WorldWideScience

Sample records for water molecular reorientation

  1. A Molecular Jump Mechanism of Water Reorientation

    National Research Council Canada - National Science Library

    Damien Laage; James T. Hynes

    2006-01-01

    .... This water reorientation mechanism involves large-amplitude angular jumps, rather than the commonly accepted sequence of small diffusive steps, and therefore calls for reinterpretation of many...

  2. 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.

  3. Junction Plasmon-Induced Molecular Reorientation

    Energy Technology Data Exchange (ETDEWEB)

    El-Khoury, Patrick Z.; Hu, Dehong; Hess, Wayne P.

    2013-10-17

    Time and frequency dependent intensity variations in sequences of Raman spectra recorded at plasmonic junctions can be assigned to molecular reorientation. This is revealed through Raman trajectories recorded at a nanojunction formed between a silver AFM tip and a corrugated silver surface coated with biphenyl-4,4’-dithiol. Molecular motion is not observed when the tip is retracted and only surface enhancement is operative. In effect, junction plasmon induced molecular reorientation is tracked.

  4. Why water reorientation slows without iceberg formation around hydrophobic solutes.

    Science.gov (United States)

    Laage, Damien; Stirnemann, Guillaume; Hynes, James T

    2009-02-26

    The dynamics of water molecules next to hydrophobic solutes is investigated, specifically addressing the recent controversy raised by the first time-resolved observations, which concluded that some water molecules are immobilized by hydrophobic groups, in strong contrast to previous NMR conclusions. Through molecular dynamics simulations and an analytic jump reorientation model, we identify the water reorientation mechanism next to a hydrophobic solute and provide evidence that no water molecules are immobilized by hydrophobic solutes. Their moderate rotational slowdown compared to bulk water (e.g., by a factor of less than 2 at low solute concentration) is mainly due to slower hydrogen-bond exchange. The slowdown is quantitatively described by a solute excluded volume effect at the transition state for the key hydrogen-bond exchange in the reorientation mechanism. We show that this picture is consistent with both ultrafast anisotropy and NMR experimental results and that the transition state excluded volume theory yields quantitative predictions of the rotational slowdown for diverse hydrophobic solutes of varying size over a wide concentration range. We also explain why hydrophobic groups slow water reorientation less than do some hydrophilic groups.

  5. Nano-confined water in the interlayers of hydrocalumite: Reorientational dynamics probed by neutron spectroscopy and molecular dynamics computer simulations

    Science.gov (United States)

    Kalinichev, A. G.; Faraone, A.; Udovic, T.; Kolesnikov, A. I.; de Souza, N. R.; Reinholdt, M. X.; Kirkpatrick, R.

    2008-12-01

    Layered double hydroxides (LDHs, anionic clays) represent excellent model systems for detailed molecular- level studies of the structure, dynamics, and energetics of nano-confined water in mineral interlayers and nano-pores, because LDH interlayers can have a well-defined structures and contain H2O molecules and a wide variety of anions in structurally well-defined positions and coordinations. [Ca2Al(OH)6]Cl·2H2O, also known as hydrocalumite or Friedel's salt, has a well- ordered Ca,Al distribution in the hydroxide layer and a very high degree of H2O,Cl ordering in the interlayer. It is also one of the only LDH phase for which a single crystal structure refinement is available. Thus, it is currently the best model compound for understanding the structure and dynamical behavior of interlayer and surface species in other, less-ordered, LDHs. We investigated the structural and dynamic behavior of water in the interlayers of hydrocalumite using inelastic (INS) and quasielastic (QENS) neutron scattering and molecular dynamics computer simulations. The comperehensive neutron scattering studies were performed for one fully hydrated and one dehydrated sample of hydrocalumite using several complementary instruments (HFBS, DCS and FANS at NCNR; HRMECS and QENS at IPNS) at temperatures above and below the previously discovered order-disorder interlayer phase transition. Together the experimental and molecular modeling results capture the important details of the dynamics of nano-confined water and the effects of the orientational ordering of H2O molecules above and below the phase transition. They provide otherwise unobtainable experimental information about the transformation of H2O librational and diffusional modes across the order-disorder phase transition and significantly add to our current understanding of the structure and dynamics of water in LDH phases based on the earlier NMR, IR, X-ray, and calorimetric measurements. The approach can now be extended to probe the

  6. Water reorientation in the hydration shells of hydrophilic and hydrophobic solutes

    Institute of Scientific and Technical Information of China (English)

    LAAGE; Damien; STIRNEMANN; Guillaume; HYNES; James; T.

    2010-01-01

    We discuss some key aspects of our recent theoretical work on water reorientation dynamics,which is important in a wide range of phenomena,including aqueous phase chemical reactions,protein folding,and drug binding to proteins and DNA. It is shown that,contrary to the standard conception that these dynamics are diffusional,the reorientation of a water molecule occurs by sudden,large amplitude angular jumps. The mechanism involves the exchange of one hydrogen bond for another by the reorienting water,and the process can be fruitfully viewed as a chemical reaction. The results for reorientation times,which can be well described analytically,are discussed in the context of the molecular level interpretation of recent ultrafast infrared spectroscopic results,focusing on the concepts of structure making/breaking and solvent ’icebergs’.

  7. Communication: On the origin of the non-Arrhenius behavior in water reorientation dynamics.

    Science.gov (United States)

    Stirnemann, Guillaume; Laage, Damien

    2012-07-21

    We combine molecular dynamics simulations and analytic modeling to determine the origin of the non-Arrhenius temperature dependence of liquid water's reorientation and hydrogen-bond dynamics between 235 K and 350 K. We present a quantitative model connecting hydrogen-bond exchange dynamics to local structural fluctuations, measured by the asphericity of Voronoi cells associated with each water molecule. For a fixed local structure the regular Arrhenius behavior is recovered, and the global anomalous temperature dependence is demonstrated to essentially result from a continuous shift in the unimodal structure distribution upon cooling. The non-Arrhenius behavior can thus be explained without invoking an equilibrium between distinct structures. In addition, the large width of the homogeneous structural distribution is shown to cause a growing dynamical heterogeneity and a non-exponential relaxation at low temperature.

  8. Femtosecond study of the effects of ions on the reorientation dynamics of water

    CERN Document Server

    van der Post, Sietse T; Bakker, Huib J

    2013-01-01

    We study the effects of ions on the reorientation dynamics of liquid water with polarization-resolved femtosecond mid-infared spectroscopy. We probe the anisotropy of the excitation of the O-D stretch vibration of HDO molecules in solutions of NaCl, NaI and tetra-alkylammonium bromide salts in 8 percent HDO:H2O. We find that the reorientation O-D groups of HDO molecules hydrating the Cl- and I- anions occurs on two different time scales with time constants of 2pm0.3 ps and 9pm2 ps. The fast component is due to a wobbling motion of the O-D group that keeps the hydrogen bond with the halogenic anion intact. For solutions of tetra-alkylammonium bromide salts we observe a very strong slowing down of the reorientation of water that is associated with the hydration of the hydrophobic alkyl groups of the tetra-alkylammonium ions.

  9. Measuring molecular reorientation at liquid surfaces with time-resolved sum-frequency spectroscopy: a theoretical framework.

    Science.gov (United States)

    Nienhuys, Han-Kwang; Bonn, Mischa

    2009-05-28

    A theoretical framework is presented for the design and analysis of ultrafast time- and polarization-resolved surface vibrational spectroscopy, aimed at elucidating surface molecular reorientational motion in real time. Vibrational excitation with linearly polarized light lifts the azimuthal symmetry of the surface transition-dipole distribution, causing marked, time-dependent changes in the surface sum-frequency generation (SFG) intensity. The subsequent recovery of the SFG signal generally reflects both vibrational relaxation and reorientational motion of surface molecules. We present experimental schemes that allow direct quantification of the time scale of surface molecular reorientational diffusive motion.

  10. Periodic structures induced by director reorientation in the lyotropic nematic phase of disodium cromoglycate-water

    Science.gov (United States)

    Hui, Y. W.; Kuzma, M. R.; San Miguel, M.; Labes, M. M.

    1985-07-01

    A nonequilibrium periodic structure is induced by a magnetic field H applied to an aligned lyotropic uniaxial nematic phase of disodium cromoglycate-water. A series of parallel lines perpendicular to H represents boundaries between 180° out-of-phase regions of director reorientation. The distance between the lines decreases with increasing H. The line spacing is also directly proportional to thickness of the sample (in a limited range of thickness), and a secondary periodicity, consisting of nodes in these lines, is observed in thicker samples. An extension of a theoretical model by Guyon et al. is used to qualitatively interpret the abovementioned dependencies.

  11. Re-orientation transition in molecular thin films: Potts model with dipolar interaction.

    Science.gov (United States)

    Hoang, Danh-Tai; Kasperski, Maciej; Puszkarski, Henryk; Diep, H T

    2013-02-06

    We study the low-temperature behavior and the phase transition of a thin film by Monte Carlo simulation. The thin film has a simple cubic lattice structure where each site is occupied by a Potts parameter which indicates the molecular orientation of the site. We take only three molecular orientations in this paper, which correspond to the three-state Potts model. The Hamiltonian of the system includes (i) the exchange interaction J(ij) between nearest-neighbor sites i and j, (ii) the long-range dipolar interaction of amplitude D truncated at a cutoff distance r(c), and (iii) a single-ion perpendicular anisotropy of amplitude A. We allow J(ij) = J(s) between surface spins, and J(ij) = J otherwise. We show that the ground state depends on the ratio D/A and r(c). For a single layer, for a given A, there is a critical value D(c) below (above) which the ground-state (GS) configuration of molecular axes is perpendicular (parallel) to the film surface. When the temperature T is increased, a re-orientation transition occurs near D(c): the low-T in-plane ordering undergoes a transition to the perpendicular ordering at a finite T, below the transition to the paramagnetic phase. The same phenomenon is observed in the case of a film with a thickness. Comparison with the Fe/Gd experiment is given. We show that the surface phase transition can occur below or above the bulk transition depending on the ratio J(s)/J. Surface and bulk order parameters as well as other physical quantities are shown and discussed.

  12. An NMR study of molecular reorientations and diffusion in solid LiBF4

    Science.gov (United States)

    Reynhardt, E. C.; Lourens, J. A. J.

    1984-06-01

    The 19F second moment and the 19F, 11B, and 7Li spin-lattice relaxation times in a powdered sample of LiBF4 have been measured as a function of temperature. The results show that the BF-4 ion reorients isotropically while the Li+ ion remains stationary. The activation energy associated with the BF-4 motion is 8.5 kcal/mol. Above ˜385 K the BF-4 and Li+ diffuse through the lattice resulting in a 19F second moment which is almost zero. The activation energy of this process is 19.2 kcal/mol. A librational motion presumably influences the 19F T1ρ results just before diffusion sets in. The migration of Li+ around the BF-4 ion, which seems to be a strong possibility in the case of an isolated LiBF4 molecule, does not take place in the solid.

  13. Strong slowing down of water reorientation in mixtures of water and tetramethylurea

    NARCIS (Netherlands)

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

    2008-01-01

    We use mid-infrared pump−probe spectroscopy to study the ultrafast dynamics of HDO molecules in mixtures of tetramethylurea (TMU) and water. The composition of the studied solutions ranges from pure water to an equimolar mixture of water and TMU. We find that the vibrational relaxation of the OD-str

  14. Temperature-pressure-induced solid-solid to reorientation in FCC metallic nanowire: a molecular dynamic study.

    Science.gov (United States)

    Sutrakar, Vijay Kumar; Roy Mahapatra, D; Pillai, A C R

    2012-01-11

    Atomistic simulation of initial oriented FCC Cu nanowires shows a novel coupled temperature-pressure dependent reorientation from to phase. A temperature-pressure-induced solid-solid to reorientation diagram is generated for Cu nanowire with varying cross-sectional sizes. A critical pressure is reported for Cu nanowires with varying cross-sectional sizes, above which an initial oriented nanowire shows temperature independent reorientation into the phase. The effect of surface stresses on the to reorientation is also studied. The results indicate that above a critical cross-sectional size for a given temperature-pressure, to reorientation is not possible. It is also reported here that for a given applied pressure, an increase in temperature is required for the to reorientation with increasing cross-sectional size of the nanowire. The temperature-pressure-induced solid-solid to reorientation diagram reported in the present paper could further be used as guidelines for controlling the reorientations/shape memory in nano-scale applications of FCC metallic nanowires.

  15. Dynamics in molecular and molecular-ionic crystals: a combined experimental and molecular simulation study of reorientational motions in benzene, pyridinium iodide, and pyridinium nitrate.

    Science.gov (United States)

    Pajzderska, A; Gonzalez, M A; Wąsicki, J

    2013-01-14

    Molecular dynamics (MD) simulations for crystalline benzene (C(6)H(6)), pyridinium iodide [C(5)NH(6)](+)I(-), and pyridinium nitrate [C(5)NH(6)](+)NO(3)(-) have been performed as a function of temperature and pressure. Despite the similar shape of the benzene molecule and the pyridinium cation, the experimental and simulated data have showed clear differences in their dynamics. Therefore, the rotational dynamics have been explored in detail by comparing thoroughly the existing experimental results together with new quasielastic neutron scattering (QENS) data obtained for (PyH)NO(3) and molecular dynamics simulations. The correlation times, activation energy, geometry of motion of benzene molecule and pyridinium cation, isothermal compressibility, and activation volume obtained from the simulations are compared with the experimental results obtained by nuclear magnetic resonance and QENS methods. MD simulations have also revealed that reorientation of the pyridinium cation in pyridinium nitrate between two inequivalent positions is strongly affected by the hydrogen bond N-H···O between the cation and the anion and the influence of temperature on strength of the hydrogen bond is much more important than that of the pressure.

  16. (1)H and (19)F spin-lattice relaxation and CH3 or CF3 reorientation in molecular solids containing both H and F atoms.

    Science.gov (United States)

    Beckmann, Peter A; Rheingold, Arnold L

    2016-04-21

    The dynamics of methyl (CH3) and fluoromethyl (CF3) groups in organic molecular (van der Waals) solids can be exploited to survey their local environments. We report solid state (1)H and (19)F spin-lattice relaxationexperiments in polycrystalline 3-trifluoromethoxycinnamic acid, along with an X-ray diffraction determination of the molecular and crystal structure, to investigate the intramolecular and intermolecular interactions that determine the properties that characterize the CF3 reorientation. The molecule is of no particular interest; it simply provides a motionless backbone (on the nuclear magnetic resonance(NMR) time scale) to investigate CF3 reorientation occurring on the NMR time scale. The effects of (19)F-(19)F and (19)F-(1)H spin-spin dipolar interactions on the complicated nonexponential NMRrelaxation provide independent inputs into determining a model for CF3 reorientation. As such, these experiments provide much more information than when only one spin species (usually (1)H) is present. In Sec. IV, which can be read immediately after the Introduction without reading the rest of the paper, we compare the barrier to CH3 and CF3 reorientation in seven organic solids and separate this barrier into intramolecular and intermolecular components.

  17. Terahertz Conductivity and Hindered Molecular Reorientation of Lithium Salt Doped Succinonitrile in its Plastic Crystal Phase

    Science.gov (United States)

    Nickel, Daniel V.; Bian, Hongtao; Zheng, Junrong; Mittleman, Daniel M.

    2014-09-01

    The terahertz complex permittivity of the molecular plastic crystal succinonitrile (SN) or 1,2 dicyanoethane (N≡C-CH2-CH2-C≡N), doped with the lithium salts LiBF4, LiPF6, LiTFSI, and LiClO4 to form solid-state plastic crystal electrolytes, is measured and compared using temperature-dependent terahertz time-domain spectroscopy (THz-TDS). In contrast to the trends at low frequency, SN's terahertz conductivity decreases slightly when doped with Li-salts. This indicates that at high frequencies the dielectric response is not dominated by ionic charge transport, but instead by relaxational processes which are hindered by the presence of the ionic dopants. Assuming a single Cole-Cole distribution of Debye-like processes dominates the measured spectra, the average relaxation times τ and Arrhenius activation energies E a are extracted for each electrolyte and are shown to increase significantly relative to undoped SN's τ and E a, indicating the relaxational processes are hindered by the presence of the ionic dopants.

  18. Reorientational dynamics in molecular liquids as revealed by dynamic light scattering: From boiling point to glass transition temperature

    Science.gov (United States)

    Schmidtke, B.; Petzold, N.; Kahlau, R.; Rössler, E. A.

    2013-08-01

    We determine the reorientational correlation time τ of a series of molecular liquids by performing depolarized light scattering experiments (double monochromator, Fabry-Perot interferometry, and photon correlation spectroscopy). Correlation times in the range 10-12 s-100 s are compiled, i.e., the full temperature interval between the boiling point and the glass transition temperature Tg is covered. We focus on low-Tg liquids for which the high-temperature limit τ ≅ 10-12 s is easily accessed by standard spectroscopic equipment (up to 440 K). Regarding the temperature dependence three interpolation formulae of τ(T) with three parameters each are tested: (i) Vogel-Fulcher-Tammann equation, (ii) the approach recently discussed by Mauro et al. [Proc. Natl. Acad. Sci. U.S.A. 106, 19780 (2009)], and (iii) our approach decomposing the activation energy E(T) in a constant high temperature value E∞ and a "cooperative part" Ecoop(T) depending exponentially on temperature [Schmidtke et al., Phys. Rev. E 86, 041507 (2012)], 10.1103/PhysRevE.86.041507. On the basis of the present data, approaches (i) and (ii) are insufficient as they do not provide the correct crossover to the high-temperature Arrhenius law clearly identified in the experimental data while approach (iii) reproduces the salient features of τ(T). It allows to discuss the temperature dependence of the liquid's dynamics in terms of a Ecoop(T)/E∞ vs. T/E∞ plot and suggests that E∞ controls the energy scale of the glass transition phenomenon.

  19. Molecular water oxidation catalysis

    CERN Document Server

    Llobet, Antoni

    2014-01-01

    Photocatalytic water splitting is a promising strategy for capturing energy from the sun by coupling light harvesting and the oxidation of water, in order to create clean hydrogen fuel. Thus a deep knowledge of the water oxidation catalysis field is essential to be able to come up with useful energy conversion devices based on sunlight and water splitting. Molecular Water Oxidation Catalysis: A Key Topic for New Sustainable Energy Conversion Schemes presents a comprehensive and state-of-the-art overview of water oxidation catalysis in homogeneous phase, describing in detail the most importan

  20. Molecular dynamics simulations of water within models of ion channels.

    Science.gov (United States)

    Breed, J; Sankararamakrishnan, R; Kerr, I D; Sansom, M S

    1996-04-01

    The transbilayer pores formed by ion channel proteins contain extended columns of water molecules. The dynamic properties of such waters have been suggested to differ from those of water in its bulk state. Molecular dynamics simulations of ion channel models solvated within and at the mouths of their pores are used to investigate the dynamics and structure of intra-pore water. Three classes of channel model are investigated: a) parallel bundles of hydrophobic (Ala20) alpha-helices; b) eight-stranded hydrophobic (Ala10) antiparallel beta-barrels; and c) parallel bundles of amphipathic alpha-helices (namely, delta-toxin, alamethicin, and nicotinic acetylcholine receptor M2 helix). The self-diffusion coefficients of water molecules within the pores are reduced significantly relative to bulk water in all of the models. Water rotational reorientation rates are also reduced within the pores, particularly in those pores formed by alpha-helix bundles. In the narrowest pore (that of the Ala20 pentameric helix bundle) self-diffusion coefficients and reorientation rates of intra-pore waters are reduced by approximately an order of magnitude relative to bulk solvent. In Ala20 helix bundles the water dipoles orient antiparallel to the helix dipoles. Such dipole/dipole interaction between water and pore may explain how water-filled ion channels may be formed by hydrophobic helices. In the bundles of amphipathic helices the orientation of water dipoles is modulated by the presence of charged side chains. No preferential orientation of water dipoles relative to the pore axis is observed in the hydrophobic beta-barrel models.

  1. Rubbing-Induced Molecular Reorientation on an Alignment Surface of an Aromatic Polyimide Containing Cyanobiphenyl Side Chains

    Science.gov (United States)

    Cheng, S. Z. D.; Ge, Jason J.; Li, Christopher Y.; Harris, Frank W.; Hong, Seok-Cheol; Zhuang, Xiaowei; Shen, Y. R.

    2002-03-01

    Surface lamellar decoration (SLD), surface enhanced Raman scattering (SERS) and optical second harmonic generation (SHG) experiments have been utilized to study the molecular orientation and conformation changes at a rubbed polyimide alignment layer surface. This aromatic polyimide containing pendent cyanobiphenyl mesogens was synthesized via a polycondensation, and abbreviated as 6FDA-6CBBP. Uniform alignment layers, possessing high pretilt angles ranging from 39^o to 43^o, have been achieved after mechanical rubbing of the polyimide thin film surface at room temperature and subsequent annealing. This is the first time that high pretilt angles have been detected to possess a negative angle [θ(c)] with respect to the rubbing direction (i.e., opposite to the rubbing direction), considerably different from the conventional pretilt angle [θc)] observed along the rubbing direction. Combined polyethylene (PE) SLD and atomic force microscopy experiments reveal that the azimuthal orientation distribution of the long axis of the edge-on PE lamellar crystals is oriented normal to the rubbing direction, indicating that the PE chains are aligned parallel to the rubbing direction. The SERS results show that mechanical rubbing causes not only tilting of the backbone moieties, but also significant conformational rearrangements of the pendent side chains at the surfaces. The molecular mechanism of this unusual alignment is due to the fact that the pendent cyanobiphenyls forms a uniformly tilted conformation on the rubbed surface, and the polar cyano groups point down towards the layer surface deduced from SHG phase measurements. This conformational rearrangement of the side chains results in the formation of fold-like bent structures on the surface, which directly leads to the long axis of cyanobiphenyls having the [θc)] pretilt angle with respect to the rubbing direction.

  2. Cotransporters as molecular water pumps

    DEFF Research Database (Denmark)

    Zeuthen, Thomas; MacAulay, Nanna

    2002-01-01

    Molecular water pumps are membrane proteins of the cotransport type in which a flux of water is coupled to substrate fluxes by a mechanism within the protein. Free energy can be exchanged between the fluxes. Accordingly, the flux of water may be relatively independent of the external water chemical...

  3. Probing equilibrium of molecular and deprotonated water on TiO 2 (110)

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhi-Tao; Wang, Yang-Gang; Mu, Rentao; Yoon, Yeohoon; Dahal, Arjun; Schenter, Gregory K.; Glezakou, Vassiliki-Alexandra; Rousseau, Roger; Lyubinetsky, Igor; Dohnálek, Zdenek

    2017-02-06

    Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociation barrier. Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. The techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.

  4. Reorienting Hypnosis Education.

    Science.gov (United States)

    Alter, David S; Sugarman, Laurence Irwin

    2017-01-01

    The legacy model of professional clinical hypnosis training presents a restrictive frame increasingly incompatible with our evolving understanding of psychobiology, health, and care. Emerging science recognizes human experience not as disease and diagnosis, but as manifestations of individual, uniquely-endowed, adaptively self-regulating systems. Hypnosis is a particularly well-suited discipline for effecting beneficial change in this paradigm. Training in clinical hypnosis must progress from the current linearly-structured, diagnosis-based, reductionist model toward a more responsive, naturalistic, and client-centered curriculum in order to remain relevant and accessible to clinicians beginning to integrate it into their practices. To that end, this article extends Hope and Sugarman's (2015) thesis of hypnosis as a skill set for systemic perturbation and reorientation to consider what those skills may be, the principles on which they are based, and how they may be taught. Parsing a clinical vignette reveals how incorporation of novelty and uncertainty results in less restrictive and more naturalistic hypnotic encounters that, in response to client-generated cues, elicit psychophysiological plasticity. This disruptive hypnosis education and training framework extends the utility and benefit of applied clinical hypnosis.

  5. Cell reorientation under cyclic stretching

    CERN Document Server

    Livne, Ariel; Geiger, Benjamin

    2014-01-01

    Mechanical cues from the extracellular microenvironment play a central role in regulating the structure, function and fate of living cells. Nevertheless, the precise nature of the mechanisms and processes underlying this crucial cellular mechanosensitivity remains a fundamental open problem. Here we provide a novel framework for addressing cellular sensitivity and response to external forces by experimentally and theoretically studying one of its most striking manifestations -- cell reorientation to a uniform angle in response to cyclic stretching of the underlying substrate. We first show that existing approaches are incompatible with our extensive measurements of cell reorientation. We then propose a fundamentally new theory that shows that dissipative relaxation of the cell's passively-stored, two-dimensional, elastic energy to its minimum actively drives the reorientation process. Our theory is in excellent quantitative agreement with the complete temporal reorientation dynamics of individual cells, measu...

  6. Molecular simulation study of water mobility in aerosol-OT reverse micelles.

    Science.gov (United States)

    Chowdhary, Janamejaya; Ladanyi, Branka M

    2011-06-16

    In this work, we present results from molecular dynamics simulations on the single-molecule relaxation of water within reverse micelles (RMs) of different sizes formed by the surfactant aerosol-OT (AOT, sodium bis(2-ethylhexyl)sulfosuccinate) in isooctane. Results are presented for RM water content w(0) = [H(2)O]/[AOT] in the range from 2.0 to 7.5. We show that translational diffusion of water within the RM can, to a good approximation, be decoupled from the translation of the RM through the isooctane solvent. Water translational mobility within the RM is restricted by the water pool dimensions, and thus, the water mean-squared displacements (MSDs) level off in time. Comparison with models of diffusion in confined geometries shows that a version of the Gaussian confinement model with a biexponential decay of correlations provides a good fit to the MSDs, while a model of free diffusion within a sphere agrees less well with simulation results. We find that the local diffusivity is considerably reduced in the interfacial region, especially as w(0) decreases. Molecular orientational relaxation is monitored by examining the behavior of OH and dipole vectors. For both vectors, orientational relaxation slows down close to the interface and as w(0) decreases. For the OH vector, reorientation is strongly affected by the presence of charged species at the RM interface and these effects are especially pronounced for water molecules hydrogen-bonded to surfactant sites that serve as hydrogen-bond acceptors. For the dipole vector, orientational relaxation near the interface slows down more than that for the OH vector due mainly to the influence of ion-dipole interactions with the sodium counterions. We investigate water OH and dipole reorientation mechanisms by studying the w(0) and interfacial shell dependence of orientational time correlations for different Legendre polynomial orders.

  7. Optimal Reorientation Of Spacecraft Orbit

    Directory of Open Access Journals (Sweden)

    Chelnokov Yuriy Nikolaevich

    2014-06-01

    Full Text Available The problem of optimal reorientation of the spacecraft orbit is considered. For solving the problem we used quaternion equations of motion written in rotating coordinate system. The use of quaternion variables makes this consideration more efficient. The problem of optimal control is solved on the basis of the maximum principle. An example of numerical solution of the problem is given.

  8. Reorientation from Altered States: Please, More Carefully.

    Science.gov (United States)

    Heikkinen, Charles A.

    1989-01-01

    Claims counselors too often appear to forget to reorient clients from altered states of consciousness used in counseling and that failure to reorient can result in unnecessary discomfort for clients. Provides suggestions for when and how to reorient to avoid unwanted, lingering aftereffects. (Author/ABL)

  9. Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties.

    Science.gov (United States)

    Martí, J; Nagy, G; Guàrdia, E; Gordillo, M C

    2006-11-30

    Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.

  10. Molecular dynamics simulation of nanosized water droplet spreading in an electric field.

    Science.gov (United States)

    Song, F H; Li, B Q; Liu, C

    2013-04-02

    Molecular dynamics (MD) simulations are performed for the spreading of a nanosized water droplet on a solid substrate subject to a parallel electric field. A combined electrostatic and Lennard-Jones potential is employed to represent the intermolecular interactions. Results show that in response to the applied field, polar water molecules realign themselves and this microscopic reorientation of molecular dipoles combines with the intermolecular forces to produce a macroscopic deformation of a free spherical water droplet into an ellipsoid. The applied field has a strong effect on the spreading of the water droplet on a solid substrate. For a weaker parallel field, the droplet spreading is asymmetric with the leading contact angle being greater than the trailing contact angle. With an increase in field strength, this asymmetry continues to increase, culminates, and then decreases until it disappears. The symmetric spreading remains with a further increase in the field strength until the saturation point is reached. This transition from the asymmetric to symmetric spreading is a manifestation of the interaction of the electric field with polar water molecules and the intermolecular forces within the droplet and between the water and solid; the interaction also leads to a change in hydrogen bonds along the droplet surface. The dynamics of the droplet spreading is entailed by the electrically induced motion of molecules along the liquid surface toward the solid substrate and is controlled by a competing mechanism among the electric, water-water, and water-solid intermolecular forces.

  11. A charge-driven molecular water pump

    Science.gov (United States)

    Gong, Xiaojing; Li, Jingyuan; Lu, Hangjun; Wan, Rongzheng; Li, Jichen; Hu, Jun; Fang, Haiping

    2007-11-01

    Understanding and controlling the transport of water across nanochannels is of great importance for designing novel molecular devices, machines and sensors and has wide applications, including the desalination of seawater. Nanopumps driven by electric or magnetic fields can transport ions and magnetic quanta, but water is charge-neutral and has no magnetic moment. On the basis of molecular dynamics simulations, we propose a design for a molecular water pump. The design uses a combination of charges positioned adjacent to a nanopore and is inspired by the structure of channels in the cellular membrane that conduct water in and out of the cell (aquaporins). The remarkable pumping ability is attributed to the charge dipole-induced ordering of water confined in the nanochannels, where water can be easily driven by external fields in a concerted fashion. These findings may provide possibilities for developing water transport devices that function without osmotic pressure or a hydrostatic pressure gradient.

  12. Water lubricates hydrogen-bonded molecular machines

    Science.gov (United States)

    Panman, Matthijs R.; Bakker, Bert H.; den Uyl, David; Kay, Euan R.; Leigh, David A.; Buma, Wybren Jan; Brouwer, Albert M.; Geenevasen, Jan A. J.; Woutersen, Sander

    2013-11-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational spectroscopy and NMR-lineshape analysis, we show that for molecular machinery consisting of hydrogen-bonded components the relative motion of the components is accelerated strongly by adding small amounts of water. The translation of a macrocycle along a thread and the rotation of a molecular wheel around an axle both accelerate significantly on the addition of water, whereas other protic liquids have much weaker or opposite effects. We tentatively assign the superior accelerating effect of water to its ability to form a three-dimensional hydrogen-bond network between the moving parts of the molecular machine. These results may indicate a more general phenomenon that helps explain the function of water as the ‘lubricant of life’.

  13. Genomic Signals of Reoriented ORFs

    Directory of Open Access Journals (Sweden)

    Paul Dan Cristea

    2004-01-01

    Full Text Available Complex representation of nucleotides is used to convert DNA sequences into complex digital genomic signals. The analysis of the cumulated phase and unwrapped phase of DNA genomic signals reveals large-scale features of eukaryote and prokaryote chromosomes that result from statistical regularities of base and base-pair distributions along DNA strands. By reorienting the chromosome coding regions, a “hidden” linear variation of the cumulated phase has been revealed, along with the conspicuous almost linear variation of the unwrapped phase. A model of chromosome longitudinal structure is inferred on these bases.

  14. Energetic and molecular water permeation mechanisms of the human red blood cell urea transporter B.

    Directory of Open Access Journals (Sweden)

    Slim Azouzi

    Full Text Available Urea transporter B (UT-B is a passive membrane channel that facilitates highly efficient permeation of urea. In red blood cells (RBC, while the major function of UT-B is to transport urea, it is assumed that this protein is able to conduct water. Here, we have revisited this last issue by studying RBCs and ghosts from human variants with defects of aquaporin 1 (AQP1 or UT-B. We found that UT-B's osmotic water unit permeability (pfunit is similar to that of AQP1. The determination of diffusional permeability coefficient (Pd allowed the calculation of the Pf/Pd ratio, which is consistent with a single-file water transport. Molecular dynamic simulations of water conduction through human UT-B confirmed the experimental finding. From these results, we propose an atomistic description of water-protein interactions involved in this permeation. Inside the UT-B pore, five water molecules were found to form a single-file and move rapidly along a channel by hydrogen bond exchange involving two critical threonines. We further show that the energy barrier for water located in the central region coincides with a water dipole reorientation, which can be related to the proton exclusion observed experimentally. In conclusion, our results indicate that UT-B should be considered as a new member of the water channel family.

  15. INIST: databases reorientation; INIST: reorientation des bases de donnees

    Energy Technology Data Exchange (ETDEWEB)

    Bidet, J.C.

    1995-08-01

    INIST is a CNRS (Centre National de la Recherche Scientifique) laboratory devoted to the treatment of scientific and technical informations and to the management of these informations compiled in a database. Reorientation of the database content has been proposed in 1994 to increase the transfer of research towards enterprises and services, to develop more automatized accesses to the informations, and to create a quality assurance plan. The catalog of publications comprises 5800 periodical titles (1300 for fundamental research and 4500 for applied research). A science and technology multi-thematic database will be created in 1995 for the retrieval of applied and technical informations. ``Grey literature`` (reports, thesis, proceedings..) and human and social sciences data will be added to the base by the use of informations selected in the existing GRISELI and Francis databases. Strong modifications are also planned in the thematic cover of Earth sciences and will considerably reduce the geological information content. (J.S.). 1 tab.

  16. Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

    Science.gov (United States)

    Fogarty, Aoife C; Laage, Damien

    2014-07-17

    Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

  17. Hydrogen Bonding and Related Properties in Liquid Water: A Car-Parrinello Molecular Dynamics Simulation Study.

    Science.gov (United States)

    Guardia, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-07-23

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water molecules have also been found to be strongly dependent on their initial hydrogen-bonding state. Finally, the dependence of the librational and vibrational modes of water molecules on the local hydrogen-bonding network has been carefully examined, revealing a significant effect upon the libration and bond-stretching peak frequencies. The calculated low frequency peaks come in agreement with previously reported interpretations of the experimental low-frequency Raman spectrum of liquid water.

  18. Escape of water molecular from Carbon Nanotubes

    Science.gov (United States)

    Li, Jiaxi; Li, Wenfeng; Zhang, Jianwei

    2014-03-01

    Understanding and controlling the transport of water molecules through nanopores have attracted great interest due to potential applications for designing novel nanofluidic devices, machines and sensors. In this work, we theoretically investigate the effects of an external nonuniform electric field on the escape of water molecules through single-walled carbon nanotubes (SWNTs) by using of molecular dynamics (MD) simulations. When polar water molecules are placed in the gradient electric field, the electric force is experienced that can drive the water molecules. Molecular dynamics simulations show that the escape probability of water obeys the Boltzmann distribution. Our results show that energy barrier delta E is independent of temperature which indicates that it is a single-barrier system. From the MD results statistics, the key parameters could be determined such that the relationship between energy barrier delta E and diameter of SWNTs and nozzle distance of the charge r would be revealed that could deepen our current theoretical understanding on transport of water molecular inside SWNTs with the nonuniform electric field.

  19. Hydrogen Bonding and Dielectric Spectra of Ethylene Glycol–Water Mixtures from Molecular Dynamics Simulations

    Science.gov (United States)

    2016-01-01

    Mixtures of ethylene glycol with water are a prominent example of media with variable viscosity. Classical molecular dynamics simulations at room temperature were performed for mixtures of ethylene glycol (EG) and water with EG mole fractions of xE = 0.0, 0.1, 0.2, 0.4, 0.6, 0.9, 1.0. The calculated dielectric loss spectra were in qualitative agreement with experiment. We found a slightly overestimated slowdown of the dynamics with increasing EG concentration compared to experimental data. Statistics of the hydrogen bond network and hydrogen bond lifetimes were derived from suitable time correlation functions and also show a slowdown in the dynamics with increasing xE. A similar picture is predicted for the time scales of EG conformer changes and for molecular reorientation. A slight blue shift was obtained for the power spectra of the molecular center of mass motion. The results were used to give a qualitative interpretation of the origin of three different relaxation times that appear in experimental complex dielectric spectra and of their change with xE. PMID:27649083

  20. Thermal Conductivity of Ordered Molecular Water

    Energy Technology Data Exchange (ETDEWEB)

    W Evans; J Fish; P Keblinski

    2006-02-16

    We use molecular dynamics simulation to investigate thermal transport characteristics of water with various degree of orientational and translational order induced by the application of an electric field. We observe that orientational ordering of the water dipole moments has a minor effect on the thermal conductivity. However, electric-field induced crystallization and associated translational order results in approximately a 3-fold increase of thermal conductivity with respect to the base water, i.e., to values comparable with those characterizing ice crystal structures.

  1. Distribution of Water Vapor in Molecular Clouds

    CERN Document Server

    Melnick, Gary J; Snell, Ronald L; Bergin, Edwin A; Hollenbach, David J; Kaufman, Michael J; Li, Di; Neufeld, David A

    2010-01-01

    We report the results of a large-area study of water vapor along the Orion Molecular Cloud ridge, the purpose of which was to determine the depth-dependent distribution of gas-phase water in dense molecular clouds. We find that the water vapor measured toward 77 spatial positions along the face-on Orion ridge, excluding positions surrounding the outflow associated with BN/KL and IRc2, display integrated intensities that correlate strongly with known cloud surface tracers such as CN, C2H, 13CO J =5-4, and HCN, and less well with the volume tracer N2H+. Moreover, at total column densities corresponding to Av < 15 mag., the ratio of H2O to C18O integrated intensities shows a clear rise approaching the cloud surface. We show that this behavior cannot be accounted for by either optical depth or excitation effects, but suggests that gas-phase water abundances fall at large Av. These results are important as they affect measures of the true water-vapor abundance in molecular clouds by highlighting the limitations...

  2. Water Abundance in Molecular Cloud Cores

    CERN Document Server

    Snell, R L; Ashby, M L N; Bergin, E A; Chin, G; Erickson, N R; Goldsmith, P F; Harwit, M; Kleiner, S C; Koch, D G; Neufeld, D A; Patten, B M; Plume, R; Schieder, R; Stauffer, J R; Tolls, V; Wang, Z; Winnewisser, G; Zhang, Y F; Melnick, G J

    2000-01-01

    We present Submillimeter Wave Astronomy Satellite (SWAS) observations of the 1_{10}-1_{01} transition of ortho-water at 557 GHz toward 12 molecular cloud cores. The water emission was detected in NGC 7538, Rho Oph A, NGC 2024, CRL 2591, W3, W3(OH), Mon R2, and W33, and was not detected in TMC-1, L134N, and B335. We also present a small map of the water emission in S140. Observations of the H_2^{18}O line were obtained toward S140 and NGC 7538, but no emission was detected. The abundance of ortho-water relative to H_2 in the giant molecular cloud cores was found to vary between 6x10^{-10} and 1x10^{-8}. Five of the cloud cores in our sample have previous water detections; however, in all cases the emission is thought to arise from hot cores with small angular extents. The water abundance estimated for the hot core gas is at least 100 times larger than in the gas probed by SWAS. The most stringent upper limit on the ortho-water abundance in dark clouds is provided in TMC-1, where the 3-sigma upper limit on the ...

  3. Molecular Density Functional Theory of Water

    CERN Document Server

    Jeanmairet, Guillaume; Vuilleumier, Rodolphe; Borgis, Daniel; 10.1021/jz301956b

    2013-01-01

    Three dimensional implementations of liquid state theories offer an efficient alternative to computer simulations for the atomic-level description of aqueous solutions in complex environments. In this context, we present a (classical) molecular density functional theory (MDFT) of water that is derived from first principles and is based on two classical density fields, a scalar one, the particle density, and a vectorial one, the multipolar polarization density. Its implementation requires as input the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric constants. It has to be complemented by a solute-solvent three-body term that reinforces tetrahedral order at short range. The approach is shown to provide the correct three-dimensional microscopic solvation profile around various molecular solutes, possibly possessing H-bonding sites, at a computer cost two-three orders of magnitude lower tha...

  4. Molecular dynamics of a tetrasaccharide subunit of chondroitin 4-sulfate in water.

    Science.gov (United States)

    Kaufmann, J; Möhle, K; Hofmann, H J; Arnold, K

    1999-05-31

    Molecular dynamics (MD) simulations on a tetrasaccharide subunit of chondroitin 4-sulfate (CS4) in aqueous solution were carried out to study its interactions with water. Pair distribution functions and diffusion coefficients were calculated from a 4 ns trajectory and the hydration of different molecular groups was analysed. The average values of the interglycosidic torsion angles found in the simulations are phi 13 = -10 degrees, psi 13 = -85 degrees and phi 13 = 80 degrees, psi 13 = 90 degrees for the beta-(1-->3) linkage, and phi 14 = -10 degrees, psi 14 = -70 degrees for the beta-(1-->4) linkage. Hydrophobic patches formed by sugar ring CH groups were found. The diffusion coefficients of the water molecules vary from 1.4 x 10(-9) to 2.3 x 10(-9) m2 s-1 depending on the distances between the water molecules and the atoms of the CS4 molecule and the type of CS4 atoms, respectively. Reorientation correlation times of the water molecules in the vicinity of different CS4 atoms were estimated to be about 1 ps at a polymer concentration of 4 wt.% CS4. The number of hydrogen bonds between the water molecules and the acceptor atoms of CS4 was determined to be about 20 per disaccharide unit, indicating a higher hydration ability of chondroitin sulfate in comparison with non-sulfated oligosaccharides. Substructures, where water molecules are involved in hydrogen bonds to different sugar rings, were found, which may be important for the stabilisation of the secondary structure of the CS4 molecule.

  5. Reorienting with terrain slope and landmarks.

    Science.gov (United States)

    Nardi, Daniele; Newcombe, Nora S; Shipley, Thomas F

    2013-02-01

    Orientation (or reorientation) is the first step in navigation, because establishing a spatial frame of reference is essential for a sense of location and heading direction. Recent research on nonhuman animals has revealed that the vertical component of an environment provides an important source of spatial information, in both terrestrial and aquatic settings. Nonetheless, humans show large individual and sex differences in the ability to use terrain slope for reorientation. To understand why some participants--mainly women--exhibit a difficulty with slope, we tested reorientation in a richer environment than had been used previously, including both a tilted floor and a set of distinct objects that could be used as landmarks. This environment allowed for the use of two different strategies for solving the task, one based on directional cues (slope gradient) and one based on positional cues (landmarks). Overall, rather than using both cues, participants tended to focus on just one. Although men and women did not differ significantly in their encoding of or reliance on the two strategies, men showed greater confidence in solving the reorientation task. These facts suggest that one possible cause of the female difficulty with slope might be a generally lower spatial confidence during reorientation.

  6. The reorientation of spatial planning in Denmark

    DEFF Research Database (Denmark)

    Galland, Daniel

    2011-01-01

    has been reoriented at national, regional and urban/local levels over time. The fundamental objective of the project is hence to explore and examine the history and evolution of Danish spatial planning through three embedded case studies from inception until most recent transformations. Respectively......, these studies embrace the reorientations of Danish national spatial planning; regional spatial planning in North Jutland; and urban planning and waterfront redevelopment in the city of Aalborg. In attaining its aim, the dissertation is guided by the general premise that the reorientations of spatial planning...... planning practices at different administrative levels. As a whole, the outcome of this dissertation confirms that there is an increasing policy and institutional mismatch between national, regional and urban/local planning practices. It further suggests that the lack of spatial reflexion embedded...

  7. SWAS Observations of Water in Molecular Outflows

    CERN Document Server

    Franklin, J; Kaufman, M J; Melnick, G J; Neufeld, D A; Hollenbach, D J; Bergin, E A

    2007-01-01

    We present SWAS detections of the ground-state 1(10)-1(01) transition of o-H2O at 557 GHz in 18 molecular outflows. These results are combined with ground-based observations of the J=1-0 transitions of 12CO and 13CO obtained at the FCRAO and, for a subset of the outflows, data from ISO. Assuming the SWAS water line emission originates from the same gas traced by CO emission, we find that the outflowing gas in most outflows has an o-H2O abundance relative to H2 of between 10(-7) and 10(-6). Analysis of the water abundance as a function of outflow velocity reveals a strong dependence. The water abundance increases with velocity, and at the highest outflow velocities some outflows have relative o-H2O abundances of order 10(-4). However the mass of gas with such elevated water abundances represents less that 1% of the total outflow gas mass. The ISO LWS observations of high-J rotational lines of CO and the 179.5 micron transition of o-H2O provide evidence for a warmer outflow component than required to produce ei...

  8. Using Perceptrons to Explore the Reorientation Task

    Science.gov (United States)

    Dawson, Michael R. W.; Kelly, Debbie M.; Spetch, Marcia L.; Dupuis, Brian

    2010-01-01

    The reorientation task is a paradigm that has been used extensively to study the types of information used by humans and animals to navigate in their environment. In this task, subjects are reinforced for going to a particular location in an arena that is typically rectangular in shape. The subject then has to find that location again after being…

  9. Reorientation of magnetic anisotropy in epitaxial cobalt ferrite thin films

    NARCIS (Netherlands)

    Lisfi, A.; Williams, C.M.; Nguyen, L.T.; Lodder, J.C.; Coleman, A.; Corcoran, H.; Johnson, A.; Chang, P.; Kumar, A.; Morgan, W.

    2007-01-01

    Spin reorientation has been observed in CoFe2O4 thin single crystalline films epitaxially grown on (100) MgO substrate upon varying the film thickness. The critical thickness for such a spin-reorientation transition was estimated to be 300 nm. The reorientation is driven by a structural transition

  10. Reorientation of magnetic anisotropy in epitaxial cobalt ferrite thin films

    NARCIS (Netherlands)

    Lisfi, A.; Williams, C.M.; Nguyen, L.T.; Lodder, J.C.; Coleman, A.; Corcoran, H.; Johnson, A.; Chang, P.; Abhishek Kumar, A.K.; Kumar, A.; Morgan, W.

    2007-01-01

    Spin reorientation has been observed in CoFe2O4 thin single crystalline films epitaxially grown on (100) MgO substrate upon varying the film thickness. The critical thickness for such a spin-reorientation transition was estimated to be 300 nm. The reorientation is driven by a structural transition

  11. Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto.

    Science.gov (United States)

    Nimmo, F; Hamilton, D P; McKinnon, W B; Schenk, P M; Binzel, R P; Bierson, C J; Beyer, R A; Moore, J M; Stern, S A; Weaver, H A; Olkin, C B; Young, L A; Smith, K E

    2016-12-01

    The deep nitrogen-covered basin on Pluto, informally named Sputnik Planitia, is located very close to the longitude of Pluto's tidal axis and may be an impact feature, by analogy with other large basins in the Solar System. Reorientation of Sputnik Planitia arising from tidal and rotational torques can explain the basin's present-day location, but requires the feature to be a positive gravity anomaly, despite its negative topography. Here we argue that if Sputnik Planitia did indeed form as a result of an impact and if Pluto possesses a subsurface ocean, the required positive gravity anomaly would naturally result because of shell thinning and ocean uplift, followed by later modest nitrogen deposition. Without a subsurface ocean, a positive gravity anomaly requires an implausibly thick nitrogen layer (exceeding 40 kilometres). To prolong the lifetime of such a subsurface ocean to the present day and to maintain ocean uplift, a rigid, conductive water-ice shell is required. Because nitrogen deposition is latitude-dependent, nitrogen loading and reorientation may have exhibited complex feedbacks.

  12. Reorientation of Sputnik Planitia implies a subsurface ocean on Pluto

    Science.gov (United States)

    Nimmo, F.; Hamilton, D. P.; McKinnon, W. B.; Schenk, P. M.; Binzel, R. P.; Bierson, C. J.; Beyer, R. A.; Moore, J. M.; Stern, S. A.; Weaver, H. A.; Olkin, C. B.; Young, L. A.; Smith, K. E.; Moore, J. M.; McKinnon, W. B.; Spencer, J. R.; Beyer, R.; Binzel, R. P.; Buie, M.; Buratti, B.; Cheng, A.; Cruikshank, D.; Ore, C. Dalle; Earle, A.; Gladstone, R.; Grundy, W.; Howard, A. D.; Lauer, T.; Linscott, I.; Nimmo, F.; Parker, J.; Porter, S.; Reitsema, H.; Reuter, D.; Roberts, J. H.; Robbins, S.; Schenk, P. M.; Showalter, M.; Singer, K.; Strobel, D.; Summers, M.; Tyler, L.; White, O. L.; Umurhan, O. M.; Banks, M.; Barnouin, O.; Bray, V.; Carcich, B.; Chaikin, A.; Chavez, C.; Conrad, C.; Hamilton, D. P.; Howett, C.; Hofgartner, J.; Kammer, J.; Lisse, C.; Marcotte, A.; Parker, A.; Retherford, K.; Saina, M.; Runyon, K.; Schindhelm, E.; Stansberry, J.; Steffl, A.; Stryk, T.; Throop, H.; Tsang, C.; Verbiscer, A.; Winters, H.; Zangari, A.; Stern, S. A.; Weaver, H. A.; Olkin, C. B.; Young, L. A.; Smith, K. E.

    2016-12-01

    The deep nitrogen-covered basin on Pluto, informally named Sputnik Planitia, is located very close to the longitude of Pluto’s tidal axis and may be an impact feature, by analogy with other large basins in the Solar System. Reorientation of Sputnik Planitia arising from tidal and rotational torques can explain the basin’s present-day location, but requires the feature to be a positive gravity anomaly, despite its negative topography. Here we argue that if Sputnik Planitia did indeed form as a result of an impact and if Pluto possesses a subsurface ocean, the required positive gravity anomaly would naturally result because of shell thinning and ocean uplift, followed by later modest nitrogen deposition. Without a subsurface ocean, a positive gravity anomaly requires an implausibly thick nitrogen layer (exceeding 40 kilometres). To prolong the lifetime of such a subsurface ocean to the present day and to maintain ocean uplift, a rigid, conductive water-ice shell is required. Because nitrogen deposition is latitude-dependent, nitrogen loading and reorientation may have exhibited complex feedbacks.

  13. Fundamental experiments on hydride reorientation in zircaloy

    Science.gov (United States)

    Colas, Kimberly B.

    In the current study, an in-situ X-ray diffraction technique using synchrotron radiation was used to follow directly the kinetics of hydride dissolution and precipitation during thermomechanical cycles. This technique was combined with conventional microscopy (optical, SEM and TEM) to gain an overall understanding of the process of hydride reorientation. Thus this part of the study emphasized the time-dependent nature of the process, studying large volume of hydrides in the material. In addition, a micro-diffraction technique was also used to study the spatial distribution of hydrides near stress concentrations. This part of the study emphasized the spatial variation of hydride characteristics such as strain and morphology. Hydrided samples in the shape of tensile dog-bones were used in the time-dependent part of the study. Compact tension specimens were used during the spatial dependence part of the study. The hydride elastic strains from peak shift and size and strain broadening were studied as a function of time for precipitating hydrides. The hydrides precipitate in a very compressed state of stress, as measured by the shift in lattice spacing. As precipitation proceeds the average shift decreases, indicating average stress is reduced, likely due to plastic deformation and morphology changes. When nucleation ends the hydrides follow the zirconium matrix thermal contraction. When stress is applied below the threshold stress for reorientation, hydrides first nucleate in a very compressed state similar to that of unstressed hydrides. After reducing the average strain similarly to unstressed hydrides, the average hydride strain reaches a constant value during cool-down to room temperature. This could be due to a greater ease of deforming the matrix due to the applied far-field strain which would compensate for the strains due to thermal contraction. Finally when hydrides reorient, the average hydride strains become tensile during the first precipitation regime and

  14. The reorientation of spatial planning in Denmark

    DEFF Research Database (Denmark)

    Galland, Daniel

    2011-01-01

    have been increasingly overridden by growth-oriented and competitiveness logics. More recently, the effects of a structural reform that changed the geographies of inter-governmental arrangements within the country have significantly transformed the orientation, scope, structure and performance...... has been reoriented at national, regional and urban/local levels over time. The fundamental objective of the project is hence to explore and examine the history and evolution of Danish spatial planning through three embedded case studies from inception until most recent transformations. Respectively...

  15. Tidal reorientation and the fracturing of Jupiter's moon Europa

    Science.gov (United States)

    Mcewen, A. S.

    1986-01-01

    The lineaments on Europa are discussed in terms of the orientation of the lineaments relative to the tensile stress trajectories due to tidal distortions and to nonsynchronous rotation. The cracks are noticeable by their darker albedo compared to the presumed water ice surrounding them. The stress trajectories for tidal distortion of a thin elastic shell are superimposed on Mercator projection maps of the lineaments. It is shown that the lineaments are mainly oriented at high angles to the tensile stress trajectories that would be expected for regularly occurring nonsynchronous rotation, i.e., extensional fractures would appear. The reorientation motions which would cause the fractures are estimated. It is suggested that the fractures occur episodically to release stresses built up on the tensile surface of the crust during the continuous nonsynchronous rotation of Europa.

  16. Reorientation of Defect Dipoles in Ferroelectric Ceramics

    Institute of Scientific and Technical Information of China (English)

    LI Bao-Shan; LI Guo-Rong; ZHAO Su-Chuan; ZHU Zhi-Gang; DING Ai-Li

    2005-01-01

    @@ We investigate the frequency, temperature, tetragonality and quenched temperature dependences of the hysteresis loops in Pb[(Zr0.52 Ti0.48)0.95 (Mn1/3Nb2/3)0.05]O3 (PMnN-PZT) ceramics. It has been demonstrated that the polarization-field hysteresis curves show "pinched" shapes when tested at room temperature, higher frequency or using the large-tetragonality specimen. While normal square-like loops are observed at 200 ℃ and 0.01 Hz or using the small-tetragonality one. Meanwhile, close relations between the P-E loops and the applied frequency,temperature or tetragonality reveal that there exists a typical relaxation time corresponding to the reorientation of the defect dipoles. It can be seen further from the quenched temperature dependences of the loops that the reorientation of the defect dipoles may influence the pinching. Compared to the intrinsic depinning procedure induced by changes of the distribution of defect dipoles, we provide new evidence for extrinsic depinning mechanism of the defect dipoles in the ferroelectric ceramics.

