a small number of molecules from a bulk solution. It traps molecules in nanofabricated chambers, or "dimples", and the trapped molecules are then studied on a fluorescence microscope at the single-molecule level. The sampling of bulk solution by dimples is representative, reproducible, and automated, enabling highthroughput single-molecule experiments. The device was applied to study hybridization of oligonucleotides, particularly in the context of reaction thermodynamics and kinetics in nanoconfinement. The DNA Pulley is a system to study protein binding and the local mechanical properties of DNA. A molecule of DNA is tethered to a surface on one end, and a superparamagnetic bead is attached to the other. A magnet pulls the DNA taut, and a silicon nitride knife with a nanoscale blade scans the DNA along its contour. Information on the local properties of the DNA is extracted by tracking the bead with nanometer precision in a white-light microscope. The system can detect proteins bound to DNA and localize their recognition sites, as shown with a model protein, EcoRI restriction enzyme. Progress on the measurements of nano-mechanical properties of DNA is included.

  6. Bounds on Generalized Huffman Codes

    CERN Document Server

    Baer, Michael B

    2007-01-01

    New lower and upper bounds are obtained for the compression of optimal binary prefix codes according to various nonlinear codeword length objectives. Like the coding bounds for Huffman coding - which concern the traditional linear code objective of minimizing average codeword length -- these are in terms of a form of entropy and the probability of the most probable input symbol. As in Huffman coding, some upper bounds can be found using sufficient conditions for the codeword corresponding to the most probable symbol being one bit long. Whereas having probability no less than 0.4 is a tight sufficient condition for this to be the case in Huffman coding, other penalties differ, some having a tighter condition, some a looser condition, and others having no such sufficient condition. The objectives explored here are ones for which optimal codes can be found using a generalized form of Huffman coding. These objectives include one related to queueing (an increasing exponential average), one related to single-shot c...

  7. The Cost of Bounded Curvature

    CERN Document Server

    Kim, Hyo-Sil

    2011-01-01

    We study the motion-planning problem for a car-like robot whose turning radius is bounded from below by one and which is allowed to move in the forward direction only (Dubins car). For two robot configurations $\\sigma, \\sigma'$, let $\\ell(\\sigma, \\sigma')$ be the shortest bounded-curvature path from $\\sigma$ to $\\sigma'$. For $d \\geq 0$, let $\\ell(d)$ be the supremum of $\\ell(\\sigma, \\sigma')$, over all pairs $(\\sigma, \\sigma')$ that are at Euclidean distance $d$. We study the function $\\dub(d) = \\ell(d) - d$, which expresses the difference between the bounded-curvature path length and the Euclidean distance of its endpoints. We show that $\\dub(d)$ decreases monotonically from $\\dub(0) = 7\\pi/3$ to $\\dub(\\ds) = 2\\pi$, and is constant for $d \\geq \\ds$. Here $\\ds \\approx 1.5874$. We describe pairs of configurations that exhibit the worst-case of $\\dub(d)$ for every distance $d$.

  8. Bounds on Black Hole Spins

    CERN Document Server

    Daly, Ruth A

    2009-01-01

    Beam powers and black hole masses of 48 extended radio sources are combined to obtain lower bounds on the spins and magnetic field strengths of supermassive black holes. This is done in the context of the models of Blandford & Znajek (1977) (the 'BZ' model) and Meier (1999); a parameterization for bounds in the context of other models is suggested. The bounds obtained for very powerful classical double radio sources in the BZ model are consistent with black hole spins of order unity for sources at high redshift. The black hole spins are largest for the highest redshift sources and decrease for sources at lower redshift; the sources studied have redshifts between zero and two. Lower power radio sources associated with central dominant galaxies may have black hole spins that are significantly less than one. Combining this analysis with other results suggests that the maximum values of black hole spin associated with powerful radio galaxies decline from values of order unity at a redshift of 2 to values of o...

  9. Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Maj, Michał; Oh, Younjun; Park, Kwanghee; Lee, Jooyong; Cho, Minhaeng, E-mail: mcho@korea.ac.kr [Department of Chemistry, Korea University, Seoul 136-713 (Korea, Republic of); Kwak, Kyung-Won [Department of Chemistry, Chung-Ang University, Seoul 156-756, SouthKorea (Korea, Republic of)

    2014-06-21

    The structure and vibrational dynamics of SCN- and SeCN-bound myoglobin have been investigated using polarization-controlled IR pump-probe measurements and quantum chemistry calculations. The complexes are found to be in low and high spin states, with the dominant contribution from the latter. In addition, the Mb:SCN high spin complex exhibits a doublet feature in the thiocyanate stretch IR absorption spectra, indicating two distinct molecular conformations around the heme pocket. The binding mode of the high spin complexes was assigned to occur through the nitrogen atom, contrary to the binding through the sulfur atom that was observed in myoglobin derived from Aplysia Limacina. The vibrational energy relaxation process has been found to occur substantially faster than those of free SCN{sup −} and SeCN{sup −} ions and neutral SCN- and SeCN-derivatized molecules reported previously. This supports the N-bound configurations of MbNCS and MbNCSe, because S- and Se-bound configurations are expected to have significantly long lifetimes due to the insulation effect by heavy bridge atom like S and Se in such IR probes. Nonetheless, even though their lifetimes are much shorter than those of corresponding free ions in water, the vibrational lifetimes determined for MbNCS and MbNCSe are still fairly long compared to those of azide and cyanide myoglobin systems studied before. Thus, thiocyanate and selenocyanate can be good local probes of local electrostatic environment in the heme pocket. The globin dependence on binding mode and vibrational dynamics is also discussed.

  10. Vibrational dynamics of thiocyanate and selenocyanate bound to horse heart myoglobin

    Science.gov (United States)

    Maj, Michał; Oh, Younjun; Park, Kwanghee; Lee, Jooyong; Kwak, Kyung-Won; Cho, Minhaeng

    2014-06-01

    The structure and vibrational dynamics of SCN- and SeCN-bound myoglobin have been investigated using polarization-controlled IR pump-probe measurements and quantum chemistry calculations. The complexes are found to be in low and high spin states, with the dominant contribution from the latter. In addition, the Mb:SCN high spin complex exhibits a doublet feature in the thiocyanate stretch IR absorption spectra, indicating two distinct molecular conformations around the heme pocket. The binding mode of the high spin complexes was assigned to occur through the nitrogen atom, contrary to the binding through the sulfur atom that was observed in myoglobin derived from Aplysia Limacina. The vibrational energy relaxation process has been found to occur substantially faster than those of free SCN- and SeCN- ions and neutral SCN- and SeCN-derivatized molecules reported previously. This supports the N-bound configurations of MbNCS and MbNCSe, because S- and Se-bound configurations are expected to have significantly long lifetimes due to the insulation effect by heavy bridge atom like S and Se in such IR probes. Nonetheless, even though their lifetimes are much shorter than those of corresponding free ions in water, the vibrational lifetimes determined for MbNCS and MbNCSe are still fairly long compared to those of azide and cyanide myoglobin systems studied before. Thus, thiocyanate and selenocyanate can be good local probes of local electrostatic environment in the heme pocket. The globin dependence on binding mode and vibrational dynamics is also discussed.