  17. RHO binding to FAM65A regulates Golgi reorientation during cell migration

    Science.gov (United States)

    Marshall, Christopher J.

    2016-01-01

    ABSTRACT Directional cell migration involves reorientation of the secretory machinery. However, the molecular mechanisms that control this reorientation are not well characterised. Here, we identify a new Rho effector protein, named FAM65A, which binds to active RHOA, RHOB and RHOC. FAM65A links RHO proteins to Golgi-localising cerebral cavernous malformation-3 protein (CCM3; also known as PDCD10) and its interacting proteins mammalian STE20-like protein kinases 3 and 4 (MST3 and MST4; also known as STK24 and STK26, respectively). Binding of active RHO proteins to FAM65A does not affect the kinase activity of MSTs but results in their relocation from the Golgi in a CCM3-dependent manner. This relocation is crucial for reorientation of the Golgi towards the leading edge and subsequent directional cell migration. Our results reveal a previously unidentified pathway downstream of RHO that regulates the polarity of migrating cells through Golgi reorientation in a FAM65A-, CCM3- and MST3- and MST4-dependent manner. PMID:27807006

  18. Physiological response, molecular analysis and water use efficiency ...

    African Journals Online (AJOL)

    SAM

    2014-07-16

    Jul 16, 2014 ... Molecular analysis of three hybrids revealed the possibility of introgressing the ...... complex and depends on both biophysical and economic ... Grant RF, Jackson BS, Kiniry KR, Arkin GF (1989) Water deficit timing effects on ...

  19. Adsorbed water on iron surface by molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Fernandes, F.W.; Campos, T.M.B.; Cividanes, L.S., E-mail: flaviano@ita.br; Simonetti, E.A.N.; Thim, G.P.

    2016-01-30

    Graphical abstract: - Highlights: • We developed a new force field to describe the Fe–H{sub 2}O interaction. • We developed a new force field to describe the flexible water model at low temperature. • We analyze the orientation of water along the iron surface. • We calculate the vibrational spectra of water near the iron surface. • We found a complex relationship between water orientation and the atomic vibrational spectra at different sites of adsorption along the iron surface. - Abstract: The adsorption of H{sub 2}O molecules on metal surfaces is important to understand the early process of water corrosion. This process can be described by computational simulation using molecular dynamics and Monte Carlo. However, this simulation demands an efficient description of the surface interactions between the water molecule and the metallic surface. In this study, an effective force field to describe the iron-water surface interactions was developed and it was used in a molecular dynamics simulation. The results showed a very good agreement between the simulated vibrational-DOS spectrum and the experimental vibrational spectrum of the iron–water interface. The water density profile revealed the presence of a water double layer in the metal interface. Furthermore, the horizontal mapping combined with the angular distribution of the molecular plane allowed the analysis of the water structure above the surface, which in turn agrees with the model of the double layer on metal surfaces.

  20. Specific Electrostatic Molecular Recognition in Water

    DEFF Research Database (Denmark)

    Li, Ming; Hoeck, Casper; Schoffelen, Sanne;

    2016-01-01

    -bead binding assay and by 2D NMR spectroscopy. Molecular dynamics (MD) studies revealed a putative mode of interaction for this unusual electrostatic binding event. High binding specificity occurred through a combination of topological matching and electrostatic and hydrogen-bond complementarities. From MD...

  1. Water lubricates hydrogen-bonded molecular machines

    NARCIS (Netherlands)

    Panman, M.R.; Bakker, B.H.; den Uyl, D.; Kay, E.R.; Leigh, D.A.; Buma, W.J.; Brouwer, A.M.; Geenevasen, J.A.J.; Woutersen, S.

    2013-01-01

    The mechanical behaviour of molecular machines differs greatly from that of their macroscopic counterparts. This applies particularly when considering concepts such as friction and lubrication, which are key to optimizing the operation of macroscopic machinery. Here, using time-resolved vibrational

  2. Spinning in the Scanner: Neural Correlates of Virtual Reorientation

    Science.gov (United States)

    Sutton, Jennifer E.; Joanisse, Marc F.; Newcombe, Nora S.

    2010-01-01

    Recent studies have used spatial reorientation task paradigms to identify underlying cognitive mechanisms of navigation in children, adults, and a range of animal species. Despite broad interest in this task across disciplines, little is known about the brain bases of reorientation. We used functional magnetic resonance imaging to examine neural…

  3. Spinning in the Scanner: Neural Correlates of Virtual Reorientation

    Science.gov (United States)

    Sutton, Jennifer E.; Joanisse, Marc F.; Newcombe, Nora S.

    2010-01-01

    Recent studies have used spatial reorientation task paradigms to identify underlying cognitive mechanisms of navigation in children, adults, and a range of animal species. Despite broad interest in this task across disciplines, little is known about the brain bases of reorientation. We used functional magnetic resonance imaging to examine neural…

  4. Molecular dynamics simulation of a polysorbate 80 micelle in water

    NARCIS (Netherlands)

    Amani, Amir; York, Peter; de Waard, Hans; Anwar, Jamshed

    2011-01-01

    The structure and dynamics of a single molecule of the nonionic surfactant polysorbate 80 (POE (20) sorbitan monooleate; Tween 80 (R)) as well as a micelle comprising sixty molecules of polysorbate 80 in water have been investigated by molecular dynamics simulation. In its free state in water the po

  5. Molecular dynamics insights into human aquaporin 2 water channel.

    Science.gov (United States)

    Binesh, A R; Kamali, R

    2015-12-01

    In this study, the first molecular dynamics simulation of the human aquaporin 2 is performed and for a better understanding of the aquaporin 2 permeability performance, the characteristics of water transport in this protein channel and key biophysical parameters of AQP2 tetramer including osmotic and diffusive permeability constants and the pore radius are investigated. For this purpose, recently recovered high resolution X-ray crystal structure of` the human aquaporin 2 is used to perform twenty nanosecond molecular dynamics simulation of fully hydrated tetramer of this protein embedded in a lipid bilayer. The resulting water permeability characteristics of this protein channel showed that the water permeability of the human AQP2 is in a mean range in comparison with other human aquaporins family. Finally, the results reported in this research demonstrate that molecular dynamics simulation of human AQP2 provided useful insights into the mechanisms of water permeation and urine concentration in the human kidney.

  6. Water and Molecular Transport across Nanopores in Monolayer Graphene Membranes

    Science.gov (United States)

    Jang, Doojoon; O'Hern, Sean; Kidambi, Piran; Boutilier, Michael; Song, Yi; Idrobo, Juan-Carlos; Kong, Jing; Laoui, Tahar; Karnik, Rohit

    2015-11-01

    Graphene's atomic thickness and high tensile strength allow it to outstand as backbone material for next-generation high flux separation membrane. Molecular dynamics simulations predicted that a single-layer graphene membrane could exhibit high permeability and selectivity for water over ions/molecules, qualifying as novel water desalination membranes. However, experimental investigation of water and molecular transport across graphene nanopores had remained barely explored due to the presence of intrinsic defects and tears in graphene. We introduce two-step methods to seal leakage across centimeter scale single-layer graphene membranes create sub-nanometer pores using ion irradiation and oxidative etching. Pore creation parameters were varied to explore the effects of created pore structures on water and molecular transport driven by forward osmosis. The results demonstrate the potential of nanoporous graphene as a reliable platform for high flux nanofiltration membranes.

  7. Molecular recognition of amidines in water.

    Science.gov (United States)

    Grawe, Thomas; Schäfer, Gerhard; Schrader, Thomas

    2003-05-15

    [structure: see text] Tetraphosphonates of the general structure shown above are biomimetic hosts for bisamidinium cations in drugs such as pentamidine and DAPI. Similar to their insertion into DNA's minor groove, these drugs are often sandwiched by two tetraphosphonate hosts (2:1). The alternative binding mode (1:2) produces extremely high association constants in water of approximately 10(8) M(-)(2) ( approximately 12 kcal/mol), which can compete with the biological process.

  8. Molecular dynamics study of the water/n-alkane interface

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Molecular dynamics simulations on the interface between liquid water and liquid n-alkane (including octane, nonane, decane, undecane and dodecane) have been performed with the purpose to study the interfacial properties: (Ⅰ) density profile; (Ⅱ) molecular orientation; (Ⅲ) interfacial tension and the temperature effect on the interfacial tension. Simulation results show that at the interface the structures of both water and n-alkane are different from those in the bulk. Water has an orientational preference due to the number of hydrogen bonds per molecule maximized. N-alkane has a more lateral orientation with respect to the interface in order to be in close contact with water. The calculated individual phase bulk density and interfacial tension of water/n-alkane systems are in good agreement with the corresponding experimental ones.

  9. Water tribology on graphene.

    Science.gov (United States)

    N'guessan, Hartmann E; Leh, Aisha; Cox, Paris; Bahadur, Prashant; Tadmor, Rafael; Patra, Prabir; Vajtai, Robert; Ajayan, Pulickel M; Wasnik, Priyanka

    2012-01-01

    Classical experiments show that the force required to slide liquid drops on surfaces increases with the resting time of the drop, t(rest), and reaches a plateau typically after several minutes. Here we use the centrifugal adhesion balance to show that the lateral force required to slide a water drop on a graphene surface is practically invariant with t(rest). In addition, the drop's three-phase contact line adopts a peculiar micrometric serrated form. These observations agree well with current theories that relate the time effect to deformation and molecular re-orientation of the substrate surface. Such molecular re-orientation is non-existent on graphene, which is chemically homogenous. Hence, graphene appears to provide a unique tribological surface test bed for a variety of liquid drop-surface interactions.

  10. Synthesis of molecular imprinted beta cyclodextrins oligomers in water

    DEFF Research Database (Denmark)

    Yu, Donghong; Nielsen, Anne Louise; Bach, Lone

    2003-01-01

    hydrophobic molecules in aqueous solution, however, with limited selectivity. Templated synthesis of Cyclodextrin polymers was introduced by Komiyama. By use of simple templates, such as cholesterol, polymers with improved selectivity for the template molecules were achieved. In most...... compounds in aqueous solution and, therefore, molecular imprinting of cyclodextrins polymers in aqueous solution is of great interest. In this paper, molecular imprinting of beta cyclodextrins has been performed in water by use of diiodobenzene as template and epichlorohydrin as a crosslinker. Inclusion...

  11. Synthesis of molecular imprinted beta cyclodextrins oligomers in water

    DEFF Research Database (Denmark)

    Yu, Donghong; Nielsen, Anne Louise; Bach, Lone

    2003-01-01

    hydrophobic molecules in aqueous solution, however, with limited selectivity. Templated synthesis of Cyclodextrin polymers was introduced by Komiyama. By use of simple templates, such as cholesterol, polymers with improved selectivity for the template molecules were achieved. In most...... compounds in aqueous solution and, therefore, molecular imprinting of cyclodextrins polymers in aqueous solution is of great interest. In this paper, molecular imprinting of beta cyclodextrins has been performed in water by use of diiodobenzene as template and epichlorohydrin as a crosslinker. Inclusion...

  12. Aquaporin water channels: molecular mechanisms for human diseases.

    Science.gov (United States)

    Agre, Peter; Kozono, David

    2003-11-27

    Although water is the major component of all biological fluids, the molecular pathways for water transport across cell membranes eluded identification until the discovery of the aquaporin family of water channels. The atomic structure of mammalian AQP1 illustrates how this family of proteins is freely permeated by water but not protons (hydronium ions, H3O+). Definition of the subcellular sites of expression predicted their physiological functions and potential clinical disorders. Analysis of several human disease states has confirmed that aquaporins are involved in multiple different illnesses including abnormalities of kidney function, loss of vision, onset of brain edema, starvation, and arsenic toxicity.

  13. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...... computations of water droplets on silica surfaces offers a useful fundamental and quantitative measurement in order to study chemical and physical properties of water-silica systems.3,16,17,18 For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence...

  14. Molecular Dynamics Simulation of Water Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    WANG Yan; YUAN Hong-Jun

    2007-01-01

    Molecular dynamics simulations are performed for water conGned in carbon nanotubes with various diameters (11.0-13.8 A). The simulations under an isobaric pressure (one atmosphere) by lowering temperatures from 300K to 190 K are carried out. Water molecules within variously sized tubes tend to transform from disorder to order with different configurations (four-water-molecule ring, six-water-molecule ring and seven-water-molecule ring) at phase transition temperatures, which may be lowered by the increasing tube radius. It is also found that the configurations of water in (10, 10) tube are not unique (seven-molecule ring and seven-molecule ring plus water chain).

  15. PIE techniques for hydride reorientation test at NDC

    Energy Technology Data Exchange (ETDEWEB)

    Tsuda, Tomohiro; Shinohara, Yasunari; Yamaguchi, Yoichiro [Nuclear Development Corporation, Ibaraki (Japan)

    2008-11-15

    Dry storage of spent fuels in the interim storage facility is being planned in Japan. However, the gradual deterioration of the mechanical property of fuel cladding due to internal pressure and temperature during the storage term is known. Therefore, the integrity of stored fuel rods should be confirmed before the start of dry storage. For the last several years, NDC had a lot of experiences on the hydride reorientation test. The specimen preparation techniques on the hydride reorientation test and the mechanical testing techniques after the hydride reorientation are shown in this paper.

  16. Interfacial molecular restructuring of plasticized polymers in water.

    Science.gov (United States)

    Hankett, Jeanne M; Lu, Xiaolin; Liu, Yuwei; Seeley, Emily; Chen, Zhan

    2014-10-07

    Upon water contact, phthalate-plasticized poly(vinyl chloride) (PVC) surfaces are highly unstable because the plasticizer molecules are not covalently bound to the polymer network. As a result, it is difficult to predict how the surface polymer chains and plasticizers may interact with water without directly probing the plastic/water interface in situ. We successfully studied the molecular surface restructuring of 10 wt% and 25 wt% bis 2-ethylhexyl phthalate (DEHP)-plasticized and pure PVC films (deposited on solid substrates) in situ due to water contact using sum frequency generation (SFG) vibrational spectroscopy. SFG spectral signals from both the top and the bottom of the plastic film were obtained simultaneously, so a thin-film model spectral analysis was applied to separately identify the molecular changes of plastics at the surface and the plastic/substrate interface in water. It was found that in water both the structures of the plastic surface and the buried plastic/substrate interface changed. After removing the samples from the water and exposing them to air again, the surface structures did not completely recover. Further SFG experiments confirmed that small amounts of DEHP were transferred into the water. The leached DEHP molecules could reorder and permanently transfer to new surfaces through water contact. Our studies indicate that small amounts of phthalates can transfer from surface to surface through water contact in an overall scope of minutes. This study yields vital new information on the molecular surface structures of DEHP plasticized PVC in water, and the transfer behaviors and environmental fate of plasticizers in polymers.

  17. Molecular dynamic simulations of the water absorbency of hydrogels.

    Science.gov (United States)

    Ou, Xiang; Han, Qiang; Dai, Hui-Hui; Wang, Jiong

    2015-09-01

    A polymer gel can imbibe solvent molecules through surface tension effect. When the solvent happens to be water, the gel can swell to a large extent and forms an aggregate called hydrogel. The large deformation caused by such swelling makes it difficult to study the behaviors of hydrogels. Currently, few molecular dynamic simulation works have been reported on the water absorbing mechanism of hydrogels. In this paper, we first use molecular dynamic simulation to study the water absorbing mechanism of hydrogels and propose a hydrogel-water interface model to study the water absorbency of the hydrogel surface. Also, the saturated water content and volume expansion rate of the hydrogel are investigated by building a hydrogel model with different cross-linking degree and by comparing the water absorption curves under different temperatures. The sample hydrogel model used consists of Polyethylene glycol diglycidyl ether (PEGDGE) as epoxy and the Jeffamine, poly-oxy-alkylene-amines, as curing agent. The conclusions obtained are useful for further investigation on PEGDGE/Jeffamine hydrogel. Moreover, the simulation methods, including hydrogel-water interface modeling, we first propose are also suitable to study the water absorbing mechanism of other hydrogels.

  18. Reorientation of the early lunar pole

    Science.gov (United States)

    Takahashi, Futoshi; Tsunakawa, Hideo; Shimizu, Hisayoshi; Shibuya, Hidetoshi; Matsushima, Masaki

    2014-06-01

    Palaeomagnetic measurements suggest that an active core dynamo operated on the Moon from 4.2 to 3.56 billion years ago. Since the Apollo era, many magnetic anomalies have been observed on the Moon. The magnetization of the lunar crust in some of these regions could preserve the signature of an early dipolar magnetic field generated by a core dynamo. Thus, the magnetic anomalies may yield information about the position of the palaeomagnetic pole during the time that the dynamo operated. Here we present a comprehensive survey of magnetic anomalies on the lunar surface using magnetometer data obtained by the Lunar Prospector and Kaguya lunar orbiters. We extract magnetization vectors from 24 magnetic anomalies using an iterative inversion method and derive the palaeomagnetic poles. We find that the north poles, as well as the antipodal south poles, cluster in two distinct locations: one near the present rotation axis and the other at mid-latitude. The clustering is consistent with a dipole-dominated magnetic field generated in the lunar core by a dynamo that was reversing, much like that of Earth. Furthermore, the two pole clusters imply that the Moon experienced a polar wander event during its ancient history due to the reorientation of the Moon with respect to its spin axis by 45°-60°.

  19. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water, at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle computations...

  20. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes.1,2,3 Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems...... and DNA microarrays technologies.4,5,6,7,8 Although extensive experimental, theoretical and computational work has been devoted to study the nature of the interaction between silica and water,2,9-16 at the molecular level a complete understanding of silica-water systems has not been reached. Contact angle...

  1. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Qi, Rui; Wang, Qiantao; Ren, Pengyu, E-mail: pren@mail.utexas.edu [Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712 (United States); Wang, Lee-Ping; Pande, Vijay S. [Department of Chemistry, Stanford University, Stanford, California 94305 (United States)

    2015-07-07

    We report the development of a united AMOEBA (uAMOEBA) polarizable water model, which is computationally 3–5 times more efficient than the three-site AMOEBA03 model in molecular dynamics simulations while providing comparable accuracy for gas-phase and liquid properties. In this coarse-grained polarizable water model, both electrostatic (permanent and induced) and van der Waals representations have been reduced to a single site located at the oxygen atom. The permanent charge distribution is described via the molecular dipole and quadrupole moments and the many-body polarization via an isotropic molecular polarizability, all located at the oxygen center. Similarly, a single van der Waals interaction site is used for each water molecule. Hydrogen atoms are retained only for the purpose of defining local frames for the molecular multipole moments and intramolecular vibrational modes. The parameters have been derived based on a combination of ab initio quantum mechanical and experimental data set containing gas-phase cluster structures and energies, and liquid thermodynamic properties. For validation, additional properties including dimer interaction energy, liquid structures, self-diffusion coefficient, and shear viscosity have been evaluated. The results demonstrate good transferability from the gas to the liquid phase over a wide range of temperatures, and from nonpolar to polar environments, due to the presence of molecular polarizability. The water coordination, hydrogen-bonding structure, and dynamic properties given by uAMOEBA are similar to those derived from the all-atom AMOEBA03 model and experiments. Thus, the current model is an accurate and efficient alternative for modeling water.

  2. Molecular level water and solute transport in reverse osmosis membranes

    Science.gov (United States)

    Lueptow, Richard M.; Shen, Meng; Keten, Sinan

    2015-11-01

    The water permeability and rejection characteristics of six solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polymeric reverse osmosis (RO) membrane using non-equilibrium molecular dynamics simulations. Results indicate that water flux increases with an increasing fraction of percolated free volume in the membrane polymer structure. Solute molecules display Brownian motion and hop from pore to pore as they pass through the membrane. The solute rejection depends on both the size of the solute molecule and the chemical interaction of the solute with water and the membrane. When the open spaces in the polymeric structure are such that solutes have to shed at least one water molecule from their solvation shell to pass through the membrane molecular structure, the water-solute pair interaction energy governs solute rejection. Organic solutes more easily shed water molecules than ions to more readily pass through the membrane. Hydrogen-bonding sites for molecules like urea also lead to a higher rejection. These findings underline the importance of the solute's solvation shell and solute-water-membrane chemistry in solute transport and rejection in RO membranes. Funded by the Institute for Sustainability and Energy at Northwestern with computing resources from XSEDE (NSF grant ACI-1053575).

  3. Molecular simulation of water behaviors on crystal faces of hydroxyapatite

    Institute of Scientific and Technical Information of China (English)

    PAN Haihua; TAO Jinhui; WU Tao; TANG Ruikang

    2007-01-01

    The water behavior on (001) and (100) crystal faces of hydroxyapatite (HAP) were studied using molecular dynamics (MD) simulations.The study showed that the water molecules between the HAP faces were under conditions of strong electrical field and high pressure,and hence formed 2-3 well-organized water layers on the crystal surfaces.These structured water layers had ice-like features.Compared with the crystallographic [100] direction of HAP,the polarity along the [001] direction was stronger,which resulted in more structured water layers on the surface.The interaction of water molecules with the calcium and phosphate sites at the HAP-water interface was also studied.The results indicated the multiple pathways of water adsorption onto the HAP surfaces.This study revealed the formation and the detailed structure of water layers on HAP surfaces and suggested that the interracial water played an important role in stabilizing the HAP particles in aqueous solutions.

  4. Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state

    CERN Document Server

    Irudayam, Sheeba J; Berkowitz, Max L

    2013-01-01

    An important step in a phospholipid membrane pore formation by melittin antimicrobial peptide is a reorientation of the peptide from a surface into a transmembrane conformation. In this work we perform umbrella sampling simulations to calculate the potential of mean force (PMF) for the reorientation of melittin from a surface-bound state to a transmembrane state and provide a molecular level insight into understanding peptide and lipid properties that influence the existence of the free energy barrier. The PMFs were calculated for a peptide to lipid (P/L) ratio of 1/128 and 4/128. We observe that the free energy barrier is reduced when the P/L ratio increased. In addition, we study the cooperative effect; specifically we investigate if the barrier is smaller for a second melittin reorientation, given that another neighboring melittin was already in the transmembrane state. We observe that indeed the barrier of the PMF curve is reduced in this case, thus confirming the presence of a cooperative effect.

  5. Molecular mechanisms of water transport in the eye

    DEFF Research Database (Denmark)

    Hamann, Steffen; Hamann, Steffen Ellitsgaard

    2002-01-01

    sites between ion and water transport remain undefined. In the retinal pigment epithelium, a H+-lactate cotransporter transports water. This protein could be the site of coupling between salt and water in this epithelium. The distribution of aquaporins does not suggest a role for these proteins......The four major sites for ocular water transport, the corneal epithelium and endothelium, the ciliary epithelium, and the retinal pigment epithelium, are reviewed. The cornea has an inherent tendency to swell, which is counteracted by its two surface cell layers, the corneal epithelium...... and endothelium. The bilayered ciliary epithelium secretes the aqueous humor into the posterior chamber, and the retinal pigment epithelium transports water from the retinal to the choroidal site. For each epithelium, ion transport mechanisms are associated with fluid transport, but the exact molecular coupling...

  6. Effect of water on structure and dynamics of [BMIM][PF6] ionic liquid: An all-atom molecular dynamics simulation investigation

    Science.gov (United States)

    Sharma, Anirban; Ghorai, Pradip Kr.

    2016-03-01

    Composition dependent structural and dynamical properties of aqueous hydrophobic 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) ionic liquid (IL) have been investigated by using all-atom molecular dynamics simulation. We observe that addition of water does not increase significant number of dissociated ions in the solution over the pure state. As a consequence, self-diffusion coefficient of the cation and anion is comparable to each other at all water concentration similar to that is observed for the pure state. Voronoi polyhedra analysis exhibits strong dependence on the local environment of IL concentration. Void and neck distributions in Voronoi tessellation are approximately Gaussian for pure IL but upon subsequent addition of water, we observe deviation from the Gaussian behaviour with an asymmetric broadening with long tail of exponential decay at large void radius, particularly at higher water concentrations. The increase in void space and neck size at higher water concentration facilitates ionic motion, thus, decreasing dynamical heterogeneity and IL reorientation time and increases self-diffusion coefficient significantly.

  7. Molecular dynamics of the water liquid-vapor interface

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

    1987-01-01

    The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

  8. Molecular dynamics of the water liquid-vapor interface

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.; Pratt, L. R.; MacElroy, R. D. (Principal Investigator)

    1987-01-01

    The results of molecular dynamics calculations on the equilibrium interface between liquid water and its vapor at 325 K are presented. For the TIP4P model of water intermolecular pair potentials, the average surface dipole density points from the vapor to the liquid. The most common orientations of water molecules have the C2 nu molecular axis roughly parallel to the interface. The distributions are quite broad and therefore compatible with the intermolecular correlations characteristic of bulk liquid water. All near-neighbor pairs in the outermost interfacial layers are hydrogen bonded according to the common definition adopted here. The orientational preferences of water molecules near a free surface differ from those near rigidly planar walls which can be interpreted in terms of patterns found in hexagonal ice 1. The mean electric field in the interfacial region is parallel to the mean polarization which indicates that attention cannot be limited to dipolar charge distributions in macroscopic descriptions of the electrical properties of this interface. The value of the surface tension obtained is 132 +/- 46 dyn/cm, significantly different from the value for experimental water of 68 dyn/cm at 325 K.

  9. Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach.

    Science.gov (United States)

    Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro

    2012-03-28

    A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.

  10. Transport Phenomena of Water in Molecular Fluidic Channels

    Science.gov (United States)

    Vo, Truong Quoc; Kim, Bohung

    2016-09-01

    In molecular-level fluidic transport, where the discrete characteristics of a molecular system are not negligible (in contrast to a continuum description), the response of the molecular water system might still be similar to the continuum description if the time and ensemble averages satisfy the ergodic hypothesis and the scale of the average is enough to recover the classical thermodynamic properties. However, even in such cases, the continuum description breaks down on the material interfaces. In short, molecular-level liquid flows exhibit substantially different physics from classical fluid transport theories because of (i) the interface/surface force field, (ii) thermal/velocity slip, (iii) the discreteness of fluid molecules at the interface and (iv) local viscosity. Therefore, in this study, we present the result of our investigations using molecular dynamics (MD) simulations with continuum-based energy equations and check the validity and limitations of the continuum hypothesis. Our study shows that when the continuum description is subjected to the proper treatment of the interface effects via modified boundary conditions, the so-called continuum-based modified-analytical solutions, they can adequately predict nanoscale fluid transport phenomena. The findings in this work have broad effects in overcoming current limitations in modeling/predicting the fluid behaviors of molecular fluidic devices.

  11. Molecular Dynamics Investigation of Benzene in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Microscopic structure and diffusion properties of benzene in ambient water (298 K, 0.1 MPa) and super critical water (673-773 K, 25-35 MPa) are investigated by molecular dynamics simulation with site-site models. It is found that at the ambient condition, the water molecules surrounding a benzene molecule form a hydrogen bond network. The hydrogen bond interaction between supercritical water molecules decreases dramatically under supercritical conditions. The diffusion coefficients of both the solute molecule and solvent molecule at supercritical conditions increase by 30-180 times than those at the ambient condition. With the temperature approaching the critical temperature, the change of diffusion coefficient with pressure becomes pronounced.

  12. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  13. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

    Walther, J. H.; Jaffe, R.; Halicioglu, T.; Koumoutsakos, P.

    2000-01-01

    We study the hydrophobic/hydrophilic behavior of carbon nanotubes using molecular dynamics simulations. The energetics of the carbon-water interface are mainly dispersive but in the present study augmented with a carbon quadrupole term acting on the charge sites of the water. The simulations indicate that this contribution is negligible in terms of modifying the structural properties of water at the interface. Simulations of two carbon nanotubes in water display a wetting and drying of the interface between the nanotubes depending on their initial spacing. Thus, initial tube spacings of 7 and 8 A resulted in a drying of the interface whereas spacing of > 9 A remain wet during the course of the simulation. Finally, we present a novel particle-particle-particle-mesh algorithm for long range potentials which allows for general (curvilinear) meshes and "black-box" fast solvers by adopting an influence matrix technique.

  14. COLD WATER VAPOR IN THE BARNARD 5 MOLECULAR CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Wirström, E. S.; Persson, C. M. [Department of Earth and Space Sciences, Chalmers University of Technology, Onsala Space Observatory, SE-439 92 Onsala (Sweden); Charnley, S. B.; Cordiner, M. A. [Astrochemistry Laboratory and The Goddard Center for Astrobiology, Mailstop 691, NASA Goddard Space Flight Center, 8800 Greenbelt Road, Greenbelt, MD 20770 (United States); Buckle, J. V. [Astrophysics Group, Cavendish Laboratory, J. J. Thomson Avenue, Cambridge CB3 0HE (United Kingdom); Takakuwa, S., E-mail: eva.wirstrom@chalmers.se [Institute of Astronomy and Astrophysics, Academia Sinica, P.O. Box 23-141, Taipei 106, Taiwan (China)

    2014-06-20

    After more than 30 yr of investigations, the nature of gas-grain interactions at low temperatures remains an unresolved issue in astrochemistry. Water ice is the dominant ice found in cold molecular clouds; however, there is only one region where cold (∼10 K) water vapor has been detected—L1544. This study aims to shed light on ice desorption mechanisms under cold cloud conditions by expanding the sample. The clumpy distribution of methanol in dark clouds testifies to transient desorption processes at work—likely to also disrupt water ice mantles. Therefore, the Herschel HIFI instrument was used to search for cold water in a small sample of prominent methanol emission peaks. We report detections of the ground-state transition of o-H{sub 2}O (J = 1{sub 10}-1{sub 01}) at 556.9360 GHz toward two positions in the cold molecular cloud, Barnard 5. The relative abundances of methanol and water gas support a desorption mechanism which disrupts the outer ice mantle layers, rather than causing complete mantle removal.

  15. A molecular density functional theory to study solvation in water

    CERN Document Server

    Jeanmairet, Guillaume

    2014-01-01

    A classical density functional theory is applied to study solvation of solutes in water. An approx- imate form of the excess functional is proposed for water. This functional requires the knowledge of pure solvent direct correlation functions. Those functions can be computed by using molecular simulations such as molecular dynamic or Monte Carlo. It is also possible to use functions that have been determined experimentally. The functional minimization gives access to the solvation free energy and to the equilibrium solvent density. Some correction to the functional are also proposed to get the proper tetrahedral order of solvent molecules around a charged solute and to reproduce the correct long range hydrophobic behavior of big apolar solutes. To proceed the numerical minimization of the functional, the theory has been discretized on two tridimensional grids, one for the space coordinates, the other for the angular coordinates, in a functional minimization code written in modern Fortran, mdft. This program i...

  16. 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.

  17. Simulation of carbohydrates, from molecular docking to dynamics in water.

    Science.gov (United States)

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

    Modeling of carbohydrates is particularly challenging because of the variety of structures resulting for the high number of monosaccharides and possible linkages and also because of their intrinsic flexibility. The development of carbohydrate parameters for molecular modeling is still an active field. Nowadays, main carbohydrates force fields are GLYCAM06, CHARMM36, and GROMOS 45A4. GLYCAM06 includes the largest choice of compounds and is compatible with the AMBER force fields and associated. Furthermore, AMBER includes tools for the implementation of new parameters. When looking at protein-carbohydrate interaction, the choice of the starting structure is of importance. Such complex can be sometimes obtained from the Protein Data Bank-although the stereochemistry of sugars may require some corrections. When no experimental data is available, molecular docking simulation is generally used to the obtain protein-carbohydrate complex coordinates. As molecular docking parameters are not specifically dedicated to carbohydrates, inaccuracies should be expected, especially for the docking of polysaccharides. This issue can be addressed at least partially by combining molecular docking with molecular dynamics simulation in water.

  18. Molecular simulation of the magnetite-water interface

    Science.gov (United States)

    Rustad, James R.; Felmy, Andrew R.; Bylaska, Eric J.

    2003-03-01

    This paper reports molecular dynamics simulations of the magnetite (001)-water interface, both in pure water and in the presence of a 2.3 molal solution of NaClO 4. The simulations are carried out using a potential model designed to allow the protonation states of the surface functional groups to evolve dynamically through the molecular dynamics trajectory. The primary structural quantities investigated are the populations of the surface functional groups, the distribution of electrolyte in the solution, and the surface hydrogen bonding relationships. The surface protonation states are dominated by extensive hydrolysis of interfacial water molecules, giving rise to a dipolar surface dominated by FeOH2+-OH 2-OH - arrangements. Triply coordinated, more deeply buried, surface sites are inert, probably due to the relative lack of solvent in their vicinity. The electrolyte distribution is oscillatory, arranging preferentially in layers defined by the solvating water molecules. The presence of electrolyte has a negligible effect on the protonation states of the surface functional groups. Steady-state behavior is obtained for the protonation states of the surface functional groups and hydrogen-bonding network. Although the overall structure of the electrolyte distribution is fairly well established, the electrolyte distribution has not fully equilibrated, as evidenced by the asymmetry in the distribution from the top to the bottom of the slab.

  19. 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.

  20. A molecular dynamics study on surface properties of supercooled water

    Institute of Scientific and Technical Information of China (English)

    L(U) Yongjun; WEI Bingbo

    2006-01-01

    Molecular dynamics simulations were performed to study the surface properties of water in a temperature range from 228 to 293 K by using the extended simple point charge (SPC/E) and four-site TIP4P potentials. The calculated surface tension increases with the decrease of temperature, and moreover the slopes of the surface tension-temperature curves show a weak rise below 273 K, whereas no obvious anomalies appear near 228 K, which accords with the previous experiments. Compared with the measured values, the SPC/E potential shows a good agreement, and the TIP4P potential scription of the surface structure of supercooled water for the SPC/E. When simulating the orientational distributions of water molecules near the surface, the SPC/E potential produces higher ordering and larger surface potentials than the TIP4P potential.

  1. Planar reorientation maneuvers of space multibody systems using internal controls

    Science.gov (United States)

    Reyhanoglu, Mahmut; Mcclamroch, N. H.

    1992-01-01

    In this paper a reorientation maneuvering strategy for an interconnection of planar rigid bodies in space is developed. It is assumed that there are no exogeneous torques, and torques generated by joint motors are used as means of control so that the total angular momentum of the multibody system is a constant, assumed to be zero in this paper. The maneuver strategy uses the nonintegrability of the expression for the angular momentum. We demonstrate that large-angle maneuvers can be designed to achieve an arbitrary reorientation of the multibody system with respect to an inertial frame. The theoretical background for carrying out the required maneuvers is briefly summarized. Specifications and computer simulations of a specific reorientation maneuver, and the corresponding control strategies, are described.

  2. Molecular dynamics of water at high temperatures and pressures

    Science.gov (United States)

    Brodholt, John; Wood, Bernard

    1990-09-01

    There are currently no precise P-V-T data for water at pressures above 8.9 kbars and temperatures above 900°C. Many petrological processes in the lower crust and upper mantle take place under more extreme conditions, however and petrologists commonly rely on empirical equations of state such as the modified Redlich-Kwong equation (MRK) to extrapolate the low pressure data. In this study we have taken an alternative approach and attempted to simulate the P-V-T properties of water using molecular dynamics. The TIP4P intermolecular potential for H 2O ( JORGENSEN et al., 1983) has had considerable success predicting the properties of water at low temperatures and pressures up to 10 kbar ( MADURA et al., 1988). We have extended its application by making molecular dynamics (MD) simulations at a density of 1.0 g/cc from 300 to 2300 K and 0.5 to 40 kbars. The results agree with the P-V-T data of BURNHAM et al. (1969) (up to 10 kbars) with an average error of under 2%. This is a much better concordance than is obtained with any of the currently used versions of MRK. At 300 kbars and 2000 K the MD simulations predict densities within 8% of those obtained in the shock wave experiments of KORMER (1968). This is a very good agreement given the fact that water ionizes to some extent at high pressures ( MITCHELL and NELLIS, 1982) and we have made no provisions for this effect. We conclude that molecular dynamics simulations provide the possibility of estimating P-V-T properties in the upper mantle P-T regime with very good accuracy.

  3. Molecular dynamics simulations of radon accumulation in water and oil

    Energy Technology Data Exchange (ETDEWEB)

    Pafong, Elvira; Drossel, Barbara [Institut fuer Festkoerperphysik, Technische Universitaet Darmstadt (Germany)

    2016-07-01

    Radon is a radioactive gas that can enter the human body from air or from ground water. Radon can accumulate to levels that considerably rise the risk of lung cancer while it is also known as a a treatment of various ailments, most notably rheumatoid arthritis. The accumulation of radon differs between tissues, with particularly high concentrations in fatty cells. In order to understand the mechanisms responsible for the different solubility of radon in water and fat, we perform molecular dynamics simulations of radon gas at ambient conditions in contact with a bulk material consisting either of water or oil. We evaluate the diffusion coefficient of radon in both media as well as the equilibrium concentration. The crucial point here is to understand the hydrophobic interaction between water and radon as compared to the dispersive interaction between radon and oil. Therefore, we artificially vary the water charges (i.e., the hydrophobicity) as well as the parameters of the van-der-Waals interaction.

  4. Molecular-dynamics of water transport through membranes - water from solvent to solute

    NARCIS (Netherlands)

    BERENDSEN, HJC; MARRINK, SJ

    1993-01-01

    An application of Molecular Dynamics computer simulation (MD) to the process of transport of water through a lipid bilayer membrane is described. The permeation process is far too slow to be modeled by straightforward MD. In stead the inverse of the permeability coefficient is expressed as an

  5. A molecular dynamics study on surface properties of supercooled water

    Institute of Scientific and Technical Information of China (English)

    Lü; Yongjun

    2006-01-01

    [1]Basu J K,Hazra S,Sanyal M K.Growth mechanism of Langmuir-Blodgett films.Phys Rev Lett,1999,82:4675-4678[2]Taylor R S,Shields R L.Molecular-dynamics simulations of the ethanol liquid-vapor interface.J Chem Phys,2003,119:12569-12576[3]Velev O D,Gurkov T D,Ivanov I B,et al.Abnormal thickness and stability of nonequilibrium liquid films.Phys Rev Lett,1995,75:264-267[4]Weng J G,Park S,Lukes J R,et al.Molecular dynamics investigation of thickness effect on liquid films.J Chem Phys,2000,113:5917-5923[5]Zakharov V V,Brodskaya E N,Laaksonen A.Surface tension of water droplets:A molecular dynamics study of model and size dependencies.J Chem Phys,1997,107:10675-10683[6]Wang J Z,Chen M,Guo Z Y.A two-dimensional molecular dynamics simulation of liquid-vapor nucleation.Chin Sci Bull,2003,48(7):623-626[7]Guissani Y,Guillot B.A computer simulation study of the liquid-vapor coexistence curve of water.J Chem Phys,1993,98:8221-8235[8]Wilson M A,Pohorille A,Pratt L R.Surface potential of the water liquid-vapor interface.J Chem Phys,1988,88:3281-3285[9]Alejandre J,Tildesley D J,Chapela G A.Molecular dynamics simulation of the orthobaric densities and surface tension of water.J Chem Phys,1995,102:4574-4583[10]Matsumoto M,Kataoka Y.Study on liquid-vapor interface of water (Ⅰ):Simulational results of thermodynamic properties and orientational structure.J Chem Phys,1988,88:3233-3245[11]Floriano M A,Angell C A.Surface tension and molar surface free energy and entropy of water to-27.2℃.J Phys Chem,1990,94:4199-4202[12]Jorgensen W L,Chandrasekhar J,Madura J D.Comparison of simple potential functions for simulating liquid water.J Chem Phys,1993,79:926-935[13]Berendsen H J C,Grigera J R,Straatsma T P.The missing term in effective pair potentials.J Phys Chem,1987,91:6269-6271[14]Arbuckle B W,Clancy P.Effects of the Ewald sum on the free energy of the extended simple point charge model for water.J Chem Phys,2002,116:5090-5098[15]Tarazona P,Chacon E,Reinaldo-Falagan M,et al

  6. Molecular mechanism for cavitation in water under tension

    CERN Document Server

    Menzl, Georg; Geiger, Philipp; Caupin, Frédéric; Abascal, Jose L F; Valeriani, Chantal; Dellago, Christoph

    2016-01-01

    Despite its relevance in biology and engineering, the molecular mechanism driving cavitation in water remains unknown. Using computer simulations, we investigate the structure and dynamics of vapor bubbles emerging from metastable water at negative pressures. We find that in the early stages of cavitation, bubbles are irregularly shaped and become more spherical as they grow. Nevertheless, the free energy of bubble formation can be perfectly reproduced in the framework of classical nucleation theory (CNT) if the curvature dependence of the surface tension is taken into account. Comparison of the observed bubble dynamics to the predictions of the macroscopic Rayleigh--Plesset (RP) equation, augmented with thermal fluctuations, demonstrates that the growth of nanoscale bubbles is governed by viscous forces. Combining the dynamical prefactor determined from the RP equation with the free energy of CNT yields an analytical expression for the cavitation rate that reproduces the simulation results very well over a w...

  7. The World Is Not Flat: Can People Reorient Using Slope?

    Science.gov (United States)

    Nardi, Daniele; Newcombe, Nora S.; Shipley, Thomas F.

    2011-01-01

    Studies of spatial representation generally focus on flat environments and visual input. However, the world is not flat, and slopes are part of most natural environments. In a series of 4 experiments, we examined whether humans can use a slope as a source of allocentric, directional information for reorientation. A target was hidden in a corner of…

  8. Reorientation of magnetic anisotropy in obliquely sputtered metallic thin films

    NARCIS (Netherlands)

    Lisfi, A.; Lodder, J.C.; Wormeester, H.; Poelsema, B.

    2002-01-01

    Reorientation in the magnetic anisotropy as a function of film thickness has been observed in Co-Ni and Co thin films, obliquely sputtered on a polyethylene terephthalate substrate at a large incidence angle (70°). This effect is a consequence of the low magnetocrystalline anisotropy of the films (f

  9. Stategic reorientation of industrial R&D towards commercial objectives.

    NARCIS (Netherlands)

    Brook, Jacques W.; de Bruijn, E.J.; McDonough III, Edward F.; Kaynak, E.; Harcar, T.D.

    2007-01-01

    In an effort to leverage R&D knowledge asset and to create more value from industrial R&D in today’s increasing liberalized and globalising business environments, some corporations adopt a strategic reorientation of their industrial R&D organisation towards commercial objectives. This study suggests

  10. Role of water states on water uptake and proton transport in Nafion using molecular simulations and bimodal network

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Gi Suk [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Mechanical Engineering; Kaviany, Massoud [Univ. of Michigan, Ann Arbor, MI (United States). Dept. of Mechanical Engineering; Gostick, Jeffrey T. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Kientiz, Brian [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Weber, Adam Z. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Energy Technologies Division; Kim, Moo Hwan [Pohang Univ. of Science and Technology (POSTECH) (Korea, Republic of). Dept. of Mechanical Engineering

    2011-04-07

    In this paper, using molecular simulations and a bimodal-domain network, the role of water state on Nafion water uptake and water and proton transport is investigated. Although the smaller domains provide moderate transport pathways, their effectiveness remains low due to strong, resistive water molecules/domain surface interactions. Finally, the water occupancy of the larger domains yields bulk-like water, and causes the observed transition in the water uptake and significant increases in transport properties.

  11. Molecular Dynamics of a Water-Lipid Bilayer Interface

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  12. Molecular Dynamics of a Water-Lipid Bilayer Interface

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1994-01-01

    We present results of molecular dynamics simulations of a glycerol 1-monooleate bilayer in water. The total length of analyzed trajectories is 5ns. The calculated width of the bilayer agrees well with the experimentally measured value. The interior of the membrane is in a highly disordered fluid state. Atomic density profile, orientational and conformational distribution functions, and order parameters indicate that disorder increases toward the center of the bilayer. Analysis of out-of-plane thermal fluctuations of the bilayer surfaces occurring at the time scale of the present calculations reveals that the distribution of modes agrees with predictions of the capillary wave model. Fluctuations of both bilayer surfaces are uncorrelated, yielding Gaussian distribution of instantaneous widths of the membrane. Fluctuations of the width produce transient thinning defects in the bilayer which occasionally span almost half of the membrane. The leading mechanism of these fluctuations is the orientational and conformational motion of head groups rather than vertical motion of the whole molecules. Water considerably penetrates the head group region of the bilayer but not its hydrocarbon core. The total net excess dipole moment of the interfacial water points toward the aqueous phase, but the water polarization profile is non-monotonic. Both water and head groups significantly contribute to the surface potential across the interface. The calculated sign of the surface potential is in agreement with that from experimental measurements, but the value is markedly overestimated. The structural and electrical properties of the water-bilayer system are discussed in relation to membrane functions, in particular transport of ions and nonelectrolytes across membranes.

  13. Environmental Geometry Aligns the Hippocampal Map during Spatial Reorientation.

    Science.gov (United States)

    Keinath, Alex T; Julian, Joshua B; Epstein, Russell A; Muzzio, Isabel A

    2017-02-06

    When a navigator's internal sense of direction is disrupted, she must rely on external cues to regain her bearings, a process termed spatial reorientation. Extensive research has demonstrated that the geometric shape of the environment exerts powerful control over reorientation behavior, but the neural and cognitive mechanisms underlying this phenomenon are not well understood. Whereas some theories claim that geometry controls behavior through an allocentric mechanism potentially tied to the hippocampus, others postulate that disoriented navigators reach their goals by using an egocentric view-matching strategy. To resolve this debate, we characterized hippocampal representations during reorientation. We first recorded from CA1 cells as disoriented mice foraged in chambers of various shapes. We found that the alignment of the recovered hippocampal map was determined by the geometry of the chamber, but not by nongeometric cues, even when these cues could be used to disambiguate geometric ambiguities. We then recorded hippocampal activity as disoriented mice performed a classical goal-directed spatial memory task in a rectangular chamber. Again, we found that the recovered hippocampal map aligned solely to the chamber geometry. Critically, we also found a strong correspondence between the hippocampal map alignment and the animal's behavior, making it possible to predict the search location of the animal from neural responses on a trial-by-trial basis. Together, these results demonstrate that spatial reorientation involves the alignment of the hippocampal map to local geometry. We hypothesize that geometry may be an especially salient cue for reorientation because it is an inherently stable aspect of the environment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Photodesorption of water ice: a molecular dynamics study

    CERN Document Server

    Andersson, S

    2008-01-01

    Absorption of ultraviolet radiation by water ice coating interstellar grains can lead to dissociation and desorption of the ice molecules. These processes are thought to be important in the gas-grain chemistry in molecular clouds and protoplanetary disks, but very few quantitative studies exist. We compute the photodesorption efficiencies of amorphous water ice and elucidate the mechanisms by which desorption occurs. Classical molecular dynamics calculations were performed for a compact amorphous ice surface at 10 K thought to be representative of interstellar ice. Dissociation and desorption of H2O molecules in the top six monolayers are considered following absorption into the first excited electronic state with photons in the 1300-1500 Angstrom range. The trajectories of the H and OH photofragments are followed until they escape or become trapped in the ice. The probability for H2O desorption per absorbed UV photon is 0.5-1% in the top three monolayers, then decreases to 0.03% in the next two monolayers, a...

  15. Learning Science Through Guided Discovery: Liquid Water and Molecular Networks

    Science.gov (United States)

    Essmann, U.; Glotzer, S.; Gyure, M.; Ostrovsky, B.; Poole, P. H.; Sastry, S.; Schwarzer, S.; Selinger, R.; Shann, M. H.; Shore, L. S.; Stanley, H. E.; Taylor, E. F.; Trunfio, P.

    In every drop of water, down at the scale of atoms and molecules, there is a world that can fascinate anyone—ranging from a non-verbal young science student to an ardent science-phobe. The objective of Learning Science through Guided Discovery: Liquid Water and Molecular Networks is to use advanced technology to provide a window into this submicroscopic world, and thereby allow students to discover by themselves a new world. We have developed a coordinated two-fold approach in which a cycle of hands-on activities, games, and experimentation is followed by a cycle of advanced computer simulations employing the full power of computer animation to "ZOOM" into the depths of his or her newly-discovered world, an interactive experience surpassing that of an OMNIMAX theater. Pairing of laboratory experiments with corresponding simulations challenges students to understand multiple representations of concepts. Answers to student questions, resolution of student misconceptions, and eventual personalized student discoveries are all guided by a clear set of "cues" which we build into the computer display. We thereby provide students with the opportunity to work in a fashion analogous to that in which practicing scientists work—e.g., by using advanced technology to "build up" to general principles from specific experiences. Moreover, the ability to visualize "real-time" dynamic motions allows for student-controlled animated graphic simulations on the molecular scale and interactive guided lessons superior to those afforded by even the most artful of existing texts.

  16. Spatial reorientation experiments for NMR of solids and partially oriented liquids.

    Science.gov (United States)

    Martin, Rachel W; Kelly, John E; Collier, Kelsey A

    2015-11-01

    on how motional reorientation experiments can be applied to current problems in chemistry, molecular biology, and materials science, given the many advances in high-field NMR magnets, fast spinning, and sample preparation realized in recent years.

  17. Modeling water adsorption in carbon micropores: study of water in carbon molecular sieves.

    Science.gov (United States)

    Rutherford, S W

    2006-01-17

    Measurements of water adsorption equilibrium in a carbon molecular sieve are undertaken in order to gain insight into the nature of water adsorption in carbon micropores. The measurements are taken at low concentrations to emphasize the role of oxygen-containing functional groups in the adsorption of water. Comparisons are made with previously published water adsorption data at higher concentrations to provide a data set spanning a wide range of loading. The assembled data set provides an opportunity for comparison of various theories for prediction of water adsorption in carbon micropores. Shortcomings of current theories are outlined, and an analytical theory that is free of these deficiencies is proposed in this investigation. With the consideration of micropore volume and pore size distribution, the experimental data and proposed isotherm model are consistent with previous studies of Takeda carbon molecular sieves. Also investigated is the uptake kinetics of water, which is characterized by a Fickian diffusion mechanism. The Maxwell-Stefan formulation is applied to characterize the dependence of the diffusional mobility upon loading.

  18. Molecular dynamics study of water and water/chlorinated hydrocargon mixtures with polarizable potential models

    Energy Technology Data Exchange (ETDEWEB)

    Dang, L.X. [Pacific Northwest National Lab., Richland, WA (United States)

    1997-12-31

    A series of molecular dynamics simulations were carried out to study water and water/chlorinated hydrocarbon mixtures. The properties of water clusters containing up to six water molecules were evaluated. A prism-like structure is predicted to be lowest in energy for the (H{sub 2}O){sub 6} cluster and a cage-like structure is the second lowest in energy with the energy about 0.2 kcal/mol higher than the prism-like structure. The computed dipole moments of water molecules in clusters indicated that there is a transition from cyclic planar configurations to three dimensional structure networks. The computed thermodynamic properties for the model including the liquid density, the enthalpy of vaporization, as well as the diffusion coefficient at room temperature, are in excellent agreement with experimental values. The computed density profile of the water of liquid/valor interface shows that the interface is not sharp at a microscopic level and has a thickness of 3.2 A at 298 K. The calculated surface tension at room temperature is in reasonably agreement with the corresponding experimental data. The computed average dipole moments of water molecules near the interface are close to their gas phase values. The thermodynamic and structural properties of water/chlorinated hydrocarbon mixtures as a function of mole fraction were evaluated.

  19. Photoanodic Hybrid Semiconductor–Molecular Heterojunction for Solar Water Oxidation

    KAUST Repository

    Joya, Khurram Saleem

    2015-06-29

    Inorganic photo-responsive semiconducting materials have been employed in photoelectrochemical(PEC) water oxidation devicesin pursuit of solar to fuel conversion.[1]The reaction kinetics in semiconductors is limited by poor contact at the interfaces, and charge transfer is impeded by surface defects and the grain boundaries.[2]It has shown that successful surface functionalization of the photo-responsive semiconducting materials with co-catalysts can maximize the charge separation, hole delivery and its effective consumption, and enhances the efficiency and performane of the PEC based water oxidation assembly.[3]We present here unique modification of photoanodic hematite (α-Fe2O3) and bismuth vanadate (BiVO4) with molecular co-catalysts for enhanced photoelectrochemical water oxidation (Figure 1). These hybrid inorganic–organometallic heterojunctions manifest impressive cathodic shifts in the onset potentials, and the photocurrent densities have been enhanced by > 90% at all potentials relative to uncatalyzed α-Fe2O3 or BiVO4, and other catalyst-semiconductor based heterojunctions.This is a novel development in the solar to fuel conversion field, and is crucially important for designing a tandem device where light interfere very little with the catalyst layer on top of semiconducting light absorber.

  20. ORNL Interim Progress Report on Hydride Reorientation CIRFT Tests

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jy-An John [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Yan, Yong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wang, Hong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2016-10-28

    A systematic study of H. B. Robinson (HBR) high burnup spent nuclear fuel (SNF) vibration integrity was performed in Phase I project under simulated transportation environments, using the Cyclic Integrated Reversible-Bending Fatigue Tester (CIRFT) hot cell testing technology developed at Oak Ridge National Laboratory in 2013–14. The data analysis on the as-irradiated HBR SNF rods demonstrated that the load amplitude is the dominant factor that controls the fatigue life of bending rods. However, previous studies have shown that the hydrogen content and hydride morphology has an important effect on zirconium alloy mechanical properties. To address the effect of radial hydrides in SNF rods, in Phase II a test procedure was developed to simulate the effects of elevated temperatures, pressures, and stresses during transfer-drying operations. Pressurized and sealed fuel segments were heated to the target temperature for a preset hold time and slow-cooled at a controlled rate. The procedure was applied to both non-irradiated/prehydrided and high-burnup Zircaloy-4 fueled cladding segments using the Nuclear Regulatory Commission-recommended 400°C maximum temperature limit at various cooling rates. Before testing high-burnup cladding, four out-of-cell tests were conducted to optimize the hydride reorientation (R) test condition with pre-hydride Zircaloy-4 cladding, which has the same geometry as the high burnup fuel samples. Test HR-HBR#1 was conducted at the maximum hoop stress of 145 MPa, at a 400°C maximum temperature and a 5°C/h cooling rate. On the other hand, thermal cycling was performed for tests HR-HBR#2, HR-HBR#3, and HR-HBR#4 to generate more radial hydrides. It is clear that thermal cycling increases the ratio of the radial hydride to circumferential hydrides. The internal pressure also has a significant effect on the radial hydride morphology. This report describes a procedure and experimental results of the four out-of-cell hydride reorientation tests of

  1. Reaction and reorientation of electronically excited H{sub 2}(B)

    Energy Technology Data Exchange (ETDEWEB)

    Pibel, C.D.

    1992-09-01

    The room temperature rate (TR) constants for fluorescence quenching fluorescence of H{sub 2}, HD, and D{sub 2} B {sup 1}{Sigma}{sub u}{sup +} by {sup 4}He were measured as a function of the initially excited rotational and vibrational level of the hydrogen molecule, and the RT rate constants for molecular angular momentum reorientation of H{sub 2}, HD and D{sub 2} (B {sup 1}{Sigma}{sub u}{sup +}. v{prime}=0, J{prime}=1, M{sub J}=0) in collisions with He, Ne, Ar and H{sub 2}(X {sup 1}{Sigma}{sub g}{sup +}) were also measured. Vibrational state dependence of the quenching cross sections fits a vibrationally adiabatic model of the quenching process. From the vibrational state dependence of the quenching cross section, the barrier height for the quenching reaction is found to be 250{plus_minus}40 cm{sup {minus}1}, and the difference in the H-H stretching frequencies between H{sub 2}(B) and the H{sub 2}-He complex at the barrier to reaction is 140{plus_minus}80 cm{sup {minus}1}. The effective cross sections for angular momentum reorientation in collisions of H{sub 2}, HD, D{sub 2} with He and Ne were found to be about 30 {Angstrom}{sup 2} and were nearly the same for each isotope and with He and Ne as collision partners. Cross sections forreorientation of HD and D{sub 2} in collisions with Ar were 10.6{plus_minus}2.0 and 13.9{plus_minus}3.0 {Angstrom}{sup 2}, respectively. Reorientation of D{sub 2}(B) in collisions with room temperature H{sub 2}(X) occurs with a 7.6{plus_minus}3.4 {Angstrom}{sup 2} cross section. Calculated cross sections using semiclassical and quantum close coupled methods give cross sections for reorientation of H{sub 2}(B) and D{sub 2}(B) in collisions with He that agree quantitatively with experiment. Discrepancy between the calculated and experimental cross sections for HD(B)-HE are likely due to rotational relaxation in HD a Turbo PASCAL version of the data-taking program is included.

  2. Reaction and reorientation of electronically excited H[sub 2](B)

    Energy Technology Data Exchange (ETDEWEB)

    Pibel, C.D.

    1992-09-01

    The room temperature rate (TR) constants for fluorescence quenching fluorescence of H[sub 2], HD, and D[sub 2] B [sup 1][Sigma][sub u][sup +] by [sup 4]He were measured as a function of the initially excited rotational and vibrational level of the hydrogen molecule, and the RT rate constants for molecular angular momentum reorientation of H[sub 2], HD and D[sub 2] (B [sup 1][Sigma][sub u][sup +]. v[prime]=0, J[prime]=1, M[sub J]=0) in collisions with He, Ne, Ar and H[sub 2](X [sup 1][Sigma][sub g][sup +]) were also measured. Vibrational state dependence of the quenching cross sections fits a vibrationally adiabatic model of the quenching process. From the vibrational state dependence of the quenching cross section, the barrier height for the quenching reaction is found to be 250[plus minus]40 cm[sup [minus]1], and the difference in the H-H stretching frequencies between H[sub 2](B) and the H[sub 2]-He complex at the barrier to reaction is 140[plus minus]80 cm[sup [minus]1]. The effective cross sections for angular momentum reorientation in collisions of H[sub 2], HD, D[sub 2] with He and Ne were found to be about 30 [Angstrom][sup 2] and were nearly the same for each isotope and with He and Ne as collision partners. Cross sections forreorientation of HD and D[sub 2] in collisions with Ar were 10.6[plus minus]2.0 and 13.9[plus minus]3.0 [Angstrom][sup 2], respectively. Reorientation of D[sub 2](B) in collisions with room temperature H[sub 2](X) occurs with a 7.6[plus minus]3.4 [Angstrom][sup 2] cross section. Calculated cross sections using semiclassical and quantum close coupled methods give cross sections for reorientation of H[sub 2](B) and D[sub 2](B) in collisions with He that agree quantitatively with experiment. Discrepancy between the calculated and experimental cross sections for HD(B)-HE are likely due to rotational relaxation in HD a Turbo PASCAL version of the data-taking program is included.

  3. Plant genetic and molecular responses to water deficit

    Directory of Open Access Journals (Sweden)

    Silvio Salvi

    2011-02-01

    Full Text Available Plant productivity is severely affected by unfavourable environmental conditions (biotic and abiotic stresses. Among others, water deficit is the plant stress condition which mostly limits the quality and the quantity of plant products. Tolerance to water deficit is a polygenic trait strictly dependent on the coordinated expression of a large set of genes coding for proteins directly involved in stress-induced protection/repair mechanisms (dehydrins, chaperonins, enzymes for the synthesis of osmoprotectants and detoxifying compounds, and others as well as genes involved in transducing the stress signal and regulating gene expression (transcription factors, kinases, phosphatases. Recently, research activities in the field evolved from the study of single genes directly involved in cellular stress tolerance (functional genes to the identification and characterization of key regulatory genes involved in stress perception and transduction and able to rapidly and efficiently activate the complex gene network involved in the response to stress. The complexity of the events occurring in response to stress have been recently approached by genomics tools; in fact the analysis of transcriptome, proteome and metabolome of a plant tissue/cell in response to stress already allowed to have a global view of the cellular and molecular events occurring in response to water deficit, by the identification of genes activated and co-regulated by the stress conditions and the characterization of new signalling pathways. Moreover the recent application of forward and reverse genetic approaches, trough mutant collection development, screening and characterization, is giving a tremendous impulse to the identification of gene functions with key role in stress tolerance. The integration of data obtained by high-throughput genomic approaches, by means of powerful informatic tools, is allowing nowadays to rapidly identify of major genes/QTLs involved in stress tolerance

  4. The reorientation of spatial planning systems and policies

    DEFF Research Database (Denmark)

    Galland, Daniel; Enemark, Stig

    2012-01-01

    spatial planning has become reoriented. This is performed through an empirical analysis regarding the transformation of spatial planning in relation with the evolving conception of planning policies at different scales, the changing role of planning in conceiving and handling growth and development......Danish spatial planning has been increasingly subjected to profound reorientations over the past two decades. The comprehensive frame wherein planning policies and practices operated across different levels of administration has become significantly altered. This has been particularly evident after...... radical shifts in terms of the scope of planning policies, the implementation of land-use tasks as well as the performance of the institutional arrangements operating within and beyond the planning system. Based on an in-depth analysis concerned with these changes, the paper endeavours into discussing how...

  5. Reorienting programme budgeting and marginal analysis (PBMA towards disinvestment

    Directory of Open Access Journals (Sweden)

    Mortimer Duncan

    2010-10-01

    Full Text Available Abstract Background Remarkable progress has been made over the past 40 years in developing rational, evidence-based mechanisms for the allocation of health resources. Much of this progress has centred on mechanisms for commissioning new medical devices and pharmaceuticals. The attention of fund-managers and policy-makers is only now turning towards development of mechanisms for decommissioning, disinvesting or redeploying resources from currently funded interventions. While Programme Budgeting and Marginal Analysis would seem well-suited to this purpose, past applications include both successes and failures in achieving disinvestment and resource release. Discussion Drawing on recent successes/failures in achieving disinvestment and resource release via PBMA, this paper identifies four barriers/enablers to disinvestment via PBMA: (i specification of the budget constraint, (ii scope of the programme budget, (iii composition and role of the advisory group, and (iv incentives for/against contributing to a 'shift list' of options for disinvestment and resource release. A number of modifications to the PBMA process are then proposed with the aim of reorienting PBMA towards disinvestment. Summary The reoriented model is differentiated by four features: (i hard budget constraint with budgetary pressure; (ii programme budgets with broad scope but specific investment proposals linked to disinvestment proposals with similar input requirements; (iii advisory/working groups that include equal representation of sectional interests plus additional members with responsibility for advocating in favour of disinvestment, (iv 'shift lists' populated and developed prior to 'wish lists' and investment proposals linked to disinvestment proposals within a relatively narrow budget area. While the argument and evidence presented here suggest that the reoriented model will facilitate disinvestment and resource release, this remains an empirical question. Likewise

  6. Rocket propellant reorientation and fluid management used in space commercialization

    Science.gov (United States)

    Hung, R. J.; Lee, C. C.; Shyu, K. L.

    1990-01-01

    In a spacecraft design, the requirements of settled propellant are different for tank pressurization, engine restart, venting, or propellant transfer. The requirement to settle or to position liquid fuel over the outlet end of the spacecraft propellant tank prior main engine restart possess a microgravity fluid behavior problem. In this paper, the dynamical behavior of liquid propellant, fluid reorientation, and propellant resettling have been carried out.

  7. A model of cytoskeletal reorientation in response to substrate stretching

    Directory of Open Access Journals (Sweden)

    Lazopoulos K.A.

    2008-01-01

    Full Text Available Living adherent cells change their orientation in response to substrate stretching such that their cytoskeletal components reorganize in a new direction. To study this phenomenon, we model the cytoskeleton as a planar system of elastic cables and struts both pinned at their endpoints to a flat flexible substrate. Tensed (pre-strained cables represent acting stress fibers, whereas compression-bearing struts represent microtubules. We assume that in response to uniaxial substrate stretching the model reorients and deforms into a new configuration that minimizes its total potential energy. Using the Maxwell's global stability criterion, we find global minima configurations during static extension and compression of the substrate. Based on these results, we predict reorientation during cyclic stretching of the substrate. We find that in response to cyclic stretching cells either reorient transversely to the direction of stretching, or exhibit multiple configurations symmetrically distributed relative to the direction of stretching. These predictions are consistent with experimental data on living cells from the literature.

  8. Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins.

    Science.gov (United States)

    Prompers, J J; Brüschweiler, R

    2001-08-01

    An approach is presented for the interpretation of heteronuclear NMR spin relaxation data in mobile protein parts in terms of reorientational eigenmode dynamics. The method is based on the covariance matrix of the spatial functions of the nuclear spin interactions that cause relaxation expressed as spherical harmonics of rank 2. The approach was applied to characterize the dynamics of a loop region of ubiquitin. The covariance matrix was determined from a conformational ensemble generated by a 5 ns molecular dynamics simulation. It was found that the time correlation functions of the dominant eigenmodes decay in good approximation with a single correlation time. From the reorientational eigenmodes, their eigenvalues, and correlation times, NMR relaxation data were calculated in accordance with Bloch-Wangsness-Redfield relaxation theory and directly compared with experimental (15)N relaxation parameters. Using a fitting procedure, agreement between calculated and experimental data was improved significantly by adjusting eigenvalues and correlation times of the dominant modes. The presented procedure provides detailed information on correlated reorientational dynamics of flexible parts in globular proteins. The covariance matrix was linked to the covariance matrix of backbone dihedral angle fluctuations, allowing one to study the motional behavior of these degrees of freedom on nano- and subnanosecond time scales.

  9. 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

  10. Molecular concepts of water splitting. Nature's approach

    Energy Technology Data Exchange (ETDEWEB)

    Cox, Nicholas; Lubitz, Wolfgang [Max-Planck-Institut fuer Chemische Energiekonversion, Muelheim an der Ruhr (Germany)

    2013-07-01

    Based on studies of natural systems, much has also been learned concerning the design principles required for biomimetic catalysis of water splitting and hydrogen evolution. In summary, these include use of abundant and inexpensive metals, the effective protection of the active sites in functional environments, repair/replacement of active components in case of damage, and the optimization of reaction rates. Biomimetic chemistry aims to mimic all these features; many labs are working toward this goal by developing new approaches in the design and synthesis of such systems, encompassing not only the catalytic center, but also smart matrices and assembly via self-organization. More stable catalysts that do not require self-repair may be obtained from fully artificial (inorganic) catalytic systems that are totally different from the biological ones and only apply some basic principles learned from nature. Metals other than Mn/Ca, Fe, and Ni could be used (e.g. Co) in new ligand spheres and other matrices. For light harvesting, charge separation/stabilization, and the effective coupling of the oxidizing/reducing equivalents to the redox catalysts, different methods have been proposed - for example, covalently linked molecular donor-acceptor systems, photo-voltaic devices, semiconductor-based systems, and photoactive metal complexes. The aim of all these approaches is to develop catalytic systems that split water with sunlight into hydrogen and oxygen while displaying high efficiency and long-term stability. Such a system - either biological, biomimetic, or bioinspired - has the potential to be used on a large scale to produce 'solar fuels' (e.g. hydrogen or secondary products thereof). (orig.)

  11. Mechanism of dynamic reorientation of cortical microtubules due to mechanical stress

    CERN Document Server

    Muratov, Alexander

    2015-01-01

    Directional growth caused by gravitropism and corresponding bending of plant cells has been explored since 19th century, however, many aspects of mechanisms underlying the perception of gravity at the molecular level are still not well known. Perception of gravity in root and shoot gravitropisms is usually attributed to gravisensitive cells, called statocytes, which exploit sedimentation of macroscopic and heavy organelles, amyloplasts, to sense the direction of gravity. Gravity stimulus is then transduced into distal elongation zone, which is several mm far from statocytes, where it causes stretching. It is suggested that gravity stimulus is conveyed by gradients in auxin flux. We propose a theoretical model that may explain how concentration gradients and/or stretching may indirectly affect the global orientation of cortical microtubules, attached to the cell membrane and induce their dynamic reorientation perpendicular to the gradients. In turn, oriented microtubules arrays direct the growth and orientatio...

  12. Spatial re-orienting of visual attention along the horizontal or the vertical axis.

    Science.gov (United States)

    Macaluso, E; Patria, F

    2007-06-01

    Neuroimaging data indicate functional segregation between voluntary and stimulus-driven control of spatial attention in dorsal and ventral fronto-parietal regions, respectively. While recent evidences demonstrated location-specific attentional effects in dorsal regions, little is known about any location or direction selectivity within the ventral network. Here, we used a spatial cueing paradigm to investigate stimulus-driven spatial re-orienting along different axes (horizontal or vertical). We found that re-orienting of attention activated the ventral attentional network, irrespective of axis-orientation. Statistical comparisons between homologous regions in the two hemispheres revealed significant main effects of attention re-orienting (common activation for the two hemispheres), irrespective of leftward or rightward re-orienting along the horizontal axis, or re-orienting along the vertical axis. We conclude that in healthy volunteers, a bilateral ventral network controls spatial covert re-orienting, and that this system is multidirectional.

  13. Young children reorient by computing layout geometry, not by matching images of the environment.

    Science.gov (United States)

    Lee, Sang Ah; Spelke, Elizabeth S

    2011-02-01

    Disoriented animals from ants to humans reorient in accord with the shape of the surrounding surface layout: a behavioral pattern long taken as evidence for sensitivity to layout geometry. Recent computational models suggest, however, that the reorientation process may not depend on geometrical analyses but instead on the matching of brightness contours in 2D images of the environment. Here we test this suggestion by investigating young children's reorientation in enclosed environments. Children reoriented by extremely subtle geometric properties of the 3D layout: bumps and ridges that protruded only slightly off the floor, producing edges with low contrast. Moreover, children failed to reorient by prominent brightness contours in continuous layouts with no distinctive 3D structure. The findings provide evidence that geometric layout representations support children's reorientation.

  14. Mechanical Characterization of Molecular Assemblies at Oil/Water Interfaces

    Science.gov (United States)

    Yuan, Wa

    The self-assembly of charged molecules in liquid phases and their ability to form functional layers at immiscible interfaces are areas of great interest. However, the implementation of these assemblies is often limited by a lack of understanding of the detailed assembly mechanisms. In order to enhance the performance of interfacial assemblies it is essential to be able to characterize the physical and mechanical properties of assembled layers, as well as develop model systems that will allow us to examine the factors that govern their interaction with the surrounding environment. The key purpose of this thesis is to develop an understanding of some of the important factors influencing interfacial assemblies at immiscible liquid interfaces. The first portion of the work involves mechanical characterization of interfacial layers formed by large amphiphilic molecules. The study of block and gradient copolymers, reveals the effect of copolymer sequence distribution on the ability of these molecules to form interfacial assemblies. Specifically, the unique network structure formed by gradient copolymers at oil/water interfaces enables us to create a robust membrane at the interface by ionic crosslinking. The second part of this thesis explores smaller molecule assemblies at liquid interfaces, including commonly used commercial surfactant (span 80) and nano particles (graphene oxide). Both studies demonstrate an interesting correlation between molecular structure and overall properties of the assembled layers. Factors such as interfacial density, particle sizes and pH can greatly influence the structure of the assembled layers, resulting in interesting phenomena such as spontaneous emulsification, wrinkling and layer collapse. The bulk of the oil/water interface study was performed using axisymmetric drop shape analysis (DSA), which successfully quantifies the mechanical tension in the interfacial layer. This analysis was further extended by a development of a double

  15. Reorientation of the high mobility plane in pentacene-based carbon nanotube enabled vertical field effect transistors.

    Science.gov (United States)

    McCarthy, Mitchell A; Liu, Bo; Jayaraman, Ramesh; Gilbert, Stephen M; Kim, Do Young; So, Franky; Rinzler, Andrew G

    2011-01-25

    The large current densities attained by carbon nanotube enabled vertical field effect transistors using crystalline organic channel materials are somewhat unexpected given the known large anisotropy in the mobility of crystalline organics and their conventional ordering on dielectric surfaces which tends to orient their high mobility axes parallel to the surface. This seeming contradiction is resolved by the finding that the nanotubes induce a molecular ordering that reorients the high mobility axes to favor current flow in a direction perpendicular to the substrate surface.

  16. The Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water with the Fragment Molecular Orbital Method

    Energy Technology Data Exchange (ETDEWEB)

    Pruitt, Spencer R.; Nakata, Hiroya; Nagata, Takeshi; Mayes, Maricris; Alexeev, Yuri; Fletcher, Graham D.; Fedorov, Dmitri G; Kitaura, Kazuo; Gordon, M

    2016-04-12

    The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted Hartree-Fock, second-order Møller-Plesset perturbation, and density functional theories. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores, are also discussed.

  17. A new twist on old ideas: how sitting reorients crawlers.

    Science.gov (United States)

    Soska, Kasey C; Robinson, Scott R; Adolph, Karen E

    2015-03-01

    Traditionally, crawling and sitting are considered distinct motor behaviors with different postures and functions. Ten- to 12-month-old infants were observed in the laboratory or in their homes while being coaxed to crawl continuously over long, straight walkways (Study 1; N = 20) and during spontaneous crawling during free play (Study 2; N = 20). In every context, infants stopped crawling to sit 3-6 times per minute. Transitions from crawling to sitting frequently turned infants' bodies away from the direction of heading; subsequent transitions back to crawling were offset by as much as 180° from the original direction of heading. Apparently, body reorientations result from the biomechanics of transitioning between crawling and sitting. Findings indicate that sustained, linear crawling is likely an epiphenomenon of how gait is studied in standard paradigms. Postural transitions between crawling and sitting are ubiquitous and can represent a functional unit of action. These transitions and the accompanying body reorientations likely have cascading effects for infants' exploration, visual perception, and spatial cognition.

  18. Surface instabilities and reorientation induced by vibration in microgravity conditions

    Science.gov (United States)

    Porter, Jeff; Laverón-Simavilla, Ana; Tinao Perez-Miravete, Ignacio; Fernandez Fraile, Jose Javier; Ezquerro Navarro, Jose Miguel

    2012-07-01

    The behavior of vibrated fluids and, in particular, the surface or interfacial instabilities that commonly arise in these systems have been the subject of continued experimental and theoretical attention since Faraday's seminal experiments in 1831. Both orientation and frequency are critical in determining the response of the fluid to excitation. Low frequencies are associated with sloshing while higher frequencies may generate Faraday waves or cross-waves, depending on whether the axis of vibration is perpendicular or parallel to the interface. In addition, high frequency vibrations are known to produce large scale reorientation of the fluid (vibroequilibria), an effect that becomes especially pronounced in the absence of gravity. We describe the results of investigations conducted at the ESA affiliated Spanish User Support and Operations Centre (E-USOC) on the effect of vibrations on fluid interfaces, particularly the interaction between Faraday waves, which arise in vertically vibrated systems, cross-waves, which are found in horizontally forced systems, and large scale reorientation (vibroequilibria). Ongoing ground experiments utilizing a dual-axis shaker configuration are described, including the effect on pattern formation of varying the two independent forcing frequencies, amplitudes, and phases. Theoretical results, based on the analysis of reduced models, and on numerical simulations, are then described and compared to experiment. Finally, the interest of a corresponding microgravity experiment is discussed and implications for fluid management strategies considered.

  19. Molecular Dynamics Simulation of a Membrane/Water Interface : The Ordering of Water and Its Relation to the Hydration Force

    NARCIS (Netherlands)

    Marrink, Siewert-Jan; Berkowitz, Max; Berendsen, Herman J.C.

    1993-01-01

    In order to obtain a better understanding of the origin of the hydration force, three molecular dynamic simulations of phospholipid/water multilamellar systems were performed. The simulated systems only differed in the amount of interbilayer water, ranging from the minimum to the maximum amount of

  20. Self consistent tight binding molecular dynamics study of Ti02 nanoclusters in water.

    Energy Technology Data Exchange (ETDEWEB)

    Erdin, S.; Lin, Y.; Halley, J. W.; Zapol, P.; Redfern, P.; Curtiss, L.; Northern Illinois Univ.; Univ. of Minnesota

    2007-09-01

    Self-consistent tight binding molecular dynamics studies of TiO{sub 2}2 anatase and rutile nanoclusters in dissociable water are reported. It is found that the structure of the particle expands as a result of interaction between the particle's surface and water. Water molecules dissociate at the nanoparticle surface during simulation.

  1. Study on fluorescence spectra of molecular association of acetic acid-water

    Institute of Scientific and Technical Information of China (English)

    Caiqin Han; Ying Liu; Yang Yang; Xiaowu Ni; Jian Lu; Xiaosen Luo

    2009-01-01

    Fluorescence spectra of acetic acid-water solution excited by ultraviolet (UV) light are studied, and the relationship between fluorescence spectra and molecular association of acetic acid is discussed. The results indicate that when the exciting light wavelength is longer than 246 nm, there are two fluorescence peaks located at 305 and 334 nm, respectively. By measuring the excitation spectra, the optimal wavelengths of the two fluorescence peaks are obtained, which are 258 and 284 nm, respectively. Fluorescence spectra of acetic acid-water solution change with concentrations, which is primarily attributed to changes of molecular association of acetic acid in aqueous solution. Through theoretical analysis, three variations of molecular association have been obtained in acetic acid-water solution, which are the hydrated monomers, the linear dimers, and the water separated dimers. This research can provide references to studies of molecular association of acetic acid-water, especially studies of hydrogen bonds.

  2. Protein Dynamics in Organic Media at Varying Water Activity Studied by Molecular Dynamics Simulation

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; Abildskov, Jens; Peters, Günther H.J.

    2012-01-01

    In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method...... relies on determining the water content of the bulk phase and uses a combination of Kirkwood−Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents...... methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme...

  3. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Zeidler, Anita [University of Bath; Salmon, Phil [University of Bath; Fischer, Henry E [Institut Laue-Langevin (ILL); Neuefeind, Joerg C [ORNL; Simonson, J Michael {Mike} [ORNL; Markland, Thomas [Columbia University

    2012-01-01

    The structure of heavy and light water at 300 K was investigated by using a joint approach in which the method of neutron di raction with oxygen isotope substitution was combined with path integral molecular dynamics simulations. The di raction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) A, were found to be in best agreement with those obtained by using the exible anharmonic TTM3-F water model. Both techniques show a di erence of '0.5% between the O-D and O-H intra-molecular bond lengths and the results support a competing quantum e ects model for water in which its structural and dynamical properties are governed by an o set between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  4. Isotope effects in water as investigated by neutron diffraction and path integral molecular dynamics

    Science.gov (United States)

    Zeidler, Anita; Salmon, Philip S.; Fischer, Henry E.; Neuefeind, Jörg C.; Simonson, J. Mike; Markland, Thomas E.

    2012-07-01

    The structures of heavy and light water at 300 K were investigated by using a joint approach in which the method of neutron diffraction with oxygen isotope substitution was complemented by path integral molecular dynamics simulations. The diffraction results, which give intra-molecular O-D and O-H bond distances of 0.985(5) and 0.990(5) Å, were found to be in best agreement with those obtained by using the flexible anharmonic TTM3-F water model. Both techniques show a difference of ≃ 0.5% between the O-D and O-H intra-molecular bond lengths, and the results support a competing quantum effects model for water in which its structural and dynamical properties are governed by an offset between intra-molecular and inter-molecular quantum contributions. Further consideration of the O-O correlations is needed in order to improve agreement with experiment.

  5. On the reorientation of non-spherical prey particles in a feeding current

    DEFF Research Database (Denmark)

    Visser, Andre; Jonsson, P.R.

    2000-01-01

    Potentially, non-spherical prey can be re-oriented in a flow field and impact on the predator's feeding structures in a non- random manner. Herein, we quantify a process whereby this passive reorientation occurs, and present a model that predicts the orientation of a spheroidal prey as a function...

  6. Molecular Dynamics Simulation of Diffusion Coefficients of Oxygen, Nitrogen and Sodium Chloride in Supercritical Water

    Institute of Scientific and Technical Information of China (English)

    肖吉; 陆九芳; 陈健; 李以圭

    2001-01-01

    Molecular dynamics simulation has been performed to determine the infinite-dilution diffusion coefficients of oxygen and nitrogen, and the diffusion coefficients of NaCl in supercritical water from 703.2- 763.2 K and 30-45 MPa.The results obtained show that the diffusion coefficients in supercritical water increase with temperature, while decreasing with pressure. Nevertheless, the diffusion coefficients in supercritical water are much larger than those in normal water.

  7. Collective Molecular Dynamics of a Floating Water Bridge

    CERN Document Server

    Del Giudice, Emilio; Vitiello, Giuseppe

    2010-01-01

    When a high voltage is applied to pure water filling two beakers kept close to each other, a connection forms spontaneously, giving the impression of a floating water bridge. This phenomenon is of special interest, since it comprises a number of phenomena currently tackled in modern water science. The formation and the main properties of this floating water bridge are analyzed in the conceptual framework of quantum electrodynamics. The necessary conditions for the formation are investigated as well as the time evolution of the dynamics. The predictions are found in agreement with the observations.

  8. Molecular cobalt pentapyridine catalysts for generating hydrogen from water

    Science.gov (United States)

    Long, Jeffrey R; Chang, Christopher J; Sun, Yujie

    2013-11-05

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition including the moiety of the general formula. [(PY5Me.sub.2)CoL].sup.2+, where L can be H.sub.2O, OH.sup.-, a halide, alcohol, ether, amine, and the like. In embodiments of the invention, water, such as tap water or sea water can be subject to low electric potentials, with the result being, among other things, the generation of hydrogen.

  9. Interfacial Properties of an Ionic Liquid by Molecular Dynamics

    NARCIS (Netherlands)

    Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.

    2010-01-01

    We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of

  10. Interfacial Properties of an Ionic Liquid by Molecular Dynamics

    NARCIS (Netherlands)

    Heggen, B.; Zhao, W.; Leroy, F.; Dammers, A.T.; Müller-Plathe, F.

    2010-01-01

    We studied the influence of a liquid-vapor interface on dynamic properties like reorientation and diffusion as well as the surface tension of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) by molecular dynamics simulations. In the interfacial region, reorientation of

  11. Development of EEM based silicon-water and silica-water wall potentials for non-reactive molecular dynamics simulations

    Science.gov (United States)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J. H.; Nedea, Silvia V.; van Steenhoven, Anton A.

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid-solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water-silicon and water-silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon-water contact angle of 129°, a quartz-water contact angle of 0°, and a cristobalite-water contact angle of 40°, which are in reasonable agreement with experimental values.

  12. The reorientation of spatial planning systems and policies

    DEFF Research Database (Denmark)

    Galland, Daniel; Enemark, Stig

    2012-01-01

    Danish spatial planning has been increasingly subjected to profound reorientations over the past two decades. The comprehensive frame wherein planning policies and practices operated across different levels of administration has become significantly altered. This has been particularly evident after...... the implementation of a structural reform that changed the political and administrative structure in the country. Most importantly, the reform abolished the county level, which caused that planning policies, functions and responsibilities were re-scaled to municipal and national levels. This situation brought about...... radical shifts in terms of the scope of planning policies, the implementation of land-use tasks as well as the performance of the institutional arrangements operating within and beyond the planning system. Based on an in-depth analysis concerned with these changes, the paper endeavours into discussing how...

  13. Thin film magnetoelectric composites near spin reorientation transition

    Energy Technology Data Exchange (ETDEWEB)

    Tiercelin, N. [Joint European Laboratory LEMAC: IEMN CNRS 8520-Ecole Centrale de Lille, Villeneuve d' Ascq 59652 (France)], E-mail: Nicolas.Tiercelin@iemn.univ-lille1.fr; Preobrazhensky, V. [Joint European Laboratory LEMAC: IEMN CNRS 8520-Ecole Centrale de Lille, Villeneuve d' Ascq 59652 (France); Joint European Laboratory LEMAC: WRC-GPI-RAS 117454, Vernadsky prosp. 78, Moscow (Russian Federation); Mortet, V. [Institute for Materials Research (IMO), Hasselt University, IMEC vzw, Division IMOMEC, B-3590 Diepenbeek (Belgium); Talbi, A. [Joint European Laboratory LEMAC: IEMN CNRS 8520-Ecole Centrale de Lille, Villeneuve d' Ascq 59652 (France); Soltani, A. [IEMN CNRS 8520, Bd Poincare, Villeneuve d' Ascq 59651 (France); Haenen, K. [Institute for Materials Research (IMO), Hasselt University, IMEC vzw, Division IMOMEC, B-3590 Diepenbeek (Belgium); Pernod, P. [Joint European Laboratory LEMAC: IEMN CNRS 8520-Ecole Centrale de Lille, Villeneuve d' Ascq 59652 (France)

    2009-06-15

    We report the use of a magnetic instability of the spin reorientation transition type to enhance the magnetoelectric sensitivity in magnetostrictive-piezoelectric structures. We present the theoretical study of a clamped beam resonant actuator composed of a piezoelectric element on a passive substrate actuated by a magnetostrictive nanostructured layer. The experiments were made on a polished 150 {mu}m thick 18x3 mm{sup 2} lead zirconate titanate (PZT) plate glued to a 50 {mu}m thick silicon plate and coated with a giant magnetostrictive nanostructured Nx(TbCo{sub 25nm}/FeCo{sub 5nm}) layer. A second set of experiments was done with magnetostrictive layer deposited on PZT plate. Finally, a film/film structure using magnetostrictive and aluminium nitride films on silicon substrate was realized, and showed ME amplitudes reaching 30 V Oe{sup -1} cm{sup -1}. Results agree with analytical theory.

  14. Understanding the reorientations and roles of spatial planning

    DEFF Research Database (Denmark)

    Galland, Daniel

    2012-01-01

    Spatial planning commonly adopts a diversity of functions and logics in contributing to handle growth and development. Being influenced by an array of contextual driving forces that result in specific institutional practices and policy agendas, spatial planning seems to be constantly reoriented...... by analytical concepts drawn from planning theory, state spatial theory and discourse analysis. Based on an in-depth study, the article then attempts to qualify, illustrate and synthesise the diverse roles that spatial planning has taken in Denmark throughout that time frame. The article concludes that spatial...... in terms of its purposes and reasoning. This article sets out to explore the diverse orientations and roles that spatial planning has assumed in Denmark over a 50-year period. In doing so, the article examines the evolution of national planning policy by means of a multi-disciplinary framework comprised...

  15. Reorienting MHD colliding flows: a shock physics mechanism for generating filaments normal to magnetic fields

    Science.gov (United States)

    Fogerty, Erica; Carroll-Nellenback, Jonathan; Frank, Adam; Heitsch, Fabian; Pon, Andy

    2017-09-01

    We present numerical simulations of reorienting oblique shocks that form in the collision layer between magnetized colliding flows. Reorientation aligns post-shock filaments normal to the background magnetic field. We find that reorientation begins with pressure gradients between the collision region and the ambient medium. This drives a lateral expansion of post-shock gas, which reorients the growing filament from the outside-in (i.e. from the flow/ambient boundary, towards the colliding flows axis). The final structures of our simulations resemble polarization observations of filaments in Taurus and Serpens South, as well as the integral-shaped filament in Orion A. Given the ubiquity of colliding flows in the interstellar medium, shock reorientation may be relevant to the formation of filaments normal to magnetic fields.

  16. Reorienting MHD Colliding Flows: A Shock Physics Mechanism for Generating Filaments Normal to Magnetic Fields

    CERN Document Server

    Fogerty, Erica L; Frank, Adam; Heitsch, Fabian; Pon, Andy

    2016-01-01

    We present numerical simulations of reorienting oblique shocks that form in the collision layer between magnetized colliding flows. Reorientation aligns parsec-scale post-shock filaments normal to the background magnetic field. We find that reorientation begins with pressure gradients between the collision region and the ambient medium. This drives a lateral expansion of post-shock gas, which reorients the growing filament from the outside-in (i.e. from the flow-ambient boundary, toward the colliding flows axis). The final structures of our simulations resemble polarization observations of filaments in Taurus and Serpens South, as well as the integral-shaped filament in Orion A. Given the ubiquity of colliding flows in the interstellar medium, shock reorientation may be relevant to the formation of filaments normal to magnetic fields.

  17. Influence of surface polarity on water dynamics at the water/rutile TiO₂(110) interface.

    Science.gov (United States)

    Ohto, Tatsuhiko; Mishra, Ankur; Yoshimune, Seiji; Nakamura, Hisao; Bonn, Mischa; Nagata, Yuki

    2014-06-18

    We report molecular dynamics (MD) simulations of the water/clean rutile TiO2 (110) interface using polarizable and non-surface polarity force field models. The effect of surface polarity on the water dynamics near the TiO2(110) surface is addressed, specifically by calculating the water hydrogen bond and reorientational dynamics. The hydrogen bond lifetime of interfacial water molecules is several times longer than that of bulk water due to the strong water-TiO2 interactions. A comparison of the dynamics simulated with the polarizable and non-surface polarity models shows that, while the hydrogen bond lifetime between the interfacial water and TiO2 surface is insensitive to the surface polarity, the reorientational dynamics around this hydrogen bond axis is significantly influenced by the surface polarity; the surface polarity of the TiO2 increases the water-TiO2 interactions, stabilizing the local structure of the interfacial water molecules and restricting their rotational motion. This reorientation occurs predominantly by rotation around the O-H group hydrogen bonded to the TiO2 surface. Furthermore, we correlate the dynamics of the induced charge on the TiO2 surface with the interfacial water dynamics. Our results show that the timescale of correlations of the atom charges induced by the local electric field in bulk water is influenced by the rotational motion, hydrogen bond rearrangement and translational motion, while the induced charge dynamics of the TiO2 surface is governed primarily by the rotational dynamics of the interfacial water molecules. This study demonstrates that the solid surface polarity has a significant impact on the dynamics of water molecules near TiO2 surfaces.

  18. Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces.

    Science.gov (United States)

    Picaud, Sylvain; Collignon, B; Hoang, Paul N M; Rayez, J C

    2006-04-27

    In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high.

  19. A molecular dynamics study of the role of molecular water on the structure and mechanics of amorphous geopolymer binders

    Science.gov (United States)

    Sadat, Mohammad Rafat; Bringuier, Stefan; Asaduzzaman, Abu; Muralidharan, Krishna; Zhang, Lianyang

    2016-10-01

    In this paper, molecular dynamics simulations are used to study the effect of molecular water and composition (Si/Al ratio) on the structure and mechanical properties of fully polymerized amorphous sodium aluminosilicate geopolymer binders. The X-ray pair distribution function for the simulated geopolymer binder phase showed good agreement with the experimentally determined structure in terms of bond lengths of the various atomic pairs. The elastic constants and ultimate tensile strength of the geopolymer binders were calculated as a function of water content and Si/Al ratio; while increasing the Si/Al ratio from one to three led to an increase in the respective values of the elastic stiffness and tensile strength, for a given Si/Al ratio, increasing the water content decreased the stiffness and strength of the binder phase. An atomic-scale analysis showed a direct correlation between water content and diffusion of alkali ions, resulting in the weakening of the AlO4 tetrahedral structure due to the migration of charge balancing alkali ions away from the tetrahedra, ultimately leading to failure. In the presence of water molecules, the diffusion behavior of alkali cations was found to be particularly anomalous, showing dynamic heterogeneity. This paper, for the first time, proves the efficacy of atomistic simulations for understanding the effect of water in geopolymer binders and can thus serve as a useful design tool for optimizing composition of geopolymers with improved mechanical properties.

  20. Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore

    2010-01-01

    We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations...... of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water....

  1. Separation of Ethanol-Water MixtureUsing Type-A Zeolite Molecular Sieve

    Directory of Open Access Journals (Sweden)

    Juan Camilo Díaz

    2010-01-01

    Full Text Available This paper presents an experimental procedure for the synthesis of a type-A zeolite molecular sieve, usable in the separation of an ethanol-water mixture. The type-A zeolite molecular sieve is obtained from a reactive mixture formed by a source of alumina, a source of silica and a promoter. Characterization of the molecular sieves obtained in this work was undertaken using X-ray diffraction (XRD, adsorption isotherms and scanning electron microscopy (SEM. The results from the characterization procedures showed that part of the product presented a pore diameter suitable for the separation of an ethanol-water mixture.

  2. [Molecular techniques for cyanobacteria detection at Riogrande II and La Fe water reservoirs, Colombia].

    Science.gov (United States)

    Hurtado-Alarcón, Julio César; Polanía-Vorenberg, Jaime

    2014-03-01

    In lentic water bodies as reservoirs occur eutrophication processes, originated mainly from human activities (i.e. agriculture, animal exploitation). This influx of nutrients in aquatic ecosystems could promote blooms of potentially toxic cyanobacteria. The purpose of this work is to detect the presence of cyanobacteria strains in water samples, using molecular techniques to help in preventive management of reservoirs dedicated to water purification. We used two molecular techniques to detect genes implied with the synthesis of hepatotoxic microcystins from potentially toxic cyanobacteria strains, and to evaluate the molecular diversity of cyanobacteria in water samples from two high-mountain reservoirs used for purification of drinking water for the metropolitan area of Medellin, Colombia. Between 2010-2011 collections of 12 water samples were taken and DNA extraction together with PCR and DGGE analyses where carried out. We amplified 22 sequences between 250-300bp of the genes mcyA and mcyE, and these sequences were related with several strains and cyanobacteria genera accessions from NCBI-GenBank databases. Moreover, sequence amplifications of the 16S small ribosomal RNA subunit - 16S rRNA- between 400-800bp were also performed in order to use them for the DGGE technique. The amplification products of DGGE were set in polyacrilamide gel with posterior denaturing electrophoresis, and the scanned images of the gel bands were analysed with the software GelCompar II. For Riogrande II and La Fe reservoirs we found 35 and 30 different DGGE bands, respectively, as a measurement of molecular diversity in these artificial ecosystems. Here, we demonstrated the utility of two molecular techniques for the detection of genes associated with toxicity and molecular diversity of cyanobacteria in reservoirs destined for drinking water in urban centers. We recommend strongly following with periodically molecular biology studies in these ecosystems combined with limnological and

  3. Molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine

    NARCIS (Netherlands)

    Cascales, J.J.L.; Berendsen, H.J.C.; delaTorre, J.G.

    1996-01-01

    A molecular dynamics simulation of water between two charged layers of dipalmitoylphosphatidylserine in its liquid-crystalline state with atomic detail was carried out. From an analysis of a trajectory of 184 ps of length, we obtained information about the dynamics and structure of water between suc

  4. Effect of water polyamorphism on the molecular vibrations of glycerol in its glassy aqueous solutions.

    Science.gov (United States)

    Suzuki, Yoshiharu; Mishima, Osamu

    2016-07-14

    A glassy dilute glycerol-water solution undergoes a mutual polyamorphic transition relating to the transition between high- and low-density amorphous ices of solvent water. The polyamorphic transition behavior depends on the glycerol concentration, indicating that the glycerol affects the water polyamorphism. Here, we used the glassy dilute glycerol-water solution of the solute molar fraction of 0.07 and examined the effect of the polyamorphic change in solvent water on the molecular vibrations of glycerol via Raman spectroscopy. It is found that the molecular vibration of glycerol in high-density liquid like solvent water is different from that in the low-density liquid like solvent water and that the change in the molecular vibration of glycerol is synchronized with the polyamorphic transition of solvent water. The dynamical change of the solute molecule relates to the polyamorphic state of solvent water. This result suggests that the polyamorphic fluctuation of water structure emanated from the presumed liquid-liquid critical point plays an important role for the function of aqueous solution under an ambient condition such as the conformational stability of solute, the functional expression of solute, and so on.

  5. Effect of water polyamorphism on the molecular vibrations of glycerol in its glassy aqueous solutions

    Science.gov (United States)

    Suzuki, Yoshiharu; Mishima, Osamu

    2016-07-01

    A glassy dilute glycerol-water solution undergoes a mutual polyamorphic transition relating to the transition between high- and low-density amorphous ices of solvent water. The polyamorphic transition behavior depends on the glycerol concentration, indicating that the glycerol affects the water polyamorphism. Here, we used the glassy dilute glycerol-water solution of the solute molar fraction of 0.07 and examined the effect of the polyamorphic change in solvent water on the molecular vibrations of glycerol via Raman spectroscopy. It is found that the molecular vibration of glycerol in high-density liquid like solvent water is different from that in the low-density liquid like solvent water and that the change in the molecular vibration of glycerol is synchronized with the polyamorphic transition of solvent water. The dynamical change of the solute molecule relates to the polyamorphic state of solvent water. This result suggests that the polyamorphic fluctuation of water structure emanated from the presumed liquid-liquid critical point plays an important role for the function of aqueous solution under an ambient condition such as the conformational stability of solute, the functional expression of solute, and so on.

  6. Nature of water molecular bridging of the soil organic matter

    Science.gov (United States)

    Kucerik, Jiri; Siewert, Christian; Quilesfogel-Esparza, Claudia; Schaumann, Gabriele E.

    2014-05-01

    Soil is a complex anisotropic and porous system consisting of both inorganic and organic parts, air and water, inhabited and successively transformed by soil biota. Processes of soil formation are influenced by several factors. Among the most important factors belong the inorganic and organic input materials, which are mixed and transformed during soil formation. As a result, specific interactions and interrelationships develop between soil compartments. Although, they are important for soil function and its stability, they are still not well understood. This work deals with water molecule bridges (WaMB), as one of those interactions, and their relation to organic matter functioning. Differential scanning calorimetry (DSC) belongs to the family of methods of thermal analysis, i.e. it uses heat as a probe of the sample's nature. In soil science, the application of this common method is quite rare. In our previous works, DSC revealed a physical stabilization of organic matter segments in soils by development of WaMB. Results suggested the development of those bridges at ambient temperature accompanied with condensation of water into small nanodroplets. In another work, we found out that water, evaporating at the same temperature as WaMB transition occurs, correlates with the activity of soil microorganisms measured via CO2respiration. In this work, the enthalpy and kinetic parameters of water evaporation are studied in two kinds of soil: in clay-rich chernozem soils originating from Siberia and a histosol collected in Germany. We discuss the details of application of DSC, experimental arrangement and advantages and disadvantages of this approach. It is shown that enthalpy of evaporation can be used for understanding the nature of water binding in soils with well-developed aggregates. In contrast, the evaporation of water from histosol, without a typical soil texture, is more complicated because of diffusion processes. Further, the connection between enthalpy of

  7. The effect of stress state on zirconium hydride reorientation

    Science.gov (United States)

    Cinbiz, Mahmut Nedim

    Prior to storage in a dry-cask facility, spent nuclear fuel must undergo a vacuum drying cycle during which the spent fuel rods are heated up to elevated temperatures of ≤ 400°C to remove moisture the canisters within the cask. As temperature increases during heating, some of the hydride particles within the cladding dissolve while the internal gas pressure in fuel rods increases generating multi-axial hoop and axial stresses in the closed-end thin-walled cladding tubes. As cool-down starts, the hydrogen in solid solution precipitates as hydride platelets, and if the multiaxial stresses are sufficiently large, the precipitating hydrides reorient from their initial circumferential orientation to radial orientation. Radial hydrides can severely embrittle the spent nuclear fuel cladding at low temperature in response to hoop stress loading. Because the cladding can experience a range of stress states during the thermo-mechanical treatment induced during vacuum drying, this study has investigated the effect of stress state on the process of hydride reorientation during controlled thermo-mechanical treatments utilizing the combination of in situ X-ray diffraction and novel mechanical testing analyzed by the combination of metallography and finite element analysis. The study used cold worked and stress relieved Zircaloy-4 sheet containing approx. 180 wt. ppm hydrogen as its material basis. The failure behavior of this material containing radial hydrides was also studied over a range of temperatures. Finally, samples from reactor-irradiated cladding tubes were examined by X-ray diffraction using synchrotron radiation. To reveal the stress state effect on hydride reorientation, the critical threshold stress to reorient hydrides was determined by designing novel mechanical test samples which produce a range of stress states from uniaxial to "near-equibiaxial" tension when a load is applied. The threshold stress was determined after thermo-mechanical treatments by

  8. Molecular dynamics modeling of a nanomaterials-water surface interaction

    Science.gov (United States)

    Nejat Pishkenari, Hossein; Keramati, Ramtin; Abdi, Ahmad; Minary-Jolandan, Majid

    2016-04-01

    In this article, we study the formation of nanomeniscus around a nanoneedle using molecular dynamics simulation approach. The results reveal three distinct phases in the time-evolution of meniscus before equilibrium according to the contact angle, meniscus height, and potential energy. In addition, we investigated the correlation between the nanoneedle diameter and nanomeniscus characteristics. The results have applications in various fields such as scanning probe microscopy and rheological measurements.

  9. Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Jaffe, Richard Lawrence; Walther, Jens Honore

    2010-01-01

    e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...... perform extensive simulations of the water- air equilibrium and calibrate the water-air interaction to match the experimental solubility of N2 and O2 in water. For the silica-water system we calibrate the water-silica interaction to match the experimental contact angle of 27º. We subsequently study...

  10. Water repellency in hydrophobic nanocapsules--molecular view on dewetting.

    Science.gov (United States)

    Müller, Achim; Garai, Somenath; Schäffer, Christian; Merca, Alice; Bögge, Hartmut; Al-Karawi, Ahmed Jasim M; Prasad, Thazhe Kootteri

    2014-05-26

    The hydrophobic effect plays a major role in a variety of important phenomena in chemistry, materials science and biology, for instance in protein folding and protein-ligand interactions. Studies--performed within cavities of the unique metal oxide based porous capsules of the type {(pentagon)12(linker)30}≡{(W)W5}12{Mo2(ligand)}30 with different acetate/water ligand ratios--have provided unprecedented results revealing segregation/repellency of the encapsulated "water" from the internal hydrophobic ligand walls of the capsules, while the disordered water molecules, interacting strongly with each other via hydrogen bonding, form in all investigated cases the same type of spherical shell. The present results can be (formally) compared--but only regarding the repellency effect--with the amazing "action" of the (super)hydrophobic Lotus (Nelumbo) leaves, which are self-cleaning based on water repellency resulting in the formation of water droplets picking up dirt. The present results were obtained by constructing deliberately suitable hydrophobic interiors within the mentioned capsules.

  11. Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

    Science.gov (United States)

    Liu, Jun; Li, Peng; Xiao, Hang; Zhang, Yayun; Shi, Xiaoyang; Lü, Xiaomeng; Chen, Xi

    2015-11-01

    Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO) as a flocculant to remove methylene blue (MB) from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion) character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

  12. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  13. Understanding flocculation mechanism of graphene oxide for organic dyes from water: Experimental and molecular dynamics simulation

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2015-11-01

    Full Text Available Flocculation treatment processes play an important role in water and wastewater pretreatment. Here we investigate experimentally and theoretically the possibility of using graphene oxide (GO as a flocculant to remove methylene blue (MB from water. Experimental results show that GO can remove almost all MB from aqueous solutions at its optimal dosages and molecular dynamics simulations indicate that MB cations quickly congregate around GO in water. Furthermore, PIXEL energy contribution analysis reveals that most of the strong interactions between GO and MB are of a van der Waals (London dispersion character. These results offer new insights for shedding light on the molecular mechanism of interaction between GO and organic pollutants.

  14. Interaction of monovalent ions with the water liquid-vapor interface - A molecular dynamics study

    Science.gov (United States)

    Wilson, Michael A.; Pohorille, Andrew

    1991-01-01

    Results of molecular dynamics calculations are presented for a series of ions at infinite dilution near the water liquid-vapor interface. The free energies of ion transfer from the bulk to the interface are discussed, as are the accompanying changes of water structure at the surface and ion mobilities as a function of their proximity to the interface. It is shown that simple dielectric models do not provide an accurate description of ions at the water surface. The results of the study should be useful in the development of better models incorporating the shape and molecular structure of the interface.

  15. Time course and auxin sensitivity of cortical microtubule reorientation in maize roots

    Science.gov (United States)

    Blancaflor, E. B.; Hasenstein, K. H.

    1995-01-01

    The kinetics of MT [microtubule] reorientation in primary roots of Zea mays cv. Merit, were examined 15, 30, 45, and 60 min after horizontal positioning. Confocal microscopy of longitudinal tissue sections showed no change in MT orientation 15 and 30 min after horizontal placement. However, after 45 and 60 min, MTs of the outer 4-5 cortical cell layers along the lower side were reoriented. In order to test whether MT reorientation during graviresponse is caused by an auxin gradient, we examined the organization of MTs in roots that were incubated for 1 h in solutions containing 10(-9) to 10(-6) M IAA. IAA treatment at 10(-8) M or less showed no major or consistent changes but 10(-7) M IAA resulted in MT reorientation in the cortex. The auxin effect does not appear to be acid-induced since benzoic acid (10(-5) M) did not cause MT reorientation. The region closest to the maturation zone was most sensitive to IAA. The data indicate that early stages of gravity induced curvature occur in the absence of MT reorientation but sustained curvature leads to reoriented MTs in the outer cortex. Growth inhibition along the lower side of graviresponding roots appears to result from asymmetric distribution of auxin following gravistimulation.

  16. Molecular detection of oomycetes species in water courses

    Directory of Open Access Journals (Sweden)

    Oszako Tomasz

    2016-12-01

    Full Text Available In Poland, about 20% of forest nurseries use irrigation water coming from natural superficial reservoirs, presumed to be the first source of infection caused by harmful pathogens belonging to the Oomycota class, especially Phytophthora genus and Pythium genus. The forest nursery is the only place where forest managers can react before pathogens leave it with asymptomatic plants or soil attached to their roots. The aim of this research was detection and identification phytopathogens in water samples. In order to recognise genus Phytophthora or Pythium in water collected from 33 places in five different forest districts in Poland, two DNA-based approaches of identification were applied: (i the TaqMan probes, and (ii sequencing of the ITS6/4 region.

  17. Molecular dynamics simulation of the behaviour of water in nano-confined ionic liquid-water mixtures

    Science.gov (United States)

    Docampo-Álvarez, B.; Gómez-González, V.; Montes-Campos, H.; Otero-Mato, J. M.; Méndez-Morales, T.; Cabeza, O.; Gallego, L. J.; Lynden-Bell, R. M.; Ivaništšev, V. B.; Fedorov, M. V.; Varela, L. M.

    2016-11-01

    This work describes the behaviour of water molecules in 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid under nanoconfinement, between graphene sheets. By means of molecular dynamics simulations, the adsorption of water molecules at the graphene surface is studied. A depletion of water molecules in the vicinity of the neutral and negatively charged graphene surfaces, and their adsorption at the positively charged surface are observed in line with the preferential hydration of the ionic liquid anions. The findings are appropriately described using a two-level statistical model. The confinement effect on the structure and dynamics of the mixtures is thoroughly analyzed using the density and the potential of mean force profiles, as well as by the vibrational densities of the states of water molecules near the graphene surface. The orientation of water molecules and the water-induced structural transitions in the layer closest to the graphene surface are also discussed.