  11. Dipole Correlation of the Electronic Structures of theConformations of Water Molecule Evolving Through theNormal Modes of Vibrations Between Angular (C2v to Linear(D∝h Shapes

    Directory of Open Access Journals (Sweden)

    Arindam Chakraborty

    2006-03-01

    Full Text Available In order to settle the issue of equivalence or non-equivalence of the two lone pairsof electrons on oxygen atom in water molecule, a quantum chemical study of the dipolecorrelation of the electronic structure of the molecule as a function of conformationsgenerated following the normal modes of vibrations between the two extremeconformations, C2v (∠HOH at 90o and D∝h (∠HOH at 180o, including the equilibrium one,has been performed. The study invokes quantum mechanical partitioning of moleculardipoles into bond moment and lone pair moment and localization of delocalized canonicalmolecular orbitals, CMO’s into localized molecular orbitals, LMO’s. An earlier suggestion,on the basis of photoelectron spectroscopy, that one lone pair is in p-type and the other is ins-type orbital of O atom of water molecule at its equilibrium shape, and also the qualitative“Squirrel Ears” structure are brought under serious scrutiny. A large number ofconformations are generated and the charge density matrix, dipole moment of eachconformation is computed in terms of the generated canonical molecular orbitals, CMO’sand then Sinanoğlu’s localization method is invoked to localize the CMO’s of eachconformation and the quantum mechanical hybridizations of all the bonds and lone pairs onO center are evaluated in terms of the localized molecular orbitals. Computed datademonstrate that the electronic structures i.e. two bond pairs and two lone pairs and itshybridization status of all conformations of water molecule are straightforward in terms ofthe LMO’s. It is further revealed that the pattern of orbital hybridization changescontinuously as a function of evolution of molecular shape. The close analysis of thegenerated LMO’s reveals that one lone pair is accommodated in a pure p orbital and anotherlone pair is in a hybrid

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

    Indian Academy of Sciences (India)

    B Deb; A Rakshit; J Hazra; D Chakraborty

    2013-01-01

    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 magneto-associative strong-coupling regimes. The significance of Fano effect in ultracold atom–molecule transitions is discussed. Quantum effects at low-energy atom–molecule interface are important for exploring coherent phenomena in hitherto unexplored parameter regimes.

  13. On interpretations of bounded arithmetic and bounded set theory

    CERN Document Server

    Pettigrew, Richard

    2008-01-01

    In a recent paper, Kaye and Wong proved the following result, which they considered to belong to the folklore of mathematical logic. THEOREM: The first-order theories of Peano arithmetic and ZF with the axiom of infinity negated are mutually interpretable with interpretations that are inverse to each other. In this note, I describe a theory of sets that stands in the same relation to the bounded arithmetic IDelta0 + exp. Because of the weakness of this theory of sets, I cannot straightforwardly adapt Kaye and Wong's interpretation of the arithmetic in the set theory. Instead, I am forced to produce a different interpretation.

  14. Crystal Structure of Phosphatidylglycerophosphatase (PGPase), a Putative Membrane-Bound Lipid Phosphatase, Reveals a Novel Binuclear Metal Binding Site and Two Proton Wires

    Energy Technology Data Exchange (ETDEWEB)

    Kumaran,D.; Bonnano, J.; Burley, S.; Swaminathan, S.

    2006-01-01

    Phosphatidylglycerophosphatase (PGPase), an enzyme involved in lipid metabolism, catalyzes formation of phosphatidylglycerol from phosphatidylglycerophosphate. Phosphatidylglycerol is a multifunctional phospholipid, found in the biological membranes of many organisms. Here, we report the crystal structure of Listeria monocytogenes PGPase at 1.8 Angstroms resolution. PGPase, an all-helical molecule, forms a homotetramer. Each protomer contains an independent active site with two metal ions, Ca{sup 2+} and Mg{sup 2+}, forming a hetero-binuclear center located in a hydrophilic cavity near the surface of the molecule. The binuclear center, conserved ligands, metal-bound water molecules, and an Asp-His dyad form the active site. The catalytic mechanism of this enzyme is likely to proceed via binuclear metal activated nucleophilic water. The binuclear metal-binding active-site environment of this structure should provide insights into substrate binding and metal-dependent catalysis. A long channel with inter-linked linear water chains, termed 'proton wires', is observed at the tetramer interface. Comparison of similar water chain structures in photosynthetic reaction centers (RCs), Cytochrome f, gramicidin, and bacteriorhodopsin, suggests that PGPase may conduct protons via proton wires.

  15. Volume Stability of Bitumen Bound Building Blocks

    Directory of Open Access Journals (Sweden)

    Thanaya I.N.A.

    2010-01-01

    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.

  16. Chemical Properties of Dipole-Bound Negative Ions

    Science.gov (United States)

    Liu, Y.

    2005-05-01

    In dipole bound negative ions the extra electron is weakly bound by the dipole potential of the neutral molecule in a diffuse orbital localized near the positive end of the dipole. In consequence, it is reasonable to expect that such species will be highly reactive and possess chemical properties similar to those of Rydberg atoms, which also contain a weakly-bound electron in a diffuse orbital. These properties are being examined using a negative ion Penning trap. Data for electron transfer in collisions with attaching targets such as SF6 show that the rate constants for this process are large, ˜ 10-7 cm^3 s-1, and similar to those for free electron attachment. This suggests that collisions can be described in terms of an essentially-free electron model. This is further reinforced by the observation that rotational energy transfer in collisions with polar molecules can lead to rapid electron detachment, again with large rate constants of ˜ 10 -7 cm^3 s-1. Results for several target species will be presented and discussed in light of a free electron model.

  17. Nanopore sensing of individual transcription factors bound to DNA

    Science.gov (United States)

    Squires, Allison; Atas, Evrim; Meller, Amit

    2015-06-01

    Transcription factor (TF)-DNA interactions are the primary control point in regulation of gene expression. Characterization of these interactions is essential for understanding genetic regulation of biological systems and developing novel therapies to treat cellular malfunctions. Solid-state nanopores are a highly versatile class of single-molecule sensors that can provide rich information about local properties of long charged biopolymers using the current blockage patterns generated during analyte translocation, and provide a novel platform for characterization of TF-DNA interactions. The DNA-binding domain of the TF Early Growth Response Protein 1 (EGR1), a prototypical zinc finger protein known as zif268, is used as a model system for this study. zif268 adopts two distinct bound conformations corresponding to specific and nonspecific binding, according to the local DNA sequence. Here we implement a solid-state nanopore platform for direct, label- and tether-free single-molecule detection of zif268 bound to DNA. We demonstrate detection of single zif268 TFs bound to DNA according to current blockage sublevels and duration of translocation through the nanopore. We further show that the nanopore can detect and discriminate both specific and nonspecific binding conformations of zif268 on DNA via the distinct current blockage patterns corresponding to each of these two known binding modes.