  18. Spin reorientation transition in Co/Au multilayers

    Energy Technology Data Exchange (ETDEWEB)

    Quispe-Marcatoma, J., E-mail: jquispem@unmsm.edu.pe [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro 22290-180 (Brazil); Facultad de Ciencias Físicas, Universidad Nacional Mayor de San Marcos, P.O. Box 14-0149, Lima 14, Perú (Peru); Tarazona, H. [Facultad de Ciencias Físicas, Universidad Nacional Mayor de San Marcos, P.O. Box 14-0149, Lima 14, Perú (Peru); Pandey, B. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro 22290-180 (Brazil); Department of Applied Science, Symbiosis Institute of Technology, SIU, Lavale, Pune 412 115, India. (India); Sousa, M.A. de [Instituto de Física, Universidade Federal de Goiás, Goiânia 74001-970 (Brazil); Carvalho, M. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro 22290-180 (Brazil); Landauro, C.V. [Facultad de Ciencias Físicas, Universidad Nacional Mayor de San Marcos, P.O. Box 14-0149, Lima 14, Perú (Peru); Pelegrini, F. [Instituto de Física, Universidade Federal de Goiás, Goiânia 74001-970 (Brazil); Baggio Saitovitch, E. [Centro Brasileiro de Pesquisas Físicas, Rio de Janeiro 22290-180 (Brazil)

    2014-10-01

    We report a study about the spin reorientation transition (SRT) from perpendicular easy axis to in-plane easy axis of magnetization in Co/Au multilayers. A series of multilayers of Si/Au(100 Å)/{[Co(t_C_o)/Au(20 Å)]_2_0}/Au(50 Å) family were studied, with Co layer thickness varying between 6 Å to 30 Å. The thickness of the Au layer was chosen large enough in order to minimize the interlayer exchange coupling between Co layers. In such thick Au-layer samples the magnetic properties are mainly the result of competition between interlayer magnetostatic coupling due to stray field, perpendicular magnetic anisotropy and shape anisotropy. The effective anisotropy constant K{sub eff} and the second order anisotropy K{sub 2} were deduced from the fit of the resonant magnetic field obtained from out of plane dependence Ferromagnetic Resonance (FMR) experiments. To study the SRT, we have plotted the phase diagram between K{sub eff} and K{sub 2}. The results show that SRT occurs through the metastable region with K{sub 2} ≤ −½ K{sub eff}, (K{sub eff} > 0). It is interesting to note that FMR shows the coexistence of two modes with different anisotropy for small Co thickness, while for thick Co layers the modes have the same anisotropy. Moreover, in thick Co layer samples, volume and surface spin wave resonance (SWR) modes were also excited by the microwave field, around the perpendicular FMR geometry, giving a clear evidence of a magnetic coupling between the Co layers. - Highlights: • Co/Au multilayers with varying Co layer thickness are prepared by DC-magnetron sputtering. • The spin reorientation transition (SRT) and flipping of magnetic moment are studied. • Effective anisotropy constant (K) and 2nd order anisotropy constant (K{sub 2}) are calculated. • K Vs K{sub 2} plot showed that SRT occurs through the metastable region with K{sub 2} ≤ −½ K, (K > 0). • Ferromagnetic Resonance spectra showed the coexistence of two resonance modes.

  19. Molecular metal-Oxo catalysts for generating hydrogen from water

    Science.gov (United States)

    Long, Jeffrey R; Chang, Christopher J; Karunadasa, Hemamala I

    2015-02-24

    A composition of matter suitable for the generation of hydrogen from water is described, the positively charged cation of the composition having the general formula [(PY5W.sub.2)MO].sup.2+, wherein PY5W.sub.2 is (NC.sub.5XYZ)(NC.sub.5H.sub.4).sub.4C.sub.2W.sub.2, M is a transition metal, and W, X, Y, and Z can be H, R, a halide, CF.sub.3, or SiR.sub.3, where R can be an alkyl or aryl group. The two accompanying counter anions, in one embodiment, can be selected from the following Cl.sup.-, I.sup.-, PF.sub.6.sup.-, and CF.sub.3SO.sub.3.sup.-. In embodiments of the invention, water, such as tap water containing electrolyte or straight sea water can be subject to an electric potential of between 1.0 V and 1.4 V relative to the standard hydrogen electrode, which at pH 7 corresponds to an overpotential of 0.6 to 1.0 V, with the result being, among other things, the generation of hydrogen with an optimal turnover frequency of ca. 1.5 million mol H.sub.2/mol catalyst per h.

  20. Molecular Dynamics Simulations of Water Droplets On Hydrophilic Silica Surfaces

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

    2009-01-01

    Wetting is essential and ubiquitous in a variety of natural and technological processes. Silicon dioxides-water systems are abundant in nature and play fundamental roles in a vast variety of novel science and engineering activities such as silicon based devices, nanoscale lab on a chip systems an...

  1. Survey of Outer Galaxy Molecular Lines Associated with Water Masers

    Science.gov (United States)

    Mochizuki, N.; Hachisuka, K.; Umemoto, T.

    2009-08-01

    H_2O masers in Young stellar objects (YSOs) in our Galaxy are one of the targets of the VSOP-2 science. The advantage of VSOP-2 observation is the highest angular resolution which can detect a proper motion of H_2O masers for distant objects over short time intervals. To find candidate sources, we observed H2O maser sources in the outer Galaxy using the VLA, and we surveyed the molecular lines toward these sources to understand the environment of YSOs. Higher H2 column densities of YSOs were found for objects with active H2O masers.

  2. Molecular characterization of water buffalo meat by proteomic techniques

    Directory of Open Access Journals (Sweden)

    L. Chianese

    2010-02-01

    Full Text Available Buffalo breeding in Campania is aimed at milk production as the starting material for the production of Mozzarella di Bufala DOP, but it does not take into account the possibility of meat production. Buffalo meat, given its low content in fat and cholesterol, represents a good alternative to bovine meat from the dietetic standpoint. One of most interesting aspects of buffalo meat is its utilization either directly or to prepare other products. Development of these products however requires suitable technological approaches based on molecular characterization, so that product evaluation and development may be carried out on rational basis.

  3. Temperature-driven spin reorientation transition of magnetron sputtered nickel thin film

    Institute of Scientific and Technical Information of China (English)

    Song Xiao-Hui; Zhang Dian-Lin

    2008-01-01

    The temperature-driven spin reorientation transition of magnetron sputtered Ni/Si(111)systems has been studied.The relationship between ac initial susceptibility and temperature of nickel films with different thicknesses shows that the magnetization orientation changes from in-plane to out-of-plane with the increase of temperature.The temperature dependence of magnetoelastic,magneto-crystalline,and magnetostatic anisotropies determines the direction of the reorientation transition.The temperature-driven spin reorientation transition is supported by Hall coefficient measurements which show that its temperature dependence is similar to that of susceptibility.

  4. Stress-induced martensite variant reorientation in magnetic shape memory Ni Mn Ga single crystal studied by neutron diffraction

    Science.gov (United States)

    Molnar, P.; Sittner, P.; Lukas, P.; Hannula, S.-P.; Heczko, O.

    2008-06-01

    Stress-induced martensite variant reorientation in magnetic shape memory Ni-Mn-Ga single crystal was studied in situ by the neutron diffraction technique. Principles of determination of individual tetragonal martensitic variants in shape memory alloys are explained. Using neutron diffraction we show that the macroscopic strain originates solely from the martensite structure reorientation or variant redistribution. Neutron diffraction also reveals that the reorientation of martensite is not fully completed even at a stress value of 25 MPa, which is about 20 times larger than the mean stress needed for reorientation. Only one twinning system is active during the reorientation process.

  5. Molecular Dynamics Simulation of Water Pore Formation in Lipid Bilayer Induced by Shock Waves

    Science.gov (United States)

    Koshiyama, Ken-ichiro; Kodama, Tetsuya; Yano, Takeru; Fujikawa, Shigeo

    2006-05-01

    Water molecule penetration into a bilayer hydrophobic region with a shock wave impulse has been investigated using molecular dynamics simulations [Koshiyama et al., AIP Conference Proceedings, 754, 104-106, (2005)]. Here we report results of simulation of spontaneous water pore formation in a bilayer that contains water molecules in the hydrophobic region in an initial state. The bilayers of 128 DPPC lipid and 3655 water molecules with insertion of 392, 784, and 1176 water molecules in the hydrophobic region are simulated. A water pore is spontaneously formed when 1176 water molecules exist in the hydrophobic region. The water pore diameter is estimated to be c.a. 1.9 nm, which is three times larger than that of 5-fluorouracil (5FU) used in cancer treatment.

  6. Molecular assemblies of perylene bisimide dyes in water.

    Science.gov (United States)

    Görl, Daniel; Zhang, Xin; Würthner, Frank

    2012-06-25

    Perylene bisimides are among the most valuable functional dyes and have numerous potential applications. As a result of their chemical robustness, photostability, and outstanding optical and electronic properties, these dyes have been applied as pigments, fluorescence sensors, and n-semiconductors in organic electronics and photovoltaics. Moreover, the extended quadrupolar π system of this class of dyes has facilitated the construction of numerous supramolecular architectures with fascinating photophysical properties. However, the supramolecular approach to the formation of perylene bisimide aggregates has been restricted mostly to organic media. Pleasingly, considerable progress has been made in the last few years in developing water-soluble perylene bisimides and their application in aqueous media. This Review provides an up-to-date overview on the self-assembly of perylene bisimides through π-π interactions in aqueous media. Synthetic strategies for the preparation of water-soluble perylene bisimides and the influence of water on the π-π stacking of perylene bisimides as well as the resulting applications are discussed.

  7. Solar water splitting in a molecular photoelectrochemical cell.

    Science.gov (United States)

    Alibabaei, Leila; Brennaman, M Kyle; Norris, Michael R; Kalanyan, Berç; Song, Wenjing; Losego, Mark D; Concepcion, Javier J; Binstead, Robert A; Parsons, Gregory N; Meyer, Thomas J

    2013-12-10

    Artificial photosynthesis and the production of solar fuels could be a key element in a future renewable energy economy providing a solution to the energy storage problem in solar energy conversion. We describe a hybrid strategy for solar water splitting based on a dye sensitized photoelectrosynthesis cell. It uses a derivatized, core-shell nanostructured photoanode with the core a high surface area conductive metal oxide film--indium tin oxide or antimony tin oxide--coated with a thin outer shell of TiO2 formed by atomic layer deposition. A "chromophore-catalyst assembly" 1, [(PO3H2)2bpy)2Ru(4-Mebpy-4-bimpy)Rub(tpy)(OH2)](4+), which combines both light absorber and water oxidation catalyst in a single molecule, was attached to the TiO2 shell. Visible photolysis of the resulting core-shell assembly structure with a Pt cathode resulted in water splitting into hydrogen and oxygen with an absorbed photon conversion efficiency of 4.4% at peak photocurrent.

  8. Structure-induced spin reorientation in magnetic nanostructures

    Science.gov (United States)

    Neumann, Alexander; Frauen, Axel; Vollmers, Julian; Meyer, Andreas; Oepen, Hans Peter

    2016-09-01

    We report on structuring-induced changes of the magnetic anisotropy of cylindrical nanostructures which are carved out of thin Pt/Co/Pt films. The magnetic properties of films and structures with a diameter of about 34 nm were investigated via magneto-optic Kerr effect. The magnetic anisotropy is determined for both films and nanostructures for varying Co thicknesses (0.5-7 nm). In general, the nanostructures exhibit larger perpendicular anisotropy than the films. On thickness increase of the Co layer two spin reorientation transitions at about 2.2 and 5 nm are found. At 2.2 nm the nanostructures exhibit the transition from perpendicular to in-plane orientation of magnetization while at 5 nm the reversed transition is found. The variation of the magnetic anisotropy of the Co nanostructures is not solely caused by the change of shape anisotropy. The net change, corrected for the shape, reveals a reduction of strain in the thinnest Co layers while the increase of the anisotropy of the nanostructures at higher Co thicknesses is caused by a transformation of the Co lattice from fcc to hcp.

  9. Resolving coiled shapes reveals new reorientation behaviors in C. elegans

    Science.gov (United States)

    Broekmans, Onno D; Rodgers, Jarlath B; Ryu, William S; Stephens, Greg J

    2016-01-01

    We exploit the reduced space of C. elegans postures to develop a novel tracking algorithm which captures both simple shapes and also self-occluding coils, an important, yet unexplored, component of 2D worm behavior. We apply our algorithm to show that visually complex, coiled sequences are a superposition of two simpler patterns: the body wave dynamics and a head-curvature pulse. We demonstrate the precise Ω-turn dynamics of an escape response and uncover a surprising new dichotomy in spontaneous, large-amplitude coils; deep reorientations occur not only through classical Ω-shaped postures but also through larger postural excitations which we label here as δ-turns. We find that omega and delta turns occur independently, suggesting a distinct triggering mechanism, and are the serpentine analog of a random left-right step. Finally, we show that omega and delta turns occur with approximately equal rates and adapt to food-free conditions on a similar timescale, a simple strategy to avoid navigational bias. DOI: http://dx.doi.org/10.7554/eLife.17227.001 PMID:27644113

  10. 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.

  11. Fourier transform infrared difference spectroscopy for studying the molecular mechanism of photosynthetic water oxidation

    Directory of Open Access Journals (Sweden)

    Hsiu-An eChu

    2013-05-01

    Full Text Available The photosystem II reaction center mediates the light-induced transfer of electrons from water to plastoquinone, with concomitant production of O2. Water oxidation chemistry occurs in the oxygen-evolving complex (OEC, which consists of an inorganic Mn4CaO5 cluster and its surrounding protein matrix. Light-induced Fourier transform infrared (FTIR difference spectroscopy has been successfully used to study the molecular mechanism of photosynthetic water oxidation. This powerful technique has enabled the characterization of the dynamic structural changes in active water molecules, the Mn4CaO5 cluster, and its surrounding protein matrix during the catalytic cycle. This mini-review presents an overview of recent important progress in FTIR studies of the OEC and implications for revealing the molecular mechanism of photosynthetic water oxidation.

  12. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino;

    2002-01-01

    by titration calorimetry. A simple dimer dissociation model was used to derive the information about the heat and the constant of dissociation from asphaltenes of Mexico and Alaska obtained from the calorimetric data. The association enthalpies calculated were found to be in excellent agreement with those......The interaction of two model asphaltene molecules from the Athabasca sand oil with a water molecule in a toluene solution was studied by means of molecular mechanics calculations. It was found that water forms bridging H bonds between the heteroatoms of asphaltenes with a considerable span...... in energies. The stronger H bond found has energies higher than those corresponding to the stacking of the aromatic areas of the same asphaltene molecules. This shows that the water molecule may generate additional mechanisms of aggregation of asphaltenes in toluene solution, as found experimentally. The H...

  13. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino

    2002-01-01

    The interaction of two model asphaltene molecules from the Athabasca sand oil with a water molecule in a toluene solution was studied by means of molecular mechanics calculations. It was found that water forms bridging H bonds between the heteroatoms of asphaltenes with a considerable span...... in energies. The stronger H bond found has energies higher than those corresponding to the stacking of the aromatic areas of the same asphaltene molecules. This shows that the water molecule may generate additional mechanisms of aggregation of asphaltenes in toluene solution, as found experimentally. The H...... bond mechanism depends on the heteroatoms involved, the extension of the aromatic regions, and the steric interference present in the asphaltene molecules. The simulation results have been compared with experimental values of enthalpy of association of two different petroleum asphaltenes obtained...

  14. Molecular-dynamic studies of carbon-water-carbon composite nanotubes.

    Science.gov (United States)

    Zou, Jian; Ji, Baohua; Feng, Xi-Qiao; Gao, Huajian

    2006-11-01

    We recently reported the discovery via molecular-dynamic simulations that single-walled carbon nanotubes (SWCNTs) with different diameters, lengths, and chiralities can coaxially self-assemble into multi-walled carbon nanotubes (MWCNTs) in water via the spontaneous insertion of smaller tubes into larger ones. Here, we extend that study to investigate the various water structures formed between two selected SWCNTs after such coaxial assembly. Depending on the tube geometry, typical water structures, besides the bulk phase, include a one-dimensional (1D) ordered water chain inside the smaller tube, a uniform or nonuniform water shell between the two tubes, and a "boundary layer" of water near the exterior wall of the larger tube. It was found that a concentric water shell consisting of up to three layers of water molecules can form between the two SWCNTs, which leads to a class of carbon-water-carbon composite nanotubes. Analysis of the potential energy of the SWCNT-water system indicated that the composite nanotubes are stabilized by both the tube-tube and tube-water van der Waals interactions. Geometrically confined between the two SWCNTs, water mono- and bilayers are found to be stable, highly condensed, and ordered, although the average number of hydrogen bonds per water molecule is reduced. In contrast, a water trilayer between the two CNTs can be easily disrupted by thermal fluctuations.

  15. Direct Calculation of Ice Homogeneous Nucleation Rate for a Molecular Model of Water

    CERN Document Server

    Haji-Akbari, Amir

    2015-01-01

    Ice formation is ubiquitous in nature, with important consequences in a variety of systems and environments, including biological cells [1], soil [2], aircraft [3], transportation infrastructure [4] and atmospheric clouds [5,6]. However, its intrinsic kinetics and microscopic mechanism are difficult to discern with current experiments. Molecular simulations of ice nucleation are also challenging, and direct rate calculations have only been performed for coarse-grained models of water [7-9]. For the more realistic molecular models, only indirect estimates have been obtained, e.g.~by assuming the validity of classical nucleation theory [10]. Here, we use a path sampling approach to perform the first direct rate calculation of homogeneous nucleation of ice in a molecular model of water. We use TIP4P/Ice [11], the most accurate among the existing molecular models for studying ice polymorphs. By using a novel topological order parameter for distinguishing different polymorphs, we are able to identify a freezing me...

  16. Water on titanium dioxide surface: a revisiting by reactive molecular dynamics simulations.

    Science.gov (United States)

    Huang, Liangliang; Gubbins, Keith E; Li, Licheng; Lu, Xiaohua

    2014-12-16

    The behavior of surface water, especially the adsorption and dissociation characteristics, is a key to understanding and promoting photocatalytic and biomedical applications of titanium dioxide materials. Using molecular dynamics simulations with the ReaxFF force field, we study the interactions between water and five different TiO2 surfaces that are of interest to both experiments and theoretical calculations. The results show that TiO2 surfaces demonstrate different reactivities for water dissociation [rutile (011) > TiO2-B (100) > anatase (001) > rutile (110)], and there is no water dissociation observed on the TiO2-B (001) surface. The simulations also reveal that the water dissociation and the TiO2 surface chemistry change, and the new surface Ti-OH and O-H functional groups affect the orientation of other near-surface water molecules. On the reactive surface, such as the rutile (110) surface, water dissociated and formed new Ti-OH and O-H bonds on the surface. Those functional groups enhanced the hydrogen bond networking with the near-surface water molecules and their configurations. On the nonreactive TiO2-B (001) surface where no molecular or dissociative water adsorption is observed, near-surface water can also form hydrogen bonds with surface oxygen atoms of TiO2, but their distance to the surface is longer than that on the rutile (011) surface.

  17. Effect of Water Concentration on the Molecular Structure of Polyacrylate Gels

    Science.gov (United States)

    Mani, Sriramvignesh; Khabaz, Fardin; Khare, Rajesh

    2015-03-01

    Recent studies have suggested pervaporation to be a promising alternative method for separation of aqueous solution of alcohol compared to distillation based separation processes. The ability to tune the hydrophobic/hydrophilic character makes polyacrylate gels attractive candidate materials for separating water-alcohol mixture by pervaporation. Experimentally, it is observed that the amount of water absorbed in the gel i.e. the degree of swelling of the gel shows a large variation with polymer chemistry. Relatively few studies exist highlighting the effects of water concentration on the membrane separation efficiency which in turn is directly related to the internal molecular structure of the water rich membranes. In this regard, an all-atom molecular dynamics (MD) simulation is employed to study water structure in polyacrylate gels. As a first step, polyacrylate copolymer systems with varying degree of hydrophobicity are prepared using the simulated annealing polymerization technique. Atomistic structures of gels containing different amounts of water are also prepared. Effect of water content on the acrylate-water system microstructure is determined by characterizing the packing of water molecules as well as the hydrogen bonding in these systems. In addition, the change in dynamics of water molecules due to the interactions with polymer is captured by monitoring the auto-correlation function of their dipole vector.

  18. Characterization of water molecular state in in-vivo thick tissues using diffuse optical spectroscopic imaging

    Science.gov (United States)

    Chung, So Hyun

    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. A bound water index (BWI) was developed that quantifies the spectral shift and shape changes observed in tissue water absorption spectra measured by broadband diffuse optical spectroscopic imaging (DOSI). DOSI quantitatively measures light absorption and scattering spectra in cm-deep tissues and therefore reveals bound water spectral shifts. BWI as a water state index was validated by comparing broadband DOSI to MRI and a conductivity cell using bound water phantoms. Non-invasive BWI measurements of malignant and normal tissues in 18 subjects showed a significantly higher fraction of free water in malignant tissues (pbreast cancer patients. The BWI and ADC correlated (R=0.8, p=<0.01) and both parameters decreased with increasing bulk water content in cancer tissues. Although BWI and ADC are positively correlated in vivo, BWI appears to be more sensitive to free water in the extracellular matrix while ADC reflects increased tumor cellularity. The relationship between ADC, BWI and bulk water concentration suggests that both parameters have potential for assessing tumor histopathological grade. My results confirm the importance of water as a critical tissue component that can potentially provide unique insight into the molecular pathophysiology of cancer.

  19. Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations

    CERN Document Server

    Shen, Meng; Lueptow, Richard M

    2016-01-01

    The Angstrom-scale transport characteristics of water and six different solutes, methanol, ethanol, 2-propanol, urea, Na+, and Cl-, were studied for a polyamide reverse osmosis (RO) membrane, FT-30, using non-equilibrium molecular dynamics (NEMD) simulations. Results indicate that water transport increases with an increasing fraction of connected percolated free volume, or water-accessible open space, in the membrane polymer structure. This free volume is enhanced by the dynamic structure of the membrane at the molecular level as it swells when hydrated and vibrates due to molecular collisions allowing a continuous path connecting the opposite membrane surfaces. The tortuous paths available for transport of solutes result in Brownian motion of solute molecules and hopping from pore to pore as they pass through the polymer network structure of the membrane. The transport of alcohol solutes decreases for solutes with larger Van der Waals volume, which corresponds to less available percolated free volume, or sol...

  20. Molecular conformation of linear alkane molecules: From gas phase to bulk water through the interface

    Science.gov (United States)

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

    2017-08-01

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

  1. Molecular dynamics simulation of adsorption of an oil-water-surfactant mixture on calcite surface

    Institute of Scientific and Technical Information of China (English)

    Lu Guiwu; Zhang Xuefen; Shao Changjin; Yang Hong

    2009-01-01

    An interface super molecular structure model for oil-water-surfactant mixture and calcite was established. By using a molecular dynamics method, the effects of rhamnolipid, sodium dodecyl benzene sulfonate and sodium hexadecyl sulfonate on the interface adsorption behavior of oil molecules were investigated. It was found that these three surfactants could reduce oil-calcite interface binding energy, and play a role of oil-displacing agent.

  2. Spin reorientation transition process in single crystal NdFeO3

    Science.gov (United States)

    Song, Gaibei; Jiang, Junjie; Kang, Baojuan; Zhang, Jincang; Cheng, Zhenxiang; Ma, Guohong; Cao, Shixun

    2015-06-01

    The spin reorientation transition in single crystal NdFeO3 is studied using AC magnetic susceptibility, hysteresis loops, and polarized terahertz (THz) time domain spectroscopy measurements. Different frequency dependence behaviors of AC susceptibility reflect that the dynamic response of magnetization inside the spin reorientation region differs from the phase outside the transition region. The magnetization hysteresis loops at different temperatures reveal that domains formed during the spin reorientation process, which coincides with the abrupt increase of AC magnetic susceptibility during the transition. In addition, temperature dependent THz wave excitation of quasi-antiferromagnetic mode indicates the process of spin reorientation as a continuous rotation of Fe3+ spins rather than a mixed phase of Γ4 and Γ2.

  3. Switching of bacterial adhesion to a glycosylated surface by reversible reorientation of the carbohydrate ligand

    DEFF Research Database (Denmark)

    Weber, Theresa; Chrasekaran, Vijayan; Stamer, Insa

    2014-01-01

    The surface recognition in many biological systems is guided by the interaction of carbohydrate-specific proteins (lectins) with carbohydrate epitopes (ligands) located within the unordered glycoconjugate layer (glycocalyx) of cells. Thus, for recognition, the respective ligand has to reorient...

  4. Molecular dynamics studies of pathways of water movement in cyanobacterial photosystem II

    Energy Technology Data Exchange (ETDEWEB)

    Gabdulkhakov, A. G., E-mail: azat@vega.protres.ru; Kljashtorny, V. G.; Dontsova, M. V. [Russian Academy of Sciences, Institute of Protein Research (Russian Federation)

    2015-01-15

    Photosystem II (PSII) catalyzes the light-induced generation of oxygen from water. The oxygen-evolving complex is buried deep in the protein on the lumenal side of PSII, and water molecules need to pass through protein subunits to reach the active site—the manganese cluster. Previous studies on the elucidation of water channels in PSII were based on an analysis of the cavities in the static PSII structure determined by X-ray diffraction. In the present study, we perform molecular dynamics simulations of the water movement in the transport system of PSII.

  5. Evaluation and molecular characterization of human adenovirus in drinking water supplies: viral integrity and viability assays.

    Science.gov (United States)

    Fongaro, Gislaine; Nascimento, Mariana A do; Rigotto, Caroline; Ritterbusch, Giseli; da Silva, Alessandra D' A; Esteves, Paulo A; Barardi, Célia R M

    2013-05-28

    Human adenoviruses (HAdVs) are the second-leading cause of childhood gastroenteritis worldwide. This virus is commonly found in environmental waters and is very resistant to water disinfection and environmental stressors, especially UV light inactivation. Molecular techniques, such as PCR-based methods (Polymerase Chain Reaction), are commonly used to detect and identify viral contamination in water, although PCR alone does not allow the discrimination between infectious and non-infectious viral particles. A combination of cell culture and PCR has allowed detection of infectious viruses that grow slowly or fail to produce cytopathic effects (CPE) in cell culture. This study aimed to assess the integrity and viability of human adenovirus (HAdV) in environmental water and evaluate circulating strains by molecular characterization in three sites of the water supply in Florianópolis, Santa Catarina Island, Brazil: Peri Lagoon water, spring source water, and water from the public water supply system. Water samples were collected, concentrated and HAdV quantified by real-time PCR. Viral integrity was evaluated by enzymatic assay (DNase I) and infectivity by plaque assay (PA) and integrated cell culture using transcribed mRNA (ICC-RT-qPCR). Samples containing particles of infectious HAdV were selected for sequencing and molecular characterization. The analyzed sites contained 83, 66 and 58% undamaged HAdV particles (defined as those in which the genetic material is protected by the viral capsid) at Peri Lagoon, spring source water and public supply system water, respectively. Of these, 66% of the particles (by PA) and 75% (by ICC-RT-qPCR) HAdV were shown to be infectious, due to being undamaged in Peri Lagoon, 33% (by PA) and 58% (by ICC-RT-qPCR) in spring source water and 8% (by PA) and 25% (by ICC-RT-qPCR) in the public water supply system. ICC-RT-qPCR, a very sensitive and rapid technique, was able to detect as low as 1 × 102 HAdV genome copies per milliliter of

  6. Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water

    Institute of Scientific and Technical Information of China (English)

    CHENG Wei; ZHANG Feng-Shou; ZHANG Bo-Yang; ZHOU Hong-Yu

    2007-01-01

    Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion ale simulated by a molecular dynamics model.The roles of Coulomb interaction effect and water effect in the relaxation process are discussed.It is found that the relaxations before and after charge transfer are similar.Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations.An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.

  7. Vibrational frequency fluctuations of ionic vibrational probe in water: Theoretical study with molecular dynamics simulation

    Science.gov (United States)

    Okuda, Masaki; Higashi, Masahiro; Ohta, Kaoru; Saito, Shinji; Tominaga, Keisuke

    2017-09-01

    The vibrational dynamics of SCN- in H2O are theoretically investigated by molecular dynamics simulations. Based on the vibrational solvatochromism theory, we calculate the frequency-frequency time correlation function of the SCN anti-symmetric stretching mode, which is characterized by time constants of 0.13 and 1.41 ps. We find that the frequency fluctuation is almost determined by the electrostatic interaction from the water molecules in the first-hydration shell. The collective dynamics of the water molecules in the first-hydration shell is found to be similar to that of bulk water, though the hydrogen bond between the ion and water molecule is very strong.

  8. On the cluster composition of supercritical water combining molecular modeling and vibrational spectroscopic data.

    Science.gov (United States)

    Tassaing, T; Garrain, P A; Bégué, D; Baraille, I

    2010-07-21

    The present study is aimed at a detailed analysis of supercritical water structure based on the combination of experimental vibrational spectra as well as molecular modeling calculations of isolated water clusters. We propose an equilibrium cluster composition model where supercritical water is considered as an ideal mixture of small water clusters (n=1-3) at the chemical equilibrium and the vibrational spectra are expected to result from the superposition of the spectra of the individual clusters, Thus, it was possible to extract from the decomposition of the midinfrared spectra the evolution of the partition of clusters in supercritical water as a function of density. The cluster composition predicted by this model was found to be quantitatively consistent with the near infrared and Raman spectra of supercritical water analyzed using the same procedure. We emphasize that such methodology could be applied to determine the portion of cluster in water in a wider thermodynamic range as well as in more complex aqueous supercritical solutions.

  9. Anisotropy of the water-carbon interaction: molecular simulations of water in low-diameter carbon nanotubes.

    Science.gov (United States)

    Pérez-Hernández, Guillermo; Schmidt, Burkhard

    2013-04-14

    Effective Lennard-Jones models for the water-carbon interaction are derived from existing high-level ab initio calculations of water adsorbed on graphene models. The resulting potential energy well (εCO + 2εCH ≈ 1 kJ mol(-1)) is deeper than most of the previously used values in the literature on water in carbon nanotubes (CNTs). Moreover, a substantial anisotropy of the water-carbon interaction (εCO ≈ 2εCH) is obtained, which is neglected in most of the literature. We systematically investigate the effect of this anisotropy on structure and dynamics of TIP5P water confined in narrow, single-walled CNTs by means of molecular dynamics simulations for T = 300 K. While for isotropic models water usually forms one-dimensional, ordered chains inside (6,6) CNTs, we find frequent chain ruptures in simulations with medium to strongly anisotropic potentials. Here, the water molecules tend to form denser clusters displaying a liquid-like behaviour, allowing for self-diffusion along the CNT axis, in contrast to all previous simulations employing spherical (εCH = 0) interaction models. For (7,7) CNTs we observe structures close to trigonal, helical ice nanotubes which exhibit a non-monotonous dependence on the anisotropy of the water-carbon interaction. Both for vanishing and for large values of εCH we find increased fluctuations leading to a more liquid-like behaviour, with enhanced axial diffusion. In contrast, structure and dynamics of water inside (8,8) CNTs are found to be almost independent of the anisotropy of the underlying potential, which is attributed to the higher stability of the non-helical fivefold water prisms. We predict this situation to also prevail for larger CNTs, as the influence of the water-water interaction dominates over that of the water-carbon interaction.

  10. What is the effective molecular polarizability of water in condensed phases?

    Science.gov (United States)

    Ge, Xiaochuan; Lu, Deyu

    Electronic polarization plays a crucial role in determining the structural and dynamical properties of water with different boundary conditions. Although it is well known that the molecular polarization in condensed phases behaves substantially differently from that in the vacuum due to the intermolecular interaction, these environmental effects have not been fully understood from first principles methods. As a result, how to rigorously define and calculate the effective molecular polarizability of a water molecule in different chemical environments remains an open question. The answer to this question not only improves our fundamental understanding of water, but also has immediate practical impact on computational modeling of water, e.g, through an accurate polarizable force field model. A main challenge to this puzzle arises from the intrinsic non-local nature of the electronic susceptibility.Recently we developed an ab initio local dielectric response theory [arxiv 1508.03563] that partitions dielectric response in real space based on a Wannier representation. In this work we apply this method to compute the effective molecular polarizability of water in the condensed phase, and discuss how the effective molecular polarizability evolves from gas phase to the condensed phase. This research used resources of the Center for Functional Nanomaterials, which is a U.S. DOE Office of Science Facility, at Brookhaven National Laboratory under Contract No. DE-SC0012704.

  11. Elucidating water dynamics in MgCl2 hydrates from molecular dynamics simulation

    Science.gov (United States)

    Huinink, Hendrik Pieter; Zahn, Dirk

    2017-07-01

    The water mobility in single crystals of MgCl2 hydrates has been investigated with molecular dynamics. Standard force fields have been benchmarked for molecular dynamics simulations of MgCl2 hydrates. To provide a reliable molecular mechanics model, force fields are selected on their ability to reproduce the structure of MgCl2·6H2O at 300 K. The selected force fields are then tested on their ability to also reproduce the structures of the different hydrates (n = 12, 8, 6, 4, 2, 1) and available thermodynamic data. For the currently best force-field available, constant-temperature, constant-pressure molecular dynamics simulations are preformed to elucidate the mechanisms of hydrate water mobility in perfect single crystals of the tetra- and hexahydrate. Long range water diffusion was not observed; each water molecule remained in the coordination sphere of its original Mg2+ host. However, collective ring-like motions of four water molecules at once within the coordination shell of a Magnesium ion were observed.

  12. Dynamics of ethanol and water mixtures observed in a self-adjusting molecularly thin slit pore.

    Science.gov (United States)

    Severin, N; Sokolov, I M; Rabe, J P

    2014-04-01

    The structure of multicomponent fluids in confined geometries is a key to understanding their properties. However, it remains an experimental challenge to gain molecular-scale resolution information on this structure. Here we show that mono- and multilayers of graphene, conforming to heterogeneous monolayers of molecules in a flexible slit pore between a mica surface and the graphene layers, allow for mapping the phase separation of water and ethanol within such a slit pore. Employing scanning force microscopy, we readily distinguish clusters of ethanol and water molecules due their different sizes, and we show that the phase separated water-ethanol structures become coarser under thicker graphenes. Moreover, we obtain a lower bound for the two-dimensional diffusion coefficient of ethanol in water of D ≥ 2 × 10(-14) m(2) s(-1). Thus, the molecularly thin slit pore provides a powerful tool to control and to investigate mixed fluids in self-adjusting nanopores.

  13. Isobaric first-principles molecular dynamics of liquid water with nonlocal van der Waals interactions

    CERN Document Server

    Miceli, Giacomo; Pasquarello, Alfredo

    2016-01-01

    We investigate the structural properties of liquid water at near ambient conditions using first-principles molecular dynamics simulations based on a semilocal density functional augmented with nonlocal van der Waals interactions. The adopted scheme offers the advantage of simulating liquid water at essentially the same computational cost of standard semilocal functionals. Applied to the water dimer and to ice Ih, we find that the hydrogen-bond energy is only slightly enhanced compared to a standard semilocal functional. We simulate liquid water through molecular dynamics in the NpH statistical ensemble allowing for fluctuations of the system density. The structure of the liquid departs from that found with a semilocal functional leading to more compact structural arrangements. This indicates that the directionality of the hydrogen-bond interaction has a diminished role as compared to the overall attractions, as expected when dispersion interactions are accounted for. This is substantiated through a detailed a...

  14. Low temperature spin reorientation in dysprosium iron garnet

    Energy Technology Data Exchange (ETDEWEB)

    Lahoubi, M; Younsi, W; Soltani, M L [Department of Physics, Badji-Mokhtar University, BP-12 Annaba, 23000 (Algeria); Voiron, J; Schmitt, D, E-mail: mlahoubi@gmail.co [Louis Neel Laboratory, CNRS-UJF, BP-166, 38042 Grenoble Cedex 9 (France)

    2009-03-01

    The spin reorientation (SR) phase transition in dysprosium iron garnet (Dy{sub 3}Fe{sub 5}O{sub 12} or DyIG) have been studied by specific heat C{sub p}(T) and high field magnetisation measurements M{sub T}(H) and M{sub H}(T) on single crystals at low temperature. A first order SR is observed with a sharp jump at T{sub SR} = 14.5+-0.5 K in the C{sub p}(T) curve which corresponds to a spontaneous change from the high temperature (HT) easy direction (111) to an (uuw) angular low temperature (LT) phases. Above T{sub SR}, the magnetic structure is described by the irreducible representation (IR) A{sub 2g} of the rhombohedral space group R 3 c. Below T{sub SR}, the magnetic structure changes in the monoclinic the space group C2/c with the IR A{sub g}. When the field H is kept aligned along the hard symmetry directions (100) and (110), we obtain respectively the variation of the angular positions theta(T) and theta'(T) from the total spontaneous magnetisation down to 1.5 K (theta = 39.23 deg. and theta' = 30.14 deg.) and the results are in good agreement with the previous observations in low fields. When the sample is allowed to rotate freely on itself, the critical field H{sub c}(T) between the HT(111) and the LT(uuw) angular phases permits us to precise the transition line up to 15 T and 40 K between the so called canted field induced (FI) and the associated collinear magnetic phases. The experimental magnetic phase diagram (MPD) is precisely determined in the (H{sub c}-T) plane and the domains of the existence and the stability of the two magnetic phases are specified.

  15. Molecular dynamics study of water molecule diffusion in oil-paper insulation materials

    Science.gov (United States)

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

    2011-03-01

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

  16. Water self-diffusivity confined in graphene nanogap using molecular dynamics simulations

    Science.gov (United States)

    Moulod, M.; Hwang, G.

    2016-11-01

    Fundamental understanding of water confined in graphene is crucial to optimally design and operate sustainable energy, water desalination, and bio-medical systems. However, the current understanding predominantly remains in the static properties near the graphene surfaces. In this paper, a key water transport property, i.e., self-diffusivity, is examined under confinement by various graphene nanogap sizes (Lz = 0.7-4.17 nm), using molecular dynamics simulations with various graphene-water interatomic potentials (Simple Point Charge (SPC/E) and TIP3P water models). It is found that the water self-diffusivity nearly linearly decreases as the graphene-water interatomic potential energy increases at a given nanogap size. It also decreases as the graphene nanogap size decreases down to Lz = 1.34 nm; however, it shows the peak water self-diffusivity at Lz = 0.8 nm and then continues to decrease. The peak water self-diffusivity is related to the significant change of the overlapping surface force, and associated, nonlinear local water density distribution. The in-plane water self-diffusivity is higher up to nearly an order of magnitude than that of the out-of-plane due to the geometrical confinement effect by the graphene nanogap. The obtained results provide a roadmap to fundamentally understand the water transport properties in the graphene geometries and surface interactions.

  17. Molecular forensic profiling of Cryptosporidium species and genotypes in raw water.

    Science.gov (United States)

    Ruecker, Norma J; Bounsombath, Niravanh; Wallis, Peter; Ong, Corinne S L; Isaac-Renton, Judith L; Neumann, Norman F

    2005-12-01

    The emerging concept of host specificity of Cryptosporidium spp. was exploited to characterize sources of fecal contamination in a watershed. A method of molecular forensic profiling of Cryptosporidium oocysts on microscope slides prepared from raw water samples processed by U.S. Environmental Protection Agency Method 1623 was developed. The method was based on a repetitive nested PCR-restriction fragment length polymorphism-DNA sequencing approach that permitted the resolution of multiple species/genotypes of Cryptosporidium in a single water sample.

  18. Molecular Dynamical Simulation of Water/Ice Phase Transitions within Carbon Nanotubes under Various Pressures

    Institute of Scientific and Technical Information of China (English)

    YIN Bing; DONG Shun-Le

    2009-01-01

    A molecular dynamics simulation is performed for water confined within carbon nanotubes with diameters 11.00 (A) and 12.38 (A).Under pressures from 0.1 MPa to 500MPa the simulations are carried out by cooling from 300K to 240 K.Water molecules tend to transform from disordered to ordered with different configurations (square,pentagonal,hexagonal and hexagonal plus a chain).It is concluded that denser structures may appear under high pressures.

  19. Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study

    OpenAIRE

    Guàrdia Manuel, Elvira; Skarmoutsos, Ioannis; Masia, Marco

    2015-01-01

    The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the ...

  20. Molecular Dynamics Simulations of the Solubility of H2S and CO2 in Water

    OpenAIRE

    Roberto López Rendón; José Alejandre

    2008-01-01

    We have performed molecular dynamics simulations at constant temperature and pressure to calculate the solubility of carbon dioxide (CO2) and hydrogen sulfide (H2S) in water. The solubility of gases in water is important in several technological problems, in particular in the petroleum industry. The calculated liquid densities as function of temperature are in good agreement with experimental data. The results at the liquid-vapor equilibrium show that at low temperatures there is an important...

  1. Bioinspired molecular adhesive for water-resistant oxygen indicator films.

    Science.gov (United States)

    Vu, Chau Hai Thai; Won, Keehoon

    2013-01-01

    Mussels can attach themselves to nearly all types of hard surfaces in wet environments. Such attractive adhesive ability of mussels is believed to rely on the amino acid composition of proteins found near the plaque-substrate interface. Dopamine (DA) is identified as a simplified mimic of mussel proteins, which are rich in 3,4-dihydroxy-L-phenylalanine and lysine, because it contains both catechol and amine functional groups. In this work, we have first applied this bioinspired adhesive to tackle a dye leaching problem of colorimetric oxygen indicator films, which are widely used to ensure the absence of oxygen inside the package of oxygen-sensitive materials. Simple immersion of packaging films into a DA solution resulted in poly(DA) deposition, decreasing the water contact angle of the films from 105° to 65°. The poly(DA) coating could reduce the thionine leakage of the UV-activated oxygen indicator film. The effects of poly(DA) coating were found to be dependent on the DA solution pH, the coating time, and the DA concentration. The film resistant to dye leaching lost its dye color by 5 min UVB irradiation and regained the color in the presence of oxygen, demonstrating that it functioned successfully as UV-activated oxygen indicators.

  2. A Molecular Thermodynamic Model for Interfacial Tension in Surfactant-Oil-Water System

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    An interfacial equation of state based on perturbation theory for surfactant-oil-water system has been developed. By combining the interfacial equation of state with Boudh-Hir and Mansoori's model, a molecular ther- modynamic model has been proposed. The interfacial tension of surfactant-oil-water systems can be calculated from the surface tensions of pure oil and water by this model. The inteffacial tension data for sodium dodecyl sulphate- heptane-water system, polyoxyethylene n-octylphenol-heptane-water system and hexadecyl trimethyl ammonium bromide-heptane-water system have been correlated. By using the adjustable parameters obtained, the interfacial tensions of these systems at other temperatures have been predicted. Both the correlated and the predicted values are satisfactory.

  3. Molecular Dynamics Simulations of Aqueous and Confined Systems Relevant to the Supercritical Water Cooled Nuclear Reactor

    Science.gov (United States)

    Kallikragas, Dimitrios Theofanis

    Supercritical water (SCW) is the intended heat transfer fluid and potential neutron moderator in the proposed GEN-IV Supercritical Water Cooled Reactor (SCWR). The oxidative environment poses challenges in choosing appropriate design materials, and the behaviour of SCW within crevices of the passivation layer is needed for developing a corrosion control strategy to minimize corrosion. Molecular Dynamics simulations have been employed to obtain diffusion coefficients, coordination number and surface density characteristics, of water and chloride in nanometer-spaced iron hydroxide surfaces. Diffusion models for hydrazine are evaluated along with hydration data. Results demonstrate that water is more likely to accumulate on the surface at low density conditions. The effect of confinement on the water structure diminishes as the gap size increases. The diffusion coefficient of chloride decreases with larger surface spacing. Clustering of water at the surface implies that the SCWR will be most susceptible to pitting corrosion and stress corrosion cracking.

  4. Hydrogen bond dynamics in liquid water: Ab initio molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Cheolhee; Kim, Eunae [College of Pharmacy, Chosun University, Gwangju (Korea, Republic of); Yeom, Min Sun [Korea Institute of Science and Technology Information, Daejeon (Korea, Republic of)

    2016-01-15

    The effect of intermolecular interaction on the distribution of the harmonic vibrational frequencies of water molecules was investigated through ab initio molecular dynamics simulations based on the Born-Oppenheimer approach. For single water, the effect of the dynamics of the oxygen atom in single water and the simulation time step on the frequency distribution were examined. The distributions of the OH stretching and HOH bending vibrational frequencies of liquid water were compared to those of single water. The probability distributions of the change in OH bond length and the lifetime of the dangling OH bond were also obtained. The distribution of the frequencies was strongly affected by the long lifetime of the dangling OH bond, resulting in the formation of hydrogen bonds between water molecules.

  5. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-12-27

    The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2 alpha 7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these stimulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.

  6. Molecular details of ovalbumin-pectin complexes at the air/water interface: A spectroscopic study

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, A. van; Jongh, H.H.J. de

    2007-01-01

    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  7. Molecular details of ovalbumin-pectin complexes at the air/water interface: a spectroscopic study.

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, van A.; Jongh, de H.H.J.

    2007-01-01

    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a

  8. DFT molecular simulations of solvated glucose dimers: explicit vs. implicit water

    Science.gov (United States)

    The behavior of Glucose dimers in solution is investigated at the DFT level of theory via optimization and constant energy DFT molecular dynamics. The effect of the solvent on the dimer is treated two different ways: using the implicit solvation method COSMO alone to treat the bulk water behavior an...

  9. Molecular details of ovalbumin-pectin complexes at the air/water interface: A spectroscopic study

    NARCIS (Netherlands)

    Kudryashova, E.V.; Visser, A.J.W.G.; Hoek, A. van; Jongh, H.H.J. de

    2007-01-01

    To stabilize air-water interfaces, as in foams, the adsorption of surface-active components is a prerequisite. An approach to controlling the surface activity of proteins is noncovalent complex formation with a polyelectrolyte in the bulk phase. The molecular properties of egg white ovalbumin in a c

  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. Chemical characterization of high molecular weight dissolved organic matter in fresh and marine waters

    Science.gov (United States)

    Repeta, Daniel J.; Quan, Tracy M.; Aluwihare, Lihini I.; Accardi, AmyMarie

    2002-03-01

    The high molecular weight fraction of dissolved organic matter in a suite of lakes, rivers, seawater, and marine sediment interstitial water samples was collected by ultrafiltration and characterized by molecular level and spectroscopic techniques. Proton nuclear magnetic resonance spectra of all samples show a high degree of similarity, with major contributions from carbohydrates, bound acetate, and lipids. Molecular level analyses of neutral sugars show seven monosaccharides, rhamnose, fucose, arabinose, xylose, mannose, glucose, and galactose, to be abundant, and to occur in comparable relative amounts in each sample. Previous studies have emphasized the distinctive composition of dissolved humic substances in fresh and marine waters, and have attributed these differences to sources and transformations of organic matter unique to each environment. In contrast we find a large fraction of freshwater high molecular weight dissolved organic matter (HMWDOM; > 1kD) to be indistinguishable from marine HMWDOM in bulk and molecular-level chemical properties. Aquatic HMWDOM is similar in chemical composition to biologically derived acylated heteropolysaccharides isolated from marine algal cultures, suggesting a biological source for some fraction of persistent HMWDOM. High molecular weight DOC contributes 51 ± 26% of the total DOC, and monosaccharides 18 ± 8% of the total HMWDOC in our freshwater samples. These contributions are on average higher and more variable, but not significantly different than for surface seawater (30% and 16% respectively). Biogeochemical processes that produce, accumulate, and recycle DOM may therefore share important similarities and be broadly comparable across a range of environmental settings.

  12. Molecular characterization of low molecular weight dissolved organic matter in water reclamation processes using Orbitrap mass spectrometry.

    Science.gov (United States)

    Phungsai, Phanwatt; Kurisu, Futoshi; Kasuga, Ikuro; Furumai, Hiroaki

    2016-09-01

    Reclaimed water has recently become an important water source for urban use, but the composition of dissolved organic matter (DOM) in reclaimed water has rarely been characterized at the compound level because of its complexity. In this study, the transformation and changes in composition of low molecular weight DOM in water reclamation processes, where secondary effluent of the municipal wastewater treatment plant was further treated by biofiltration, ozonation and chlorination, were investigated by "unknown" screening analysis using Orbitrap mass spectrometry (Orbitrap MS). The intense ions were detected over an m/z range from 100 to 450. In total, 2412 formulae with various heteroatoms were assigned, and formulae with carbon (C), hydrogen (H) and oxygen (O) only and C, H, O and sulfur (S) were the most abundant species. During biofiltration, CHO-only compounds with relatively high hydrogen to carbon (H/C) ratio or with saturated structure were preferentially removed, while CHOS compounds were mostly removed. Ozonation induced the greatest changes in DOM composition. CHOS compounds were mostly decreased after ozonation while ozone selectively removed CHO compounds with relatively unsaturated structure and produced compounds that were more saturated and with a higher degree of oxidation. After chlorination, 168 chlorine-containing formulae, chlorinated disinfection by-products (DBPs), were additionally detected. Candidate DBP precursors were determined by tracking chlorinated DBPs formed via electrophilic substitution, half of which were generated during the ozonation.

  13. Hydration of methanol in water. A DFT-based molecular dynamics study

    CERN Document Server

    Van Erp, T S; Erp, Titus S. van; Meijer, Evert Jan

    2000-01-01

    We studied the hydration of a single methanol molecule in aqueous solution by first-principle DFT-based molecular dynamics simulation. The calculations show that the local structural and short-time dynamical properties of the water molecules remain almost unchanged by the presence of the methanol, confirming the observation from recent experimental structural data for dilute solutions. We also see, in accordance with this experimental work, a distinct shell of water molecules that consists of about 15 molecules. We found no evidence for a strong tangential ordering of the water molecules in the first hydration shell.

  14. Covalent features in the hydrogen bond of a water dimer: molecular orbital analysis

    CERN Document Server

    Wang, Bo; Dai, Xing; Gao, Yang; Wang, Zhigang; Zhang, Rui-Qin

    2015-01-01

    The covalent-like characteristics of hydrogen bonds offer a new perspective on intermolecular interactions. Here, using density functional theory and post-Hartree-Fock methods, we reveal that there are two bonding molecular orbitals (MOs) crossing the O and H atoms of the hydrogen-bond in water dimer. Energy decomposition analysis also shows a non-negligible contribution of the induction term. These results illustrate the covalent-like character of the hydrogen bond between water molecules, which contributes to the essential understanding of ice, liquid water, related materials, and life sciences.

  15. Enhanced heating of salty water and ice under microwaves: Molecular dynamics study

    OpenAIRE

    Tanaka, Motohiko; Sato, Motoyasu

    2008-01-01

    By molecular dynamics simulations, we have studied the enhanced heating process of salty ice and water by the electric field of applied microwaves at 2.5 GHz, and those in the range 2.5-10 GHz for the frequency dependence. We show that water molecules in salty ice are allowed to rotate in response to the microwave electric field to the extent comparable to those in pure water, because the molecules in salty ice are loosely tied by hydrogen bonds with adjacent molecules unlike the case of rigi...

  16. Molecular dynamics simulation of nanoscale distribution and mobility of water and dimethylmethylphosphonate in sulfonated polystyrene.

    Science.gov (United States)

    Vishnyakov, Aleksey; Neimark, Alexander V

    2008-11-27

    The interest in a better understanding of the specific interactions of phosphor-organic compounds and water with sulfonated polystyrene (sPS) is motivated by the use of block copolymers as protective membranes against chemical warfare agents. Using classical molecular dynamics simulations, we explored the nanoscale segregation and diffusion of water and nerve gas simulant dimethylmethylphosphonate (DMMP) in sPS neutralized with calcium counterions at different sulfonation and hydration levels. The water content was varied from 15 to 54% of dry polymer weight, and the DMMP content was varied from 0 to 100 wt %. We found that, in the 40% sulfonated polystyrene, water forms well defined aggregates, which grow in size as the hydration increases, reaching approximately 20 A at the maximum water content. In the 100% sulfonated polystyrene, the overall structure of hydrated polymer is more uniform with smaller water aggregates. Diffusion of water at the same number of water molecules per sulfonate group is faster at a lower sulfonation level. The solvation of sPS in water-DMMP binary mixtures was found to differ substantially from Nafion, where DMMP forms a layer between the hydropholic and hydrophobic subphases. In sPS with divalent Ca(2+) counterions, DMMP and water compete for the solvation of the sulfonate group. At high water and DMMP contents, the diffusion of DMMP turned out to be rather fast with a diffusion coefficient of ca. 30% of that of water. At the same time, water diffusion slows down as the DMMP concentration increases. This observation suggests that although sPS is permeable for both solvents, water and DMMP are partially segregated on the scale of 1-2 nm and have different pathways through the system. The nonuniform nanoscale distribution of water and DMMP in sPS is confirmed by analyses of different pair correlation functions. This feature may significantly affect the perm-selective properties of sPS-contained block copolymer membranes.

  17. Mechanical tuning of molecular machines for nucleotide recognition at the air-water interface

    Directory of Open Access Journals (Sweden)

    Shinoda Satoshi

    2011-01-01

    Full Text Available Abstract Molecular machines embedded in a Langmuir monolayer at the air-water interface can be operated by application of lateral pressure. As part of the challenge associated with versatile sensing of biologically important substances, we here demonstrate discrimination of nucleotides by applying a cholesterol-armed-triazacyclononane host molecule. This molecular machine can discriminate ribonucleotides based on a twofold to tenfold difference in binding constants under optimized conditions including accompanying ions in the subphase and lateral surface pressures of its Langmuir monolayer. The concept of mechanical tuning of the host structure for optimization of molecular recognition should become a novel methodology in bio-related nanotechnology as an alternative to traditional strategies based on increasingly complex and inconvenient molecular design strategies.

  18. A trinuclear ruthenium complex as a highly efficient molecular catalyst for water oxidation.

    Science.gov (United States)

    Zhang, L L; Gao, Y; Liu, Z; Ding, X; Yu, Z; Sun, L C

    2016-03-01

    A trinuclear ruthenium complex, 3, was designed and synthesized with the ligand 2,2'-bipyridine-6,6'-dicarboxylic acid (bda) and we found that this complex could function as a highly efficient molecular catalyst for water oxidation in homogeneous systems. This trinuclear molecular water oxidation catalyst, 3, displayed much higher efficiencies in terms of turnover numbers and initial oxygen evolution rate than its counterparts, a binuclear catalyst, 2, and a mononuclear catalyst, 1, in both chemically driven and photochemically driven water oxidation based on either the whole catalytic molecules or just the active Ru centers. The reasons for the superior performance of catalyst 3 were discussed and we believe that multiple Ru centers in a single molecule are indeed beneficial for increasing the probability of the formation of O-O bonds through an intramolecular radical coupling pathway.

  19. Molecular Density Functional Theory of Water describing Hydrophobicity at Short and Long Length Scales

    CERN Document Server

    Jeanmairet, Guillaume; Borgis, Daniel

    2013-01-01

    We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619, 2013] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields, the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional ...

  20. Water hexamer: Self-consistent phonons versus reversible scaling versus replica exchange molecular dynamics

    CERN Document Server

    Brown, Sandra E

    2014-01-01

    Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.

  1. Molecular Density Functional Theory for water with liquid-gas coexistence and correct pressure

    CERN Document Server

    Jeanmairet, Guillaume; Sergiievskyi, Volodymyr; Borgis, Daniel

    2015-01-01

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. With this correction, molecular density functional theory gives, at a modest computational cost, quantita...

  2. Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water.

    Science.gov (United States)

    Comez, L; Paolantoni, M; Sassi, P; Corezzi, S; Morresi, A; Fioretto, D

    2016-07-07

    When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.

  3. The Silica-Water Interface from the Analysis of Molecular Dynamic Simulations

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

    Surface chemistry is an emerging field that can give detailed insight about the elec- tronic properties and the interaction of complex material surfaces with their neigh- bors. This is for both solid-solid and solid-liquid interfaces. Among the latter class, the silica-water interface plays a major role in nature. Silica is among the most abundant materials on earth, as well in advanced technological applications such as catalysis and nanotechnology. This immediately indicates the relevance of a detailed understanding of the silica-water interface. In this study, we investigate the details of this interaction at microscopic level by analyzing trajectories obtained with ab initio molecular dynamic simulations. The system we consider consists of bulk liquid water confined between two β-cristobalite silica surfaces. The molecular dynamics were generated with the CP2K, an ab initio molecular dynamic simulation tool. The simulations are 25 picoseconds long, and the CP2K program was run on 64 cores on a supercomputer cluster. During the simulations the program integrates Newton’s equations of motion for the system and generates the trajectory for analysis. For analysis, we focused on the following properties that characterize the silica water interface. We calculated the density profile of the water layers from the silica surface, and we also calculated the radial distribution function (RDF) of the hydrogen bond at the silanols on the silica surface. The main focus of this thesis is to write the programs for calculating the atom density profile and the RDF from the generated MD trajectories. The atomic probability density profile shows that water is strongly adsorbed on the (001) cristobalite surface, while the RDF indicates differently ad- sorbed water molecules in the first adsorption layer. As final remark, the protocol and the tools developed in this thesis can be applied to the study of basically any crystal-water interface.

  4. High Resolution Surveys of the Water and Methanol Star Formation Masers in the Central Molecular Zone

    Science.gov (United States)

    Rickert, Matthew; Yusef-Zadeh, Farhad; Ott, Juergen; Meier, David S.; Krieger, Nico; SWAG

    2017-01-01

    We present some of the first high resolution fully interferometric surveys of 6.7 GHz methanol and 22 GHz water masers towards the Central Molecular Zone (CMZ). These masers are good signposts for early (methanol masers with resolutions of 0.9” (0.04 pc) and 0.4 km/s (8 kHz) and an average channel sensitivity of ~0.01 Jy/beam. With this high resolution and sensitivity, we have detected ~100 methanol masers, which is over a factor of two more than has previously been detected. We have also conducted two surveys of water masers in this region. As part of the Survey of Water and Ammonia in the Galactic Center (SWAG), the Australia Telescope Compact Array (ATCA) was used to survey a variety of molecular lines, including the 22 GHz water line. With the ATCA, we have detected over 200 water masers using resolutions of 26” (1 pc) and 2 km/s (60 kHz) and an average channel sensitivity of ~0.01 Jy/beam. Afterward, we conducted the first on-the-fly (OTF) VLA survey of water masers with improved resolutions of 0.7” (0.03 pc) and 0.4 km/s (26 kHz) and an average channel sensitivity of ~0.05 Jy/beam. Although the analysis of this OTF survey is not yet complete, we have already identified water masers that were not visible in the SWAG data.The improvement in the number of detected masers allows us to better analyze the distribution of these masers. We show that the SWAG water masers appear uniformly distributed along the Galactic plane, despite the asymmetry of the molecular gas distribution, where ~2/3 of the gas mass is located at positive Galactic longitudes. The methanol masers follow the molecular gas distribution, with a majority of the masers being found at positive longitudes. This could indicate a difference in the star forming history of these two parts of the CMZ and/or that the 22 GHz water masers are contaminated by water masers produced from evolved stars as well as star forming regions, indicating that a larger percentage of 22 GHz water masers are produced

  5. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Science.gov (United States)

    Wong, C. H.; Vijayaraghavan, V.

    2014-01-01

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  6. Water dynamics: relation between hydrogen bond bifurcations, molecular jumps, local density & hydrophobicity.

    Science.gov (United States)

    Titantah, John Tatini; Karttunen, Mikko

    2013-10-21

    Structure and dynamics of water remain a challenge. Resolving the properties of hydrogen bonding lies at the heart of this puzzle. We employ ab initio Molecular Dynamics (AIMD) simulations over a wide temperature range. The total simulation time was ≈ 2 ns. Both bulk water and water in the presence of a small hydrophobic molecule were simulated. We show that large-angle jumps and bond bifurcations are fundamental properties of water dynamics and that they are intimately coupled to both local density and hydrogen bond strength oscillations in scales from about 60 to a few hundred femtoseconds: Local density differences are the driving force for bond bifurcations and the consequent large-angle jumps. The jumps are intimately connected to the recently predicted hydrogen bond energy asymmetry. Our analysis also appears to confirm the existence of the so-called negativity track provided by the lone pairs of electrons on the oxygen atom to enable water rotation.

  7. Compressive characteristics of single walled carbon nanotube with water interactions investigated by using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Wong, C.H., E-mail: chwong@ntu.edu.sg; Vijayaraghavan, V.

    2014-01-24

    The elastic properties of single walled carbon nanotube (SWCNT) with surrounding water interactions are studied using molecular dynamics simulation technique. The compressive loading characteristic of carbon nanotubes (CNTs) in a fluidic medium such as water is critical for its role in determining the lifetime and stability of CNT based nano-fluidic devices. In this paper, we conducted a comprehensive analysis on the effect of geometry, chirality and density of encapsulated water on the elastic properties of SWCNT. Our studies show that defect density and distribution can strongly impact the compressive resistance of SWCNTs in water. Further studies were conducted on capped SWCNTs with varying densities of encapsulated water, which is necessary to understand the strength of CNT as a potential drug carrier. The results obtained from this paper will help determining the potential applications of CNTs in the field of nano-electromechanical systems (NEMS) such as nano-biological and nano-fluidic devices.

  8. Molecular Dynamics Simulations of CO2/Water/Quartz Interfacial Properties: Impact of CO2 Dissolution in Water.

    Science.gov (United States)

    Javanbakht, Gina; Sedghi, Mohammad; Welch, William; Goual, Lamia

    2015-06-01

    The safe trapping of carbon dioxide (CO2) in deep saline aquifers is one of the major concerns of CO2 sequestration. The amount of capillary trapping is dominated by the capillary pressure of water and CO2 inside the reservoir, which in turn is controlled by the interfacial tension (IFT) and the contact angle (CA) of CO2/water/rock systems. The measurement of IFT and CA could be very challenging at reservoir conditions, especially in the presence of toxic cocontaminants. Thus, the ability to accurately predict these interfacial properties at reservoir conditions is very advantageous. Although the majority of existing molecular dynamics (MD) studies of CO2/water/mineral systems were able to capture the trends in IFT and CA variations with pressure and temperature, their predictions often deviated from experimental data, possibly due to erroneous models and/or overlooked chemical reactions. The objective of this study was to improve the MD predictions of IFT and CA of CO2/water/quartz systems at various pressure and temperature conditions by (i) considering the chemical reactions between CO2 and water and (ii) using a new molecular model for α-quartz surface. The results showed that the presence of carbonic acid at the CO2/water interface improved the predictions of IFT, especially at low temperature and high pressure where more CO2 dissolution occurs. On the other hand, the effect on CA was minor. The slight decrease in CA observed across the pressure range investigated could be attributed to an increase in the total number of H-bonds between fluid molecules and quartz surface.

  9. Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

    Science.gov (United States)

    Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

  10. Occurrence, molecular characterization and antibiogram of water quality indicator bacteria in river water serving a water treatment plant

    Energy Technology Data Exchange (ETDEWEB)

    Okeke, Benedict C., E-mail: bokeke@aum.edu [Department of Biology, Auburn University at Montgomery, P.O. Box 244023, Montgomery, AL 36124 (United States); Thomson, M. Sue [Department of Biology, Auburn University at Montgomery, P.O. Box 244023, Montgomery, AL 36124 (United States); Moss, Elica M. [Department of Natural Resources and Environmental Science, Alabama A and M University, AL 35762 (United States)

    2011-11-01

    Water pollution by microorganisms of fecal origin is a current world-wide public health concern. Total coliforms, fecal coliforms (Escherichia coli) and enterococci are indicators commonly used to assess the microbiological safety of water resources. In this study, influent water samples and treated water were collected seasonally from a water treatment plant and two major water wells in a Black Belt county of Alabama and evaluated for water quality indicator bacteria. Influent river water samples serving the treatment plant were positive for total coliforms, fecal coliforms (E. coli), and enterococci. The highest number of total coliform most probable number (MPN) was observed in the winter (847.5 MPN/100 mL) and the lowest number in the summer (385.6 MPN/100 mL). Similarly E. coli MPN was substantially higher in the winter (62.25 MPN/100 mL). Seasonal variation of E. coli MPN in influent river water samples was strongly correlated with color (R{sup 2} = 0.998) and turbidity (R{sup 2} = 0.992). Neither E. coli nor other coliform type bacteria were detected in effluent potable water from the treatment plant. The MPN of enterococci was the highest in the fall and the lowest in the winter. Approximately 99.7 and 51.5 enterococci MPN/100 mL were recorded in fall and winter seasons respectively. One-way ANOVA tests revealed significant differences in seasonal variation of total coliforms (P < 0.05), fecal coliforms (P < 0.01) and enterococci (P < 0.01). Treated effluent river water samples and well water samples revealed no enterococci contamination. Representative coliform bacteria selected by differential screening on Coliscan Easygel were identified by 16S ribosomal RNA gene sequence analysis. E. coli isolates were sensitive to gentamicin, trimethoprim/sulfamethazole, ciprofloxacin, vancomycin, tetracycline, ampicillin, cefixime, and nitrofurantoin. Nonetheless, isolate BO-54 displayed decreased sensitivity compared to other E. coli isolates. Antibiotic sensitivity

  11. Solubility of cellulose in supercritical water studied by molecular dynamics simulations.

    Science.gov (United States)

    Tolonen, Lasse K; Bergenstråhle-Wohlert, Malin; Sixta, Herbert; Wohlert, Jakob

    2015-04-02

    The insolubility of cellulose in ambient water and most aqueous systems presents a major scientific and practical challenge. Intriguingly though, the dissolution of cellulose has been reported to occur in supercritical water. In this study, cellulose solubility in ambient and supercritical water of varying density (0.2, 0.7, and 1.0 g cm(-3)) was studied by atomistic molecular dynamics simulations using the CHARMM36 force field and TIP3P water. The Gibbs energy of dissolution was determined between a nanocrystal (4 × 4 × 20 anhydroglucose residues) and a fully dissociated state using the two-phase thermodynamics model. The analysis of Gibbs energy suggested that cellulose is soluble in supercritical water at each of the studied densities and that cellulose dissolution is typically driven by the entropy gain upon the chain dissociation while simultaneously hindered by the loss of solvent entropy. Chain dissociation caused density augmentation around the cellulose chains, which improved water-water bonding in low density supercritical water whereas the opposite occurred in ambient and high density supercritical water.

  12. Molecular view modeling of atmospheric organic particulate matter: Incorporating molecular structure and co-condensation of water

    Science.gov (United States)

    Pankow, James F.; Marks, Marguerite C.; Barsanti, Kelley C.; Mahmud, Abdullah; Asher, William E.; Li, Jingyi; Ying, Qi; Jathar, Shantanu H.; Kleeman, Michael J.

    2015-12-01

    Most urban and regional models used to predict levels of organic particulate matter (OPM) are based on fundamental equations for gas/particle partitioning, but make the highly simplifying, anonymized-view (AV) assumptions that OPM levels are not affected by either: a) the molecular characteristics of the condensing organic compounds (other than simple volatility); or b) co-condensation of water as driven by non-zero relative humidity (RH) values. The simplifying assumptions have allowed parameterized chamber results for formation of secondary organic aerosol (SOA) (e.g., ;two-product; (2p) coefficients) to be incorporated in chemical transport models. However, a return towards a less simplistic (and more computationally demanding) molecular view (MV) is needed that acknowledges that atmospheric OPM is a mixture of organic compounds with differing polarities, water, and in some cases dissolved salts. The higher computational cost of MV modeling results from a need for iterative calculations of the composition-dependent gas/particle partition coefficient values. MV modeling of OPM that considered water uptake (but not dissolved salts) was carried out for the southeast United States for the period August 29 through September 7, 2006. Three model variants were used at three universities: CMAQ-RH-2p (at PSU), UCD/CIT-RH-2p (at UCD), and CMAQ-RH-MCM (at TAMU). With the first two, MV structural characteristics (carbon number and numbers of functional groups) were assigned to each of the 2p products used in CMAQv.4.7.1 such that resulting predicted Kp,i values matched those in CMAQv.4.7.1. When water uptake was allowed, most runs assumed that uptake occurred only into the SOA portion, and imposed immiscibility of SOA with primary organic aerosol (POA). (POA is often viewed as rather non-polar, while SOA is commonly viewed as moderately-to-rather polar. Some runs with UCD/CIT-RH-2p were used to investigate the effects of POA/SOA miscibility.) CMAQ-RH-MCM used MCM to

  13. Polarizability effects in molecular dynamics simulations of the graphene-water interface

    Science.gov (United States)

    Ho, Tuan A.; Striolo, Alberto

    2013-02-01

    The importance of including the polarizability of both water and graphene in molecular dynamics simulations of the water/graphene system was quantified. A thin film of either rigid single point charge extended (SPC/E) water or polarizable simple 4-site water model with Drude polarizability (SWM4_DP) water on non-polarizable and polarizable graphene surfaces was simulated. The graphene surface was either maintained neutral or charged, positively and negatively. The results suggest that SPC/E and SWM4_DP water models yield very similar predictions for the water structural properties on neutral non-polarizable graphene, although they yield slightly different dynamical properties of interfacial water on neutral non-polarizable graphene. More pronounced were the differences obtained when graphene was modeled with a polarizable force field. In particular, the polarizability of graphene was found to enhance the number of interfacial SWM4_DP water molecules pointing one of their OH bonds towards the neutral surface. Despite this structural difference, the dynamical properties predicted for the interfacial SWM4_DP water were found to be independent on polarizability as long as the polarizability of a carbon atom is smaller than α = 0.878 Å. On charged graphene surfaces, the effect of polarizability of graphene on structural properties and some dynamical properties of SWM4_DP water is negligible because electrostatic forces due to surface charge dominate polarization forces, as expected. For all cases, our results suggest that the hydrogen bond network is insensitive to the polarizability of both water and graphene. Understanding how these effects will determine the accumulation of ions near neutral or charged graphene could have important implications for applications in the fields of energy storage and water desalination.

  14. Molecular dynamics simulation of single-walled silicon carbide nanotubes immersed in water.

    Science.gov (United States)

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

    2013-07-01

    The structure and dynamics of water confined in single-walled silicon carbon nanotubes (SWSiCNTs) are investigated using molecular dynamics (MD) simulations. The density of water inside SWSiCNTs is reported, and an equation is suggested to predict the density of water inside SWSiCNTs. Interestingly, the water diffusion coefficients (D) here are larger compared with those in SWCNTs and single-walled boron-nitride nanotubes (SWBNNTs). Furthermore, water inside zigzag SWCNTs has a lower diffusion coefficient than water inside armchair SWCNTs. A thorough analysis of the density profiles, hydrogen bonding, and water molecule orientation inside SWSiCNTs is presented to explore the mechanism behind the diffusive behavior of water observed here. It is shown here, by mean square displacement (MSD) analysis, that water molecules inside SWSiCNTs diffuse with a ballistic motion mechanism for up to 500ps. Additionally it is confirmed here for the first time that water molecules confined in the SWSiCNTs with diameters of less than 10Å obey the single-file diffusion mechanism at time scales in excess of 500ps. The orientation of water molecules inside SWSiCNTs could be a good explanation for the difference between the diffusion coefficient in (6,6) and (10,0) SWSiCNTs. Finally, a PMF analysis explains the difficulty of water entrance into SWSiCNTs and also the different water self-diffusion inside armchair and zigzag SWSiCNTs. These results are motivating reasons to use SWSiCNTs in nanoscale biochannels, for instance, in drug-delivery applications.

  15. Nonequilibrium molecular dynamics simulation of water transport through carbon nanotube membranes at low pressurea)

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2012-07-01

    Nonequilibrium molecular dynamics (NEMD) simulations are used to investigate pressure-driven water flow passing through carbon nanotube (CNT) membranes at low pressures (5.0 MPa) typical of real nanofiltration (NF) systems. The CNT membrane is modeled as a simplified NF membrane with smooth surfaces, and uniform straight pores of typical NF pore sizes. A NEMD simulation system is constructed to study the effects of the membrane structure (pores size and membrane thickness) on the pure water transport properties. All simulations are run under operating conditions (temperature and pressure difference) similar to a real NF processes. Simulation results are analyzed to obtain water flux, density, and velocity distributions along both the flow and radial directions. Results show that water flow through a CNT membrane under a pressure difference has the unique transport properties of very fast flow and a non-parabolic radial distribution of velocities which cannot be represented by the Hagen-Poiseuille or Navier-Stokes equations. Density distributions along radial and flow directions show that water molecules in the CNT form layers with an oscillatory density profile, and have a lower average density than in the bulk flow. The NEMD simulations provide direct access to dynamic aspects of water flow through a CNT membrane and give a view of the pressure-driven transport phenomena on a molecular scale.

  16. Molecular modeling of water interactions with fossil wood from Victorian brown coal

    Energy Technology Data Exchange (ETDEWEB)

    Tham Vu; Irene Yarovsky; Alan L. Chaffee [Monash University, Vic. (Australia). School of Chemistry

    2005-07-01

    The chemical structure of a fossil wood sample (Podocarpus sp.) taken from the Latrobe Valley coal measures (Victoria) was probed by {sup 13}C solid-state NMR, ultimate analyses and functional group analyses. This information was then used to create a molecular model (C{sub 100}H{sub 80}O{sub 2}) of fossil wood based on polymerized, but degraded lignin subunits. Molecular dynamics methods were used to observe both static and dynamic aspects of the coal-water interactions at ambient temperature, and to compare these with the analogous interactions for model lignin systems based on both guaiacyl (common to most woods) and syringyl (specific to angiosperms) structural units, as well as with bulk water. Na- and Ca-exchanged forms of the fossil wood model were also considered. The mobility of water was significantly reduced in all systems relative to bulk water, with the fossil wood and guaiacyl systems providing very similar values (global diffusion constants {approximately} 2.2 x 10{sup -5}cm{sup 2}{center_dot}s{sup -1}) and the Ca-exchanged system exhibiting the lowest value of all. A further reduction in the mobility of water molecules was observed in regions where hydrogen bonding could occur. For the fossil wood system, water molecules in the vicinity of carboxylic groups were significantly less mobile than those in the vicinity of OH groups generally. 22 refs., 8 figs., 2 tabs.

  17. Structured Ionomer Thin Films at Water Interface: Molecular Dynamics Simulation Insight.

    Science.gov (United States)

    Aryal, Dipak; Agrawal, Anupriya; Perahia, Dvora; Grest, Gary S

    2017-09-08

    Controlling the structure and dynamics of thin films of ionizable polymers at water interfaces is critical to their many applications. As the chemical diversity within one polymer is increased, controlling the structure and dynamics of the polymer, which is a key to their use, becomes a challenge. Here molecular dynamics simulations (MD) are used to obtain molecular insight into the structure and dynamics of thin films of one such macromolecule at the interface with water. The polymer consists of an ABCBA topology with randomly sulfonated polystyrene (C), tethered symmetrically to flexible poly(ethylene-r-propylene) blocks (B), and end-capped by a poly(t-butylstyrene) block (A). The compositions of the interfacial and bulk regions of thin films of the ABCBA polymers are followed as a function of exposure time to water. We find that interfacial rearrangements take place where buried ionic segments migrate toward the water interface. The hydrophobic blocks collapse and rearrange to minimize their exposure to water. The water that initially drives interfacial reengagements breaks the ionic clusters within the film, forming a dynamic hydrophilic internal network within the hydrophobic segments.

  18. CALCULATION OF COEFFICIENT OF SHARING OCTANOL-WATER OF ORGANIC COMPOUNDS USING MOLECULAR DESCRIPTORS

    Directory of Open Access Journals (Sweden)

    B. Souyei

    2010-12-01

    Full Text Available A quantitative structure-property relationship (QSPR study is carried out to develop correlations that relate the molecular structures of organic compounds to their Octanol- Water partition coefficients, Kow , using molecular descriptors. The correlations are simple in application with good accuracy, which provide an easy, direct and relatively accurate way to calculate Kow. Such calculation gives us a model that gives results in remarkable correlation with the descriptors of blocks fragments of the atom-centered and functional groups (R2 = 0.949, δ = 0477 (R2 = 0.926,δ = 0,548 respectively.

  19. Development of EEM based silicon–water and silica–water wall potentials for non-reactive molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Junghan; Iype, Eldhose; Frijns, Arjan J.H.; Nedea, Silvia V.; Steenhoven, Anton A. van

    2014-07-01

    Molecular dynamics simulations of heat transfer in gases are computationally expensive when the wall molecules are explicitly modeled. To save computational time, an implicit boundary function is often used. Steele's potential has been used in studies of fluid–solid interface for a long time. In this work, the conceptual idea of Steele's potential was extended in order to simulate water–silicon and water–silica interfaces. A new wall potential model is developed by using the electronegativity-equalization method (EEM), a ReaxFF empirical force field and a non-reactive molecular dynamics package PumMa. Contact angle simulations were performed in order to validate the wall potential model. Contact angle simulations with the resulting tabulated wall potentials gave a silicon–water contact angle of 129°, a quartz–water contact angle of 0°, and a cristobalite–water contact angle of 40°, which are in reasonable agreement with experimental values.

  20. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S.; Dickson, James M.

    2013-03-01

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  1. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation.

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-28

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm(-1)); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  2. Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow

    Science.gov (United States)

    Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.

    2016-07-01

    Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.

  3. Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes.

    Science.gov (United States)

    Wang, Luying; Dumont, Randall S; Dickson, James M

    2013-03-28

    Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.

  4. Hydrogen bonding and vibrational energy relaxation of interfacial water: A full DFT molecular dynamics simulation

    Science.gov (United States)

    Jeon, Jonggu; Hsieh, Cho-Shuen; Nagata, Yuki; Bonn, Mischa; Cho, Minhaeng

    2017-07-01

    The air-water interface has been a subject of extensive theoretical and experimental studies due to its ubiquity in nature and its importance as a model system for aqueous hydrophobic interfaces. We report on the structure and vibrational energy transfer dynamics of this interfacial water system studied with equilibrium and non-equilibrium molecular dynamics simulations employing a density functional theory -based description of the system and the kinetic energy spectral density analysis. The interfacial water molecules are found to make fewer and weaker hydrogen (H)-bonds on average compared to those in the bulk. We also find that (i) the H-bonded OH groups conjugate to the free OH exhibit rather low vibrational frequencies (3000-3500 cm-1); (ii) the presence of a significant fraction (>10%) of free and randomly oriented water molecules at the interface ("labile water"), neither of whose OH groups are strong H-bond donors; (iii) the inertial rotation of free OH groups, especially from the labile water, contribute to the population decay of excited free OH groups with comparable rate and magnitude as intramolecular energy transfer between the OH groups. These results suggest that the labile water, which might not be easily detectable by the conventional vibrational sum frequency generation method, plays an important role in the surface water dynamics.

  5. Influence of Molecular Oxygen on Ortho-Para Conversion of Water Molecules

    Science.gov (United States)

    Valiev, R. R.; Minaev, B. F.

    2017-07-01

    The mechanism of influence of molecular oxygen on the probability of ortho-para conversion of water molecules and its relation to water magnetization are considered within the framework of the concept of paramagnetic spin catalysis. Matrix elements of the hyperfine ortho-para interaction via the Fermi contact mechanism are calculated, as well as the Maliken spin densities on water protons in H2O and O2 collisional complexes. The mechanism of penetration of the electron spin density into the water molecule due to partial spin transfer from paramagnetic oxygen is considered. The probability of ortho-para conversion of the water molecules is estimated by the quantum chemistry methods. The results obtained show that effective ortho-para conversion of the water molecules is possible during the existence of water-oxygen dimers. An external magnetic field affects the ortho-para conversion rate given that the wave functions of nuclear spin sublevels of the water protons are mixed in the complex with oxygen.

  6. Spontaneous assembly of HSP90 inhibitors at water/octanol interface: A molecular dynamics simulation study

    Science.gov (United States)

    Zolghadr, Amin Reza; Boroomand, Samaneh

    2017-02-01

    Drug absorption at an acceptable dose depends on the pair of solubility and permeability. There are many potent therapeutics that are not active in vivo, presumably due to the lack of capability to cross the cell membrane. Molecular dynamics simulation of radicicol, diol-radicicol, cyclopropane-radicicol and 17-DMAG were performed at water/octanol interface to suggest interfacial activity as a physico-chemical characteristic of these heat shock protein 90 (HSP90) inhibitors. We have observed that orally active HSP90 inhibitors form aggregates at the water/octanol and DPPC-lipid/water interfaces by starting from an initial configuration with HSP90 inhibitors embedded in the water matrix.

  7. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    Science.gov (United States)

    Wang, Qi; Suzuki, Kimichi; Nagashima, Umpei; Tachikawa, Masanori; Yan, Shiwei

    2013-11-01

    The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH∗ stretching and intermolecular ion-water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion-water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water-water hydrogen bond interactions.

  8. Molecular dynamics simulations of water on a hydrophilic silica surface at high air pressures

    DEFF Research Database (Denmark)

    Zambrano, H.A.; Walther, Jens Honore; Jaffe, R.L.

    2014-01-01

    of air in water at different pressures. Using the calibrated force field, we conduct MD simulations to study the interface between a hydrophilic silica substrate and water surrounded by air at different pressures. We find that the static water contact angle is independent of the air pressure imposed......Wepresent a force field forMolecular Dynamics (MD) simulations ofwater and air in contactwith an amorphous silica surface. We calibrate the interactions of each species present in the systemusing dedicated criteria such as the contact angle of a water droplet on a silica surface, and the solubility...... on the system. Our simulations reveal the presence of a nanometer thick layer of gas at the water–silica interface. We believe that this gas layer could promote nucleation and stabilization of surface nanobubbles at amorphous silica surfaces. © 2014 Elsevier B.V. All rights reserved....

  9. Molecular Dynamics Simulation of Water Nanodroplets on Silica Surfaces at High Air Pressures

    DEFF Research Database (Denmark)

    Zambrano, Harvey A; Jaffe, Richard Lawrence; Walther, Jens Honore

    2010-01-01

    e.g., nanobubbles. In the present work we study the role of air on the wetting of hydrophilic systems. We conduct molecular dynamics simulations of a water nanodroplet on an amorphous silica surface at different air pressures. The interaction potentials describing the silica, water, and air...... not been reached. Contact angle measurements of droplets on solid surfaces offer useful quantitative measurements of the physiochemical properties of the solid-liquid interface. For hydrophobic systems the properties the solid- liquid interface are now known to be strongly influenced by the presence of air...... are obtained from the literature. The silica surface is modeled by a large 32 ⨯ 32 ⨯ 2 nm amorphous SiO2 structure consisting of 180000 atoms. The water consists of 18000 water molecules surrounded by N2 and O2 air molecules corresponding to air pressures of 0 bar (vacuum), 50 bar, 100 bar and 200 bar. We...

  10. Optimizing Water Transport through Graphene-Based Membranes: Insights from Nonequilibrium Molecular Dynamics.

    Science.gov (United States)

    Muscatello, Jordan; Jaeger, Frederike; Matar, Omar K; Müller, Erich A

    2016-05-18

    Recent experimental results suggest that stacked layers of graphene oxide exhibit strong selective permeability to water. To construe this observation, the transport mechanism of water permeating through a membrane consisting of layered graphene sheets is investigated via nonequilibrium and equilibrium molecular dynamics simulations. The effect of sheet geometry is studied by changing the offset between the entrance and exit slits of the membrane. The simulation results reveal that the permeability is not solely dominated by entrance effects; the path traversed by water molecules has a considerable impact on the permeability. We show that contrary to speculation in the literature, water molecules do not pass through the membrane as a hydrogen-bonded chain; instead, they form well-mixed fluid regions confined between the graphene sheets. The results of the present work are used to provide guidelines for the development of graphene and graphene oxide membranes for desalination and solvent separation.

  11. Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation.

    Science.gov (United States)

    Hong, Seung Do; Ha, Man Yeong; Balachandar, S

    2009-11-01

    The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. With increasing characteristic energy, the static contact angle in equilibrium with a solid surface in the absence of a body force decreases because the hydrophobic surface changes its characteristics to the hydrophilic surface. In order to consider the effect of moving water droplet on the dynamic contact angles, we apply the constant acceleration to an individual oxygen and hydrogen atom. In the presence of a body force, the water droplet changes its shape with larger advancing contact angle than the receding angle. The dynamic contact angles are compared with the static contact angle in order to see the effect of the presence of a body force.

  12. The hydrophobic effect: Molecular dynamics simulations of water confined between extended hydrophobic and hydrophilic surfaces

    DEFF Research Database (Denmark)

    Jensen, Morten Østergaard; Mouritsen, Ole G.; Peters, Günther H.J.

    2004-01-01

    experimental data from x-ray reflectivity measurements, reveal a uniform weak de-wetting characteristic for the extended hydrophobic surface, while the hydrophilic surface is weakly wetted. These microscopic data are consistent with macroscopic contact angle measurements. Specific water orientation is present......-correlation functions reveal that water molecules have characteristic diffusive behavior and orientational ordering due to the lack of hydrogen bonding interactions with the surface. These observations suggest that the altered dynamical properties of water in contact with extended hydrophobic surfaces together......Structural and dynamic properties of water confined between two parallel, extended, either hydrophobic or hydrophilic crystalline surfaces of n-alkane C36H74 or n-alcohol C35H71OH, are studied by molecular dynamics simulations. Electron density profiles, directly compared with corresponding...

  13. Molecular Dynamics Simulations of a Flexible Polyethylene: A Protein-Like Behaviour in a Water Solvent

    CERN Document Server

    Kretov, D A

    2005-01-01

    We used molecular dynamics (MD) simulations to study the density and the temperature behaviour of a flexible polyethylene (PE) subjected to various heating conditions and to investigate the PE chain conformational changes in a water solvent. First, we have considered the influence of the heating process on the final state of the polymeric system and the sensitivity of its thermodynamic characteristics (density, energy, etc.) for different heating regimes. For this purpose three different simulations were performed: fast, moderate, and slow heating. Second, we have investigated the PE chain conformational dynamics in water solvent for various simulation conditions and various configurations of the environment. From the obtained results we have got the pictures of the PE dynamical motions in water. We have observed a protein-like behaviour of the PE chain, like that of the DNA and the proteins in water, and have also estimated the rates of the conformational changes. For the MD simulations we used the optimized...

  14. Molecular dynamics simulations of the surface tension of oxygen-supersaturated water

    Directory of Open Access Journals (Sweden)

    S. Jain

    2017-04-01

    Full Text Available In this work, non-reactive molecular dynamic simulations were conducted to determine the surface tension of water as a function of the concentration of the dissolved gaseous molecules (O2, which would in turn help to predict the pressure inside the nanobubbles under supersaturation conditions. Knowing the bubble pressure is a prerequisite for understanding the mechanisms behind the spontaneous combustion of the H2/O2 gases inside the nanobubbles. First, the surface tension of pure water was determined using the planar interface method and the Irving and Kirkwood formula. Next, the surface tension of water containing four different supersaturation concentrations (S of O2 gas molecules was computed considering the curved interface of a nanobubble. The surface tension of water was found to decrease with an increase in the supersaturation ratio or the concentration of the dissolved O2 gas molecules.

  15. Equilibrium and kinetics of water adsorption in carbon molecular sieve: theory and experiment.

    Science.gov (United States)

    Rutherford, S W; Coons, J E

    2004-09-28

    Measurements of water adsorption equilibrium and kinetics in Takeda carbon molecular sieve (CMS) were undertaken in an effort to characterize fundamental mechanisms of adsorption and transport. Adsorption equilibrium revealed a type III isotherm that was characterized by cooperative multimolecular sorption theory. Water adsorption was found to be reversible and did not display hysteresis upon desorption over the conditions studied. Adsorption kinetics measurements revealed that a Fickian diffusion mechanism governed the uptake of water and that the rate of adsorption decreased with increasing relative pressure. Previous investigations have attributed the observed decreasing trend in the rate of adsorption to blocking of micropores. Here, it is proposed that the decrease is attributed to the thermodynamic correction to Fick's law which is formulated on the basis of the chemical potential as the driving force for transport. The thermodynamically corrected formulation accounted for observations of transport of water and other molecules in CMS.

  16. Reorientation phenomena in imidazolium methyl sulfonate as probed by advanced solid-state NMR.

    Science.gov (United States)

    Goward, Gillian R; Saalwächter, Kay; Fischbach, Ingrid; Spiess, Hans Wolfgang

    2003-01-01

    Evidence for reorientation of imidazolium rings in imidazolium methylsulfonate is demonstrated using solid-state NMR. This material is a model system for exciting new proton-conducting materials based on imidazole. Two advanced NMR methods, including 1H-13C and 1H-15N recoupled polarization transfer with dipolar sideband pattern analysis and analysis of the coalescence of 13C lineshapes are used to characterize the ring reorientation. The process is found to occur at temperatures well below the melting point of the salt, between 240 and 380 K, and is described by a single activation energy, of 38+/-5 kJ/mol. This material is considered as a model system for quantifying the ring reorientation process, which is often proposed to be the rate-limiting step in proton transport in imidazole-based proton conducting materials.

  17. Influence of Rayleigh-Taylor Instability on Liquid Propellant Reorientation in a Low-Gravity Environment

    Institute of Scientific and Technical Information of China (English)

    LI Zhang-Guo; LIU Qiu-Sheng; LIU Rong; HU Wei; DENG Xin-Yu

    2009-01-01

    A computational simulation is conducted to investigate the influence of Rayleigh-Taylor instability on liquid propellant reorientation flow dynamics for the tank of CZ-3A launch vehicle series fuel tanks in a low-gravity environment. The volume-of-fluid (VOF) method is used to simulate the free surface flow of gas-liquid. The process of the liquid propellant reorientation started from initially fiat and curved interfaces are numerically studied. These two different initial conditions of the gas-liquid interface result in two modes of liquid flow. It is found that the Rayleigh-Taylor instability can be reduced evidently at the initial gas-liquid interface with a high curve during the process of liquid reorientation in a low-gravity environment.

  18. Reorientation of single-wall carbon nanotubes in negative anisotropy liquid crystals by an electric field

    Directory of Open Access Journals (Sweden)

    Amanda García-García

    2016-06-01

    Full Text Available Single-wall carbon nanotubes (SWCNT are anisotropic nanoparticles that can cause modifications in the electrical and electro-optical properties of liquid crystals. The control of the SWCNT concentration, distribution and reorientation in such self-organized fluids allows for the possibility of tuning the liquid crystal properties. The alignment and reorientation of CNTs are studied in a system where the liquid crystal orientation effect has been isolated. Complementary studies including Raman spectroscopy, microscopic inspection and impedance studies were carried out. The results reveal an ordered reorientation of the CNTs induced by an electric field, which does not alter the orientation of the liquid crystal molecules. Moreover, impedance spectroscopy suggests a nonnegligible anchoring force between the CNTs and the liquid crystal molecules.

  19. Reorientation response of magnetic microspheres attached to gold electrodes under an applied magnetic field

    Energy Technology Data Exchange (ETDEWEB)

    De Los Santos Valladares, L.; Reeve, R.M.; Mitrelias, T.; Langford, R.M.; Barnes, C.H.W., E-mail: luis_d_v@hotmail.com [Cavendish Laboratory, Department of Physics, University of Cambridge Materials and Structures Laboratory (United Kingdom); Bustamante Dominguez, A. [Laboratorio de Ceramicos y Nanomateriales, Facultad de Ciencias Fisicas, Universidad Nacional Mayor de San Marcos, Lima (Peru); Aguiar, J. Albino [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Departamento de Fisica; Azuma, Y. [Materials and Structures Laboratory, Tokyo Institute of Technology, Midori-ku, Yokohama (Japan); Majima, Y. [CREST, Japan Science and Technology Agency (JST), Midori-ku, Yokohama (Japan)

    2013-08-15

    In this work, we report the mechanical reorientation of thiolated ferromagnetic microspheres bridging a pair of gold electrodes under an external magnetic field. When an external magnetic field (7 kG) is applied during the measurement of the current-voltage characteristics of a carboxyl ferromagnetic microsphere (4 μm diameter) attached to two gold electrodes by self-assembled monolayers (SAMs) of octane dithiol (C{sub 8}H{sub 18}S{sub 2}), the current signal is distorted. Rather than due to magnetoresistance, this effect is caused by a mechanical reorientation of the ferromagnetic sphere, which alters the number of SAMs between the sphere and the electrodes and therefore affects conduction. To study the physical reorientation of the ferromagnetic particles, we measure their hysteresis loops while suspended in a liquid solution. (author)

  20. Fluidization, resolidification, and reorientation of the endothelial cell in response to slow tidal stretches.

    Science.gov (United States)

    Krishnan, Ramaswamy; Canovic, Elizabeth Peruski; Iordan, Andreea L; Rajendran, Kavitha; Manomohan, Greeshma; Pirentis, Athanassios P; Smith, Michael L; Butler, James P; Fredberg, Jeffrey J; Stamenovic, Dimitrije

    2012-08-15

    Mechanical stretch plays an important role in regulating shape and orientation of the vascular endothelial cell. This morphological response to stretch is basic to angiogenesis, neovascularization, and vascular homeostasis, but mechanism remains unclear. To elucidate mechanisms, we used cell mapping rheometry to measure traction forces in primary human umbilical vein endothelial cells subjected to periodic uniaxial stretches. Onset of periodic stretch of 10% strain amplitude caused a fluidization response typified by attenuation of traction forces almost to zero. As periodic stretch continued, the prompt fluidization response was followed by a slow resolidification response typified by recovery of the traction forces, but now aligned along the axis perpendicular to the imposed stretch. Reorientation of the cell body lagged reorientation of the traction forces, however. Together, these observations demonstrate that cellular reorientation in response to periodic stretch is preceded by traction attenuation by means of cytoskeletal fluidization and subsequent traction recovery transverse to the stretch direction by means of cytoskeletal resolidification.

  1. Effect of spin reorientation on magnetocaloric and transport properties of NdAl2

    Science.gov (United States)

    de Souza, M. V.; da Silva, J. A.; Silva, L. S.

    2017-01-01

    We report the magneto-thermal and resistive properties of rare-earth dialuminide NdAl2, including spin reorientation transition. To this purpose, we used a theoretical model that considers the interactions of exchange and Zeeman, besides the anisotropy due to the electrical crystal field. The theoretical results obtained were compared to experimental data of the NdAl2 in single crystal and bulk forms. Explicitly, we have calculated the anisotropic variation of magnetic entropy with the magnetic field oriented along the three principal crystallographic directions: [100], [110], and [111] of NdAl2 single crystal, where a signature of the spin reorientation is observed in the [110] and [111] directions. Moreover, of magnetoresistivity we consider the applied magnetic field along the crystallographic directions [100] and [110]. In turn, for the polycrystalline form, the good agreement between theory and experiment confirms the presence of spin reorientation, which was predicted theoretically in magnetization curves.

  2. Chaotic attitude and reorientation maneuver for completely liquid-filled spacecraft with flexible appendage

    Institute of Scientific and Technical Information of China (English)

    Baozeng Yue

    2009-01-01

    The present paper investigates the chaotic attitude dynamics and reorientation maneuver for completely viscous liquid-filled spacecraft with flexible appendage. All of the equations of motion are derived by using Lagrangian mechanics and then transformed into a form consisting of an unperturbed part plus perturbed terms so that the system's nonlinear characteristics can be exploited in phase space.Emphases are laid on the chaotic attitude dynamics produced from certain sets of physical parameter values of the spacecraft when energy dissipation acts to derive the body from minor to major axis spin. Numerical solutions of these equations show that the attitude dynamics of liquid-filled flexible spacecraft possesses characteristics common to random, nonperiodic solutions and chaos, and it is demonstrated that the desired reorientation maneuver is guaranteed by using a pair of thruster impulses. The control strategy for reorientation maneuver is designed and the numerical simulation results are presented for both the uncontrolled and controlled spins transition.

  3. Reorientation of single-wall carbon nanotubes in negative anisotropy liquid crystals by an electric field

    Science.gov (United States)

    García-García, Amanda; Vergaz, Ricardo; Algorri, José F; Zito, Gianluigi; Cacace, Teresa; Marino, Antigone; Otón, José M

    2016-01-01

    Summary Single-wall carbon nanotubes (SWCNT) are anisotropic nanoparticles that can cause modifications in the electrical and electro-optical properties of liquid crystals. The control of the SWCNT concentration, distribution and reorientation in such self-organized fluids allows for the possibility of tuning the liquid crystal properties. The alignment and reorientation of CNTs are studied in a system where the liquid crystal orientation effect has been isolated. Complementary studies including Raman spectroscopy, microscopic inspection and impedance studies were carried out. The results reveal an ordered reorientation of the CNTs induced by an electric field, which does not alter the orientation of the liquid crystal molecules. Moreover, impedance spectroscopy suggests a nonnegligible anchoring force between the CNTs and the liquid crystal molecules. PMID:27547599

  4. Delirium prevention in critically ill adults through an automated reorientation intervention - A pilot randomized controlled trial.

    Science.gov (United States)

    Munro, Cindy L; Cairns, Paula; Ji, Ming; Calero, Karel; Anderson, W McDowell; Liang, Zhan

    Explore the effect of an automated reorientation intervention on ICU delirium in a prospective randomized controlled trial. Delirium is common in ICU patients, and negatively affects outcomes. Few prevention strategies have been tested. Thirty ICU patients were randomized to 3 groups. Ten received hourly recorded messages in a family member's voice during waking hours over 3 ICU days, 10 received the same messages in a non-family voice, and 10 (control) did not receive any automated reorientation messages. The primary outcome was delirium free days during the intervention period (evaluated by CAM-ICU). Groups were compared by Fisher's Exact Test. The family voice group had more delirium free days than the non-family voice group, and significantly more delirium free days (p = 0.0437) than the control group. Reorientation through automated, scripted messages reduced incidence of delirium. Using identical scripted messages, family voice was more effective than non-family voice. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. Molecular characterization of Cryptosporidium and Giardia occurring in natural water bodies in Poland.

    Science.gov (United States)

    Adamska, Małgorzata

    2015-02-01

    Cryptosporidium and Giardia protozoa are zoonotic parasites that cause human gastroenteritis and can be transmitted to human through the fecal-oral route and water or food. Several species belong to these genera and their resistant forms occur in water, but only some of them are infectious to human. Health risk depends on the occurrence of infectious Cryptosporidium and Giardia species and genotypes in water, and only molecular techniques allow detecting them, as well as enable to identify the contamination source. In this work, genotyping and phylogenetic analysis have been performed on the basis of 18S rDNA and ß-giardin genes sequences of Cryptosporidium and Giardia, respectively, in order to provide the molecular characterization of these parasites detected earlier in five natural water bodies in Poland and to track possible sources of their (oo)cysts in water. Genotyping revealed a high similarity (over 99 up to 100 %) of analyzed sequences to cattle genotype of C. parvum isolated from cattle and human and to G. intestinalis assemblage B isolated from human. The sequences obtained by others originated from patients with clinical symptoms of cryptosporidiosis or giardiasis and/or with the infection confirmed by different methods. The contamination of three examined lakes is probably human-originated, while the sources of contamination of two remaining lakes are wild and domestic animals. Obtained phylogenetic trees support suggestions of other authors that the bovine genotype of C. parvum should be a separate species, as well as A and B assemblages of G. intestinalis.

  6. Sensitive Limits on the Water Abundance in Cold Low Mass Molecular Cores

    CERN Document Server

    Bergin, E A; Bergin, Edwin A.; Snell, Ronald L.

    2002-01-01

    We present SWAS observations of water vapor in two cold star-less clouds, B68 and Core D in rho Ophiuchus. Sensitive non-detections of the 1(10)-1(01) transition of o-H2O are reported for each source. Both molecular cores have been previously examined by detailed observations that have characterized the physical structure. Using these rather well defined physical properties and a Monte-Carlo radiation transfer model we have removed one of the largest uncertainties from the abundance calculation and set the lowest water abundance limit to date in cold low-mass molecular cores. These limits are < 3 x 10^{-8} (relative to H2) and < 8 x 10^{-9} in B68 and rho Oph D, respectively. Such low abundances confirm the general lack of ortho-water vapor in cold (T < 20 K) cores. Provided that the ortho/para ratio of water is not near zero, these limits are well below theoretical predictions and appear to support the suggestion that most of the water in dense low-mass cores is frozen onto the surfaces of cold dust...

  7. On the relation between hydrogen bonds, tetrahedral order and molecular mobility in model water

    CERN Document Server

    Pereyra, R G; Malaspina, D C; Carignano, M A

    2013-01-01

    We studied by molecular dynamics simulations the relation existing between the lifetime of hydrogen bonds, the tetrahedral order and the diffusion coefficient of model water. We tested four different models: SPC/E, TIP4P-Ew, TIP5P-Ew and Six-site, these last two having sites explicitly resembling the water lone pairs. While all the models perform reasonably well at ambient conditions, their behavior is significantly different for temperatures below 270 K. The models with explicit lone-pairs have a longer hydrogen bond lifetime, a better tetrahedral order and a smaller diffusion coefficient than the models without them.

  8. Smart polyelectrolyte microcapsules as carriers for water-soluble small molecular drug.

    Science.gov (United States)

    Song, Weixing; He, Qiang; Möhwald, Helmuth; Yang, Yang; Li, Junbai

    2009-10-15

    Heat treatment is introduced as a simple method for the encapsulation of low molecular weight water-soluble drugs within layer-by-layer assembled microcapsules. A water-soluble drug, procainamide hydrochloride, could thus be encapsulated in large amount and enriched by more than 2 orders of magnitude in the assembled PDADMAC/PSS capsules. The shrunk capsules could control the unloading rate of drugs, and the drugs could be easily unloaded using ultrasonic treatment. The encapsulated amount could be quantitatively controlled via the drug concentration in the bulk. We also found that smaller capsules possess higher encapsulation capability.

  9. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation

    OpenAIRE

    Zhang, Jun; Borg, Matthew; Sefiane, Khellil; Reese, Jason

    2015-01-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an ...

  10. Electron spin relaxation due to reorientation of a permanent zero field splitting tensor.

    Science.gov (United States)

    Schaefle, Nathaniel; Sharp, Robert

    2004-09-15

    Electron spin relaxation of transition metal ions with spin S> or =1 results primarily from thermal modulation of the zero field splitting (zfs) tensor. This occurs both by distortion of the zfs tensor due to intermolecular collisions and, for complexes with less than cubic symmetry, by reorientational modulation of the permanent zfs tensor. The reorientational mechanism is much less well characterized in previous work than the distortional mechanism although it is an important determinant of nuclear magnetic resonance (NMR) paramagnetic relaxation enhancement phenomena (i.e., the enhancement of NMR relaxation rates produced by paramagnetic ions in solution or NMR-PRE). The classical density matrix theory of spin relaxation does not provide an appropriate description of the reorientational mechanism at low Zeeman field strengths because the zero-order spin wave functions are stochastic functions of time. Using spin dynamics simulation techniques, the time correlation functions of the spin operators have been computed and used to determine decay times for the reorientational relaxation mechanism for S=1. In the zfs limit of laboratory field strengths (H(Zeem)spin decay is exponential, the spin relaxation time, tau(S) (composite function) approximately 0.53tau(R)((1)), where tau(R)((1)) is the reorientational correlation time of a molecule-fixed vector. The value of tau(S) (composite function) is independent of the magnitude of the cylindrical zfs parameter (D), but it depends strongly on low symmetry zfs terms (the E/D ratio). Other spin dynamics (SD) simulations examined spin decay in the intermediate regime of field strengths where H(Zeem) approximately H(zfs) (composite function), and in the vicinity of the Zeeman limit. The results demonstrate that the reorientational electron spin relaxation mechanism is often significant when H(zfs) (composite function)> or =H(Zeem), and that its neglect can lead to serious errors in the interpretation of NMR-PRE data.

  11. The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

    Science.gov (United States)

    Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

    2009-01-01

    Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

  12. 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...

  13. Molecular Forensic Profiling of Cryptosporidium Species and Genotypes in Raw Water

    OpenAIRE

    Ruecker, Norma J.; Bounsombath, Niravanh; Wallis, Peter; Ong, Corinne S.L.; Isaac-Renton, Judith L.; Neumann, Norman F.

    2005-01-01

    The emerging concept of host specificity of Cryptosporidium spp. was exploited to characterize sources of fecal contamination in a watershed. A method of molecular forensic profiling of Cryptosporidium oocysts on microscope slides prepared from raw water samples processed by U.S. Environmental Protection Agency Method 1623 was developed. The method was based on a repetitive nested PCR-restriction fragment length polymorphism-DNA sequencing approach that permitted the resolution of multiple sp...

  14. Separation of ethanol-water mixtures using 3A molecular sieve

    Energy Technology Data Exchange (ETDEWEB)

    Carton, A.; Gonzalez, G.; Iniguez de la Torre, A.; Cabezas, J.L.

    1987-01-01

    An experimental study of 3A molecular sieve behavior, in order to obtain anhydrous ethanol, was developed. The adsorption of water in vapor phase was performed in an essentially isothermal fixed bed. 99.9 wt% ethanol was recovered operating with azeotropic distillation and different flow rates. A simple model in terms of a driving force and linear equilibrium was tested. Runs in liquid phase were also carried out, obtaining lower treatment-capacities than when working in vapor phase.

  15. Hollow Nanospheres with Fluorous Interiors for Transport of Molecular Oxygen in Water

    KAUST Repository

    Vu, Khanh B.

    2016-08-11

    A dispersion system for saturated fluorocarbon (SFC) liquids based on permeable hollow nanospheres with fluorous interiors is described. The nanospheres are well dispersible in water and are capable of immediate uptake of SFCs. The nanosphere shells are gas-permeable and feature reactive functional groups for easy modification of the exterior. These features make the SFC-filled nanospheres promising vehicles for respiratory oxygen storage and transport. Uptake of molecular oxygen into nanosphere-stabilized SFC dispersions is demonstrated.

  16. Dynamic Water Networks in Cytochrome c Oxidase from Paracoccus denitrificans Investigated by Molecular Dynamics Simulations

    OpenAIRE

    Olkhova, Elena; Hutter, Michael C; Lill, Markus A.; Helms, Volkhard; Michel, Hartmut

    2004-01-01

    We present a molecular dynamics study of cytochrome c oxidase from Paracoccus denitrificans in the fully oxidized state, embedded in a fully hydrated dimyristoylphosphatidylcholine lipid bilayer membrane. Parallel simulations with different levels of protein hydration, 1.125 ns each in length, were carried out under conditions of constant temperature and pressure using three-dimensional periodic boundary conditions and full electrostatics to investigate the distribution and dynamics of water ...

  17. Molecular density functional theory of water including density–polarization coupling

    OpenAIRE

    Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

    2016-01-01

    International audience; We present a three-dimensional molecular density functional theory of water derived fromfirst-principles that relies on the particle’s density and multipolar polarization density andincludes the density–polarization coupling. This brings two main benefits: (i) scalar densityand vectorial multipolar polarization density fields are much more tractable and give morephysical insight than the full position and orientation densities, and (ii) it includes the fulldensity–pola...

  18. Molecular and dissociative adsorption of water at a defective Cu(110) surface

    Science.gov (United States)

    Lousada, Cláudio M.; Johansson, Adam Johannes; Korzhavyi, Pavel A.

    2017-04-01

    We performed a density functional theory (DFT) investigation of the molecular and dissociative adsorption of water at the perfect Cu(110) and at a defective Cu surface that provides a broad spectrum of adsorption sites in terms of coordination of Cu atoms, with the aim of understanding the role of surface defects in the dissociation of water molecules. The molecular adsorption of water is spontaneous at both surfaces but at the defective surface we found two stable molecular adsorption structures that differ slightly in the disposition of the O-atoms of H2O on the surface plane but differ considerably on the orientation of their H-atoms. Additionally we studied the dissociative adsorption of water accompanied with formation of H2(g). At the defective surface, starting from 1 ML of molecularly adsorbed H2O, the dissociation of 0.22 ML of H2O leading to 0.22 ML of HO, 0.78 ML H2O and H2(g) is exergonic but the dissociation of 0.44 ML or more H2O molecules is endergonic. These findings are discussed in terms of the two main factors that affect the adsorption energies: the existence of exposed adatoms provides an environment that facilitates the interaction with small adsorbates leading to stronger bonds between the surface and such adsorbates; and at the same time, the limited polarizability of the defect sites causes high coverages of adsorbates that drag electron density from the surface to be unfavorable. The overall effect is that at the defective Cu(110) formation of low coverages of HO groups is more favorable than at the perfect Cu(110) while forming coverages higher than 0.44 ML of HO is less favorable than at the perfect Cu(110). These effects have their origin in the extent of the polarization of the Cu-O bonds.