  18. Spectroscopy of ultracold LiRb molecules using ionization detection

    Science.gov (United States)

    Altaf, Adeel

    We present spectroscopic studies of ultracold LiRb molecules using ionization detection. The molecules are created by cooling and trapping Li and Rb atoms in overlapping magneto-optical traps (MOTs) and using light resonant with a free-bound transition to create weakly bound excited state molecules in a process known as photoassociation (PA). We explore weakly bound vibrational levels of LiRb with PA spectroscopy using ionization detection and, where possible, compare our results with earlier measurements performed in our lab using trap-loss spectroscopy. In addition, we also probe vibrational levels of the ground triplet electronic state and excited electronic states using resonantly enhanced multiphoton ionization (REMPI) spectroscopy. We identify several vibrational levels of the alpha3Sigma+, (3)3piO and (4)3Sigma + states and compare our observations with theoretical calculations. As LiRb is one of the least studied heteronuclear diatomic molecules, these studies are aimed towards exploring the molecular structure. The spectroscopic work is also in line with the long-term project goals of transferring ultracold LiRb molecules into the lowest rotational and vibrational levels of the ground singlet electronic state. Molecules in this rovibronic ground state possess a large electric dipole moment, which is essential for application of ultracold molecules in various quantum computation schemes. The rovibronic ground state will also be an ideal starting point for investigating molecular entangled states.

  19. 水蒸气分子在金属钚表面吸附的量子力学计算%Adsorption Study of Water Vapor Molecule on Metal Pu Surface by Quantum Mechanism Computation

    Institute of Scientific and Technical Information of China (English)

    陈军; 蒙大桥; 孙希媛; 杜际广; 蒋刚

    2012-01-01

    Employing density functional method (B3LYP) with the relativistic effective core potential (RECP) for Pu atom and all-electron basis set aug-cc-pVTZ for O and H atoms, the equilibrium geometrical structures of PuO2 molecule were optimized. In addition, four structures for Pu-water were proposed and studied. The results indicate that water molecule tends to dissociate to form more stable structure with Pu. Due to the lager difference of electronegativity for Pu and O atoms, the stable structure is from the interaction of Pu and O atoms. The thermodynamic functions of adsorption and dissociation reactions of Pu and H2O were calculated according to electronic-vibration approximation. The results show that the water vapor molecule can't adsorb on Pu surface even at low temperature, in contrast, dissociation reactions of H2O on Pu surface can occur spontaneously.%采用密度泛函理论(B3LYP)方法,钚原子采用相对论有效原子实势(RECP) SDD基组,氢、氧原子采用aug-cc-pVTZ全电子基组,优化了PuO2的分子结构,得到了相应的平衡几何构型.同时优化了Pu-H2O的4个稳定异构体.比较能量发现水分子易于解离,从而与Pu形成更稳定的结构.由于Pu与O原子的电负性相差很大易发生电荷转移,分子的稳定性主要源于Pu-O之间的相互作用.根据电子-振动近似理论,计算了不同温度下金属Pu与H2O吸附与解离反应的生成热力学函数.计算表明,即使在低温下,H2O蒸汽分子也无法在金属钚表面形成分子吸附,相反,在金属钚表面水分子的解离可自发进行.

  20. In vivo water state measurements in breast cancer using broadband diffuse optical spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chung, S H; Cerussi, A E; Tromberg, B J [Beckman Laser Institute, University of California, Irvine, 1002 Health Sciences Road, Irvine 92612, CA (United States); Klifa, C [Magnetic Resonance Science Center, Radiology, University of California, San Francisco, 505 Parnassus Avenue, Box 0628, San Francisco, CA 94143-0628 (United States); Baek, H M; Birgul, O; Gulsen, G [Tu and Yuen Center for Functional Onco Imaging, Department of Radiological Sciences, University of California, Irvine, 108 Irvine Hall, Irvine, CA, 92697-5020 (United States); Merritt, S I [Masimo Corporation, 40 Parker, Irvine, CA 92618 (United States); Hsiang, D [Department of Surgery, Chao Family Comprehensive Cancer Center, University of California, Irvine, Healthcare, 101 The City Drive South, Orange, CA 92868 (United States)], E-mail: bjtrombe@uci.edu

    2008-12-07

    Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. We introduce a bound water index (BWI) that quantifies shifts observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopy (DOS). DOS quantitatively measures light absorption and scattering spectra and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOS to magnetic resonance spectroscopy, diffusion-weighted MRI and conductivity in bound water tissue phantoms. Non-invasive DOS measurements of malignant and normal breast tissues performed in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p < 0.0001) compared to normal tissues. BWI of breast cancer tissues inversely correlated with Nottingham-Bloom-Richardson histopathology scores. These results highlight broadband DOS sensitivity to molecular disposition of water and demonstrate the potential of BWI as a non-invasive in vivo index that correlates with tissue pathology.

  1. In vivo water state measurements in breast cancer using broadband diffuse optical spectroscopy

    Science.gov (United States)

    Chung, S. H.; Cerussi, A. E.; Klifa, C.; Baek, H. M.; Birgul, O.; Gulsen, G.; Merritt, S. I.; Hsiang, D.; Tromberg, B. J.

    2008-12-01

    Structural changes in water molecules are related to physiological, anatomical and pathological properties of tissues. Near infrared (NIR) optical absorption methods are sensitive to water; however, detailed characterization of water in thick tissues is difficult to achieve because subtle spectral shifts can be obscured by multiple light scattering. In the NIR, a water absorption peak is observed around 975 nm. The precise NIR peak's shape and position are highly sensitive to water molecular disposition. We introduce a bound water index (BWI) that quantifies shifts observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopy (DOS). DOS quantitatively measures light absorption and scattering spectra and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOS to magnetic resonance spectroscopy, diffusion-weighted MRI and conductivity in bound water tissue phantoms. Non-invasive DOS measurements of malignant and normal breast tissues performed in 18 subjects showed a significantly higher fraction of free water in malignant tissues (p breast cancer tissues inversely correlated with Nottingham-Bloom-Richardson histopathology scores. These results highlight broadband DOS sensitivity to molecular disposition of water and demonstrate the potential of BWI as a non-invasive in vivo index that correlates with tissue pathology.