  19. Molecular Dynamics Analysis of Lysozyme Protein in Ethanol- Water Mixed Solvent

    Science.gov (United States)

    2012-01-01

    Hermans , 1981; Levitt & Warshel, 1975). The idea for molecular dynamic simulation was born out of the quest to solve and understand the following  To...GROMACS is the MD analysis code employed in the present work. Groningen machine for chemical simulations( GROMACS)(Lindahl, Hess , & Van Der Spoel...Physical Chemistry B, 106(14), 3668-3672. Berendsen, H., Postma, J., Van Gunsteren, W., & Hermans , J. (1981). Interaction models for water in

  20. Orbital magnetic moment instability at the spin reorientation transition of Nd2Fe14B

    Science.gov (United States)

    Garcia; Chaboy; Bartolome; Goedkoop

    2000-07-10

    Highly accurate soft-XMCD data recorded on a Nd2Fe14B single crystal, through the spin reorientation transition show that the average Fe orbital moment (a) is proportional to the macroscopic Fe anisotropy constant, and (b) diverges 15 K below the reorientation transition temperature. This divergence is indicative of a critical behavior and it is related to a tetragonal distortion. These results give experimental evidence of the mutual dependence between orbital moment, macroscopic magnetic anisotropy, and tetragonal distortion. Furthermore, it is argued that the critical behavior of the orbital moment is at the origin of similar divergences previously observed in Mossbauer and Hall-effect data.

  1. New fractal math tool providing simultaneous reorientation and acceleration of spacecraft

    Science.gov (United States)

    Yefremov, Alexander P.

    2017-10-01

    Quaternion based math system of spacecraft reorientation is extended by admitting imaginary rotation parameters, thus involving hyperbolic functions. For simplicity only one simple hyperbolic rotation is added as the last one in the series of orthogonal matrices. The scheme is reduced to a single rotation about instant axis, and to transformation of primitive basis on a 2D fractal space of dimension ½. This new tool is proved to simultaneously reorient the spacecraft and to accelerate it the kinematics automatically described as relativistic. With a small speed the problem becomes a classical one.

  2. Molecular density functional theory of water describing hydrophobicity at short and long length scales.

    Science.gov (United States)

    Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

    2013-10-21

    We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619 (2013)] to the solvation of hydrophobic solutes of various sizes, going from angstroms to nanometers. The theory is based on the quadratic expansion of the excess free energy in terms of two classical density fields: the particle density and the multipolar polarization density. Its implementation requires as input a molecular model of water and three measurable bulk properties, namely, the structure factor and the k-dependent longitudinal and transverse dielectric susceptibilities. The fine three-dimensional water structure around small hydrophobic molecules is found to be well reproduced. In contrast, the computed solvation free-energies appear overestimated and do not exhibit the correct qualitative behavior when the hydrophobic solute is grown in size. These shortcomings are corrected, in the spirit of the Lum-Chandler-Weeks theory, by complementing the functional with a truncated hard-sphere functional acting beyond quadratic order in density, and making the resulting functional compatible with the Van-der-Waals theory of liquid-vapor coexistence at long range. Compared to available molecular simulations, the approach yields reasonable solvation structure and free energy of hard or soft spheres of increasing size, with a correct qualitative transition from a volume-driven to a surface-driven regime at the nanometer scale.

  3. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    Science.gov (United States)

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces.

  4. Diffusion measurements for molecular capsules: pulse sequences effect on water signal decay.

    Science.gov (United States)

    Avram, Liat; Cohen, Yoram

    2005-04-20

    Diffusion NMR and, more recently, diffusion ordered spectroscopy (DOSY) are gaining popularity as efficient tools for the characterization of supramolecular systems in solution. Here, using diffusion NMR of hydrogen-bond molecular capsules, we demonstrate that the use of different diffusion sequences may have a dramatic effect on exchanging peaks. In fact, we found that the signal decay of the water peak in [(1a)(6)(H(2)O)(8)] is monoexponential in the pulsed gradient spin-echo (PGSE) and stimulated echo (PGSTE) sequences and biexponential in the longitudinal eddy current delay (LED) and the bipolar longitudinal eddy current delay (BPLED) sequences, routinely used in modern DOSY experiments. By performing these diffusion measurements on molecular capsules, in which water is not part of the molecular capsules, we demonstrate that this phenomenon is observed only for water molecules that exchange between two sites that differ considerably in their diffusion coefficients. Degeneration of the LED or the BPLED sequences into PGSTE-type sequences by shortening the te period resulted in the disappearance of the extra slow diffusing component. The origin, as well as the implications of the different results obtained from conventional diffusion sequences, such as the PGSE and PGSTE as compared with the LED and BPLED sequences generally used in DOSY experiments, are briefly discussed.

  5. Re-orienting crop improvement for the changing climatic conditions of the 21st century

    Directory of Open Access Journals (Sweden)

    Mba Chikelu

    2012-06-01

    Full Text Available Abstract A 70% increase in food production is required over the next four decades to feed an ever-increasing population. The inherent difficulties in achieving this unprecedented increase are exacerbated by the yield-depressing consequences of climate change and variations and by the pressures on food supply by other competing demographic and socioeconomic demands. With the dwindling or stagnant agricultural land and water resources, the sought-after increases will therefore be attained mainly through the enhancement of crop productivity under eco-efficient crop production systems. ‘Smart’ crop varieties that yield more with fewer inputs will be pivotal to success. Plant breeding must be re-oriented in order to generate these ‘smart’ crop varieties. This paper highlights some of the scientific and technological tools that ought to be the staple of all breeding programs. We also make the case that plant breeding must be enabled by adequate policies, including those that spur innovation and investments. To arrest and reverse the worrisome trend of declining capacities for crop improvement, a new generation of plant breeders must also be trained. Equally important, winning partnerships, including public-private sector synergies, are needed for 21st century plant breeding to bear fruits. We also urge the adoption of the continuum approach to the management of plant genetic resources for food and agriculture as means to improved cohesion of the components of its value chain. Compellingly also, the National Agricultural Research and Extension System of developing countries require comprehensive overhauling and strengthening as crop improvement and other interventions require a sustained platform to be effective. The development of a suite of actionable policy interventions to be packaged for assisting countries in developing result-oriented breeding programs is also called for.

  6. Water accommodation on ice and organic surfaces: insights from environmental molecular beam experiments.

    Science.gov (United States)

    Kong, Xiangrui; Thomson, Erik S; Papagiannakopoulos, Panos; Johansson, Sofia M; Pettersson, Jan B C

    2014-11-26

    Water uptake on aerosol and cloud particles in the atmosphere modifies their chemistry and microphysics with important implications for climate on Earth. Here, we apply an environmental molecular beam (EMB) method to characterize water accommodation on ice and organic surfaces. The adsorption of surface-active compounds including short-chain alcohols, nitric acid, and acetic acid significantly affects accommodation of D2O on ice. n-Hexanol and n-butanol adlayers reduce water uptake by facilitating rapid desorption and function as inefficient barriers for accommodation as well as desorption of water, while the effect of adsorbed methanol is small. Water accommodation is close to unity on nitric-acid- and acetic-acid-covered ice, and accommodation is significantly more efficient than that on the bare ice surface. Water uptake is inefficient on solid alcohols and acetic acid but strongly enhanced on liquid phases including a quasi-liquid layer on solid n-butanol. The EMB method provides unique information on accommodation and rapid kinetics on volatile surfaces, and these studies suggest that adsorbed organic and acidic compounds need to be taken into account when describing water at environmental interfaces.

  7. Removal of phenolic estrogen pollutants from different sources of water using molecularly imprinted polymeric microspheres.

    Science.gov (United States)

    Lin, Yi; Shi, Yun; Jiang, Ming; Jin, Yuan; Peng, Yan; Lu, Bin; Dai, Kang

    2008-05-01

    The efficiency and effects of using Bisphenol A-molecularly imprinted polymeric microspheres (MIPMs) to remove phenolic estrogens from different sources of water were evaluated. MIPMs prepared by precipitation polymerization removed a group of phenolic estrogens from different kinds of water selectively and effectively. The highest removal efficiency was observed at pH=5. Fifty millimoles per litre ions or 10mg/L humid acid improved removal efficiency. MIPMs were more suitable to remove trace estrogens in large volume than high concentration of estrogens in small volume. The removal efficiency of spiked tap water, lake water and river water were better than that of distilled water. Hundred milligrams of MIPMs had higher removal selectivity and efficiency than those of 100mg or 300mg activated carbons. Moreover, MIPMs can be re-used for at least 30 times without losing any removal efficiency. MIPMs provided a selective, simple, reliable and practicable solution to remove trace phenolic estrogens from different sources of water.

  8. Molecular Structure and Dynamics of Water on Pristine and Strained Phosphorene: Wetting and Diffusion at Nanoscale

    Science.gov (United States)

    Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong

    2016-12-01

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.

  9. MOLECULAR MECHANICS OF WATER AND ITS ROLE IN INCREASE OF VIABILITY OF BIOSYSTEMS (STATE-OF-THE-ART REVIEW

    Directory of Open Access Journals (Sweden)

    E. Sh. Ismailov

    2013-01-01

    Full Text Available In work modern data on molecular structure of water in the form of the state-of-the-art review are considered. The irreplaceable role of water in activity processes is shown. Ways of effective use of active forms of water in technologies are defined.

  10. MOLECULAR MECHANICS OF WATER AND ITS ROLE IN INCREASE OF VIABILITY OF BIOSYSTEMS (STATE-OF-THE-ART REVIEW)

    OpenAIRE

    E. Sh. Ismailov; M. K. Kazimagomedov; G. M. Abacarov

    2013-01-01

    In work modern data on molecular structure of water in the form of the state-of-the-art review are considered. The irreplaceable role of water in activity processes is shown. Ways of effective use of active forms of water in technologies are defined.

  11. Quantify Water Extraction by TBP/Dodecane via Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Khomami, Bamin [Univ. of Tennessee, Knoxville, TN (United States); Cui, Shengting [Univ. of Tennessee, Knoxville, TN (United States); de Almeida, Valmor F. [Oak Ridge National Lab., Oak Ridge, TN (United States); Felker, Kevin [Oak Ridge National Lab., Oak Ridge, TN (United States)

    2013-05-16

    The purpose of this project is to quantify the interfacial transport of water into the most prevalent nuclear reprocessing solvent extractant mixture, namely tri-butyl- phosphate (TBP) and dodecane, via massively parallel molecular dynamics simulations on the most powerful machines available for open research. Specifically, we will accomplish this objective by evolving the water/TBP/dodecane system up to 1 ms elapsed time, and validate the simulation results by direct comparison with experimentally measured water solubility in the organic phase. The significance of this effort is to demonstrate for the first time that the combination of emerging simulation tools and state-of-the-art supercomputers can provide quantitative information on par to experimental measurements for solvent extraction systems of relevance to the nuclear fuel cycle. Results: Initially, the isolated single component, and single phase systems were studied followed by the two-phase, multicomponent counterpart. Specifically, the systems we studied were: pure TBP; pure n-dodecane; TBP/n-dodecane mixture; and the complete extraction system: water-TBP/n-dodecane two phase system to gain deep insight into the water extraction process. We have completely achieved our goal of simulating the molecular extraction of water molecules into the TBP/n-dodecane mixture up to the saturation point, and obtained favorable comparison with experimental data. Many insights into fundamental molecular level processes and physics were obtained from the process. Most importantly, we found that the dipole moment of the extracting agent is crucially important in affecting the interface roughness and the extraction rate of water molecules into the organic phase. In addition, we have identified shortcomings in the existing OPLS-AA force field potential for long-chain alkanes. The significance of this force field is that it is supposed to be optimized for molecular liquid simulations. We found that it failed for dodecane and

  12. Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution%Molecular Dynamics Simulation of Diffusion of Vitamin C in Water Solution

    Institute of Scientific and Technical Information of China (English)

    曾建平; 王爱民; 贡雪东; 陈景文; 陈松; 薛锋

    2012-01-01

    Under different temperatures and concentrations, the diffusion of Vitamin C (VC) in water solution was exam- ined by molecular dynamics simulation. The diffusion coefficients were calculated based on the Einstein equation. The influences of temperature, concentration, and simulation time on the diffusion coefficient were discussed. The results showed that at higher temperature and lower concentration the normal diffusions appear relatively late, but the linear range of mean square displacement curves continues longer than that at lower temperature and higher concentration. At the same temperature, the normal diffusion time increases and the diffusion coefficient decreases as the simulation concentration increases. These simulation results are in good agreement with experiments. Analyses of the pair correlation functions of the simulation systems showed that hydrogen bonds are mainly formed be- tween the hydrogen atoms of VC molecules and oxygen atoms of H20 molecules, rather than between the O atoms of VC molecules and H atoms of H20 molecules. The diffusion coefficient is higher as the interaction between water molecules and VC molecules is stronger when VC concentration is lower. The water in the model systems affects the diffusion of VC molecules by the short-range repulsion of O(H20)-O(H20) pairs and the non-bond interaction of H(H20)-H(H20) pairs. The short-range repulsion of O(H20)-O(H20) pairs is greater when VC concentration is higher, the diffusion of VC is weaker. The greater the non-bond interaction of H(H20)-H(H20) pairs is, the higher the VC diffusion is. It is expected that this study can provide a theoretical direction for the experiments on the mass transfer of VC in water solution.

  13. Molecular dynamics simulations of NMR relaxation and diffusion of bulk hydrocarbons and water

    Science.gov (United States)

    Singer, Philip M.; Asthagiri, Dilip; Chapman, Walter G.; Hirasaki, George J.

    2017-04-01

    Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1,2 in the fast motion regime where T1 =T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.

  14. Metastable liquid-liquid transition in a molecular model of water

    Science.gov (United States)

    Palmer, Jeremy C.; Martelli, Fausto; Liu, Yang; Car, Roberto; Panagiotopoulos, Athanassios Z.; Debenedetti, Pablo G.

    2014-06-01

    Liquid water's isothermal compressibility and isobaric heat capacity, and the magnitude of its thermal expansion coefficient, increase sharply on cooling below the equilibrium freezing point. Many experimental, theoretical and computational studies have sought to understand the molecular origin and implications of this anomalous behaviour. Of the different theoretical scenarios put forward, one posits the existence of a first-order phase transition that involves two forms of liquid water and terminates at a critical point located at deeply supercooled conditions. Some experimental evidence is consistent with this hypothesis, but no definitive proof of a liquid-liquid transition in water has been obtained to date: rapid ice crystallization has so far prevented decisive measurements on deeply supercooled water, although this challenge has been overcome recently. Computer simulations are therefore crucial for exploring water's structure and behaviour in this regime, and have shown that some water models exhibit liquid-liquid transitions and others do not. However, recent work has argued that the liquid-liquid transition has been mistakenly interpreted, and is in fact a liquid-crystal transition in all atomistic models of water. Here we show, by studying the liquid-liquid transition in the ST2 model of water with the use of six advanced sampling methods to compute the free-energy surface, that two metastable liquid phases and a stable crystal phase exist at the same deeply supercooled thermodynamic condition, and that the transition between the two liquids satisfies the thermodynamic criteria of a first-order transition. We follow the rearrangement of water's coordination shell and topological ring structure along a thermodynamically reversible path from the low-density liquid to cubic ice. We also show that the system fluctuates freely between the two liquid phases rather than crystallizing. These findings provide unambiguous evidence for a liquid-liquid transition in

  15. Molecular dynamics simulations of proton-ordered water confined in low-diameter carbon nanotubes.

    Science.gov (United States)

    Li, Shujuan; Schmidt, Burkhard

    2015-03-21

    The present work deals with molecular dynamics simulations of water confined in single-walled carbon nanotubes (CNTs), with emphasis on the proton-ordering of water and its polarization. First, the water occupancy of open-ended armchair and zigzag CNTs immersed in water under ambient NPT conditions is calculated for various water models, and for varying Lennard-Jones parameters of the water-carbon interaction. As a function of the CNT diameter, the water density displays several oscillations before converging to the bulk value. Based on these results, the water structures encapsulated in 10 nm long armchair CNTs (n,n) with 5 ≤ n ≤ 10, are investigated under NVT conditions. Inside the smallest nanotubes (n = 5, 6) highly ferroelectric (FE), quasi-one-dimensional water chains are found while inside the other CNTs water molecules assemble into single-walled ice nanotubes (INTs). There are several, near-degenerate minimum energy INT structures: single helical structures were found for 7 ≤ n ≤ 10, in all cases in FE arrangement. In addition, a double helical INT structure was found for n = 8 with an even higher polarization. Prism-like structures were found only for 8 ≤ n ≤ 10 with various FE, ferrielectric (FI), and antiferroelectric (AF, n = 9, 10) proton ordering. The coexistence of the nearly iso-energetic FE, FI, and AF INT structures separated by high barriers renders the molecular dynamics highly metastable, typically with nanosecond timescales at room temperature. Hence, the replica exchange simulation method is used to obtain populations of different INT states at finite temperatures. Many of the FE INT structures confined in low-diameter CNTs are still prevalent at room temperature. Both helix-helix and helix-prism structural transitions are detected which can be either continuous (around 470 K for n = 8) or discontinuous (at 218 K for n = 9). Also melting-like transitions are found in which the INT structures are disrupted leading to a loss of FE

  16. Selective removal of diclofenac from contaminated water using molecularly imprinted polymer microspheres

    Energy Technology Data Exchange (ETDEWEB)

    Dai Chaomeng [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China); Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Geissen, Sven-Uwe, E-mail: sven.geissen@tu-berlin.de [Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Zhang Yalei, E-mail: zhangyalei@tongji.edu.cn [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China); Zhang Yongjun [Department of Environmental Technology, Chair of Environmental Process Engineering, Technical University of Berlin, Berlin (Germany); Zhou Xuefei [State Key Laboratory of Pollution Control and Resource Reuse, Tongji University, Shanghai 200092 (China)

    2011-06-15

    A molecularly imprinted polymer (MIP) was synthesized by precipitation polymerization using diclofenac (DFC) as a template. Binding characteristics of the MIP were evaluated using equilibrium binding experiments. Compared to the non-imprinted polymer (NIP), the MIP showed an outstanding affinity towards DFC in an aqueous solution with a binding site capacity (Q{sub max}) of 324.8 mg/g and a dissociation constant (K{sub d}) of 3.99 mg/L. The feasibility of removing DFC from natural water by the MIP was demonstrated by using river water spiked with DFC. Effects of pH and humic acid on the selectivity and adsorption capacity of MIP were evaluated in detail. MIP had better selectivity and higher adsorption efficiency for DFC as compared to that of powdered activated carbon (PAC). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance, which is a definite advantage over single-use activated carbon. - Highlights: > A MIP was synthesized by precipitation polymerization using DFC as template. > The MIP had better selectivity and higher adsorption efficiency for DFC. > The MIP is an effective method for selective removal of DFC from complex water. > MIP reusability is a definite advantage over single-use activated carbon. - A diclofenac molecularly imprinted polymer synthesized by precipitation polymerization was used for the selective removal of diclofenac from contaminated water.

  17. Cholesterol effect on water permeability through DPPC and PSM lipid bilayers: a molecular dynamics study.

    Science.gov (United States)

    Saito, Hiroaki; Shinoda, Wataru

    2011-12-29

    Water permeability of two different lipid bilayers of dipalmitoylphosphatidylcholine (DPPC) and palmitoylsphingomyelin (PSM) in the absence and presence of cholesterol (0-50 mol %) have been studied by molecular dynamics simulations to elucidate the molecular mechanism of the reduction in water leakage across the membranes by the addition of cholesterol. An enhanced free energy barrier was observed in these membranes with increased cholesterol concentration, and this was explained by the reduced cavity density around the cholesterol in the hydrophobic membrane core. There was an increase of trans conformers in the hydrophobic lipid chains adjacent to the cholesterol, which reduced the cavity density. The enhanced free energy barrier was found to be the main reason to reduce the water permeability with increased cholesterol concentration. At low cholesterol concentrations the PSM bilayer exhibited a higher free energy barrier than the DPPC bilayer for water permeation, while at greater than 30 mol % of cholesterol the difference became minor. This tendency for the PSM and DPPC bilayers to resemble each other at higher cholesterol concentrations was similar to commonly observed trends in several structural properties, such as order parameters, cross-sectional area per molecule, and cavity density profiles in the hydrophobic regions of bilayer membranes. These results demonstrate that DPPC and PSM bilayers with high cholesterol contents possess similar physical properties, which suggests that the solubility of cholesterol in these lipid bilayers has importance for an understanding of multicomponent lipid membranes with cholesterol.

  18. Animal Hairs as Water-stimulated Shape Memory Materials: Mechanism and Structural Networks in Molecular Assemblies

    Science.gov (United States)

    Xiao, Xueliang; Hu, Jinlian

    2016-05-01

    Animal hairs consisting of α-keratin biopolymers existing broadly in nature may be responsive to water for recovery to the innate shape from their fixed deformation, thus possess smart behavior, namely shape memory effect (SME). In this article, three typical animal hair fibers were first time investigated for their water-stimulated SME, and therefrom to identify the corresponding net-points and switches in their molecular and morphological structures. Experimentally, the SME manifested a good stability of high shape fixation ratio and reasonable recovery rate after many cycles of deformation programming under water stimulation. The effects of hydration on hair lateral size, recovery kinetics, dynamic mechanical behaviors and structural components (crystal, disulfide and hydrogen bonds) were then systematically studied. SME mechanisms were explored based on the variations of structural components in molecular assemblies of such smart fibers. A hybrid structural network model with single-switch and twin-net-points was thereafter proposed to interpret the water-stimulated shape memory mechanism of animal hairs. This original work is expected to provide inspiration for exploring other natural materials to reveal their smart functions and natural laws in animals including human as well as making more remarkable synthetic smart materials.

  19. Molecular density functional theory of water including density-polarization coupling.

    Science.gov (United States)

    Jeanmairet, Guillaume; Levy, Nicolas; Levesque, Maximilien; Borgis, Daniel

    2016-06-22

    We present a three-dimensional molecular density functional theory of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: (i) scalar density and vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and (ii) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

  20. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  1. Enhanced heating of salty ice and water under microwaves: molecular dynamics study.

    Science.gov (United States)

    Tanaka, Motohiko; Sato, Motoyasu

    2008-01-01

    Through the use of molecular dynamics simulations, we have studied the enhanced heating of salty ice and water by the electric field of applied microwaves at 2.5 GHz, and in the range of 2.5-10 GHz for the frequency dependence. We show that water molecules in salty ice are allowed to rotate in response to the microwave electric field to the extent comparable to those in pure water because the molecules in salty ice are loosely tied by hydrogen bonds with adjacent molecules unlike rigidly bonded pure ice. The weakening of hydrogen-bonded network of molecules in salty ice is mainly due to the electrostatic effect of salt ions rather than the short-range geometrical (size) effect of salt since the presence of salt ions with small radii causes similar enhanced heating.

  2. Molecular density functional theory of water including density-polarization coupling

    CERN Document Server

    Jeanmairet, Guillaume; Levesque, Maximilien; Borgis, Daniel

    2016-01-01

    We present a three-dimensional molecular density functional theory (MDFT) of water derived from first-principles that relies on the particle's density and multipolar polarization density and includes the density-polarization coupling. This brings two main benefits: ($i$) a scalar density and a vectorial multipolar polarization density fields are much more tractable and give more physical insight than the full position and orientation densities, and ($ii$) it includes the full density-polarization coupling of water, that is known to be non-vanishing but has never been taken into account. Furthermore, the theory requires only the partial charge distribution of a water molecule and three measurable bulk properties, namely the structure factor and the Fourier components of the longitudinal and transverse dielectric susceptibilities.

  3. Theoretical Structures of Triflic Acid-Water Clusters and the Molecular Mechanism of Proton Dissociation

    Energy Technology Data Exchange (ETDEWEB)

    Paddison, S.J.; Pratt, L.R.; Zawodzinski, T.A.

    1998-11-01

    Structural and energetic information required for recently proposed quasi-chemical theories of solution chemistry have been obtained for clusters of water with triflic acid, CF{sub 3}SO{sub 3}H(H{sub 2}O){sub n} for n=1-6. Quantum mechanical calculations on the clusters indicate that the acid proton does not dissociate with n=1 or 2 hydrating water molecules, but does dissociate for n>=3 water molecule partners. The computed minimum energy structures indicate that both ''Eigen'' (H{sub 9}O{sub 4}{sup +}) (n=3,4,6) and ''Zundel'' (H{sub 5}O{sub 2}{sup +}) (n=5) structures are likely to play a role in the molecular mechanism of acid dissociation in Nafion{reg_sign}.

  4. Molecular Dynamics Studies of Structure and Functions of Water-Membrane Interfaces

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A large number of essential cellular processes occur at the interfaces between water and membranes. The selectivity and dynamics of these processes are largely determined by the structural and electrical properties of the water-membrane interface. We investigate these properties by the molecular dynamics method. Over the time scales of the simulations, the membrane undergoes fluctuations described by the capillary wave model. These fluctuations produce occasional thinning defects in the membrane which provide effective pathways for passive transport of ions and small molecules across the membrane. Ions moving through the membrane markedly disrupt its structure and allow for significant water penetration into the membrane interior. Selectivity of transport, with respect to ionic charge, is determined by the interfacial electrostatic potential. Many small molecules. of potential significance in catalysis, bioenergetics and pharmacology, are shown to bind to the interface. The energetics and dynamics of this process will be discussed.

  5. Molecular dynamics simulations of the orthoclase (001)- and (010)-water interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Liu, Chongxuan; Ilton, Eugene S.

    2008-03-15

    Molecular dynamics simulations of water in contact with the (001) and (010) surfaces of orthoclase (KAlSi3O8) were carried out to investigate the structure and dynamics of the feldspar-water interface, contrast the intrinsic structural properties of the two surfaces, and provide a basis for future work on the diffusion of ions and molecules in microscopic mineral fractures. Electron density profiles were computed from the molecular dynamics trajectories and compared with those derived experimentally from high-resolution X-ray reflectivity measurements by Fenter and co-workers (Fenter et al., 2003a). For each surface, three scenarios were considered whereby the interfacial species is potassium, water, or a hydronium ion. Excellent agreement was obtained for the (001) surface when potassium is the predominant interfacial species. Good agreement was found for the (010) surface with some discrepancies which could be due in part to the fact that our model does not take into account the increased roughness of the (010) surface compared to the (001) surface. The two surfaces showed similarities in the extent of water ordering at the interface, the activation energies for water and potassium desorption, and the adsorption localization of interfacial species. However, there are also important differences between the two surfaces in the coordination of a given adsorbed species, adsorption sites density, and the propensity for water molecules in the adsorbed and first hydration layers to coordinate to surface bridging oxygen atoms. These differences may have implications for the extent of dissolution in the proton-promoted regime since hydrolysis of Si(Al)-O-Si(Al) bonds is thought to be the major dissolution mechanism.

  6. Water radiolysis by low-energy carbon projectiles from first-principles molecular dynamics

    Science.gov (United States)

    Kohanoff, Jorge

    2017-01-01

    Water radiolysis by low-energy carbon projectiles is studied by first-principles molecular dynamics. Carbon projectiles of kinetic energies between 175 eV and 2.8 keV are shot across liquid water. Apart from translational, rotational and vibrational excitation, they produce water dissociation. The most abundant products are H and OH fragments. We find that the maximum spatial production of radiolysis products, not only occurs at low velocities, but also well below the maximum of energy deposition, reaching one H every 5 Å at the lowest speed studied (1 Bohr/fs), dissociative collisions being more significant at low velocity while the amount of energy required to dissociate water is constant and much smaller than the projectile’s energy. A substantial fraction of the energy transferred to fragments, especially for high velocity projectiles, is in the form of kinetic energy, such fragments becoming secondary projectiles themselves. High velocity projectiles give rise to well-defined binary collisions, which should be amenable to binary approximations. This is not the case for lower velocities, where multiple collision events are observed. H secondary projectiles tend to move as radicals at high velocity, as cations when slower. We observe the generation of new species such as hydrogen peroxide and formic acid. The former occurs when an O radical created in the collision process attacks a water molecule at the O site. The latter when the C projectile is completely stopped and reacts with two water molecules. PMID:28267804

  7. Dynamics of biological water: insights from molecular modeling of light scattering in aqueous trehalose solutions.

    Science.gov (United States)

    Lupi, Laura; Comez, Lucia; Paolantoni, Marco; Fioretto, Daniele; Ladanyi, Branka M

    2012-06-28

    Extended depolarized light scattering (EDLS) measurements have been recently employed to investigate the dynamics of water solvating biological molecules, giving evidence of the presence of two different dynamical regimes among water molecules. An interpretation of EDLS has been proposed that provides an independent estimate of the retardation factor of slowdown with respect to fast water molecules and of the number of solvent molecules affected by this slowing down. Nevertheless this measure is an inherently complex one, due to the collective nature of the physical property probed. In the present work a molecular dynamics (MD) approach has been used to more deeply understand experimental results. Time correlation functions of the collective polarizability anisotropy have been calculated for the prototype disaccharide trehalose in aqueous solutions as a function of concentration. The unique capability of MD to disentangle the contributions to the dynamics arising from solute, solvent, and cross terms between the two allowed us to check the reliability of an interpretation that assumes a spectral separation of water and sugar dynamics, as well as to highlight the very presence of two distinct relaxation processes in water. The two processes have been attributed to the dynamics of bulk and hydration water, respectively. A retardation factor of ~5 and concentration dependent hydration numbers have been observed, in good agreement with experimental results [Paolantoni, M.; et al. J. Phys. Chem. B 2009, 113, 7874-7878].

  8. Molecular dynamics study of oil detachment from an amorphous silica surface in water medium

    Science.gov (United States)

    Chen, Jiaxuan; Si, Hao; Chen, Wenyang

    2015-10-01

    In this paper, the mechanism of oil detachment from optical glass in water medium is studied by using molecular dynamics simulation. At the beginning, some undecane molecules are adsorbed on the amorphous silica surface to get contaminated glass. Upon addition of 6000 water molecules, most of the undecane molecules on the substrate surface can be detached from an amorphous silica surface through three stages. The formation of different directions of water channels is vital for oil detachment. The electrostatic interaction of water substrate contributes to disturbing the aggregates of undecane molecules and the H-bonding interaction between the water molecules is helpful for the oil puddle away from the substrate. However, there is still some oil molecules residue on the substrate surface after water cleaning. The simulation results showed that the specific ring potential well of amorphous silica surface will hinder the detachment of oil molecules. We also find that the formation of the specific ring potential well is related to the number of atoms and the average radius in silica atomic rings. Increasing the upward lift force, which acts on the hydrocarbon tail of oil molecules, will be benefit to clear the oil pollution residues from the glass surface.

  9. Curvature induced L-defects in water conduction in carbon nanotubes.

    Science.gov (United States)

    Zimmerli, Urs; Gonnet, Pedro G; Walther, Jens H; Koumoutsakos, Petros

    2005-06-01

    We conduct molecular dynamics simulations to study the effect of the curvature induced static dipole moment of small open-ended single-walled carbon nanotubes (CNTs) immersed in water. This dipole moment generates a nonuniform electric field, changing the energy landscape in the CNT and altering the water conduction process. The CNT remains practically filled with water at all times, whereas intermittent filling is observed when the dipole term is not included. In addition, the dipole moment induces a preferential orientation of the water molecules near the end regions of the nanotube, which in turn causes a reorientation of the water chain in the middle of the nanotube. The most prominent feature of this reorientation is an L-defect in the chain of water molecules inside the CNT. The analysis of the water energetics and structural characteristics inside and in the vicinity of the CNT helps to identify the role of the dipole moment and to suggest possible mechanisms for controlled water and proton transport at the nanoscale.

  10. The molecular structure of the interface between water and a hydrophobic substrate is liquid-vapor like.

    Science.gov (United States)

    Willard, Adam P; Chandler, David

    2014-11-14

    With molecular simulation for water and a tunable hydrophobic substrate, we apply the instantaneous interface construction [A. P. Willard and D. Chandler, "Instantaneous liquid interfaces," J. Phys. Chem. B 114, 1954-1958 (2010)] to examine the similarity between a water-vapor interface and a water-hydrophobic surface interface. We show that attractive interactions between a hydrophobic surface and water affect capillary wave fluctuations of the instantaneous liquid interface, but these attractive interactions have essentially no effect on the intrinsic interface. The intrinsic interface refers to molecular structure in terms of distances from the instantaneous interface. Further, the intrinsic interface of liquid water and a hydrophobic substrate differs little from that of water and its vapor. The same is not true, we show, for an interface between water and a hydrophilic substrate. In that case, strong directional substrate-water interactions disrupt the liquid-vapor-like interfacial hydrogen bonding network.

  11. Spatial variations in the molecular diversity of dissolved organic matter in water moving through a boreal forest in eastern Finland

    Science.gov (United States)

    Ide, Jun’ichiro; Ohashi, Mizue; Takahashi, Katsutoshi; Sugiyama, Yuko; Piirainen, Sirpa; Kortelainen, Pirkko; Fujitake, Nobuhide; Yamase, Keitaro; Ohte, Nobuhito; Moritani, Mina; Hara, Miyako; Finér, Leena

    2017-01-01

    Dissolved organic matter (DOM) strongly affects water quality within boreal forest ecosystems. However, how the quality of DOM itself changes spatially is not well understood. In this study, to examine how the diversity of DOM molecules varies in water moving through a boreal forest, the number of DOM molecules in different water samples, i.e., rainwater, throughfall, soil water, groundwater, and stream water was determined using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in Norway spruce and Scots pine stands in eastern Finland during May and June 2010. The number of molecular compounds identified by FT-ICR MS (molecular diversity) ranged from 865 to 2,194, revealing large DOM molecular diversity in the water samples. Additionally, some of the molecular compounds were shared between different water samples. The DOM molecular diversity linearly correlated with the number of low-biodegradable molecules, such as, lignin-like molecules (lignins), but not with dissolved organic carbon concentration. The number of lignins shared between different sampling locations was larger than that of any other biomolecular class. Our results suggest that low-biodegradable molecules, especially lignins, regulate spatial variations in DOM molecular diversity in boreal forests. PMID:28186141

  12. Social reorientation in adolescence : neurobiological changes and individual differences in empathic concern

    NARCIS (Netherlands)

    Overgaauw, Sandy

    2015-01-01

    One of the most prominent changes in adolescence is social reorientation. In other words, adolescents develop more intimate relationships with peers, they discover what it is like to be involved in a romantic relationship, and they take (social) risks by for example showing risky driving in the pres

  13. Use of Geometry for Spatial Reorientation in Children Applies Only to Symmetric Spaces

    Science.gov (United States)

    Lew, Adina R.; Gibbons, Bryony; Murphy, Caroline; Bremner, J. Gavin

    2010-01-01

    Proponents of the geometric module hypothesis argue that following disorientation, many species reorient by use of macro-environment geometry. It is suggested that attention to the surface layout geometry of natural terrain features may have been selected for over evolutionary time due to the enduring and unambiguous location information it…

  14. Why Size Counts: Children's Spatial Reorientation in Large and Small Enclosures

    Science.gov (United States)

    Learmonth, Amy E.; Newcombe, Nora S.; Sheridan, Natalie; Jones, Meredith

    2008-01-01

    When mobile organisms are spatially disoriented, for instance by rapid repetitive movement, they must re-establish orientation. Past research has shown that the geometry of enclosing spaces is consistently used for reorientation by a wide variety of species, but that non-geometric features are not always used. Based on these findings, some…

  15. Time-dependent solution for reorientation of rotating tidally deformed visco-elastic bodies

    Science.gov (United States)

    Hu, Haiyang; van der Wal, Wouter; Vermeersen, Bert

    2017-04-01

    Many icy satellites or planets contain features which suggest a (past) reorientation of the body, such as the tiger stripes on Enceladus and the heart-shaped Sputnik Planum on Pluto. Most of these icy bodies are tidally locked and this creates a large tidal bulge which is about three times of its centrifugal (equatorial) bulge. To study the reorientation of such rotating tidally deformed body is complicated and most previous studies apply the so-called fluid limit method. The fluid limit approach ignores the viscous response of the body and assumes that it immediately reaches its fluid limit when simulating the reorientation due to a changing load. As a result, this method can only simulate cases when the change in the load is much slower than the dominant viscous modes of the body. For other kinds of load, for instance, a Heaviside load due to an impact which creates an instant relocation of mass, it does not give us a prediction of how the reorientation is accomplished (e.g. How fast? Along which path?). We establish a new method which can give an accurate time-dependent solution for reorientation of rotating tidally deformed bodies. Our method can be applied both semi-analytically or numerically (with finite element method) to include features such as lateral heterogeneity or non-linear material. We also present an extension of our method to simulate the e ffect of a fossil bulge. With our method, we show that reorientation of a tidally deformed body driven by a positive mass anomaly near the poles has a preference for rotating around the tidal axis instead of towards it, contrary to predictions in previous studies. References Hu, H., W. van der Wal and L.L.A. Vermeersen (2017). A numerical method for reorientation of rotating tidally deformed visco-elastic bodies. Journal of Geophysical Research: Planets, doi:10.1002/2016JE005114, 2016JE005114. Matsuyama, I. and Nimmo, F. (2007). Rotational stability of tidally deformed planetary bodies. Journal of Geophysical

  16. Molecular resolution friction microscopy of Cu phthalocyanine thin films on dolomite (104) in water.

    Science.gov (United States)

    Nita, Paweł; Pimentel, Carlos; Luo, Feng; Milián-Medina, Begoña; Gierschner, Johannes; Pina, Carlos M; Gnecco, Enrico

    2014-07-21

    The reliability of ultrathin organic layers as active components for molecular electronic devices depends ultimately on an accurate characterization of the layer morphology and ability to withstand mechanical stresses on the nanoscale. To this end, since the molecular layers need to be electrically decoupled using thick insulating substrates, the use of AFM becomes mandatory. Here, we show how friction force microscopy (FFM) in water allows us to identify the orientation of copper(ii)phthalocyanine (CuPc) molecules previously self-assembled on a dolomite (104) mineral surface in ultra-high vacuum. The molecular features observed in the friction images show that the CuPc molecules are stacked in parallel rows with no preferential orientation with respect to the dolomite lattice, while the stacking features resemble well the single CuPc crystal structure. This proves that the substrate induction is low and makes friction force microscopy in water a suitable alternative to more demanding dynamic AFM techniques in ultra-high vacuum.

  17. Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)-Water Interface

    Energy Technology Data Exchange (ETDEWEB)

    Kerisit, Sebastien N.; Zarzycki, Piotr P.; Rosso, Kevin M.

    2015-04-30

    The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.

  18. Formation and growth of molecular clusters containing sulfuric acid, water, ammonia, and dimethylamine.

    Science.gov (United States)

    DePalma, Joseph W; Doren, Douglas J; Johnston, Murray V

    2014-07-24

    The structures and thermochemistry of molecular clusters containing sulfuric acid, water, ammonia, and/or dimethylamine ((CH3)2NH or DMA) are explored using a combination of Monte Carlo configuration sampling, semiempirical calculations, and density functional theory (DFT) calculations. Clusters are of the general form [(BH(+))n(HSO4(-))n(H2O)y], where B = NH3 or DMA, 2 ≤ n ≤ 8, and 0 ≤ y ≤ 10. Cluster formulas are written based on the computed structures, which uniformly show proton transfer from each sulfuric acid molecule to a base molecule while the water molecules remain un-ionized. Cluster formation is energetically favorable, owing to strong electrostatic attraction among the ions. Water has a minor effect on the energetics of cluster formation, lowering the free energy of formation by ∼ 10% depending on the cluster size and number of water molecules. Cluster growth (addition of one base molecule and one sulfuric acid molecule to a pre-existing cluster) and base substitution (substituting DMA for ammonia) are also energetically favorable processes for both anhydrous and hydrated clusters. However, the effect of water is different for different bases. Hydrated ammonium bisulfate clusters have a more favorable free energy for growth (i.e., incrementing n with fixed y) than anhydrous clusters, while the reverse is observed for dimethylammonium bisulfate clusters, where the free energy for growth is more favorable for anhydrous clusters. The substitution of DMA for ammonia in bisulfate clusters is favorable but exhibits a complex water dependence. Base substitution in smaller bisulfate clusters is enhanced by the presence of water, while base substitution in larger bisulfate clusters is less favorable for hydrated clusters than that for anhydrous clusters. While DMA substitution can stabilize small clusters containing one or a few sulfuric acid molecules, the free energy advantage of forming amine clusters relative to ammonia clusters becomes less

  19. Investigating the quartz (1010)/water interface using classical and ab initio molecular dynamics.

    Science.gov (United States)

    Skelton, A A; Wesolowski, D J; Cummings, P T

    2011-07-19

    Two different terminations of the (1010) surface of quartz (α and β) interacting with water are simulated by classical (CMD) (using two different force fields) and ab initio molecular dynamics (AIMD) and compared with previously published X-ray reflectivity (XR) experiments. Radial distribution functions between hydroxyl and water show good agreement between AIMD and CMD using the ClayFF force field for both terminations. The Lopes et al. (Lopes, P. E. M.; Murashov, V.; Tazi, M.; Demchuk, E.; MacKerell, A. D. J. Phys. Chem. B2006, 110, 2782-2792) force field (LFF), however, underestimates the extent of hydroxyl-water hydrogen bonding. The β termination is found to contain hydroxyl-hydroxyl hydrogen bonds; the quartz surface hydroxyl hydrogens and oxygens that hydrogen bond with each other exhibit greatly reduced hydrogen bonding to water. Conversely, the hydroxyl hydrogen and oxygens that are not hydrogen bonded to other surface hydroxyls but are connected to those that are show a considerable amount of hydrogen bonding to water. The electron density distribution of an annealed surface of quartz (1010) obtained by XR is in qualitative agreement with electron densities calculated by CMD and AIMD. In all simulation methods, the interfacial water peak appears farther from the surface than observed by XR. Agreement among AIMD, LFF, and XR is observed for the relaxation of the near-surface atoms; however, ClayFF shows a larger discrepancy. Overall, results show that for both terminations of (1010), LFF treats the near-surface structure more accurately whereas ClayFF treats the interfacial water structure more accurately. It is shown that the number of hydroxyl and water hydrogen bonds to the bridging Si-O-Si oxygens connecting the surface silica groups to the rest of the crystal is much greater for the α than the β termination. It is suggested that this may play a role in the greater resistance to dissolution of the β termination than that of the α termination.

  20. Mechanics and molecular filtration performance of graphyne nanoweb membranes for selective water purification

    Science.gov (United States)

    Lin, Shangchao; Buehler, Markus J.

    2013-11-01

    Two-dimensional carbon materials such as the 2D nanoweb-like graphyne membrane are promising as molecular sieves for energy and environmental applications. Based on the application of water purification - the removal of contaminants from wastewater and seawater - here we use molecular dynamics (MD) simulations to investigate the interplay between mechanical forces, filtration mechanisms, and overall performance for graphyne membranes with different pore sizes. We carry out biaxial tensile tests and verify the superior mechanical robustness and tolerance of graphyne membranes against possible deformations from the membrane installation process. A possible ultimate stress in excess of 15 GPa and an ultimate strain of 1.2-2.7% are determined. We also demonstrate their excellent filtration performance with barrier-free water permeation and perfect rejection of the representative contaminants considered here, including divalent heavy metal salts (copper sulfate), hydrophobic organic chemicals (benzene and carbon tetrachloride), and inorganic monovalent salts (sodium chloride). We find that graphtriyne, with an effective pore diameter of 3.8 Å, exhibits an optimal purification performance, because the contaminant rejection rate is more sensitive to pore size than water permeability. In addition, we find that the hydrophobic graphyne membranes exhibit higher rejection rates for hydrophilic contaminants compared to the hydrophobic ones. This size exclusion effect is a result of the larger hydrated radii of hydrophilic species due to stronger interactions between them and water molecules. Finally, we find that the maximum deformation of graphtriyne at the ultimate strain before material failure has only a minor impact on its filtration performance. One of the advantages of using graphyne for water purification is that no chemical functionalization or defects need to be introduced, which maintains the structural integrity of the membrane, and possibly, the long-term device

  1. Calculation of heat capacities of light and heavy water by path-integral molecular dynamics

    Science.gov (United States)

    Shiga, Motoyuki; Shinoda, Wataru

    2005-10-01

    As an application of atomistic simulation methods to heat capacities, path-integral molecular dynamics has been used to calculate the constant-volume heat capacities of light and heavy water in the gas, liquid, and solid phases. While the classical simulation based on conventional molecular dynamics has estimated the heat capacities too high, the quantum simulation based on path-integral molecular dynamics has given reasonable results based on the simple point-charge/flexible potential model. The calculated heat capacities (divided by the Boltzmann constant) in the quantum simulation are 3.1 in the vapor H2O at 300 K, 6.9 in the liquid H2O at 300 K, and 4.1 in the ice IhH2O at 250 K, respectively, which are comparable to the experimental data of 3.04, 8.9, and 4.1, respectively. The quantum simulation also reproduces the isotope effect. The heat capacity in the liquid D2O has been calculated to be 10% higher than that of H2O, while it is 13% higher in the experiment. The results demonstrate that the path-integral simulation is a promising approach to quantitatively evaluate the heat capacities for molecular systems, taking account of quantum-mechanical vibrations as well as strongly anharmonic motions.

  2. Selective Adsorption on Fluorinated Plastic Enables the Optical Detection of Molecular Pollutants in Water

    Science.gov (United States)

    Lanfranco, R.; Giavazzi, F.; Salina, M.; Tagliabue, G.; Di Nicolò, E.; Bellini, T.; Buscaglia, M.

    2016-05-01

    Amorphous fluorinated plastic can be produced with a refractive index similar to that of water, a condition that makes it essentially invisible when immersed in aqueous solutions. Because of this property, even a small amount of adsorbed molecules on the plastic-water interface provides a detectable optical signal. We investigate two distinct substrates made of this material, characterized by different interface areas: a prism and a microporous membrane. We demonstrate that both substrates enable the label-free detection of molecular compounds in water even without any surface functionalization. The adsorption of molecules on the planar surface of the prism provides an increase of optical reflectivity, whereas the adsorption on the internal surface of the microporous membrane yields an increase of scattered light. Despite the different mechanisms, we find a similar optical response upon adsorption. We confirm this result by a theoretical model accounting for both reflection and scattering. We investigate the spontaneous adsorption process for different kinds of molecules: surfactants with different charges, a protein (lysozyme), and a constituent of gasoline (hexane). The measured equilibrium and kinetic constants for adsorption differ by orders of magnitudes among the different classes of molecules. By suitable analytical models, accounting for the effects of mass limitation and transport, we find a simple and general scaling of the adsorption parameters with the molecular size.

  3. The Aqueous Solvation of Water A Comparison of Continuum Methods with Molecular Dynamics

    CERN Document Server

    Rick, S W; Rick, Steven W.

    1994-01-01

    The calculation of the solvation properties of a single water molecule in liquid water is carried out in two ways. In the first, the water molecule is placed in a cavity and the solvent is treated as a dielectric continuum. This model is analyzed by numerically solving the Poisson equation using the DelPhi program. The resulting solvation properties depend sensitively on the shape and size of the cavity. In the second method, the solvent and solute molecules are treated explicitly in molecular dynamics simulations using Ewald boundary conditions. We find a 2 kcal/mole difference in solvation free energies predicted by these two methods when standard cavity radii are used. In addition, dielectric continuum theory assumes that the solvent reacts solely by realigning its electric moments linearly with the strength of the solute's electric field; the results of the molecular simulation show important non-linear effects. Non-linear solvent effects are generally of two types: dielectric saturation, due to solvent-s...

  4. Molecular density functional theory for water with liquid-gas coexistence and correct pressure

    Energy Technology Data Exchange (ETDEWEB)

    Jeanmairet, Guillaume, E-mail: g.jeanmairet@fkf.mpg.de; Levesque, Maximilien, E-mail: maximilien.levesque@ens.fr [École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris (France); Sergiievskyi, Volodymyr [SIS2M, LIONS, CEA, Saclay (France); Borgis, Daniel [École Normale Supérieure - PSL Research University, Département de Chimie, Sorbonne Universités - UPMC Univ. Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris (France); Maison de la Simulation, USR 3441, CEA - CNRS - INRIA - Univ. Paris-Sud - Univ. de Versailles, 91191 Gif-sur-Yvette Cedex (France)

    2015-04-21

    The solvation of hydrophobic solutes in water is special because liquid and gas are almost at coexistence. In the common hypernetted chain approximation to integral equations, or equivalently in the homogenous reference fluid of molecular density functional theory, coexistence is not taken into account. Hydration structures and energies of nanometer-scale hydrophobic solutes are thus incorrect. In this article, we propose a bridge functional that corrects this thermodynamic inconsistency by introducing a metastable gas phase for the homogeneous solvent. We show how this can be done by a third order expansion of the functional around the bulk liquid density that imposes the right pressure and the correct second order derivatives. Although this theory is not limited to water, we apply it to study hydrophobic solvation in water at room temperature and pressure and compare the results to all-atom simulations. The solvation free energy of small molecular solutes like n-alkanes and hard sphere solutes whose radii range from angstroms to nanometers is now in quantitative agreement with reference all atom simulations. The macroscopic liquid-gas surface tension predicted by the theory is comparable to experiments. This theory gives an alternative to the empirical hard sphere bridge correction used so far by several authors.

  5. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study.

    Science.gov (United States)

    Demontis, Pierfranco; Gulín-González, Jorge; Masia, Marco; Sant, Marco; Suffritti, Giuseppe B

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130-350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between "fragile" (at higher temperatures) and "strong" (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between "fragile" (at lower temperatures) and "strong" (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T(∗) ∼ 315 ± 5 K, was spotted at T(∗) ∼ 283 K and T(∗) ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible mechanisms of the two

  6. The molecular mobility of water in natural polymers : Silk Bombyx mori with a low water content as studied by H-1 DQF NMR

    NARCIS (Netherlands)

    Rodin, VV; Knight, DP

    2004-01-01

    The molecular mobility of water in fibres of natural silk (Bombyx mori) was studied by the double-quantum-filtered (DQF) and single-pulse H-1 NMR techniques. The results obtained showed a slow motion of water molecules and their strong interaction with silk macromolecules. At different model

  7. The molecular mobility of water in natural polymers : Silk Bombyx mori with a low water content as studied by H-1 DQF NMR

    NARCIS (Netherlands)

    Rodin, VV; Knight, DP

    2004-01-01

    The molecular mobility of water in fibres of natural silk (Bombyx mori) was studied by the double-quantum-filtered (DQF) and single-pulse H-1 NMR techniques. The results obtained showed a slow motion of water molecules and their strong interaction with silk macromolecules. At different model functio

  8. 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.

  9. Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water

    Science.gov (United States)

    Habershon, Scott; Fanourgakis, George S.; Manolopoulos, David E.

    2008-08-01

    The ring polymer molecular dynamics (RPMD) and partially adiabatic centroid molecular dynamics (PA-CMD) methods are compared and contrasted in an application to the infrared absorption spectrum of a recently parametrized flexible, polarizable, Thole-type potential energy model for liquid water. Both methods predict very similar spectra in the low-frequency librational and intramolecular bending region at wavenumbers below 2500 cm-1. However, the RPMD spectrum is contaminated in the high-frequency O-H stretching region by contributions from the internal vibrational modes of the ring polymer. This problem is avoided in the PA-CMD method, which adjusts the elements of the Parrinello-Rahman mass matrix so as to shift the frequencies of these vibrational modes beyond the spectral range of interest. PA-CMD does not require any more computational effort than RPMD and it is clearly the better of the two methods for simulating vibrational spectra.

  10. Physiological and molecular mechanisms of salt and water homeostasis in the nematode Caenorhabditis elegans.

    Science.gov (United States)

    Choe, Keith P

    2013-08-01

    Intracellular salt and water homeostasis is essential for all cellular life. Extracellular salt and water homeostasis is also important for multicellular organisms. Many fundamental mechanisms of compensation for osmotic perturbations are well defined and conserved. Alternatively, molecular mechanisms of detecting salt and water imbalances and regulating compensatory responses are generally poorly defined for animals. Throughout the last century, researchers studying vertebrates and vertebrate cells made critical contributions to our understanding of osmoregulation, especially mechanisms of salt and water transport and organic osmolyte accumulation. Researchers have more recently started using invertebrate model organisms with defined genomes and well-established methods of genetic manipulation to begin defining the genes and integrated regulatory networks that respond to osmotic stress. The nematode Caenorhabditis elegans is well suited to these studies. Here, I introduce osmoregulatory mechanisms in this model, discuss experimental advantages and limitations, and review important findings. Key discoveries include defining genetic mechanisms of osmolarity sensing in neurons, identifying protein damage as a sensor and principle determinant of hypertonic stress resistance, and identification of a putative sensor for hypertonic stress associated with the extracellular matrix. Many of these processes and pathways are conserved and, therefore, provide new insights into salt and water homeostasis in other animals, including mammals.

  11. First principles molecular dynamics of metal/water interfaces under bias potential

    Science.gov (United States)

    Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre; Fernandez-Serra, Marivi

    2014-03-01

    Understanding the interaction of the water-metal system at an atomic level is extremely important in electrocatalysts for fuel cells, photocatalysis among other systems. The question of the interface energetics involves a detailed study of the nature of the interactions between water-water and water-substrate. A first principles description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemically processes. In this work we describe, using first principles molecular dynamics simulations, the dynamics of a combined surface(Au and Pd)/water system both in the presence and absence of an external bias potential applied to the electrodes, as one would come across in electrochemistry. This is accomplished using a combination of density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), thus accounting for the fact that one is dealing with an out-of-equilibrium open system, with and without van der Waals interactions. DOE Early Career Award No. DE-SC0003871.

  12. Isolation and Molecular Characterization of Free-Living Amoebae from Different Water Sources in Italy

    Directory of Open Access Journals (Sweden)

    Margherita Montalbano Di Filippo

    2015-03-01

    Full Text Available Free-living amoebae (FLA are protozoa ubiquitous in Nature, isolated from a variety of environments worldwide. In addition to their natural distribution, some species have been found to be pathogenic to humans. In the present study a survey was conducted in order to evaluate the presence and to characterize at molecular level the isolates of amoebic organisms collected from different water sources in Italy. A total of 160 water samples were analyzed by culture and microscopic examination. FLA were found in 46 (28.7% of the investigated water samples. Groundwater, well waters, and ornamental fountain waters were the sources with higher prevalence rates (85.7%, 50.0%, and 45.9%, respectively. Identification of FLA species/genotypes, based on the 18S rDNA regions, allowed to identify 18 (39.1% Acanthamoeba isolates (genotypes T4 and T15 and 21 (45.6% Vermamoeba vermiformis isolates. Other FLA species, including Vahlkampfia sp. and Naegleria spp., previously reported in Italy, were not recovered. The occurrence of potentially pathogenic free-living amoebae in habitats related to human population, as reported in the present study, supports the relevance of FLA as a potential health threat to humans.

  13. Isolation and molecular characterization of free-living amoebae from different water sources in Italy.

    Science.gov (United States)

    Montalbano Di Filippo, Margherita; Santoro, Maristella; Lovreglio, Piero; Monno, Rosa; Capolongo, Carmen; Calia, Carla; Fumarola, Luciana; D'Alfonso, Rossella; Berrilli, Federica; Di Cave, David

    2015-03-24

    Free-living amoebae (FLA) are protozoa ubiquitous in Nature, isolated from a variety of environments worldwide. In addition to their natural distribution, some species have been found to be pathogenic to humans. In the present study a survey was conducted in order to evaluate the presence and to characterize at molecular level the isolates of amoebic organisms collected from different water sources in Italy. A total of 160 water samples were analyzed by culture and microscopic examination. FLA were found in 46 (28.7%) of the investigated water samples. Groundwater, well waters, and ornamental fountain waters were the sources with higher prevalence rates (85.7%, 50.0%, and 45.9%, respectively). Identification of FLA species/genotypes, based on the 18S rDNA regions, allowed to identify 18 (39.1%) Acanthamoeba isolates (genotypes T4 and T15) and 21 (45.6%) Vermamoeba vermiformis isolates. Other FLA species, including Vahlkampfia sp. and Naegleria spp., previously reported in Italy, were not recovered. The occurrence of potentially pathogenic free-living amoebae in habitats related to human population, as reported in the present study, supports the relevance of FLA as a potential health threat to humans.

  14. Understanding the structure of hydrophobic surfactants at the air/water interface from molecular level.

    Science.gov (United States)

    Zhang, Li; Liu, Zhipei; Ren, Tao; Wu, Pan; Shen, Jia-Wei; Zhang, Wei; Wang, Xinping

    2014-11-25

    Understanding the behavior of fluorocarbon surfactants at the air/water interface is crucial for many applications, such as lubricants, paints, cosmetics, and fire-fighting foams. In this study, molecular dynamics (MD) simulations were employed to investigate the microscopic properties of non-ionic fluorocarbon surfactants at the air/water interface. Several properties, including the distribution of head groups, the distribution probability of the tilt angle between hydrophobic tails with respect to the xy plane, and the order parameter of surfactants, were computed to probe the structure of hydrophobic surfactants at the air/water interface. The effects of the monomer structure on interfacial phenomena of non-ionic surfactants were investigated as well. It is observed that the structure of fluorocarbon surfactants at the air/water interface is more ordered than that of hydrocarbons, which is dominated by the van der Waals interaction between surfactants and water molecules. However, replacing one or two CF2 with one or two CH2 group does not significantly influence the interfacial structure, suggesting that hydrocarbons may be promising alternatives to perfluorinated surfactants.

  15. Identification of Viable Helicobacter pylori in Drinking Water Supplies by Cultural and Molecular Techniques.

    Science.gov (United States)

    Santiago, Paula; Moreno, Yolanda; Ferrús, M Antonía

    2015-08-01

    Helicobacter pylori is one of the most common causes of chronic bacterial infection in humans, directly related to peptic ulcer and gastric cancer. It has been suggested that H. pylori can be acquired through different transmission routes, including water. In this study, culture and qPCR were used to detect and identify the presence of H. pylori in drinking water. Furthermore, the combined techniques PMA-qPCR and DVC-FISH were applied for detection of viable cells of H. pylori. Among 24 drinking water samples, 16 samples were positive for the presence of H. pylori, but viable cells were only detected in six samples. Characteristic colonies, covered by a mass of bacterial unspecific growth, were observed on selective agar plates from an only sample, after enrichment. The mixed culture was submitted to DVC-FISH and qPCR analysis, followed by sequencing of the amplicons. Molecular techniques confirmed the growth of H. pylori on the agar plate. Our results demonstrate for the first time that H. pylori can survive and be potentially infective in drinking water, showing that water distribution systems could be a potential route for H. pylori transmission. © 2015 John Wiley & Sons Ltd.

  16. Molecular simulations of mixed self-assembled monolayer coated gold nanoparticles in water.

    Science.gov (United States)

    J, Meena Devi

    2015-06-01

    Molecular dynamics simulations have been employed to study the hydration of a series of nanoparticles, each of which was coated with a mixed self-assembled monolayer (SAM) comprising methyl- and hydroxy-terminated alkane thiol chains. The mixing ratio of those chains are different for each nanoparticle. The simulations focused on the wetting behavior of the SAM-coated gold nanoparticles and the distribution and structure of their interfacial water molecules. The interactions of the mixed SAM-coated gold nanoparticles with water were analyzed by evaluating the radial distribution function, hydrogen bonds, the dipole orientations of the water molecules, and the water residence time in the interfacial region. The wettability of the mixed SAM-coated gold nanoparticles improved as the concentration of terminal hydroxy moieties was increased. The distribution and dynamics of the interfacial water molecules were found to be influenced by the mixing ratio of the terminal moieties of the SAM chains. The results of our simulations suggest that the surface interactions of the mixed SAM-coated gold nanoparticles with the aqueous medium can be modulated by systematically altering the mixing ratio of the terminal methyl and hydroxy moieties. This work may lead to new biological and technological applications and inspire the development of novel biomimetic materials. Graphical Abstract Mixed SAM-coated gold nanoparticles.

  17. Molecular dynamics simulations of the ice temperature dependence of water ice photodesorption

    CERN Document Server

    Arasa, C; Cuppen, H M; van Dishoweck, E F; Kroes, G -J; 10.1063/1.3422213

    2010-01-01

    The ultraviolet (UV) photodissociation of amorphous water ice at different ice temperatures is investigated using molecular dynamics (MD) simulations and analytical potentials. Previous MD calculations of UV photodissociation of amorphous and crystalline water ice at 10 K [S. Andersson et al., J. Chem. Phys. 124, 064715 (2006)] revealed -for both types of ice- that H atom, OH, and H2O desorption are the most important processes after photoexcitation in the uppermost layers of the ice. Water desorption takes place either by direct desorption of recombined water, or when, after dissociation, an H atom transfers part of its kinetic energy to one of the surrounding water molecules which is thereby kicked out from the ice. We present results of MD simulations of UV photodissociation of amorphous ice at 10, 20, 30, and 90 K in order to analyze the effect of ice temperature on UV photodissociation processes. Desorption and trapping probabilities are calculated for photoexcitation of H2O in the top four monolayers an...

  18. Solubilization of poorly water-soluble compounds using amphiphilic phospholipid polymers with different molecular architectures.

    Science.gov (United States)

    Mu, Mingwei; Konno, Tomohiro; Inoue, Yuuki; Ishihara, Kazuhiko

    2017-06-29

    To achieve stable and effective solubilization of poorly water-soluble bioactive compounds, water-soluble and amphiphilic polymers composed of hydrophilic 2-methacryloyloxyethyl phosphorylcholine (MPC) units and hydrophobic n-butyl methacrylate (BMA) units were prepared. MPC polymers having different molecular architectures, such as random-type monomer unit sequences and block-type sequences, formed polymer aggregates when they were dissolved in aqueous media. The structure of the random-type polymer aggregate was loose and flexible. On the other hand, the block-type polymer formed polymeric micelles, which were composed of very stable hydrophobic poly(BMA) cores and hydrophilic poly(MPC) shells. The solubilization of a poorly water-soluble bioactive compound, paclitaxel (PTX), in the polymer aggregates was observed, however, solubilizing efficiency and stability were strongly depended on the polymer architecture; in other words, PTX stayed in the poly(BMA) core of the polymer micelle formed by the block-type polymer even when plasma protein was present in the aqueous medium. On the other hand, when the random-type polymer was used, PTX was transferred from the polymer aggregate to the protein. We conclude that water-soluble and amphiphilic MPC polymers are good candidates as solubilizers for poorly water-soluble bioactive compounds. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

    Science.gov (United States)

    Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

    2013-02-01

    Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

  20. Microbial quality and molecular identification of cultivable microorganisms isolated from an urban drinking water distribution system (Limassol, Cyprus).

    Science.gov (United States)

    Botsaris, George; Kanetis, Loukas; Slaný, Michal; Parpouna, Christiana; Makris, Konstantinos C

    2015-12-01

    Microorganisms can survive and multiply in aged urban drinking water distribution systems, leading to potential health risks. The objective of this work was to investigate the microbial quality of tap water and molecularly identify its predominant cultivable microorganisms. Tap water samples collected from 24 different households scattered in the urban area of Limassol, Cyprus, were microbiologically tested following standard protocols for coliforms, E. coli, Pseudomonas spp., Enterococcus spp., and total viable count at 22 and 37 °C. Molecular identification was performed on isolated predominant single colonies using 16SrRNA sequencing. Approximately 85% of the household water samples were contaminated with one or more microorganisms belonging to the genera of Pseudomonas, Corynebacterium, Agrobacterium, Staphylococcus, Bacillus, Delftia, Acinetobacter, Enterococcus, Enterobacter, and Aeromonas. However, all samples tested were free from E. coli. This is the first report in Cyprus molecularly confirming specific genera of relevant microbial communities in tap water.

  1. Effect of nanostructure on rapid boiling of water on a hot copper plate: a molecular dynamics study

    Science.gov (United States)

    Fu, Ting; Mao, Yijin; Tang, Yong; Zhang, Yuwen; Yuan, Wei

    2016-08-01

    Molecular dynamic simulations are performed to study the effects of nanostructure on rapid boiling of water that is suddenly heated by a hot copper plate. The results show that the nanostructure has significant effects on energy transfer from solid copper plate to liquid water and phase change process from liquid water to vapor. The liquid water on the solid surface rapidly boil after contacting with an extremely hot copper plate and consequently a cluster of liquid water moves upward during phase change. The temperature of the water film when it separates from solid surface and its final temperature when the system is at equilibrium strongly depend on the size of the nanostructure. These temperatures increase with increasing size of nanostructure. Furthermore, a non-vaporized molecular layer is formed on the surface of the copper plate even continuous heat flux is passing into water domain through the plate.

  2. Wide-ranging molecular mobilities of water in active pharmaceutical ingredient (API) hydrates as determined by NMR relaxation times.

    Science.gov (United States)

    Yoshioka, Sumie; Aso, Yukio; Osako, Tsutomu; Kawanishi, Toru

    2008-10-01

    In order to examine the possibility of determining the molecular mobility of hydration water in active pharmaceutical ingredient (API) hydrates by NMR relaxation measurement, spin-spin relaxation and spin-lattice relaxation were measured for the 11 API hydrates listed in the Japanese Pharmacopeia using pulsed (1)H-NMR. For hydration water that has relatively high mobility and shows Lorentzian decay, molecular mobility as determined by spin-spin relaxation time (T(2)) was correlated with ease of evaporation under both nonisothermal and isothermal conditions, as determined by DSC and water vapor sorption isotherm analysis, respectively. Thus, T(2) may be considered a useful parameter which indicates the molecular mobility of hydration water. In contrast, for hydration water that has low mobility and shows Gaussian decay, T(2) was found not to correlate with ease of evaporation under nonisothermal conditions, which suggests that in this case, the molecular mobility of hydration water was too low to be determined by T(2). A wide range of water mobilities was found among API hydrates, from low mobility that could not be evaluated by NMR relaxation time, such as that of the water molecules in pipemidic acid hydrate, to high mobility that could be evaluated by this method, such as that of the water molecules in ceftazidime hydrate. (c) 2008 Wiley-Liss, Inc. and the American Pharmacists Association

  3. 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.

  4. Molecular recognition of Acanthamoeba spp from surface waters in Qaen county, north of Southern Khorasan province

    Directory of Open Access Journals (Sweden)

    Mahmoodreza Behravan

    2016-06-01

    Full Text Available Background& Aims of the Study: Free living amoebae (FLA are frequently distributed in environment, such as air, water, dust and soil. Some strains of Acanthamoebaspp are non-pathogen, while others are pathogenic in immunocompromised patients or even healthy persons. So, due to their medical importance, identification of free living amoeba in water resources, as a source of human infection, is necessary.The aim of this study was to isolate of Acanthamoebaspp from surface waters in Qaen county, north of Southern Khorasan province, during 2015-2016 by Morphological and molecular method. Materials and Methods: In a cross-sectional study, 40 samples were collected from different localities in Qaen county including surface waters, pools and fountains in parks and squares from November 2015 to April 2016. Each sample was filtered through a nitrocellulose membrane filters and cultured on non-nutrient agar (NNA with Escherichia coli suspension and incubated for 1 week to 2 months at room temperature.The cultures media were microscopically examined for the presence of trophozoitesand cysts ofAcanthamoeba spp. Positive cultures for amoebae were examined by PCR (polymerase chain reaction method using specific primers for the genus of Acanthamoeba. Results: Out of 40 water samples, 13 (32.5% were positive for Acanthamoebatrophozoites and cysts according to morphological criteria. In addition, Acanthamoebaspp was identified by PCR method using genus specific primers pairs in 10 (76.93% cases of positive cultures showing anearly 500bp band. Conclusion:According to prevalent of Acanthamoebaspp in surface stagnant waters in this crowded city to buy the saffron from all over the Iran and the world, more attention to the potential role of such waters in transmission of infection by the regional clinicians and health practitioners is necessary.

  5. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  6. Water bath synthesis of tin oxide nanostructure coating for a molecular sensor.

    Science.gov (United States)

    Masuda, Yoshitake; Ohji, Tatsuki; Kato, Kazumi

    2014-03-01

    Tin oxide nanostructures were fabricated using a water bath technique. The structures were modified with dye-labeled DNAs for a molecular sensor. Sensing mechanism of the sensor was based on a photoelectric conversion effect. Photoluminescence intensities from the tin oxide nanostructures reached to 16 times larger than that from SnO2:F films. High photocurrent of 5.5 x 10(-6) A and high signal-to-noise ratio of 29 were achieved in this system. Photoelectric conversion on a combination of the dye-labeled DNA and the tin oxide was an essence of the sensing system. Surface nanospaces were effectively utilized to increase photoluminescence and photocurrent.

  7. On the influence of molecular structure on the conductivity of electrolyte solutions - sodium nitrate in water

    Directory of Open Access Journals (Sweden)

    H. Krienke

    2013-01-01

    Full Text Available Theoretical calculations of the conductivity of sodium nitrate in water are presented and compared with experimental measurements. The method of direct correlation force in the framework of the interionic theory is used for the calculation of transport properties in connection with the associative mean spherical approximation (AMSA. The effective interactions between ions in solutions are derived with the help of Monte Carlo and Molecular Dynamics calculations on the Born-Oppenheimer level. This work is based on earlier theoretical and experimental studies of the structure of concentrated aqueous sodium nitrate solutions.

  8. Evaporative cooling of microscopic water droplets in vacuo: Molecular dynamics simulations and kinetic gas theory.

    Science.gov (United States)

    Schlesinger, Daniel; Sellberg, Jonas A; Nilsson, Anders; Pettersson, Lars G M

    2016-03-28

    In the present study, we investigate the process of evaporative cooling of nanometer-sized droplets in vacuum using molecular dynamics simulations with the TIP4P/2005 water model. The results are compared to the temperature evolution calculated from the Knudsen theory of evaporation which is derived from kinetic gas theory. The calculated and simulation results are found to be in very good agreement for an evaporation coefficient equal to unity. Our results are of interest to experiments utilizing droplet dispensers as well as to cloud micro-physics.

  9. Path-integral molecular dynamics simulations for water anion clusters (HO)5- and (DO)5-

    Science.gov (United States)

    Takayanagi, Toshiyuki; Yoshikawa, Takehiro; Motegi, Haruki; Shiga, Motoyuki

    2009-11-01

    Quantum path-integral molecular dynamics simulations have been performed for the (HO)5- and (DO)5- anion clusters on the basis of a semiempirical one-electron pseudopotential-polarization model. Due to larger zero-point vibrational amplitudes for H atoms than that of D atoms, hydrogen-bond lengths in the (HO)5- cluster are slightly larger than those in (DO)5-. The distribution of the vertical detachment energies for (HO)5- also show a broader feature than that for (DO)5-. The present PIMD simulations thus demonstrate the importance of nuclear quantum effects in water anion clusters.

  10. Molecular solubilization of fullerene C60 in water by γ-cyclodextrin thioethers

    Directory of Open Access Journals (Sweden)

    Hai Ming Wang

    2012-09-01

    Full Text Available Various hydrophilic γ-cyclodextrin (CD thioethers, containing neutral or ionic side arms were found to form molecular disperse solutions of C60 in water reaching concentrations of 15 mg/L. Equilibrium state was approached after seven days without the use of organic cosolvents. The 1:2 stoichiometry of the C60/γ-CD thioether complexes was demonstrated by a parabolic phase-solubility diagram. In contrast, native γ-CD forms nanoparticles with C60. Particle sizes of C60 were determined by dynamic light scattering.

  11. Acanthamoeba Species Keratitis in a Soft Contact Lens Wearer Molecularly Linked to Well Water

    Directory of Open Access Journals (Sweden)

    Samira Mubareka

    2006-01-01

    Full Text Available Acanthamoeba species keratitis has been associated with soft contact lens wear. In the present report, an epidemiological link was established between the patient's isolate and well water from the home using molecular methods. To the authors' knowledge, this is the first case in Canada where such a link has been established. Primary care practitioners and specialists, including ophthalmologists and infectious diseases specialists, must maintain a high degree of clinical suspicion in soft contact lens wearers with keratitis unresponsive to conventional topical and systemic treatment.

  12. Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24

    Science.gov (United States)

    Owenson, Brian; Macelroy, Robert D.; Pohorille, Andrew

    1988-01-01

    The molecular dynamics of chloride capture from water by the tetraprotonated cryptand SC24 has been studied for the cases of 19 distances between the criptand and the chloride. The chloride capture is found to be characterized by a rapid cooperative change in the conformation of the cryptand when the Cl(-) begins to enter the ligand and just as it encounters the energy barrier. The conformational transition is associated with a shift of three N-H bonds from the pure endo orientation, such that they point toward the chloride.

  13. New Insights into the Dynamics of Zwitterionic Micelles and Their Hydration Waters by Gigahertz-to-Terahertz Dielectric Spectroscopy

    CERN Document Server

    George, Deepu K; Hull, Olivia A; Mishra, Archana; Capelluto, Daniel G S; Mitchell-Koch, Katie R; Vinh, Nguyen Q

    2016-01-01

    Gigahertz-to-terahertz spectroscopy of macromolecules in aqueous environments provides an important approach for identifying their global and transient molecular structures, as well as directly assessing hydrogen-bonding. We report dielectric properties of zwitterionic dodecylphosphocholine (DPC) micelles in aqueous solutions over a wide frequency range, from 50 MHz to 1.12 THz. The dielectric relaxation spectra reveal different polarization mechanisms at the molecular level, reflecting the complexity of DPC micelle-water interactions. We have made a deconvolution of the spectra into different components and combined them with the effective-medium approximation to separate delicate processes of micelles in water. Our measurements demonstrate reorientational motion of the DPC surfactant head groups within the micelles, and two levels of hydration water shells, including tightly- and loosely-bound hydration water layers. From the dielectric strength of bulk water in DPC solutions, we found that the number of wa...

  14. Water Vapor Adsorption Capacity of Thermally Fluorinated Carbon Molecular Sieves for CO2 Capture

    Directory of Open Access Journals (Sweden)

    Jin-Young Jung

    2013-01-01

    Full Text Available The surfaces of carbon molecular sieves (CMSs were thermally fluorinated to adsorb water vapor. The fluorination of the CMSs was performed at various temperatures (100, 200, 300, and 400°C to investigate the effects of the fluorine gas (F2 content on the surface properties. Fluorine-related functional groups formed were effectively generated on the surface of the CMSs via thermal fluorination process, and the total pore volume and specific surface area of the pores in the CMSs increased during the thermal fluorination process, especially those with diameters ≤ 8 Å. The water vapor adsorption capacity of the thermally fluorinated CMSs increased compared with the as-received CMSs, which is attributable to the increased specific surface area and to the semicovalent bonds of the C–F groups.

  15. Water rotational jump driven large amplitude molecular motions of nitrate ions in aqueous potassium nitrate solution

    CERN Document Server

    Banerjee, Puja; Bagchi, Biman

    2016-01-01

    Molecular dynamics simulations of aqueous potassium nitrate solution reveal a highly complex rotational dynamics of nitrate ions where, superimposed on the expected continuous Brownian motion, are large amplitude angular jumps that are coupled to and at least partly driven by similar large amplitude jump motions in water molecules which are associated with change in the hydrogen bonded water molecule. These jumps contribute significantly to rotational and translational motions of these ions. We explore the detailed mechanism of these correlated (or, coupled) jumps and introduce a new time correlation function to decompose the coupled orientational- jump dynamics of solvent and solute in the aqueous electrolytic solution. Time correlation function provides for the unequivocal determination of the time constant involved in orientational dynamics originating from making and breaking of hydrogen bonds. We discover two distinct mechanisms-both are coupled to density fluctuation but are of different types.

  16. Interaction of the model alkyltrimethylammonium ions with alkali halide salts: an explicit water molecular dynamics study

    Directory of Open Access Journals (Sweden)

    M. Druchok

    2013-01-01

    Full Text Available We present an explicit water molecular dynamics simulation of dilute solutions of model alkyltrimethylammonium surfactant ions (number of methylene groups in the tail is 3, 5, 8, 10, and 12 in mixture with NaF, NaCl, NaBr, and NaI salts, respectively. The SPC/E model is used to describe water molecules. Results of the simulation at 298 K are presented in form of the radial distribution functions between nitrogen and carbon atoms of CH2 groups on the alkyltrimethylammonium ion, and the counterion species in the solution. The running coordination numbers between carbon atoms of surfactants and counterions are also calculated. We show that I- counterion exhibits the highest, and F- the lowest affinity to "bind" to the model surfactants. The results are discussed in view of the available experimental and simulation data for this and similar solutions.

  17. A classical reactive potential for molecular clusters of sulphuric acid and water

    CERN Document Server

    Stinson, Jake L; Ford, Ian J

    2016-01-01

    We present a two-state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent.

  18. Labyrinthine water flow across multilayer graphene-based membranes: molecular dynamics versus continuum predictions

    CERN Document Server

    Yoshida, Hiroaki

    2016-01-01

    In this paper we investigate the hydrodynamic permeance of water through graphene-based membranes, inspired by recent experimental findings on graphene-oxide membranes. We consider the flow across multiple graphene layers having nanoslits in a staggered alignment, with an inter-layer distance ranging from sub- nanometer to a few nanometers. We compare results for the permeability obtained by means of molecular dynamics simulations to continuum predictions obtained by using the lattice Boltzmann calculations and hydrodynamic modelization. This highlights that, in spite of extreme confinement, the permeability across the graphene-based membrane is quantitatively predicted on the basis of a continuum expression, taking properly into account entrance and slippage effects of the confined water flow. Our predictions refute the breakdown of hydrodynamics at small scales in these membrane systems. They constitute a benchmark to which we compare published experimental data.

  19. Proton momentum distributions in water: A path integral molecular dynamics study

    Science.gov (United States)

    Srinivasan, Varadharajan; Morrone, Joseph A.; Sebastiani, Daniel; Car, Roberto

    2007-03-01

    Recent neutron Compton scattering experiments have detected the proton momentum distributions of water. This density in momentum space is a quantum mechanical property of the proton, due to the confining anharmonic potential from covalent and hydrogen bonds. The theoretical calculation of this property can be carried out via ``open'' path integral expressions. In this work, we present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize the SPC/F2 empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.

  20. Proton momentum distribution in water: an open path integral molecular dynamics study

    Science.gov (United States)

    Morrone, Joseph A.; Srinivasan, Varadharajan; Sebastiani, Daniel; Car, Roberto

    2007-06-01

    Recent neutron Compton scattering experiments have detected the proton momentum distribution in water. The theoretical calculation of this property can be carried out via "open" path integral expressions. In this work, present an extension of the staging path integral molecular dynamics method, which is then employed to calculate the proton momentum distributions of water in the solid, liquid, and supercritical phases. We utilize a flexible, single point charge empirical force field to model the system's interactions. The calculated momentum distributions depict both agreement and discrepancies with experiment. The differences may be explained by the deviation of the force field from the true interactions. These distributions provide an abundance of information about the environment and interactions surrounding the proton.

  1. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    Energy Technology Data Exchange (ETDEWEB)

    Zen, Andrea, E-mail: a.zen@ucl.ac.uk [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); London Centre for Nanotechnology, University College London, London WC1E 6BT (United Kingdom); Luo, Ye, E-mail: xw111luoye@gmail.com; Mazzola, Guglielmo, E-mail: gmazzola@phys.ethz.ch; Sorella, Sandro, E-mail: sorella@sissa.it [SISSA–International School for Advanced Studies, Via Bonomea 26, 34136 Trieste (Italy); Democritos Simulation Center CNR–IOM Istituto Officina dei Materiali, 34151 Trieste (Italy); Guidoni, Leonardo, E-mail: leonardo.guidoni@univaq.it [Dipartimento di Fisica, “La Sapienza” - Università di Roma, piazzale Aldo Moro 5, 00185 Rome (Italy); Dipartimento di Scienze Fisiche e Chimiche, Università degli Studi dell’ Aquila, via Vetoio, 67100 L’ Aquila (Italy)

    2015-04-14

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems.

  2. Solvation structures and dynamics of alkaline earth metal halides in supercritical water: A molecular dynamics study

    Science.gov (United States)

    Keshri, Sonanki; Mandal, Ratnamala; Tembe, B. L.

    2016-09-01

    Constrained molecular dynamics simulations of alkaline earth metal halides have been carried out to investigate their structural and dynamical properties in supercritical water. Potentials of mean force (PMFs) for all the alkaline earth metal halides in supercritical water have been computed. Contact ion pairs (CIPs) are found to be more stable than all other configurations of the ion pairs except for MgI2 where solvent shared ion pair (SShIP) is more stable than the CIP. There is hardly any difference in the PMFs between the M2+ (M = Mg, Ca, Sr, Ba) and the X- (X = F, Cl, Br, I) ions whether the second X- ion is present in the first coordination shell of the M2+ ion or not. The solvent molecules in the solvation shells diffuse at a much slower rate compared to the bulk. Orientational distribution functions of solvent molecules are sharper for smaller ions.

  3. Ab-initio molecular dynamics simulation of liquid water by Quantum Monte Carlo

    CERN Document Server

    Zen, Andrea; Mazzola, Guglielmo; Guidoni, Leonardo; Sorella, Sandro

    2014-01-01

    Despite liquid water is ubiquitous in chemical reactions at roots of life and climate on earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in excellent agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous Density Functional Theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab-initio simulations of complex chemical systems.

  4. Molecular dynamics of dewetting of ultra-thin water films on solid substrate

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Molecular dynamics simulation is applied to study the instability and rupture process of ultra-thin water films on a solid substrate. Results show the small disturbance of the film will develop linearly due to the spinodal instability, whereas the interaction between solid and liquid has less influences on the initial growth. Then the rupture occurs and the rim recedes with a dynamic contact angle. The radius of the rim varies with time as the square root of t, which is consistent with the macroscopic theory available.Stronger interaction between solid and liquid will postpone rupture time, decline the dynamic contact angle and raise the density of water near the interface between solid and liquid.

  5. Water adsorption and proton conduction in metal-organic frameworks: Insights from molecular simulations

    Science.gov (United States)

    Paesani, Francesco

    2014-03-01

    Metal-organic frameworks (MOFs) are a relatively new class of porous materials that hold great potential for a wide range of applications in chemistry, materials science, and nanoengineering. Compared to other porous materials such as zeolites, MOF properties are highly tunable. In particular, it has been shown that both size and shape of the MOF pores can be rationally designed for specific applications. For example, the ability to modify the framework properties with respect to hydrophilicity/hydrophobicity and acidity/basicity can enable the direct control of proton conduction through carrier molecules adsorbed inside the pores. Here, I report on our current efforts aimed at providing a molecular-level characterization of water-mediated proton conduction through the MOF pores. Particular emphasis will be put on correlation between proton conduction and both structural and chemical properties of the frameworks as well as on the dynamical behavior of water confined in the MOF pores. NSF award number: DMR-130510

  6. A molecular dynamics implementation of the 3D Mercedes-Benz water model

    Science.gov (United States)

    Hynninen, T.; Dias, C. L.; Mkrtchyan, A.; Heinonen, V.; Karttunen, M.; Foster, A. S.; Ala-Nissila, T.

    2012-02-01

    The three-dimensional Mercedes-Benz model was recently introduced to account for the structural and thermodynamic properties of water. It treats water molecules as point-like particles with four dangling bonds in tetrahedral coordination, representing H-bonds of water. Its conceptual simplicity renders the model attractive in studies where complex behaviors emerge from H-bond interactions in water, e.g., the hydrophobic effect. A molecular dynamics (MD) implementation of the model is non-trivial and we outline here the mathematical framework of its force-field. Useful routines written in modern Fortran are also provided. This open source code is free and can easily be modified to account for different physical context. The provided code allows both serial and MPI-parallelized execution. Program summaryProgram title: CASHEW (Coarse Approach Simulator for Hydrogen-bonding Effects in Water) Catalogue identifier: AEKM_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKM_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 20 501 No. of bytes in distributed program, including test data, etc.: 551 044 Distribution format: tar.gz Programming language: Fortran 90 Computer: Program has been tested on desktop workstations and a Cray XT4/XT5 supercomputer. Operating system: Linux, Unix, OS X Has the code been vectorized or parallelized?: The code has been parallelized using MPI. RAM: Depends on size of system, about 5 MB for 1500 molecules. Classification: 7.7 External routines: A random number generator, Mersenne Twister ( http://www.math.sci.hiroshima-u.ac.jp/m-mat/MT/VERSIONS/FORTRAN/mt95.f90), is used. A copy of the code is included in the distribution. Nature of problem: Molecular dynamics simulation of a new geometric water model. Solution method: New force-field for

  7. Source-specific sewage pollution detection in urban river waters using pharmaceuticals and personal care products as molecular indicators.

    Science.gov (United States)

    Kiguchi, Osamu; Sato, Go; Kobayashi, Takashi

    2016-11-01

    Source-specific elucidation of domestic sewage pollution caused by various effluent sources in an urban river water, as conducted for this study, demands knowledge of the relation between concentrations of pharmaceuticals and personal care products (PPCPs) as molecular indicators (caffeine, carbamazepine, triclosan) and water quality concentrations of total nitrogen (T-N) and total phosphorous (T-P). River water and wastewater samples from the Asahikawa River Basin in northern Japan were analyzed using derivatization-gas chromatography/mass spectrometry. Caffeine, used as an indicator of domestic sewage in the Asahikawa River Basin, was more ubiquitous than either carbamazepine or triclosan (92-100 %). Its concentration was higher than any target compound used to assess the basin:  0.759) reflect the contribution of septic tank system effluents to the lower Asahikawa River Basin. Results of relative molecular indicators in combination with different molecular indicators (caffeine/carbamazepine and triclosan/carbamazepine) and cluster analysis better reflect the contribution of sewage than results obtained using concentrations of respective molecular indicators and cluster analysis. Relative molecular indicators used with water quality parameters (e.g., caffeine/T-N ratio) in this study provide results more clearly, relatively, and quantitatively than results obtained using molecular indicators alone. Moreover, the caffeine/T-N ratio reflects variations of caffeine flux from effluent sources. These results suggest strongly relative molecular indicators are also useful indicators, reflecting differences in spatial contributions of domestic sources for PPCPs in urban areas.

  8. Highly efficient bioinspired molecular Ru water oxidation catalysts with negatively charged backbone ligands.

    Science.gov (United States)

    Duan, Lele; Wang, Lei; Li, Fusheng; Li, Fei; Sun, Licheng

    2015-07-21

    -coordinate Ru(IV) species was isolated as a reaction intermediate, shedding light on the reaction mechanisms of Ru-catalyzed water oxidation chemistry. Auxiliary ligands have dramatic effects on the water oxidation catalysis in terms of the reactivity and the reaction mechanism. For instance, Ru-bda (H2bda = 2,2'-bipyridine-6,6'-dicarboxylic acid) water oxidation catalysts catalyze Ce(IV)-driven water oxidation extremely fast via the radical coupling of two Ru(V)═O species, while Ru-pda (H2pda = 1,10-phenanthroline-2,9-dicarboxylic acid) water oxidation catalysts catalyze the same reaction slowly via water nucleophilic attack on a Ru(V)═O species. With a number of active Ru catalysts in hands, light driven water oxidation was accomplished using catalysts with low catalytic onset potentials. The structures of molecular catalysts could be readily tailored to introduce additional functional groups, which favors the fabrication of state-of-the-art Ru-based water oxidation devices, such as electrochemical water oxidation anodes and photo-electrochemical anodes. The development of efficient water oxidation catalysts has led to a step forward in the sustainable energy system.

  9. Molecular dynamic simulations of iron (II) hydroxide in high temperature and supercritical water

    Science.gov (United States)

    Meng, Yuanliang

    In this study, the iron (II) hydroxide -- water system has been investigated at high temperatures by using molecular dynamics (MD) simulations. The simulation results reveal that at infinite dilution both Fe2+ cation and OH- anion have 6 water molecules within their first hydration shell and both types of ionic species experience a dramatic increase in their diffusion coefficients at near and supercritical conditions. The process of iron (II) hydroxide cluster formation has been simulated. The nano-clusters of larger sizes formed in supercritical water tend to be in an amorphous state. After having been quenched by an inert gas bath, iron (II) hydroxide nano-clusters with various structures have been produced. The geometries and associated binding energies of these species are given in detail. The vibrational spectra of iron (II) hydroxide clusters are also derived and compared with the spectrum of a bulk solid. The obtained results have a practical value for the analysis of potential corrosion products in supercritical water-cooled reactor (SCWR) which is employed in the new generation nuclear power plant design (GEN IV). This work also illustrates the process of hydrothermal synthesis of oxide nano-particles.

  10. Water and Methanol Maser Survey of Protostars in the Orion Molecular Cloud Complex

    CERN Document Server

    Kang, Miju; Choi, Minho; Choi, Yunhee; Kim, Kee-Tae; Di Francesco, James; Park, Yong-Sun

    2013-01-01

    The results of a maser survey toward ninety-nine protostars in the Orion molecular cloud complex are presented. The target sources are low-mass protostars identified from infrared observations. Single-dish observations were carried out in the water maser line at 22 GHz and the methanol class I maser lines at 44, 95, and 133 GHz. Most of the detected sources were mapped to determine the source positions. Five water maser sources were detected, and they are excited by HH 1-2 VLA 3, HH 1-2 VLA 1, L1641N MM1/3, NGC 2071 IRS 1/3, and an object in the OMC 3 region. The water masers showed significant variability in intensity and velocity with time scales of a month or shorter. Four methanol emission sources were detected, and those in the OMC 2 FIR 3/4 and L1641N MM1/3 regions are probably masers. The methanol emission from the other two sources in the NGC 2071 IRS 1-3 and V380 Ori NE regions are probably thermal. For the water masers, the number of detections per protostar in the survey region is about 2%, which s...

  11. A molecular dynamics study of water nucleation using the TIP4P/2005 model

    Science.gov (United States)

    Pérez, Alejandro; Rubio, Angel

    2011-12-01

    Extensive molecular dynamics simulations were conducted using the TIP4P/2005 water model of Abascal and Vega [J. Chem. Phys. 123, 234505 (2005)] to investigate its condensation from supersaturated vapor to liquid at 330 K. The mean first passage time method [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); L. S. Bartell and D. T. Wu, 125, 194503 (2006)] was used to analyze the influence of finite size effects, thermostats, and charged species on the nucleation dynamics. We find that the Nosé-Hoover thermostat and the one proposed by Bussi et al. [J. Chem. Phys. 126, 014101 (2007)] give essentially the same averages. We identify the maximum thermostat coupling time to guarantee proper thermostating for these simulations. The presence of charged species has a dramatic impact on the dynamics, inducing a marked change towards a pure growth regime, which highlights the importance of ions in the formation of liquid droplets in the atmosphere. It was found a small but noticeable sign preference at intermediate cluster sizes (between 5 and 30 water molecules) corresponding mostly to the formation of the second solvation shell around the ion. The TIP4P/2005 water model predicts that anions induce faster formation of water clusters than cations of the same magnitude of charge.

  12. Molecular Dynamics of a Water-Absorbent Nanoscale Material Based on Chitosan.

    Science.gov (United States)

    Borca, Carlos H; Arango, Carlos A

    2016-04-21

    Although hydrogels have been widely investigated for their use in materials science, nanotechnology, and novel pharmaceuticals, mechanistic details explaining their water-absorbent features are not well understood. We performed an all-atom molecular dynamics study of the structural transformation of chitosan nanohydrogels due to water absorption. We analyzed the conformation of dry, nanoscaled chitosan, the structural modifications that emerge during the process of water inclusion, and the dynamics of this biopolymer in the presence of nature's solvent. Two sets of nanoscaled, single-chained chitosan models were simulated: one to study the swelling dependence upon the degree of self-cross-linking and other to observe the response with respect to the degree of protonation. We verified that nanohydrogels keep their ability to absorb water and grow, regardless of their degree of cross-linking. Noteworthy, we found that the swelling behavior of nanoscaled chitosan is pH-dependent, and it is considerably more limited than that of larger scale hydrogels. Thus, our study suggests that properties of nanohydrogels are significantly different from those of larger hydrogels. These findings might be important in the design of novel controlled-release and targeted drug-delivery systems based on chitosan.

  13. Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight

    Science.gov (United States)

    Aryal, Dipak; Perahia, Dvora; Grest, Gary

    The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.

  14. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K.; Sefiane, Khellil; Reese, Jason M.

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  15. Molecular restructuring of water and lipids upon the interaction of DNA with lipid monolayers.

    Science.gov (United States)

    Campen, R Kramer; Ngo, Thuy T M; Sovago, Maria; Ruysschaert, Jean-Marie; Bonn, Mischa

    2010-06-16

    Understanding the molecular mechanism of DNA/lipid interaction is critical in optimizing the use of lipid cofactors in gene therapy. Here, we address this question by employing label-free vibrational sum frequency (VSF) spectroscopy to study the interaction of DNA with lipid monolayers of the cationic lipids DPTAP(1,2-dipalmitoyl-3-trimethylammonium-propane) and diC14-amidine as well as the zwitterionic lipid DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) in the presence and absence of calcium. Our approach has the advantage both of allowing us to explicitly probe intermolecular interactions and of providing insight into the structure of water and lipids around DNA at the lipid interface. We find, by examination of the OD stretch of interfacial D(2)O, that water structure differs markedly between systems containing DNA adsorbed to cationic and those that contain DNA adsorbed to zwitterionic lipid monolayers (in the presence or absence of Ca(2+)). The spectral response of interfacial water in the cationic system is consistent with a highly structured, undercoordinated, structural 'type' of water. Further, by investigation of CH stretch modes of the diC14-amidine lipid tails, we demonstrate that the adsorption of DNA to this lipid leads to increased ordering of lipid tails.

  16. Wetting and evaporation of salt-water nanodroplets: A molecular dynamics investigation.

    Science.gov (United States)

    Zhang, Jun; Borg, Matthew K; Sefiane, Khellil; Reese, Jason M

    2015-11-01

    We employ molecular dynamics simulations to study the wetting and evaporation of salt-water nanodroplets on platinum surfaces. Our results show that the contact angle of the droplets increases with the salt concentration. To verify this, a second simulation system of a thin salt-water film on a platinum surface is used to calculate the various surface tensions. We find that both the solid-liquid and liquid-vapor surface tensions increase with salt concentration and as a result these cause an increase in the contact angle. However, the evaporation rate of salt-water droplets decreases as the salt concentration increases, due to the hydration of salt ions. When the water molecules have all evaporated from the droplet, two forms of salt crystals are deposited, clump and ringlike, depending on the solid-liquid interaction strength and the evaporation rate. To form salt crystals in a ring, it is crucial that there is a pinned stage in the evaporation process, during which salt ions can move from the center to the rim of the droplets. With a stronger solid-liquid interaction strength, a slower evaporation rate, and a higher salt concentration, a complete salt crystal ring can be deposited on the surface.

  17. Water's structure around hydrophobic solutes and the iceberg model.

    Science.gov (United States)

    Galamba, N

    2013-02-21

    The structure of water in the hydration shells of small hydrophobic solutes was investigated through molecular dynamics. The results show that a subset of water molecules in the first hydration shell of a nonpolar solute have a significantly enhanced tetrahedrality and a slightly larger number of hydrogen bonds, relative to the molecules in water at room temperature, consistent with the experimentally observed negative excess entropy and increased heat capacity of hydrophobic solutions at room temperature. This ordering results from the rearrangement of a small number of water molecules near the nonpolar solutes that occupy one to two vertices of the enhanced water tetrahedra. Although this structuring is not nearly like that often associated with a literal interpretation of the term "iceberg" in the Frank and Evans iceberg model, it does support a moderate interpretation of this model. Thus, the tetrahedral orientational order of this ensemble of water molecules is comparable to that of liquid water at ~10 °C, although not accompanied by the small contraction of the O-O distance observed in cold water. Further, we show that the structural changes of water in the vicinity of small nonpolar solutes cannot be inferred from the water radial distribution functions, explaining why this increased ordering is not observed through neutron diffraction experiments. The present results restore a molecular view where the slower translational and reorientational dynamics of water near hydrophobic groups has a structural equivalent resembling water at low temperatures.

  18. Wastewater contamination in Antarctic melt-water streams evidenced by virological and organic molecular markers.

    Science.gov (United States)

    Tort, L F L; Iglesias, K; Bueno, C; Lizasoain, A; Salvo, M; Cristina, J; Kandratavicius, N; Pérez, L; Figueira, R; Bícego, M C; Taniguchi, S; Venturini, N; Brugnoli, E; Colina, R; Victoria, M

    2017-12-31

    Human activities in the Antarctica including tourism and scientific research have been raised substantially in the last century with the concomitant impact on the Antarctic ecosystems through the release of wastewater mainly from different scientific stations activities. The aim of this study was to assess the wastewater contamination of surface waters and sediments of three melt-water streams (11 sites) by leaking septic tanks located in the vicinity of the Uruguayan Scientific Station in the Fildes Peninsula, King George Island, Antarctica, during summer 2015. For this purpose, we combined the analysis of fecal steroids in sediments by using gas chromatography and six enteric viruses in surface waters by quantitative and qualitative PCR. Coprostanol concentrations (from 0.03 to 3.31μgg(-1)) and fecal steroids diagnostic ratios indicated that stations C7 and C8 located in the kitchen stream presented sewage contamination. Rotavirus was the only enteric virus detected in five sites with concentration ranging from 1.2×10(5)gcL(-)(1) to 5.1×10(5)gcL(-)(1) being three of them located downstream from the leaking AINA and Kitchen septic tanks. This study shows for the first time the presence of both virological and molecular biomarkers of wastewater pollution in surface waters and sediments of three melt-water streams in the vicinity of a scientific station in the Antarctica. These results highlight the importance of the complementation of these biomarkers in two different matrices (surface waters and sediments) to assess wastewater pollution in an Antarctic environment related to anthropogenic activities in the area. Copyright © 2017. Published by Elsevier B.V.

  19. 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.

  20. Water Orientation at Ceramide/Water Interfaces Studied by Heterodyne-Detected Vibrational Sum Frequency Generation Spectroscopy and Molecular Dynamics Simulation

    KAUST Repository

    Adhikari, Aniruddha

    2016-10-10

    Lipid/water interaction is essential for many biological processes. The water structure at the nonionic lipid interface remains little known, and there is no scope of a priori prediction of water orientation at nonionic interfaces, either. Here, we report our study combining advanced nonlinear spectroscopy and molecular dynamics simulation on the water orientation at the ceramide/water interface. We measured χ spectrum in the OH stretch region of ceramide/isotopically diluted water interface using heterodyne-detected vibrational sum-frequency generation spectroscopy and found that the interfacial water prefers an overall hydrogen-up orientation. Molecular dynamics simulation indicates that this preferred hydrogen-up orientation of water is determined by a delicate balance between hydrogen-up and hydrogen-down orientation induced by lipid-water and intralipid hydrogen bonds. This mechanism also suggests that water orientation at neutral lipid interfaces depends highly on the chemical structure of the lipid headgroup, in contrast to the charged lipid interfaces where the net water orientation is determined solely by the charge of the lipid headgroup.

  1. Preparation of diclofenac-imprinted polymer beads for selective molecular separation in water.

    Science.gov (United States)

    Zhou, Tongchang; Kamra, Tripta; Ye, Lei

    2017-01-13

    Molecular imprinting technique is an attractive strategy to prepare materials for target recognition and rapid separation. In this work, a new type of diclofenac (DFC)-imprinted polymer beads was synthesized by Pickering emulsion polymerization using 2-(dimethylamino)ethyl methacrylate as the functional monomer. The selectivity and capacity of the molecularly imprinted polymers (MIPs) were investigated in aqueous solution. Equilibrium binding results show that the MIPs have a high selectivity to bind DFC in a wide range of pH values. Moreover, in liquid chromatography experiment, the imprinted polymer beads were packed into column to investigate the binding selectivity under nonequilibrium conditions. The retention time of DFC on the MIP column is significantly longer than its structural analogues. Also, retention of DFC on the MIP column was significantly longer than on the nonimprinted polymer column under aqueous condition. As the new MIP beads can be used to achieve direct separation of DFC from water, the synthetic method and the affinity beads developed in this work opened new possibilities for removing toxic chemicals from environmental and drinking water.

  2. Prediction of water-phosphatidylcholine membrane partition coefficient of some drugs from their molecular structures.

    Science.gov (United States)

    Fatemi, Mohammad Hossein; Moghaddam, Masoomeh Raei

    2012-10-01

    In this work, the phosphatidylcholine membrane-water partition coefficients (MA) of some drugs were estimated from their theoretical derived molecular descriptors by applying quantitative structure-activity relationship (QSAR) methodology. The data set consisted of 46 drugs where their log MA were determined experimentally. Descriptors used in this work were calculated by DRAGON (version 1) package, on the basis of optimized molecular structures, and the most relevant descriptors were selected by stepwise multilinear regressions (MLRs). These descriptors were used to developing linear and nonlinear models by using MLR and artificial neural networks (ANNs), respectively. During this investigation, the best QSAR model was identified when using the ANN model that produced a reasonable level of correlation coefficients (R(train) = 0.995, R(test) = 0.948) and low standard error (SE(train) = 0.099, SE(test) = 0.326). The built model was fully assessed by various validation methods, including internal and external validation test, Y-randomization test, and cross-validation (Q(2) = 0.805). The results of this investigation revealed the applicability of QSAR approaches in the estimation of phosphatidylcholine membrane-water partition coefficients.

  3. A Survey of 557 GHz Water Vapor Emission in the NGC 1333 Molecular Cloud

    CERN Document Server

    Bergin, E A; Melnick, G J; Snell, R L; Howe, J E; Bergin, Edwin A.; Kaufman, Michael J.; Melnick, Gary J.; Snell, Ronald L.; Howe, John E.

    2003-01-01

    Using NASA's Submillimeter Wave Astronomy Satellite (SWAS) we have examined the production of water in quiescent and shocked molecular gas through a survey of the 556.936 GHz transition of ortho-H2O in the NGC 1333 molecular core. These observations reveal broad emission lines associated with the IRAS~2, IRAS~4, IRAS~7, and HH7-11 outflows. Towards 3 positions we detect narrow (~2-3 km/s) emission lines clearly associated with the ambient gas. The SWAS observations, with a resolution of 4', are supplemented with observations from the Infrared Space Observatory (ISO) and by an unbiased survey of a 17' x 15' area, with 50" resolution, in the low-J transitions of CO, 13CO, C18O, N2H+, CH3OH, and SiO. Using these combined data sets, with consistent assumptions, we find beam-averaged o-H2O abundances of > 10^{-6} relative to H2O for all four outflows. A comparison of SWAS and ISO water data is consistent with non-dissociative shock models, provided the majority of the 557 GHz emission arises from cool post-shock m...

  4. Hidden force stiffening molecular clusters, surface skins, and ultrathin films of water

    CERN Document Server

    Sun, Chang Q

    2013-01-01

    A slight, molecular-undercoordination-induced contraction of the stiffer O-H real-bond and a significant, inter-electron-pair repulsion driven, elongation of the softer H:O non-bond, and the associated stiffness relaxation, of the segmented O-H:O bond, are recognized as the key to stiffening molecular clusters, surface skins, and ultrathin films of water. Agreement between calculations and measurements verified our expectations that the shortened-and-stiffened real-bond stiffens the stiffer phonons (>3000 cm-1), densifies bonding electrons, entraps binding energy, and elevates the melting point and hence the viscosity, surface tension, and elasticity, and that the lengthened-and-softened non-bond softens the softer phonons (<300 cm-1), expands the volume, and polarizes the electron pairs of the undercoordinated molecules in freestanding and encapsuled clusters, water surfaces, and ultrathin films that exhibit ice- or glue-like and hydrophobic nature at the ambient. This effect becomes more significant as N...

  5. A Comprehensive Study of Hydrogen Adsorbing to Amorphous Water ice: Defining Adsorption in Classical Molecular Dynamics

    Science.gov (United States)

    Dupuy, John L.; Lewis, Steven P.; Stancil, P. C.

    2016-11-01

    Gas-grain and gas-phase reactions dominate the formation of molecules in the interstellar medium (ISM). Gas-grain reactions require a substrate (e.g., a dust or ice grain) on which the reaction is able to occur. The formation of molecular hydrogen (H2) in the ISM is the prototypical example of a gas-grain reaction. In these reactions, an atom of hydrogen will strike a surface, stick to it, and diffuse across it. When it encounters another adsorbed hydrogen atom, the two can react to form molecular hydrogen and then be ejected from the surface by the energy released in the reaction. We perform in-depth classical molecular dynamics simulations of hydrogen atoms interacting with an amorphous water-ice surface. This study focuses on the first step in the formation process; the sticking of the hydrogen atom to the substrate. We find that careful attention must be paid in dealing with the ambiguities in defining a sticking event. The technical definition of a sticking event will affect the computed sticking probabilities and coefficients. Here, using our new definition of a sticking event, we report sticking probabilities and sticking coefficients for nine different incident kinetic energies of hydrogen atoms [5-400 K] across seven different temperatures of dust grains [10-70 K]. We find that probabilities and coefficients vary both as a function of grain temperature and incident kinetic energy over the range of 0.99-0.22.

  6. Molecular trajectories provide signatures of protein clustering and crowding at the oil/water interface.

    Science.gov (United States)

    McUmber, Aaron C; Larson, Nicholas R; Randolph, Theodore W; Schwartz, Daniel K

    2015-06-02

    Using high throughput single-molecule total internal reflection fluorescence microscopy (TIRFM), we have acquired molecular trajectories of bovine serum albumin (BSA) and hen egg white lysozyme during protein layer formation at the silicone oil-water interface. These trajectories were analyzed to determine the distribution of molecular diffusion coefficients, and for signatures of molecular crowding/caging, including subdiffusive motion and temporal anticorrelation of the instantaneous velocity vector. The evolution of these properties with aging time of the interface was compared with dynamic interfacial tension measurements. For both lysozyme and BSA, we observed an overall slowing of protein objects, the onset of both subdiffusive and anticorrelated motion (associated with crowding), and a decrease in the interfacial tension with aging time. For lysozyme, all of these phenomena occurred virtually simultaneously, consistent with a homogeneous model of layer formation that involves gradual crowding of weakly interacting proteins. For BSA, however, the slowing occurred first, followed by the signatures of crowding/caging, followed by a decrease in interfacial tension, consistent with a heterogeneous model of layer formation involving the formation of protein clusters. The application of microrheological methods to single molecule trajectories described here provides an unprecedented level of mechanistic interpretation of interfacial events that occurred over a wide range of interfacial protein coverage.

  7. Effect of thermo-mechanical cycling on zirconium hydride reorientation studied in situ with synchrotron X-ray diffraction

    Science.gov (United States)

    Colas, Kimberly B.; Motta, Arthur T.; Daymond, Mark R.; Almer, Jonathan D.