  2. Bound Polaron Pair Formation in Poly (phenylenevinylenes)

    Science.gov (United States)

    Rothberg, Lewis

    The following sections are included: * INTRODUCTION * PHOTOGENERATED YIELD OF SINGLET EXCITONS * AGGREGRATION EFFECTS ON EXCITED STATE PHOTO-GENERATION * ASSIGNMENT TO BOUND POLARON PAIRS AND DISCUSSION * PROBLEMS WITH THE BOUND POLARON PAIR PICTURE AND CONCLUSION * REFERENCES

  3. An Exponential Bound for Cox Regression☆

    Science.gov (United States)

    Kosorok, M. R.

    2012-01-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold. PMID:23565013

  4. An Exponential Bound for Cox Regression.

    Science.gov (United States)

    Goldberg, Y; Kosorok, M R

    2012-07-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold.

  5. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    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...... quantities of interest. To be able to utilise the evidence about the derivative it is suggested to adapt the ‘conventional’ problem statement to variational calculus and the way to do so is demonstrated. A number of examples are given throughout the paper....

  6. Two applications of the thermogram of the alcohol/water binary system with compositions of cryobiological interests.

    Science.gov (United States)

    Weng, Lindong; Li, Weizhong; Zuo, Jianguo

    2011-06-01

    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.

  7. New bounds for multi-dimensional packing

    OpenAIRE

    Seiden, S.; Stee, van, Rob

    2001-01-01

    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d=2, are as follows: A new upper bound of 2.66013 for online box packing, a new $14/9 + varepsilon$ polynomial time offline approximation algorithm for square packing, a new upper bound ...

  8. Is JPC = 3-+ molecule possible?

    Science.gov (United States)

    Zhu, Wei; Liu, Yan-Rui; Yao, Tao

    2015-02-01

    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

  9. Synchrotron X-ray footprinting as a method to visualize water in proteins.

    Science.gov (United States)

    Gupta, Sayan; Feng, Jun; Chan, Leanne Jade G; Petzold, Christopher J; Ralston, Corie Y

    2016-09-01

    The vast majority of biomolecular processes are controlled or facilitated by water interactions. In enzymes, regulatory proteins, membrane-bound receptors and ion-channels, water bound to functionally important residues creates hydrogen-bonding networks that underlie the mechanism of action of the macromolecule. High-resolution X-ray structures are often difficult to obtain with many of these classes of proteins because sample conditions, such as the necessity of detergents, often impede crystallization. Other biophysical techniques such as neutron scattering, nuclear magnetic resonance and Fourier transform infrared spectroscopy are useful for studying internal water, though each has its own advantages and drawbacks, and often a hybrid approach is required to address important biological problems associated with protein-water interactions. One major area requiring more investigation is the study of bound water molecules which reside in cavities and channels and which are often involved in both the structural and functional aspects of receptor, transporter and ion channel proteins. In recent years, significant progress has been made in synchrotron-based radiolytic labeling and mass spectroscopy techniques for both the identification of bound waters and for characterizing the role of water in protein conformational changes at a high degree of spatial and temporal resolution. Here the latest developments and future capabilities of this method for investigating water-protein interactions and its synergy with other synchrotron-based methods are discussed.

  10. The Acquisition of Bound and Free Anaphora.

    Science.gov (United States)

    Koster, Jan; Koster, Charlotte

    Most linguists assume that bound anaphors such as "himself" are connected with their antecedents in a different way from free anaphors such as "him." Bound anaphora resolution is deterministic, based on Principle A of Chomsky's binding theory. Free anaphors, pronominals, cannot be bound in the domain of reflexives (principle…

  11. Computing the bounds on the loss rates

    OpenAIRE

    Fourneau J.-M.; Mokdad L.; Pekergin N.

    2002-01-01

    We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.

  12. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil

    2014-01-01

    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...

  13. Tight adversary bounds for composite functions

    NARCIS (Netherlands)

    Hoyer, P.; Spalek, R.

    2005-01-01

    The quantum adversary method is a very versatile method for proving lower bounds on quantum algorithms. It has many equivalent formulations, yields tight bounds for many computational problems, and has natural connections to classical lower bounds. One of its formulations is in terms of the spectral

  14. Bound entangled states invariant under Ux

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Wang Zhi-Xi

    2008-01-01

    This paper obtains an entangled condition for isotropic-like states by using an atomic map. It constructs a class of bound entangled states from the entangled condition and shows that the partial transposition of the state from the constructed bound entangled class is an edge bound entangled state by using range criterion.

  15. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    D. Massaro

    2012-01-01

    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

  16. Counting Young Tableaux of Bounded Height

    Science.gov (United States)

    Bergeron, Francois; Gascon, Francis

    2000-03-01

    We show that formulas of Gessel, for the generating functions for Young standard tableaux of height bounded by k (see [2]), satisfy linear differential equations, with polynomial coefficients, equivalent to P-recurrences conjectured by Favreau, Krob and the first author (see [1]) for the number of bounded height tableaux and pairs of bounded height tableaux.

  17. Dwell time of a Brownian interacting molecule in a cellular microdomain

    CERN Document Server

    Taflia, A; Taflia, Adi; Holcman, David

    2006-01-01

    The time spent by an interacting Brownian molecule inside a bounded microdomain has many applications in cellular biology, because the number of bounds is a quantitative signal, which can initiate a cascade of chemical reactions and thus has physiological consequences. In the present article, we propose to estimate the mean time spent by a Brownian molecule inside a microdomain $\\Omega$ which contains small holes on the boundary and agonist molecules located inside. We found that the mean time depends on several parameters such as the backward binding rate (with the agonist molecules), the mean escape time from the microdomain and the mean time a molecule reaches the binding sites (forward binding rate). In addition, we estimate the mean and the variance of the number of bounds made by a molecule before it exits $\\Omega$. These estimates rely on a boundary layer analysis of a conditional mean first passage time, solution of a singular partial differential equation. In particular, we apply the present results ...

  18. Water

    Science.gov (United States)

    Leopold, Luna Bergere; Baldwin, Helene L.

    1962-01-01

    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. Impact of deformation energy on the hydrogen bonding interactions in gas phase 3-X catechol ⋯ H2O complexes (X = H, F, Cl, Br): The effect of approach of a water molecule

    Science.gov (United States)

    Deb, Debojit Kumar; Sarkar, Biplab

    2016-06-01

    The conformations and nature of hydrogen bonding interactions for 3-X catechol ⋯ H2O (X = H, F, Cl, Br) has been investigated by ab initio MP2, CCSD(T), and density functional B3LYP, wB97XD and M06-2X methods. The changes in interaction energies due to deformation of the structures has been studied in detail. The intra- and intermolecular hydrogen bonding interactions due to the different direction of approach of water molecule have been discussed. A detailed natural bond orbital (NBO) analysis and the symmetry-adapted perturbation theory (SAPT) based energy decomposition analysis has been carried out to elucidate interaction strength and properties in these hydrogen bonded systems. The charge transfer percentage (CTP) has been derived which will be universally useful for correlating binding energy, deformation energy and the geometrical parameters such as angles, bond lengths, etc. for other systems as well.

  20. Asymmetric dark matter bound state

    Science.gov (United States)

    Bi, Xiao-Jun; Kang, Zhaofeng; Ko, P.; Li, Jinmian; Li, Tianjun

    2017-02-01

    We propose an interesting framework for asymmetric scalar dark matter (ADM), which has novel collider phenomenology in terms of an unstable ADM bound state (ADMonium) produced via Higgs portals. ADMonium is a natural consequence of the basic features of ADM: the (complex scalar) ADM is charged under a dark local U (1 )d symmetry which is broken at a low scale and provides a light gauge boson X . The dark gauge coupling is strong and then ADM can annihilate away into X -pair effectively. Therefore, the ADM can form a bound state due to its large self-interaction via X mediation. To explore the collider signature of ADMonium, we propose that ADM has a two-Higgs doublet portal. The ADMonium can have a sizable mixing with the heavier Higgs boson, which admits a large cross section of ADMonium production associated with b b ¯. The resulting signature at the LHC depends on the decays of X . In this paper we consider a case of particular interest: p p →b b ¯ +ADMonium followed by ADMonium→2 X →2 e+e- where the electrons are identified as (un)converted photons. It may provide a competitive explanation to heavy di-photon resonance searches at the LHC.

  1. Boosting equal time bound states

    CERN Document Server

    Dietrich, Dennis D; Jarvinen, Matti

    2012-01-01

    We present an explicit and exact boost of a relativistic bound state defined at equal time of the constituents in the Born approximation (lowest order in hbar). To this end, we construct the Poincar\\'e generators of QED and QCD in D=1+1 dimensions, using Gauss' law to express A^0 in terms of the fermion fields in A^1=0 gauge. We determine the fermion-antifermion bound states in the Born approximation as eigenstates of the time and space translation generators P^0 and P^1. The boost operator is combined with a gauge transformation so as to maintain the gauge condition A^1=0 in the new frame. We verify that the boosted state remains an eigenstate of P^0 and P^1 with appropriately transformed eigenvalues and determine the transformation law of the equal-time, relativistic wave function. The shape of the wave function is independent of the CM momentum when expressed in terms of a variable, which is quadratically related to the distance x between the fermions. As a consequence, the Lorentz contraction of the wave ...

  2. Endurance bounds of aerial systems

    Science.gov (United States)

    Harrington, Aaron M.; Kroninger, Christopher M.

    2014-06-01

    Within the past few years micro aerial vehicles (MAVs) have received much more attention and are starting to proliferate into military as well as civilian roles. However, one of the major drawbacks for this technology currently, has been their poor endurance, usually below 10 minutes. This is a direct result of the inefficiencies inherent in their design. Often times, designers do not consider the various components in the vehicle design and match their performance to the desired mission for the vehicle. These vehicles lack a prescribed set of design guidelines or empirically derived design equations which often limits their design to selection of commercial off-the-shelf components without proper consideration of their affect on vehicle performance. In the current study, the design space for different vehicle configurations has been examined including insect flapping, avian flapping, rotary wing, and fixed wing, and their performance bounds are established. The propulsion system typical of a rotary wing vehicle is analyzed to establish current baselines for efficiency of vehicles at this scale. The power draw from communications is analyzed to determine its impact on vehicle performance. Finally, a representative fixed wing MAV is examined and the effects of adaptive structures as a means for increasing vehicle endurance and range are examined. This paper seeks to establish the performance bounds for micro air vehicles and establish a path forward for future designs so that efficiency may be maximized.

  3. catena-Poly[[[(oxamide dioxime-κ2N,N')copper(II)]-μ-L-tartrato-κ4O1,O2:O3,O4] tetrahydrate]: a chiral nanochannel framework hosting solvent water molecules.

    Science.gov (United States)

    Bélombé, Michel M; Nenwa, Justin; Kouamo, Jean S T Wankap; Ponou, Siméon; Fischer, Andreas

    2012-05-01

    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.

  4. Formation of Ultracold Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Cote, Robin [Univ. of Connecticut, Storrs, CT (United States)

    2016-01-28

    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.

  5. Structured free-water clusters near lubricating surfaces are essential in water-based lubrication.

    Science.gov (United States)

    Hou, Jiapeng; Veeregowda, Deepak H; de Vries, Joop; Van der Mei, Henny C; Busscher, Henk J

    2016-10-01

    Water-based lubrication provides cheap and environmentally friendly lubrication and, although hydrophilic surfaces are preferred in water-based lubrication, often lubricating surfaces do not retain water molecules during shear. We show here that hydrophilic (42° water contact angle) quartz surfaces facilitate water-based lubrication to the same extent as more hydrophobic Si crystal surfaces (61°), while lubrication by hydrophilic Ge crystal surfaces (44°) is best. Thus surface hydrophilicity is not sufficient for water-based lubrication. Surface-thermodynamic analyses demonstrated that all surfaces, regardless of their water-based lubrication, were predominantly electron donating, implying water binding with their hydrogen groups. X-ray photoelectron spectroscopy showed that Ge crystal surfaces providing optimal lubrication consisted of a mixture of -O and =O functionalities, while Si crystal and quartz surfaces solely possessed -O functionalities. Comparison of infrared absorption bands of the crystals in water indicated fewer bound-water layers on hydrophilic Ge than on hydrophobic Si crystal surfaces, while absorption bands for free water on the Ge crystal surface indicated a much more pronounced presence of structured, free-water clusters near the Ge crystal than near Si crystal surfaces. Accordingly, we conclude that the presence of structured, free-water clusters is essential for water-based lubrication. The prevalence of structured water clusters can be regulated by adjusting the ratio between surface electron-donating and electron-accepting groups and between -O and =O functionalities.

  6. Water

    Science.gov (United States)

    ... Lead Poisoning Prevention Training Center (HHLPPTC) Training Tracks Water Language: English Español (Spanish) Recommend on Facebook Tweet Share Compartir For information about lead in water in Flint, MI, please visit http://www.phe. ...

  7. Decoherence in time evolution of bound entanglement

    CERN Document Server

    Sun, Z; Sun, C P; Wang, X; Sun, Zhe; Wang, Xiaoguang

    2007-01-01

    We study a dynamic process of disentanglement by considering the time evolution of bound entanglement for a quantum open system, two qutrits coupling to a common environment. Here, the initial quantum correlations of the two qutrits are characterized by the bound entanglement. In order to show the universality of the role of environment on bound entanglement, both bosonic and spin environments are considered. We found that the bound entanglement displays collapses and revivals, and it can be stable against small temperature and time change. The thermal fluctuation effects on bound entanglement are also considered.

  8. The nature of water within bacterial spores: protecting life in extreme environments

    Science.gov (United States)

    Rice, Charles V.; Friedline, Anthony; Johnson, Karen; Zachariah, Malcolm M.; Thomas, Kieth J., III

    2011-10-01

    The bacterial spore is a formidable container of life, protecting the vital contents from chemical attack, antimicrobial agents, heat damage, UV light degradation, and water dehydration. The exact role of the spore components remains in dispute. Nevertheless, water molecules are important in each of these processes. The physical state of water within the bacterial spore has been investigated since the early 1930's. The water is found two states, free or bound, in two different areas, core and non-core. It is established that free water is accessible to diffuse and exchange with deuterated water and that the diffusible water can access all areas of the spore. The presence of bound water has come under recent scrutiny and has been suggested the water within the core is mobile, rather than bound, based on the analysis of deuterium relaxation rates. Using an alternate method, deuterium quadrupole-echo spectroscopy, we are able to distinguish between mobile and immobile water molecules. In the absence of rapid motion, the deuterium spectrum of D2O is dominated by a broad line, whose line shape is used as a characteristic descriptor of molecular motion. The deuterium spectrum of bacterial spores reveals three distinct features: the broad peak of immobilized water, a narrow line of water in rapid motion, and a signal of intermediate width. This third signal is assigned this peak from partially deuterated proteins with the spore in which N-H groups have undergone exchange with water deuterons to form N-D species. As a result of these observations, the nature of water within the spore requires additional explanation to understand how the spore and its water preserve life.

  9. Thermodynamic law from the entanglement entropy bound

    CERN Document Server

    Park, Chanyong

    2015-01-01

    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamics-like law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we also find that a global quench unlike the excitation does not preserve the entanglement entropy bound.

  10. Exact entanglement bases and general bound entanglement

    CERN Document Server

    Zhong, Z Z

    2004-01-01

    In this paper, we give the more general bound entangled states associated with the unextendible product bases (UPB), i.e. by using of the exact entanglement bases (EEB) and the complete basis with unextendible product bases (CBUPB), we prove that the arbitrary convex sums of the uniform mixtures (bound entangled states) associated with UPBs are still bound entangled states. Further, we discuss the equivalent transformation group and classification of the CBUPBs, and by using this classification, we prove that in the meaning of indistinguishability, the set of the above all possible bound entangled states can be reduced to the set of all possible mixtures of some fixed basic bound entangled states. At last, we prove that every operating of the partial transposition (PT) map acting upon a density matrix under any bipartite partitioning induces a mapping from the above reduced set of bound entangled states to oneself, which corresponds to a non-identical permutation of the basic bound entangled states.

  11. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    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.

  12. Bound states of Dipolar Bosons in One-dimensional Systems

    DEFF Research Database (Denmark)

    G. Volosniev, A.; R. Armstrong, J.; V. Fedorov, D.;

    2013-01-01

    -body structures in this geometry are determined as function of polarization angles and dipole strength by using both essentially exact stochastic variational methods and the harmonic approximation. The main focus is on the three, four, and five-body problems in two or more tubes. Our results indicate...... that in the weakly-coupled limit the inter-tube interaction is similar to a zero-range term with a suitable rescaled strength. This allows us to address the corresponding many-body physics of the system by constructing a model where bound chains with one molecule in each tube are the effective degrees of freedom...

  13. Proposal for field-based definition of soil bound pesticide residues.

    Science.gov (United States)

    Boesten, J J T I

    2016-02-15

    The environmental significance of soil bound pesticide residues (SBPR) is potentially large because approximately one third of the applied mass of the pesticides in agriculture ends up as SBPR. At EU level, there is little regulatory guidance available on the environmental risk assessment of SBPR in spite of some 50 years of SBPR research. This lack of guidance is partially caused by the fact that the current definitions of SBPR are founded on non-extractability in soil in the laboratory whereas for the environmental risk assessment not the soil in the laboratory but the soil in the field is the system of interest. Therefore a definition of SBPR is proposed that is based on the field soil: a molecule (further called 'the mother molecule') is soil bound if a relevant part of this molecule has become part of the solid phase in the soil and if this relevant part will never be released again to the liquid phase in soil under relevant field conditions in the form of this mother molecule or in the form of another molecule that may possibly raise environmental or human toxicological concerns. This mother molecule may be the parent substance that is applied to the soil but it may also be a metabolite of this parent substance. A consequence of the definition is that the SBPR terminology becomes more precise because the mother molecule of the soil bound residue has to be specified. A further consequence is that very strong but reversible sorption of molecules such as paraquat is not considered soil-bound residue anymore (as may be demonstrated by a self-exchange extraction procedure). Furthermore, the definition requires that risk managers have to define what they consider as 'relevant field conditions' (e.g. include also changes of agricultural fields into forests?).

  14. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    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...

  15. Trapping molecules on chips

    CERN Document Server

    Santambrogio, Gabriele

    2015-01-01

    In the last years, it was demonstrated that neutral molecules can be loaded on a microchip directly from a supersonic beam. The molecules are confined in microscopic traps that can be moved smoothly over the surface of the chip. Once the molecules are trapped, they can be decelerated to a standstill, for instance, or pumped into selected quantum states by laser light or microwaves. Molecules are detected on the chip by time-resolved spatial imaging, which allows for the study of the distribution in the phase space of the molecular ensemble.

  16. [Endothelial cell adhesion molecules].

    Science.gov (United States)

    Ivanov, A N; Norkin, I A; Puchin'ian, D M; Shirokov, V Iu; Zhdanova, O Iu

    2014-01-01

    The review presents current data concerning the functional role of endothelial cell adhesion molecules belonging to different structural families: integrins, selectins, cadherins, and the immunoglobulin super-family. In this manuscript the regulatory mechanisms and factors of adhesion molecules expression and distribution on the surface of endothelial cells are discussed. The data presented reveal the importance of adhesion molecules in the regulation of structural and functional state of endothelial cells in normal conditions and in pathology. Particular attention is paid to the importance of these molecules in the processes of physiological and pathological angiogenesis, regulation of permeability of the endothelial barrier and cell transmigration.

  17. The formation of bound residues of diazinon in four UK soils: Implications for risk assessment

    Energy Technology Data Exchange (ETDEWEB)

    Fenlon, Katie A., E-mail: katefenlon@hotmail.com [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom); Andreou, Kostas; Jones, Kevin C.; Semple, Kirk T. [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom)

    2011-03-15

    The behaviour of diazinon in the soil determines the likelihood of further pollution incidents, particularly leaching to water. The most significant processes in the control of the fate of diazinon in the soil are microbial degradation and the formation of bound residues. Soils from four sites in the UK were amended with diazinon and its {sup 14}C labelled analogue and incubated for 100 days. After 0, 10, 21, 50 and 100 days, the formation of bound residues was assessed by solvent extraction, and the microbial degradation of diazinon by mineralisation assay. In microbially active soils, diazinon is degraded rapidly, reducing the risk of future pollution incidents. However, where there was limited mineralisation there was also significantly lower formation of bound residues, which may lead to water pollution via leaching. The formation of bound residues was dependent on extraction type. Acetonitrile extraction identified bound residues in all soils, with the bound residue fraction increasing with increasing incubation time. - Research highlights: > Bound residues are defined by extraction method. > Microbial degradation is limited by the formation of bound residues. > Bioavailability of diazinon maybe estimated by chemical extraction. - The formation of bound residues and biodegradation of diazinon are dependent on soil type and the presence of degrading bacteria.

  18. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.

    1996-07-01

    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.

  19. ISOLATED MOLECULES IN METALS

    NARCIS (Netherlands)

    1992-01-01

    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.

  20. Algebraic theory of molecules

    CERN Document Server

    Iachello, F

    1995-01-01

    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

  1. Layers of Cold Dipolar Molecules in the Harmonic Approximation

    DEFF Research Database (Denmark)

    R. Armstrong, J.; Zinner, Nikolaj Thomas; V. Fedorov, D.;

    2012-01-01

    We consider the N-body problem in a layered geometry containing cold polar molecules with dipole moments that are polarized perpendicular to the layers. A harmonic approximation is used to simplify the hamiltonian and bound state properties of the two-body inter-layer dipolar potential are used...

  2. Molecules in galaxies

    CERN Document Server

    Omont, Alain

    2007-01-01

    The main achievements, current developments and prospects of molecular studies in external galaxies are reviewed. They are put in the context of the results of several decades of studies of molecules in local interstellar medium, their chemistry and their importance for star formation. CO observations have revealed the gross structure of molecular gas in galaxies. Together with other molecules, they are among the best tracers of star formation at galactic scales. Our knowledge about molecular abundances in various local galactic environments is progressing. They trace physical conditions and metallicity, and they are closely related to dust processes and large aromatic molecules. Major recent developments include mega-masers, and molecules in Active Galactic Nuclei; millimetre emission of molecules at very high redshift; and infrared H2 emission as tracer of warm molecular gas, shocks and photodissociation regions. The advent of sensitive giant interferometers from the centimetre to sub-millimetre range, espe...

  3. Synthesis and characterization of lower generation broom molecules

    Institute of Scientific and Technical Information of China (English)

    Jun Wang; Cui Qin Li; Shu Yan Zhang; Fang Sun; Teng Jie Ge

    2008-01-01

    Dendritic molecules with dodecyl groups as the hyperbranchs were synthesized in methanol by Michael addition withdodecylamine and methyl acrylate as raw materials. This new-type dendritic molecules were called vividly "broom molecules" inthis report. The surface tension of the aqueous solution of broom molecule terminated amino group was measured by using the drop-volume method. The demulsification performance of the broom molecules for the oil/water (O/W) simulated crude oil emulsion wasexamined. The experimental results revealed that, as a new-type of surfactants, the broom molecules terminated amino groupsshowed demulsification for the O/W simulated crude oil emulsion.

  4. Thermodynamic law from the entanglement entropy bound

    Science.gov (United States)

    Park, Chanyong

    2016-04-01

    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamicslike law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we show that the deformed modular Hamiltonian under a global quench also satisfies the generalized entanglement entropy boundary after introducing a new quantity called the entanglement chemical potential.

  5. Bounds on double-diffusive convection

    Science.gov (United States)

    Balmforth, Neil J.; Ghadge, Shilpa A.; Kettapun, Atichart; Mandre, Shreyas D.

    2006-12-01

    We consider double-diffusive convection between two parallel plates and compute bounds on the flux of the unstably stratified species using the background method. The bound on the heat flux for Rayleigh Bénard convection also serves as a bound on the double-diffusive problem (with the thermal Rayleigh number equal to that of the unstably stratified component). In order to incorporate a dependence of the bound on the stably stratified component, an additional constraint must be included, like that used by Joseph (Stability of Fluid Motion, 1976, Springer) to improve the energy stability analysis of this system. Our bound extends Joseph's result beyond his energy stability boundary. At large Rayleigh number, the bound is found to behave like R_T(1/2) for fixed ratio R_S/R_T, where R_T and R_S are the Rayleigh numbers of the unstably and stably stratified components, respectively.

  6. Process expression of bounded Petri nets

    Institute of Scientific and Technical Information of China (English)

    吴哲辉

    1996-01-01

    The concept of process expression of bounded Petri nets is presented.Moreover,an algorithm to find the process expression for a bounded Petri net is given.A process expression of a bounded Petri net is a regular expression whose every alphabet symbol represents a basic subprocess of the net.The regular set expressed by the regular expression is the set of all surjective processes of a bounded Petri net.A surjective process of a bounded Petri net is a process of this net in which every s-cut corresponds to a reachable marking of the net.Therefore,all surjective processes of a bounded Petri net can be obtained as long as its process expression and the basic subprocess represented by the alphabet symbols of the process expression are given.

  7. 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

    2013-06-15

    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.

  8. A New and Simple Approach to Determine the Abundance of Hydrogen Molecules on Interstellar Ice Mantles

    CERN Document Server

    Hincelin, Ugo; Herbst, Eric

    2014-01-01

    Water is usually the main component of ice mantles, which cover the cores of dust grains in cold portions of dense interstellar clouds. When molecular hydrogen is adsorbed onto an icy mantle through physisorption, a common assumption in gas-grain rate equation models is to use an adsorption energy for molecular hydrogen on a pure water substrate. However, at high density and low temperature, when H2 is efficiently adsorbed onto the mantle, its surface abundance can be strongly overestimated if this assumption is still used. Unfortunately, the more detailed microscopic Monte Carlo treatment cannot be used to study the abundance of H2 in ice mantles if a full gas-grain network is utilized. We present a numerical method adapted for rate-equation models that takes into account the possibility that an H2 molecule can, while diffusing on the surface, find itself bound to another hydrogen molecule, with a far weaker bond than the H2-water bond, which can lead to more efficient desorption. We label the ensuing desorp...

  9. Computing the bounds on the loss rates

    Directory of Open Access Journals (Sweden)

    Fourneau J.-M.

    2002-01-01

    Full Text Available We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.

  10. Conditionally bounding analytic ranks of elliptic curves

    CERN Document Server

    Bober, Jonathan W

    2011-01-01

    We describe a method for bounding the rank of an elliptic curve under the assumptions of the Birch and Swinnerton-Dyer conjecture and the generalized Riemann hypothesis. As an example, we compute, under these conjectures, exact upper bounds for curves which are known to have rank at least as large as 20, 21, 22, 23, and 24. For the known curve of rank at least 28, we get a bound of 30.

  11. Scalable Capacity Bounding Models for Wireless Networks

    OpenAIRE

    Du, Jinfeng; Medard, Muriel; Xiao, Ming; Skoglund, Mikael

    2014-01-01

    The framework of network equivalence theory developed by Koetter et al. introduces a notion of channel emulation to construct noiseless networks as upper (resp. lower) bounding models, which can be used to calculate the outer (resp. inner) bounds for the capacity region of the original noisy network. Based on the network equivalence framework, this paper presents scalable upper and lower bounding models for wireless networks with potentially many nodes. A channel decoupling method is proposed...

  12. Glycerol inhibits water permeation through Plasmodium falciparum aquaglyceroporin.

    Science.gov (United States)

    Chen, Liao Y

    2013-01-01

    Plasmodium falciparum aquaglyceroporin (PfAQP) is a multifunctional membrane protein in the plasma membrane of P. falciparum, the parasite that causes the most severe form of malaria. The current literature has established the science of PfAQP's structure, functions, and hydrogen-bonding interactions but left unanswered the following fundamental question: does glycerol modulate water permeation through aquaglyceroporin that conducts both glycerol and water? This paper provides an affirmative answer to this question of essential importance to the protein's functions. On the basis of the chemical-potential profile of glycerol from the extracellular bulk region, throughout PfAQP's conducting channel, to the cytoplasmic bulk region, this study shows the existence of a bound state of glycerol inside aquaglyceroporin's permeation pore, from which the dissociation constant is approximately 14μM. A glycerol molecule occupying the bound state occludes the conducting pore through which permeating molecules line up in single file by hydrogen-bonding with one another and with the luminal residues of aquaglyceroporin. In this way, glycerol inhibits permeation of water and other permeants through aquaglyceroporin. The biological implications of this theory are discussed and shown to agree with the existent in vitro data. It turns out that the structure of aquaglyceroporin is perfect for the van der Waals interactions between the protein and glycerol to cause the existence of the bound state deep inside the conducting pore and, thus to play an unexpected but significant role in aquaglyceroporin's functions.

  13. Conductivity bounds in probe brane models

    CERN Document Server

    Ikeda, Tatsuhiko N; Nakai, Yuichiro

    2016-01-01

    We discuss upper and lower bounds on the electrical conductivity of finite temperature strongly coupled quantum field theories, holographically dual to probe brane models, within linear response. In a probe limit where disorder is introduced entirely through an inhomogeneous background charge density, we find simple lower and upper bounds on the electrical conductivity in arbitrary dimensions. In field theories in two spatial dimensions, we show that both bounds persist even when disorder is included in the bulk metric. We discuss the challenges with finding sharp lower bounds on conductivity in three or more spatial dimensions when the metric is inhomogeneous.

  14. Risk Bounds for Infinitely Divisible Distribution

    CERN Document Server

    Zhang, Chao

    2012-01-01

    In this paper, we study the risk bounds for samples independently drawn from an infinitely divisible (ID) distribution. In particular, based on a martingale method, we develop two deviation inequalities for a sequence of random variables of an ID distribution with zero Gaussian component. By applying the deviation inequalities, we obtain the risk bounds based on the covering number for the ID distribution. Finally, we analyze the asymptotic convergence of the risk bound derived from one of the two deviation inequalities and show that the convergence rate of the bound is faster than the result for the generic i.i.d. empirical process (Mendelson, 2003).

  15. Dynamics of Activated Molecules

    Energy Technology Data Exchange (ETDEWEB)

    Mullin, Amy S. [Univ. of Maryland, College Park, MD (United States)

    2016-11-16

    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.

  16. How tight is the Lieb-Oxford bound?

    CERN Document Server

    Odashima, Mariana M

    2007-01-01

    Density-functional theory requires ever better exchange-correlation (xc) functionals for the ever more precise description of many-body effects on electronic structure. Universal constraints on the xc energy are important ingredients in the construction of improved functionals. Here we investigate one such universal property of xc functionals: the Lieb-Oxford lower bound on the exchange-correlation energy, $E_{xc}[n] \\ge -C \\int d^3r n^{4/3}$, where $C\\leq C_{LO}=1.68$. To this end, we perform a survey of available exact or near-exact data on xc energies of atoms, ions, molecules, solids, and some model Hamiltonians (the electron liquid, Hooke's atom and the Hubbard model). All physically realistic density distributions investigated are consistent with the tighter limit $C \\leq 1$. For large classes of systems one can obtain class-specific (but not fully universal) similar bounds. The Lieb-Oxford bound with $C_{LO}=1.68$ is a key ingredient in the construction of modern xc functionals, and a substantial chang...

  17. A Stronger LP Bound for Formula Size Lower Bounds via Clique Constraints

    CERN Document Server

    Ueno, Kenya

    2009-01-01

    We introduce a new technique proving formula size lower bounds based on the linear programming bound originally introduced by Karchmer, Kushilevitz and Nisan [11] and the theory of stable set polytope. We apply it to majority functions and prove their formula size lower bounds improved from the classical result of Khrapchenko [13]. Moreover, we introduce a notion of unbalanced recursive ternary majority functions motivated by a decomposition theory of monotone self-dual functions and give integrally matching upper and lower bounds of their formula size. We also show monotone formula size lower bounds of balanced recursive ternary majority functions improved from the quantum adversary bound of Laplante, Lee and Szegedy [15].

  18. An outer bound for 2-receiver discrete memoryless broadcast channels

    OpenAIRE

    Nair, Chandra

    2008-01-01

    An outer bound to the two-receiver discrete memoryless broadcast channel is presented. We compare it to the known outer bounds and show that the outer bound presented is at least as tight as the existing bounds.

  19. Electron correlation in molecules

    CERN Document Server

    Wilson, S

    2007-01-01

    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

  20. Minimal surfaces bounded by elastic lines

    CERN Document Server

    Giomi, L

    2011-01-01

    The classical Plateau's problem consists of finding the surface of least area that spans a given rigid boundary curve. A physical realization of the problem is obtained by dipping a stiff wire frame of some given shape in soapy water and then removing it. But what happens if a soap film spans a loop of inextensible but flexible wire? We consider this simple query that couples the Plateau's problem to Euler's Elastica: a special class of curves of given length that minimize their total squared curvature energy. The natural marriage of two of the oldest geometrical problems linking physics and mathematics leads to a quest for the shape of a minimal surface bounded by an elastic line: the Euler-Plateau problem. We use a combination of simple physical experiments with soap films that span soft filaments, scaling concepts, exact and asymptotic analysis combined with numerical simulations to explore some of the richness of the shapes that result. Our study also raises a number of interesting questions of intrinsic ...