    2013-09-01

    The circumferential hydrides normally present in nuclear reactor fuel cladding after reactor exposure may dissolve during drying for dry storage and re-precipitate when cooled under load into a more radial orientation, which could embrittle the fuel cladding. It is necessary to study the rates and conditions under which hydride reorientation may happen in order to assess fuel integrity in dry storage. The objective of this work is to study the effect of applied stress and thermal cycling on the hydride morphology in cold-worked stress-relieved Zircaloy-4 by combining conventional metallography and in situ X-ray diffraction techniques. Metallography is used to study the evolution of hydride morphology after several thermo-mechanical cycles. In situ X-ray diffraction performed at the Advanced Photon Source synchrotron provides real-time information on the process of hydride dissolution and precipitation under stress during several thermal cycles. The detailed study of diffracted intensity, peak position and full-width at half-maximum provides information on precipitation kinetics, elastic strains and other characteristics of the hydride precipitation process. The results show that thermo-mechanical cycling significantly increases the radial hydride fraction as well as the hydride length and connectivity. The radial hydrides are observed to precipitate at a lower temperature than circumferential hydrides. Variations in the magnitude and range of hydride strains due to reorientation and cycling have also been observed. These results are discussed in light of existing models and experiments on hydride reorientation. The study of hydride elastic strains during precipitation shows marked differences between circumferential and radial hydrides, which can be used to investigate the reorientation process. Cycling under stress above the threshold stress for reorientation drastically increases both the reoriented hydride fraction and the hydride size. The reoriented hydride

  8. Diverging effects of isotopic fractionation upon molecular diffusion of noble gases in water: mechanistic insights through ab initio molecular dynamics simulations.

    Science.gov (United States)

    Pinto de Magalhães, Halua; Brennwald, Matthias S; Kipfer, Rolf

    2017-03-22

    Atmospheric noble gases are routinely used as natural tracers to analyze gas transfer processes in aquatic systems. Their isotopic ratios can be employed to discriminate between different physical transport mechanisms by comparison to the unfractionated atmospheric isotope composition. In many applications of aquatic systems molecular diffusion was thought to cause a mass dependent fractionation of noble gases and their isotopes according to the square root ratio of their masses. However, recent experiments focusing on isotopic fractionation within a single element challenged this broadly accepted assumption. The determined fractionation factors of Ne, Ar, Kr and Xe isotopes revealed that only Ar follows the prediction of the so-called square root relation, whereas within the Ne, Kr and Xe elements no mass-dependence was found. The reason for this unexpected divergence of Ar is not yet understood. The aim of our computational exercise is to establish the molecular-resolved mechanisms behind molecular diffusion of noble gases in water. We make the hypothesis that weak intermolecular interactions are relevant for the dynamical properties of noble gases dissolved in water. Therefore, we used ab initio molecular dynamics to explicitly account for the electronic degrees of freedom. Depending on the size and polarizability of the hydrophobic particles such as noble gases, their motion in dense and polar liquids like water is subject to different diffusive regimes: the inter-cavity hopping mechanism of small particles (He, Ne) breaks down if a critical particle size achieved. For the case of large particles (Kr, Xe), the motion through the water solvent is governed by mass-independent viscous friction leading to hydrodynamical diffusion. Finally, Ar falls in between the two diffusive regimes, where particle dispersion is propagated at the molecular collision time scale of the surrounding water molecules.

  9. Molecular mechanisms for the destabilization and restabilization of reactivated spatial memory in the Morris water maze

    Directory of Open Access Journals (Sweden)

    Kim Ryang

    2011-02-01

    Full Text Available Abstract Background Memory retrieval is not a passive process. Recent studies have shown that reactivated memory is destabilized and then restabilized through gene expression-dependent reconsolidation. Molecular studies on the regulation of memory stability after retrieval have focused almost exclusively on fear memory, especially on the restabilization process of the reactivated fear memory. We previously showed that, similarly with fear memories, reactivated spatial memory undergoes reconsolidation in the Morris water maze. However, the underlying molecular mechanisms by which reactivated spatial memory is destabilized and restabilized remain poorly understood. In this study, we investigated the molecular mechanism that regulates the stability of the reactivated spatial memory. Results We first showed that pharmacological inactivation of the N-methyl-D-aspartate glutamate receptor (NMDAR in the hippocampus or genetic inhibition of cAMP-responsible element binding protein (CREB-mediated transcription disrupted reactivated spatial memory. Finally, we showed that pharmacological inhibition of cannabinoid receptor 1 (CB1 and L-type voltage gated calcium channels (LVGCCs in the hippocampus blocked the disruption of the reactivated spatial memory by the inhibition of protein synthesis. Conclusions Our findings indicated that the reactivated spatial memory is destabilized through the activation of CB1 and LVGCCs and then restabilized through the activation of NMDAR- and CREB-mediated transcription. We also suggest that the reactivated spatial memory undergoes destabilization and restabilization in the hippocampus, through similar molecular processes as those for reactivated contextual fear memories, which require CB1 and LVGCCs for destabilization and NMDAR and CREB for restabilization.

  10. A simplified molecular method for distinguishing among species and ploidy levels in European water frogs (Pelophylax).

    Science.gov (United States)

    Hauswaldt, J Susanne; Höer, Manuela; Ogielska, Maria; Christiansen, Ditte G; Dziewulska-Szwajkowska, Daria; Czernicka, Elżbieta; Vences, Miguel

    2012-09-01

    Western Palearctic water frogs in the genus Pelophylax are a set of morphologically similar anuran species that form hybridogenetic complexes. Fully reliable identification of species and especially of hybrid ploidy depends on karyological and molecular methods. In central Europe, native water frog populations consist of the Pelophylax esculentus complex, that is, P. lessonae (LL), P. ridibundus (RR) and the hybrid form P. esculentus that can have different karyotypes (RL, LLR and RRL). We developed existing molecular methods further and propose a simple PCR method based on size-differences in the length of the serum albumin intron-1 and the RanaCR1, a non-LTR retrotransposon of the chicken repeat (CR) family. This PCR yields taxon-specific banding patterns that can easily be screened by standard agarose gel electrophoresis and correctly identify species in all of the 160 samples that had been identified to karyotype with other methods. To distinguish ploidy levels in LR, LLR and RRL specimens, we used the ratio of the peak heights of the larger (ridibundus specific) to the smaller (lessonae specific) bands of fluorescently labelled PCR products resolved on a capillary DNA sequencer and obtained a correct assignment of the karyotype in 93% of cases. Our new method will cut down time and expenses drastically for a reliable identification of water frogs of the P. esculentus complex and potentially for identification of other hybridogenetic complexes and/or taxa, and it even serves as a good indicator of the ploidy status of hybrid individuals.

  11. Effect of dopant nanoparticles on reorientation process in polymer-dispersed liquid crystals

    Science.gov (United States)

    Zobov, K. V.; Zharkova, G. M.; Syzrantsev, V. V.

    2016-01-01

    The analysis of the experimental data of the nanoscale powders application for doping polymer-dispersed liquid crystals (PDLC) was represented in this work. A model based on the separation of the liquid crystals reorientation process on the surface mode and the volume mode was proposed and tested. In the research the wide-spread model mixture PDLC were used. But alumina nanoparticles were the distinctive ones obtained by electron beam evaporation. The proposed model allowed to conclude that the nanoparticles localization at the surface of the droplets (as in the Pickering emulsion) lead to the variation of the connection force between the liquid crystals and the polymer. The effect of nanoparticles resulted in an acceleration of the reorientation process near the surface when the control field is turned on and in a deceleration when it is turned off. The effect for the different size particles was confirmed.

  12. A mechanism for reorientation of cortical microtubule arrays driven by microtubule severing.

    Science.gov (United States)

    Lindeboom, Jelmer J; Nakamura, Masayoshi; Hibbel, Anneke; Shundyak, Kostya; Gutierrez, Ryan; Ketelaar, Tijs; Emons, Anne Mie C; Mulder, Bela M; Kirik, Viktor; Ehrhardt, David W

    2013-12-06

    Environmental and hormonal signals cause reorganization of microtubule arrays in higher plants, but the mechanisms driving these transitions have remained elusive. The organization of these arrays is required to direct morphogenesis. We discovered that microtubule severing by the protein katanin plays a crucial and unexpected role in the reorientation of cortical arrays, as triggered by blue light. Imaging and genetic experiments revealed that phototropin photoreceptors stimulate katanin-mediated severing specifically at microtubule intersections, leading to the generation of new microtubules at these locations. We show how this activity serves as the basis for a mechanism that amplifies microtubules orthogonal to the initial array, thereby driving array reorientation. Our observations show how severing is used constructively to build a new microtubule array.

  13. Transient Reorientation of a Doped Liquid Crystal System under a Short Laser Pulse

    Institute of Scientific and Technical Information of China (English)

    LI Tao; XIANG Ying; LIU Yi-Kun; WANG Jian; YANG Shun-Lin

    2009-01-01

    The transient optical nonlinearity of a nematic liquid crystal doped with azo-dye DRW is examined.The optical reorientation threshold of a 25-μm-thick planar-aligned sample of 5CB using a 50 ns pulse duration 532 nm YAG laser pulse is observed to decrease from 800 mJ/mm2 to 0.6 mJ/mm2 after the addition of 1 vol% azo dopant,a reduction of three orders of magnitude.When using a laser pulse duration of 10 ns,no such effect is observed.Experimental results indicate that the azo dopant molecules undergo photoisomerization from trans-isomer to cis-isomer under exposure to light,and this conformation change reorients the 5CB molecules via intermolecular coupling between guest and host.This guest-host couphng also affects the azo photoisomerization process.

  14. Optimal reorientation of underactuated spacecraft using genetic algorithm with wavelet approximation

    Institute of Scientific and Technical Information of China (English)

    Xinsheng Ge; Liqun Chen

    2009-01-01

    The optimal attitude control of an underactuated spacecraft is investigated in this paper. The flywheels of the spacecraft can somehow only provide control inputs in two independent directions. The dynamic equations are formulated for the spacecraft under a nonholonomic constraint resulting from the constant time-rate of the total angular momentum of the system. The reorientation of such underactuated spacecraft is transformed into an optimal control problem. A ggnetic algorithm is proposed to derive the control laws of the two flywheels angle velocity inputs. The control laws are approximated by the discrete orthogonal wavelets.The numerical simulations indicate that the genetic algorithm with the wavelet approximation is an effective approach to deal with the optimal reorientation of underactuated spacecraft.

  15. Paleomagnetic reorientation of San Andreas Fault Observatory at Depth (SAFOD) core

    Science.gov (United States)

    Pares, J.M.; Schleicher, A.M.; van der Pluijm, B.A.; Hickman, S.

    2008-01-01

    We present a protocol for using paleomagnetic analysis to determine the absolute orientation of core recovered from the SAFOD borehole. Our approach is based on determining the direction of the primary remanent magnetization of a spot core recovered from the Great Valley Sequence during SAFOD Phase 2 and comparing its direction to the expected reference field direction for the Late Cretaceous in North America. Both thermal and alternating field demagnetization provide equally resolved magnetization, possibly residing in magnetite, that allow reorientation. Because compositionally similar siltstones and fine-grained sandstones were encountered in the San Andreas Fault Zone during Stage 2 rotary drilling, we expect that paleomagnetic reorientation will yield reliable core orientations for continuous core acquired from directly within and adjacent to the San Andreas Fault during SAFOD Phase 3, which will be key to interpretation of spatial properties of these rocks. Copyright 2008 by the American Geophysical Union.

  16. Stimulus-driven reorienting in the ventral frontoparietal attention network: the role of emotion

    Directory of Open Access Journals (Sweden)

    David Witt Frank

    2012-05-01

    Full Text Available Activity in the human temporoparietal junction and inferior frontal gyrus is hypothesized to underlie stimulus-driven, or bottom-up attention reorienting. Demanding tasks require focused attention, and as task difficulty increases, activity suppression in the ventral network correlates positively with task performance, an effect thought to reflect the gating of irrelevant cues. However, activation in these structures is elicited by a range of stimulus features and task demands that vary across multiple characteristics, complicating the interpretation of the functional role of this pathway. Consideration of several current studies suggests that, in addition to task difficulty, the motivational relevance or emotional intensity of distractor stimuli may supersede ongoing task priority, and evoke ventral network activation. Support for this possibility is offered from a review of recent reports, and the import of this perspective for models of attention reorienting are discussed.

  17. Influence of an electric field on the spin-reorientation transition in Ni/Cu(100)

    Energy Technology Data Exchange (ETDEWEB)

    Gerhard, Lukas [Institut für Nanotechnologie, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen (Germany); Bonell, Frédéric; Suzuki, Yoshishige [CREST, Japan Science Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Graduate School of Engineering Science, Osaka University, Osaka 560-8531 (Japan); Wulfhekel, Wulf [Institut für Nanotechnologie, Karlsruhe Institute of Technology, 76344 Eggenstein-Leopoldshafen (Germany); Physikalisches Institut, Karlsruhe Institute of Technology, 76131 Karlsruhe (Germany)

    2014-10-13

    Magnetoelectric coupling offers the possibility to change the magnetic state of a material by an applied electric field. Over the last few years, metallic systems have come up as simple prototypes for this interaction. While the previous studies focused on Fe and Co thin films or their alloys, here we demonstrate magnetoelectric coupling in a Ni thin film which is close to a spin-reorientation transition. Our magneto-optic Kerr effect measurements on 10 ML of Ni/Cu(100) show a considerable influence of the applied electric field on the magnetism. This rounds off the range of magnetic metals that exhibit magnetoelectric coupling, and it reveals the possibility of an electric field control of a spin-reorientation transition.

  18. A structured continuum modelling framework for martensitic transformation and reorientation in shape memory materials.

    Science.gov (United States)

    Bernardini, Davide; Pence, Thomas J

    2016-04-28

    Models for shape memory material behaviour can be posed in the framework of a structured continuum theory. We study such a framework in which a scalar phase fraction field and a tensor field of martensite reorientation describe the material microstructure, in the context of finite strains. Gradients of the microstructural descriptors naturally enter the formulation and offer the possibility to describe and resolve phase transformation localizations. The constitutive theory is thoroughly described by a single free energy function in conjunction with a path-dependent dissipation function. Balance laws in the form of differential equations are obtained and contain both bulk and surface terms, the latter in terms of microstreses. A natural constraint on the tensor field for martensite reorientation gives rise to reactive fields in these balance laws. Conditions ensuring objectivity as well as the relation of this framework to that provided by currently used models for shape memory alloy behaviour are discussed.

  19. Interactions of anesthetics with the water-hexane interface. A molecular dynamics study

    Science.gov (United States)

    Chipot, C.; Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles characterizing the transfer of nine solutes across the liquid-vapor interfaces of water and hexane and across the water-hexane interface were calculated from molecular dynamics simulations. Among the solutes were n-butane and three of its halogenated derivatives, as well as three halogenated cyclobutanes. The two remaining molecules, dichlorodifluoromethane and 1,2-dichloroperfluoroethane, belong to series of halo-substituted methanes and ethanes, described in previous studies (J. Chem. Phys. 1996, 104, 3760; Chem. Phys. 1996, 204, 337). Each series of molecules contains structurally similar compounds that differ greatly in anesthetic potency. The accuracy of the simulations was tested by comparing the calculated and the experimental free energies of solvation of all nine compounds in water and in hexane. In addition. the calculated and the measured surface excess concentrations of n-butane at the water liquid-vapor interface were compared. In all cases, good agreement with experimental results was found. At the water-hexane interface, the free energy profiles for polar molecules exhibited significant interfacial minima, whereas the profiles for nonpolar molecules did not. The existence of these minima was interpreted in terms of a balance between the free energy contribution arising from solute-solvent interactions and the work to form a cavity that accommodates the solute. These two contributions change monotonically, but oppositely, across the interface. The interfacial solubilities of the solutes, obtained from the free energy profiles, correlate very well with their anesthetic potencies. This is the case even when the Meyer-Overton hypothesis, which predicts a correlation between anesthetic potency and solubility in oil, fails.

  20. Pluto followed its heart: reorientation and faulting of Pluto due to volatile loading in Sputnik Planum

    Science.gov (United States)

    Tuttle Keane, James; Matsuyama, Isamu; Kamata, Shunichi; Steckloff, Jordan

    2016-10-01

    The New Horizons flyby of Pluto revealed the dwarf planet to be a strikingly diverse, geologically active world. Perhaps the most intriguing feature on the New Horizons encounter hemisphere is Sputnik Planum—a 1000 km diameter, probable impact basin, filled with several kilometers of actively convecting volatile ices (N2, CH4, CO). One salient characteristic of Sputnik Planum is its curious alignment with the Pluto-Charon tidal axis. The alignment of large geologic features with principal axis of inertia (such as the tidal axis) is the hallmark of global reorientation, i.e. true polar wander. Here we show that the present location of Sputnik Planum is a natural consequence of loading of 1-2 km of volatile ices within the Sputnik Planum basin. Larger volatile ice thicknesses (like those inferred from studies of ice convection within Sputnik Planum) betray an underlying negative gravity anomaly associated with the basin. As Pluto reoriented in response to the loading of volatile ices within Sputnik Planum, stresses accumulated within the lithosphere (as each geographic location experiences a change in tidal/rotational potential). These reorientation stresses, coupled with loading stresses, and stresses from the freezing of a subsurface ocean resulted in the fracturing of Pluto's lithosphere in a characteristic, global pattern of extensional faults. Our predicted pattern of extensional faults due to this reorientation closely replicates the observed distribution of faults on Pluto (more so than global expansion, orbit migration, de-spinning, or loading alone). Sputnik Planum likely formed ~60° northwest of its present location, and was loaded with volatile ices over millions of years due to seasonal volatile transport cycles. This result places Pluto in a truly unique category of planetary bodies where volatiles are not only controlling surface geology and atmospheric processes, but they are also directly controlling the orientation of the entire dwarf planet

  1. Geometric and featural systems, separable and combined: Evidence from reorientation in people with Williams syndrome

    Science.gov (United States)

    Ferrara, Katrina; Landau, Barbara

    2015-01-01

    Spatial reorientation by humans and other animals engages geometric representations of surface layouts as well as featural landmarks; however, the two types of information are thought to be behaviorally and neurally separable. In this paper, we examine the use of these two types of information during reorientation among children and adults with Williams syndrome (WS), a genetic disorder accompanied by abnormalities in brain regions that support use of both geometry and landmarks. Previous studies of reorientation in adolescents and adults with WS have shown deficits in the ability to use geometry for reorientation, but intact ability to use features, suggesting that the two systems can be differentially impaired by genetic disorder. Using a slightly modified layout, we found that many WS participants could use geometry, and most could use features along with geometry. However, the developmental trajectories for the two systems were quite different from one other, and different from those found in typical development. Purely geometric responding was not correlated with age in WS, and search processes appeared similar to those in typically developing (TD) children. In contrast, use of features in combination with geometry was correlated with age in WS, and search processes were distinctly different from TD children. The results support the view that use of geometry and features stem from different underlying mechanisms, that the developmental trajectories and operation of each are altered in WS, and that combination of information from the two systems is atypical. Given brain abnormalities in regions supporting the two kinds of information, our findings suggest that the co-operation of the two systems is functionally altered in this genetic syndrome. PMID:26275835

  2. Giant magnetostrictive superlattices: from spin reorientation transition to MEMS. Static and dynamical properties

    CERN Document Server

    Tiercelin, N; Preobrazhensky, V; Pernod, P; Gall, H L

    2002-01-01

    The results of development of 'giant magnetostrictive' multilayers with spin reorientation transition (SRT) for microactuators are presented. Manifestations of magneto-mechanical instability and nonlinearity near SRT are studied experimentally and simulated numerically. Improvement of magneto-mechanical sensitivity near SRT is demonstrated for various modes of linear and nonlinear actuation of magnetostrictive unimorph. Limitations of sensitivity caused by magnetic field distortions are described by a numerical model, the results are compared with the experimental data.

  3. GOLPH3 drives cell migration by promoting Golgi reorientation and directional trafficking to the leading edge.

    Science.gov (United States)

    Xing, Mengke; Peterman, Marshall C; Davis, Robert L; Oegema, Karen; Shiau, Andrew K; Field, Seth J

    2016-12-01

    The mechanism of directional cell migration remains an important problem, with relevance to cancer invasion and metastasis. GOLPH3 is a common oncogenic driver of human cancers, and is the first oncogene that functions at the Golgi in trafficking to the plasma membrane. Overexpression of GOLPH3 is reported to drive enhanced cell migration. Here we show that the phosphatidylinositol-4-phosphate/GOLPH3/myosin 18A/F-actin pathway that is critical for Golgi-to-plasma membrane trafficking is necessary and limiting for directional cell migration. By linking the Golgi to the actin cytoskeleton, GOLPH3 promotes reorientation of the Golgi toward the leading edge. GOLPH3 also promotes reorientation of lysosomes (but not other organelles) toward the leading edge. However, lysosome function is dispensable for migration and the GOLPH3 dependence of lysosome movement is indirect, via GOLPH3's effect on the Golgi. By driving reorientation of the Golgi to the leading edge and driving forward trafficking, particularly to the leading edge, overexpression of GOLPH3 drives trafficking to the leading edge of the cell, which is functionally important for directional cell migration. Our identification of a novel pathway for Golgi reorientation controlled by GOLPH3 provides new insight into the mechanism of directional cell migration with important implications for understanding GOLPH3's role in cancer. © 2016 Xing, Peterman, et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  4. The interplay between dynamic heterogeneities and structure of bulk liquid water: A molecular dynamics simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Demontis, Pierfranco; Suffritti, Giuseppe B. [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Gulín-González, Jorge [Grupo de Matemática y Física Computacionales, Universidad de las Ciencias Informáticas (UCI), Carretera a San Antonio de los Baños, Km 21/2, La Lisa, La Habana (Cuba); Masia, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy); Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM), Unità di ricerca di Sassari, Via Vienna, 2, I-07100 Sassari (Italy); Istituto Officina dei Materiali del CNR, UOS SLACS, Via Vienna 2, 07100 Sassari (Italy); Sant, Marco [Dipartimento di Chimica e Farmacia, Università degli studi di Sassari, Sassari (Italy)

    2015-06-28

    In order to study the interplay between dynamical heterogeneities and structural properties of bulk liquid water in the temperature range 130–350 K, thus including the supercooled regime, we use the explicit trend of the distribution functions of some molecular properties, namely, the rotational relaxation constants, the atomic mean-square displacements, the relaxation of the cross correlation functions between the linear and squared displacements of H and O atoms of each molecule, the tetrahedral order parameter q and, finally, the number of nearest neighbors (NNs) and of hydrogen bonds (HBs) per molecule. Two different potentials are considered: TIP4P-Ew and a model developed in this laboratory for the study of nanoconfined water. The results are similar for the dynamical properties, but are markedly different for the structural characteristics. In particular, for temperatures higher than that of the dynamic crossover between “fragile” (at higher temperatures) and “strong” (at lower temperatures) liquid behaviors detected around 207 K, the rotational relaxation of supercooled water appears to be remarkably homogeneous. However, the structural parameters (number of NNs and of HBs, as well as q) do not show homogeneous distributions, and these distributions are different for the two water models. Another dynamic crossover between “fragile” (at lower temperatures) and “strong” (at higher temperatures) liquid behaviors, corresponding to the one found experimentally at T{sup ∗} ∼ 315 ± 5 K, was spotted at T{sup ∗} ∼ 283 K and T{sup ∗} ∼ 276 K for the TIP4P-Ew and the model developed in this laboratory, respectively. It was detected from the trend of Arrhenius plots of dynamic quantities and from the onset of a further heterogeneity in the rotational relaxation. To our best knowledge, it is the first time that this dynamical crossover is detected in computer simulations of bulk water. On the basis of the simulation results, the possible

  5. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  6. Quantification of Salmonella Typhi in water and sediments by molecular-beacon based qPCR.

    Science.gov (United States)

    Rani, Neetika; Vajpayee, Poornima; Bhatti, Saurabh; Singh, Smriti; Shanker, Rishi; Gupta, Kailash Chand

    2014-10-01

    A molecular-beacon based qPCR assay targeting staG gene was designed for specific detection and quantification of S. Typhi and validated against water and sediment samples collected from the river Ganga, Yamuna and their confluence on two days during Mahakumbha mela 2012-2013 (a) 18 December, 2012: before six major religious holy dips (Makar Sankranti, Paush Poornima, Mauni Amavasya, Basant Panchami, Maghi Poornima and Mahashivratri) (b) 10 February, 2013: after the holy dip was taken by over 3,00,00,000 devotees led by ascetics of Hindu sects at Sangam on 'Mauni Amavasya' (the most auspicious day of ritualistic mass bathing). The assay could detect linearly lowest 1 genomic equivalent per qPCR and is highly sensitive and selective for S. Typhi detection in presence of non specific DNA from other bacterial strains including S. Paratyphi A and S. Typhimurium. It has been observed that water and sediment samples exhibit S. Typhi. The mass holy dip by devotees significantly affected the water and sediment quality by enhancing the number of S. Typhi in the study area. The qPCR developed in the study might be helpful in planning the intervention and prevention strategies for control of enteric fever outbreaks in endemic regions.

  7. Geometric isotope effects on small chloride ion water clusters with path integral molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qi [Department of Chemistry, Tsukuba University, 1-1-1 Tennodai, Tsukuba 305-8571 (Japan); Suzuki, Kimichi [Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Nagashima, Umpei, E-mail: u.nagashima@aist.go.jp [Department of Chemistry, Tsukuba University, 1-1-1 Tennodai, Tsukuba 305-8571 (Japan); Research Institute for Nanosystem, National Institute of Advanced Industrial Science and Technology, Chuo-2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568 (Japan); Tachikawa, Masanori [Quantum Chemistry Division, Graduate School of Science, Yokohama-City University, Seto 22-2, Kanazawa-ku, Yokohama 236-0027 (Japan); Yan, Shiwei [College of Nuclear Science and Technology, Beijing Normal University, Beijing 100875 (China)

    2013-11-29

    Highlights: • PIMD simulations with PM6-DH+ potential are carried out for Cl{sup −}(H{sub 2}O){sub n} clusters. • The geometric isotope effects on the rearrangement of single and multi shell structures are presented. • The competition of intramolecular and intermolecular nuclear quantum effects on the cluster structures is shown. • The correlations between r(Cl…O) and other vibration motions are discussed. - Abstract: The geometric isotope effects on the structures of hydrated chloride ionic hydrogen bonded clusters are explored by carrying out path integral molecular dynamics simulations. First, an outer shell coordinate is selected to display the rearrangement of single and multi hydration shell cluster structures. Next, to show the competition of intramolecular and intermolecular nuclear quantum effects, the intramolecular OH{sup ∗} stretching and intermolecular ion–water wagging motions are studied for single and multi shell structures, respectively. The results indicate that the intermolecular nuclear quantum effects stabilize the ionic hydrogen bonds in single shell structures, while they are destabilized through the competition with intramolecular nuclear quantum effects in multi shell structures. In addition, the correlations between ion–water stretching motion and other cluster vibrational coordinates are discussed. The results indicate that the intermolecular nuclear quantum effects on the cluster structures are strongly related to the cooperation of the water–water hydrogen bond interactions.

  8. Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study

    Science.gov (United States)

    Wilson, M. A.; Pohorille, A.

    1997-01-01

    The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.

  9. Reorientation and faulting of Pluto due to volatile loading within Sputnik Planitia.

    Science.gov (United States)

    Keane, James T; Matsuyama, Isamu; Kamata, Shunichi; Steckloff, Jordan K

    2016-12-01

    Pluto is an astoundingly diverse, geologically dynamic world. The dominant feature is Sputnik Planitia-a tear-drop-shaped topographic depression approximately 1,000 kilometres in diameter possibly representing an ancient impact basin. The interior of Sputnik Planitia is characterized by a smooth, craterless plain three to four kilometres beneath the surrounding rugged uplands, and represents the surface of a massive unit of actively convecting volatile ices (N2, CH4 and CO) several kilometres thick. This large feature is very near the Pluto-Charon tidal axis. Here we report that the location of Sputnik Planitia is the natural consequence of the sequestration of volatile ices within the basin and the resulting reorientation (true polar wander) of Pluto. Loading of volatile ices within a basin the size of Sputnik Planitia can substantially alter Pluto's inertia tensor, resulting in a reorientation of the dwarf planet of around 60 degrees with respect to the rotational and tidal axes. The combination of this reorientation, loading and global expansion due to the freezing of a possible subsurface ocean generates stresses within the planet's lithosphere, resulting in a global network of extensional faults that closely replicate the observed fault networks on Pluto. Sputnik Planitia probably formed northwest of its present location, and was loaded with volatiles over million-year timescales as a result of volatile transport cycles on Pluto. Pluto's past, present and future orientation is controlled by feedbacks between volatile sublimation and condensation, changing insolation conditions and Pluto's interior structure.

  10. Optimal reorientation of asymmetric underactuated spacecraft using differential flatness and receding horizon control

    Science.gov (United States)

    Cai, Wei-wei; Yang, Le-ping; Zhu, Yan-wei

    2015-01-01

    This paper presents a novel method integrating nominal trajectory optimization and tracking for the reorientation control of an underactuated spacecraft with only two available control torque inputs. By employing a pseudo input along the uncontrolled axis, the flatness property of a general underactuated spacecraft is extended explicitly, by which the reorientation trajectory optimization problem is formulated into the flat output space with all the differential constraints eliminated. Ultimately, the flat output optimization problem is transformed into a nonlinear programming problem via the Chebyshev pseudospectral method, which is improved by the conformal map and barycentric rational interpolation techniques to overcome the side effects of the differential matrix's ill-conditions on numerical accuracy. Treating the trajectory tracking control as a state regulation problem, we develop a robust closed-loop tracking control law using the receding-horizon control method, and compute the feedback control at each control cycle rapidly via the differential transformation method. Numerical simulation results show that the proposed control scheme is feasible and effective for the reorientation maneuver.

  11. Is height a core geometric cue for navigation? Young children's use of height in reorientation.

    Science.gov (United States)

    Hu, Qingfen; Zhang, Jing; Wu, Di; Shao, Yi

    2015-02-01

    With respect to reorientation, children older than 1.5 to 2 years can use geometric cues (distance and left/right sense). However, because previous studies have focused mainly on the plane geometric properties, little is known about the role of information with respect to vertical dimension in children's reorientation. The current study aimed to examine whether and how 3- and 4-year-old children use height information to search for a hidden toy when disoriented in a small enclosure. In a slant-ceiling rectangular room and a slant-ceiling square room, 4-year-olds were able to use height information to reorient and search for the toy in the correct corner, whereas 3-year-olds were not able to do so. Our results suggest that children can, at least by the age of 4 years, use height information and that height is not used as early as other geometric properties that are in the core geometry system for navigation. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Spatial reorientation decline in aging: the combination of geometry and landmarks.

    Science.gov (United States)

    Caffò, Alessandro O; Lopez, Antonella; Spano, Giuseppina; Serino, Silvia; Cipresso, Pietro; Stasolla, Fabrizio; Savino, Michelina; Lancioni, Giulio E; Riva, Giuseppe; Bosco, Andrea

    2017-07-20

    The study is focused on the assessment of reorientation skills in a sample of community-dwelling elderly people, manipulating landmarks and geometric (layout) information. A neuropsychological assessment was administered to 286 elderly participants, divided into six groups (healthy controls, HC; four subgroups of participants with mild cognitive impairment, MCI; participants with probable dementia, Prob_D) and tested with the Virtual Reorientation Test (VReoT). VReoT manipulated different spatial cues: geometry and landmarks (proximal and distal). Compared with HC, participants with MCI and Prob_D showed to be impaired in tasks involving geometry, landmarks and a combination of them. Both single and multiple domain impairment in MCI had an impact on reorientation performance. Moreover, VReoT was marginally able to discriminate between amnesic and non-amnesic MCI. The occurrence of getting lost events seemed to be associated to learning of geometric information. The associative strength between landmark and target plays an important role in affecting spatial orientation performance of cognitively impaired participants. Geometry significantly supports landmark information and becomes helpful with the increase of cognitive impairment which is linked to a decrement in landmark encoding. VReoT seems to represent a reliable evaluation supplement for spatial orientation deficits in prodromal stages of dementia.

  13. Hypergravity induces reorientation of cortical microtubules and modifies growth anisotropy in azuki bean epicotyls.

    Science.gov (United States)

    Soga, Kouichi; Wakabayashi, Kazuyuki; Kamisaka, Seiichiro; Hoson, Takayuki

    2006-11-01

    We examined the changes in the orientation of cortical microtubules during the hypergravity-induced modification of growth anisotropy (inhibition of elongation growth and promotion of lateral growth) in azuki bean (Vigna angularis Ohwi et Ohashi) epicotyls. The percentage of cells with transverse microtubules was decreased, while that with longitudinal microtubules was increased, in proportion to the logarithm of the magnitude of gravity. The percentage of cells with longitudinal microtubules showed an increase within 0.5 h of transfer of the 1g-grown seedlings to a 300g-hypergravity condition. Lanthanum and gadolinium, blockers of calcium channels, nullified the modification of growth anisotropy and reorientation of microtubules by hypergravity. Horizontal and acropetal hypergravity modified growth anisotropy and reorientation of microtubules, as did basipetal hypergravity, and these changes were not seen in the presence of lanthanum or gadolinium. These results suggest that hypergravity changes activities of lanthanum- and gadolinium-sensitive calcium channels independently of its direction, which may lead to reorientation of cortical microtubules and modification of growth anisotropy in azuki bean epicotyls.

  14. Stable panoramic views facilitate snap-shot like memories for spatial reorientation in homing pigeons.

    Directory of Open Access Journals (Sweden)

    Tommaso Pecchia

    Full Text Available Following spatial disorientation, animals can reorient themselves by relying on geometric cues (metric and sense specified both by the macroscopic surface layout of an enclosed space and prominent visual landmarks in arrays. Whether spatial reorientation in arrays of landmarks is based on explicit representation of the geometric cues is a matter of debate. Here we trained homing pigeons (Columba livia to locate a food-reward in a rectangular array of four identical or differently coloured pipes provided with four openings, only one of which allowed the birds to have access to the reward. Pigeons were trained either with a stable or a variable position of the opening on pipes, so that they could view the array either from the same or a variable perspective. Explicit mapping of configural geometry would predict successful reorientation irrespective of access condition. In contrast, we found that a stable view of the array facilitated spatial learning in homing pigeons, likely through the formation of snapshot-like memories.

  15. Age-related differences during a gaze reorientation task while standing or walking on a treadmill.

    Science.gov (United States)

    Cinelli, Michael; Patla, Aftab; Stuart, Bethany

    2008-02-01

    Falls among adults over the age of 65 years have become a growing concern. Two factors related to high incidence of falls in this group of adults are decreased head stability and impaired balance. Older adults' level of control of head stability or balance is unknown when they must reorient their gaze. In the current study, ten older adults (69 +/- 3.27 years) performed a gaze reorienting task while standing or walking on a treadmill. The task was the same as that used on young adults by Cinelli et al. (2007). The results show that older adults use a different strategy than young adults when reorienting gaze. Shoulder and hip rotations occurred synchronously when standing and were more variable when walking on a treadmill. As well, there was a larger difference between the onset of eye movements and body segment movement in the older adults. These differences can be accounted for by decreases in physiological subsystems. The visual presence of a visual target helped the older adults stabilize their heads-in-space by incorporating information from more than one sensory system.

  16. Involvement of the head and trunk during gaze reorientation during standing and treadmill walking.

    Science.gov (United States)

    Cinelli, Michael; Patla, Aftab; Stuart, Bethany

    2007-07-01

    As individuals stand or walk in an environment their gaze may be reoriented from one location to another in response to auditory or visual stimuli. In order to reorient gaze, the eyes and/or the head and trunk must rotate. However, what determines the exact degree of rotation of each segment while standing or walking is not fully understood. In the current study we show that when participants were asked to reorient their gaze towards light cues positioned at eccentric locations of up to 90 degrees while standing or walking on a treadmill their eyes and head mainly facilitated the action. Rotations of the head-in-space were similar for both tasks, but the rotation of the shoulders- and hips-in-space were lower for the treadmill walking condition. It is argued that this difference in the level of head-on-trunk rotation during the two tasks is controlled by the vestibular feedback loop. The regulation of this feedback loop is performed by the cerebellum in response to the level of threat to postural stability.

  17. Neural mechanisms underlying pain's ability to reorient attention: evidence for sensitization of somatic threat detectors.

    Science.gov (United States)

    Dowman, Robert

    2014-06-01

    Pain typically signals damage to the body, and as such can be perceived as threatening and can elicit a strong emotional response. This ecological significance undoubtedly underlies pain's well-known ability to demand attention. However, the neural mechanisms underlying this ability are poorly understood. Previous work from the author's laboratory has reported behavioral evidence suggesting that participants disengage their attention from an incorrectly cued visual target stimulus and reorient it toward a somatic target more rapidly when the somatic target is painful than when it is nonpainful. Furthermore, electrophysiological data suggest that this effect is mediated by a stimulus-driven process, in which somatic threat detectors located in the dorsal posterior insula activate the medial and lateral prefrontal cortex areas involved in reorienting attention toward the painful target. In these previous studies, the painful and nonpainful somatic targets were given in separate experiments involving different participants. Here, the nonpainful and painful somatic targets were presented in random order within the same block of trials. Unlike in the previous studies, both the nonpainful and painful somatic targets activated the somatic threat detectors, and the times taken to disengage and reorient attention were the same for both. These electrophysiological and behavioral data suggest that somatic threat detectors can become sensitized to nonpainful somatic stimuli that are presented in a context that includes painful stimuli.

  18. Reorientation dynamics of nematics encapsulated in microscopic volumes in a strong electric field

    Science.gov (United States)

    Zakharov, A. V.; Vakulenko, A. A.; Pasechnik, S. V.

    2016-09-01

    We theoretically describe a new regime of reorientation of the director field widehat n and velocity v of a nematic liquid crystal (LC) encapsulated in a rectangular cell under the action of strong electric field E directed at angle α ( π/2) to the horizontal surfaces bounding the LC cell. The numerical calculations in the framework of nonlinear generalization of the classical Eriksen-Leslie theory showed that at certain relations between the torques and momenta affecting the unit LC volume and E ≫ E th, transition periodic structures can arise during reorientation of widehat n, if the corresponding distortion mode has the fastest response and, thus, suppresses all the rest of the modes, including uniform ones. The position of sites of these periodic structures is affected by the value of field E, angle α, and the character of anchoring of LC molecules to the bounding surfaces. The calculations performed for the nematic formed by 4-n-penthyl-4'-cyanobiphenyl showed that several vortexes can form in an LC cell under the action of reorientation of the nematic field; the boundaries of these vortexes are determined by the positions of periodic structure sites.

  19. Performance of Traditional and Molecular Methods for Detecting Biological Agents in Drinking Water

    Science.gov (United States)

    Francy, Donna S.; Bushon, Rebecca N.; Brady, Amie M.G.; Bertke, Erin E.; Kephart, Christopher M.; Likirdopulos, Christina A.; Mailot, Brian E.; Schaefer, Frank W.; Lindquist, H.D. Alan

    2009-01-01

    To reduce the impact from a possible bioterrorist attack on drinking-water supplies, analytical methods are needed to rapidly detect the presence of biological agents in water. To this end, 13 drinking-water samples were collected at 9 water-treatment plants in Ohio to assess the performance of a molecular method in comparison to traditional analytical methods that take longer to perform. Two 100-liter samples were collected at each site during each sampling event; one was seeded in the laboratory with six biological agents - Bacillus anthracis (B. anthracis), Burkholderia cepacia (as a surrogate for Bu. pseudomallei), Francisella tularensis (F. tularensis), Salmonella Typhi (S. Typhi), Vibrio cholerae (V. cholerae), and Cryptospordium parvum (C. parvum). The seeded and unseeded samples were processed by ultrafiltration and analyzed by use of quantiative polymerase chain reaction (qPCR), a molecular method, and culture methods for bacterial agents or the immunomagnetic separation/fluorescent antibody (IMS/FA) method for C. parvum as traditional methods. Six replicate seeded samples were also processed and analyzed. For traditional methods, recoveries were highly variable between samples and even between some replicate samples, ranging from below detection to greater than 100 percent. Recoveries were significantly related to water pH, specific conductance, and dissolved organic carbon (DOC) for all bacteria combined by culture methods, but none of the water-quality characteristics tested were related to recoveries of C. parvum by IMS/FA. Recoveries were not determined by qPCR because of problems in quantifying organisms by qPCR in the composite seed. Instead, qPCR results were reported as detected, not detected (no qPCR signal), or +/- detected (Cycle Threshold or 'Ct' values were greater than 40). Several sample results by qPCR were omitted from the dataset because of possible problems with qPCR reagents, primers, and probes. For the remaining 14 qPCR results

  20. A new biomarker to examine the role of hippocampal function in the development of spatial reorientation in children: a review

    OpenAIRE

    Vanessa eVieites; Alina eNazareth; Reeb-Sutherland, Bethany C.; Shannon M Pruden

    2015-01-01

    Spatial navigation is an adaptive skill that involves determining the route to a particular goal or location, and then travelling that path. A major component of spatial navigation is spatial reorientation, or the ability to reestablish a sense of direction after being disoriented. The hippocampus is known to be critical for navigating, and has more recently been implicated in reorienting in adults, but relatively little is known about the development of the hippocampus in relation to these l...

  1. Arousal and attention re-orienting in autism spectrum disorders: evidence from auditory event-related potentials

    OpenAIRE

    2014-01-01

    The extended phenotype of autism spectrum disorders (ASD) includes a combination of arousal regulation problems, sensory modulation difficulties, and attention re-orienting deficit. A slow and inefficient re-orienting to stimuli that appear outside of the attended sensory stream is thought to be especially detrimental for social functioning. Event-related potentials (ERPs) and magnetic fields (ERFs) may help to reveal which processing stages underlying brain response to unattended but salient...

  2. Arousal and attention re-orienting in autism spectrum disorders: evidence from auditory event-related potentials

    OpenAIRE

    2014-01-01

    The extended phenotype of autism spectrum disorders (ASD) includes a combination of arousal regulation problems, sensory modulation difficulties, and attention re-orienting deficit. A slow and inefficient re-orienting to stimuli that appear outside of the attended sensory stream is thought to be especially detrimental for social functioning. Event-related potentials (ERPs) and magnetic fields (ERFs) may help to reveal which processing stages underlying brain response to unattended but salien...

  3. Origins of Water Molecules in the Photosystem II Crystal Structure.

    Science.gov (United States)

    Sakashita, Naoki; Watanabe, Hiroshi C; Ikeda, Takuya; Saito, Keisuke; Ishikita, Hiroshi

    2017-06-20

    The cyanobacterial photosystem II (PSII) crystal structure includes more than 1300 water molecules in each monomer unit; however, their precise roles in water oxidation are unclear. To understand the origins of water molecules in the PSII crystal structure, the accessibility of bulk water molecules to channel inner spaces in PSII was investigated using the water-removed PSII structure and molecular dynamics (MD) simulations. The inner space of the channel that proceeds toward the D1-Glu65/D2-Glu312 pair (E65/E312 channel) was entirely filled with water molecules from the bulk region. In the same channel, a diamond-shaped cluster of water molecules formed near redox-active TyrZ in MD simulations. Reorientation of the D2-Leu352 side chain resulted in formation of a hexagonal water network at the Cl(-)2 binding site. Water molecules could not enter the main region of the O4-water chain, which proceeds from the O4 site of the Mn4CaO5 cluster. However, in the O4-water chain, the two water binding sites that are most distant from the protein bulk surface were occupied by water molecules that approached along the E65/E312 channel, one of which formed an H-bond with the O4 site. These findings provide key insights into the significance of the channel ends, which may utilize water molecules during the PSII photocycle.

  4. Gauge-origin independent magnetizabilities from hybrid quantum mechanics/molecular mechanics models: Theory and applications to liquid water

    Science.gov (United States)

    Aidas, Kestutis; Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-07-01

    The theory of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach for gauge-origin independent calculations of the molecular magnetizability using Hartree-Fock or Density Functional Theory is presented. The method is applied to liquid water using configurations generated from classical Molecular Dynamics simulation to calculate the statistical averaged magnetizability. Based on a comparison with experimental data, treating only one water molecule quantum mechanically appears to be insufficient, while a quantum mechanical treatment of also the first solvation shell leads to good agreement between theory and experiment. This indicates that the gas-to-liquid phase shift for the molecular magnetizability is to a large extent of non-electrostatic nature.

  5. Void-induced dissolution in molecular dynamics simulations of NaCl and water.

    Science.gov (United States)

    Bahadur, Ranjit; Russell, Lynn M; Alavi, Saman; Martin, Scot T; Buseck, Peter R

    2006-04-21

    To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100 ps, in contrast with a much longer time scale of 1 mus expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300 K and 1 atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100 K increase in temperature, and a weak dependence on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.

  6. First molecular characterisation of Cryptosporidium and Giardia from Bubalus bubalis (water buffalo) in Victoria, Australia.

    Science.gov (United States)

    Abeywardena, Harshanie; Jex, Aaron R; von Samson-Himmelstjerna, Georg; Haydon, Shane R; Stevens, Melita A; Gasser, Robin B

    2013-12-01

    We conducted a molecular epidemiological survey of Cryptosporidium and Giardia from Bubalus bubalis (water buffalo) on two extensive farms (450 km apart) in Victoria, Australia. Faecal samples (n=476) were collected from different age groups of water buffalo at two time points (six months apart) and tested using a PCR-based mutation scanning-targeted sequencing-phylogenetic approach, employing markers within the small subunit of ribosomal RNA (designated pSSU) and triose phosphate isomerase (ptpi) genes. Based on pSSU data, Cryptosporidium parvum, Cryptosporidium bovis and Cryptosporidium genotypes 1, 2 (each 99% similar genetically to Cryptosporidium ryanae) and 3 (99% similar to Cryptosporidium suis) were detected in two (0.4%), one (0.2%), 38 (8.0%), 16 (3.4%) and one (0.2%) of the 476 samples tested, respectively. Using ptpi, Giardia duodenalis assemblages A and E were detected in totals of 56 (11.8%) and six (1.3%) of these samples, respectively. Cryptosporidium was detected on both farms, whereas Giardia was detected only on farm B, and both genera were detected in 1.5% of all samples tested. The study showed that water buffaloes on these farms excreted C. parvum and/or G. duodenalis assemblage A, which are consistent with those found in humans, inferring that these particular pathogens are of zoonotic significance. Future work should focus on investigating, in a temporal and spatial manner, the prevalence and intensity of such infections in water buffaloes in various geographical regions in Australia and in other countries.

  7. Revisiting Molecular Dynamics on a CPU/GPU system: Water Kernel and SHAKE Parallelization.

    Science.gov (United States)

    Ruymgaart, A Peter; Elber, Ron

    2012-11-13

    We report Graphics Processing Unit (GPU) and Open-MP parallel implementations of water-specific force calculations and of bond constraints for use in Molecular Dynamics simulations. We focus on a typical laboratory computing-environment in which a CPU with a few cores is attached to a GPU. We discuss in detail the design of the code and we illustrate performance comparable to highly optimized codes such as GROMACS. Beside speed our code shows excellent energy conservation. Utilization of water-specific lists allows the efficient calculations of non-bonded interactions that include water molecules and results in a speed-up factor of more than 40 on the GPU compared to code optimized on a single CPU core for systems larger than 20,000 atoms. This is up four-fold from a factor of 10 reported in our initial GPU implementation that did not include a water-specific code. Another optimization is the implementation of constrained dynamics entirely on the GPU. The routine, which enforces constraints of all bonds, runs in parallel on multiple Open-MP cores or entirely on the GPU. It is based on Conjugate Gradient solution of the Lagrange multipliers (CG SHAKE). The GPU implementation is partially in double precision and requires no communication with the CPU during the execution of the SHAKE algorithm. The (parallel) implementation of SHAKE allows an increase of the time step to 2.0fs while maintaining excellent energy conservation. Interestingly, CG SHAKE is faster than the usual bond relaxation algorithm even on a single core if high accuracy is expected. The significant speedup of the optimized components transfers the computational bottleneck of the MD calculation to the reciprocal part of Particle Mesh Ewald (PME).

  8. Void-induced dissolution in molecular dynamics simulations of NaCl and water

    Science.gov (United States)

    Bahadur, Ranjit; Russell, Lynn M.; Alavi, Saman; Martin, Scot T.; Buseck, Peter R.

    2006-04-01

    To gain a better understanding of the interaction of water and NaCl at the surface during dissolution, we have used molecular dynamics to simulate the interface with two equal-sized slabs of solid NaCl and liquid water in contact. The introduction of voids in the bulk of the salt, as well as steps or pits on the surface of the NaCl slab results in a qualitative change of system structure, as defined by radial distribution functions (RDFs). As an example, the characteristic Na-Na RDF for the system changes from regularly spaced narrow peaks (corresponding to an ordered crystalline structure), to a broad primary and smaller secondary peak (corresponding to a disordered structure). The change is observed at computationally short time scales of 100ps, in contrast with a much longer time scale of 1μs expected for complete mixing in the absence of defects. The void fraction (which combines both bulk and surface defects) required to trigger dissolution varies between 15%-20% at 300K and 1atm, and has distinct characteristics for the physical breakdown of the crystal lattice. The void fraction required decreases with temperature. Sensitivity studies show a strong dependence of the critical void fraction on the quantity and distribution of voids on the surface, with systems containing a balanced number of surface defects and a rough surface showing a maximum tendency to dissolve. There is a moderate dependence on temperature, with a 5% decrease in required void fraction with a 100K increase in temperature, and a weak dependance on water potential model used, with the SPC, SPC/E, TIP4P, and RPOL models giving qualitatively identical results. The results were insensitive to the total quantity of water available for dissolution and the duration of the simulation.

  9. Ionothermal synthesis process for aluminophosphate molecular sieves in the mixed water/ionic liquid system.

    Science.gov (United States)

    Zhao, Zhenchao; Zhang, Weiping; Xu, Renshun; Han, Xiuwen; Tian, Zhijian; Bao, Xinhe

    2012-01-21

    The synthesis process of aluminophosphate AlPO(4)-11 molecular sieve in the mixed water/1-butyl- 3-methylimidazolium bromide ([bmim]Br) ionic liquid was investigated by XRD, multinuclear solid-state NMR, scanning electron microscopy (SEM) and X-ray energy dispersive spectroscopy (EDS). It was observed that a tablet phase, named SIZ-2, was formed at the early stage of crystallization. During crystallization metastable SIZ-2 with an incompletely condensed framework phosphorus disappeared gradually, and the phosphorous species became fully condensed through hydroxyl reaction with tetrahedral aluminum to form thermodynamically stable AlPO(4)-11 in the final product. It was found that [bmim]Br, acting as the structure-directing agent, was occluded into the AlPO(4)-11 channel.

  10. Hydration and translocation of an excess proton in water clusters: An ab initio molecular dynamics study

    Indian Academy of Sciences (India)

    Arindam Bankura; Amalendu Chandra

    2005-10-01

    The hydration structure and translocation of an excess proton in hydrogen bonded water clusters of two different sizes are investigated by means of finite temperature quantum simulations. The simulations are performed by employing the method of Car–Parrinello molecular dynamics where the forces on the nuclei are obtained directly from `on the fly' quantum electronic structure calculations. Since no predefined interaction potentials are used in this scheme, it is ideally suited to study proton translocation processes which proceed through breaking and formation of chemical bonds. The coordination number of the hydrated proton and the index of oxygen to which the excess proton is attached are calculated along the simulation trajectories for both the clusters.

  11. Molecular dynamics simulations of the contact angle between water droplets and graphite surfaces

    CERN Document Server

    Sergi, Danilo; Ortona, Alberto

    2012-01-01

    Wetting is a widespread phenomenon, most prominent in a number of cases, both in nature and technology. Droplets of pure water with initial radius ranging from 20 to 80 [\\AA] spreading on graphitic surfaces are studied by molecular dynamics simulations. The equilibrium contact angle is determined and the transition to the macroscopic limit is discussed using Young equation in its modified form. While the largest droplets are almost perfectly spherical, the profiles of the smallest ones are no more properly described by a circle. For the sake of accuracy, we employ a more general fitting procedure based on local linear regressions. Furthermore, our results reveal that there is a possible transition to the macroscopic limit. The modified Young equation is particularly precise for characteristic lengths (radii and contact-line curvatures) around 40 [\\AA].

  12. High density gas state at water/graphite interface studied by molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Wang Chun-Lei; Li Zhao-Xia; Li Jing-Yuan; Xiu Peng; Hu Jun; Fang Hai-Ping

    2008-01-01

    In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results: gas films (pancake-like) for a larger ratio and nanobubbles for a Smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film (pancake-like) and nanobubbles.

  13. Molecular molybdenum persulfide and related catalysts for generating hydrogen from water

    Energy Technology Data Exchange (ETDEWEB)

    Long, Jeffrey R.; Chang, Christopher J.; Karunadasa, Hemamala I.; Majda, Marcin

    2016-11-22

    New metal persulfido compositions of matter are described. In one embodiment the metal is molybdenum and the metal persulfido complex mimics the structure and function of the triangular active edge site fragments of MoS.sub.2, a material that is the current industry standard for petroleum hydro desulfurization, as well as a promising low-cost alternative to platinum for electrocatalytic hydrogen production. This molecular [(PY5W.sub.2)MoS.sub.2].sup.x+ containing catalyst is capable of generating hydrogen from acidic-buffered water or even seawater at very low overpotentials at a turnover frequency rate in excess of 500 moles H.sub.2 per mole catalyst per second, with a turnover number (over a 20 hour period) of at least 19,000,000 moles H.sub.2 per mole of catalyst.

  14. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  15. Molecular molybdenum persulfide and related catalysts for generating hydrogen from water

    Energy Technology Data Exchange (ETDEWEB)

    Long, Jeffrey R.; Chang, Christopher J.; Karunadasa, Hemamala I.; Majda, Marcin

    2016-04-19

    New metal persulfido compositions of matter are described. In one embodiment the metal is molybdenum and the metal persulfido complex mimics the structure and function of the triangular active edge site fragments of MoS.sub.2, a material that is the current industry standard for petroleum hydro desulfurization, as well as a promising low-cost alternative to platinum for electrocatalytic hydrogen production. This molecular [(PY5W.sub.2)MoS.sub.2].sup.x+ containing catalyst is capable of generating hydrogen from acidic-buffered water or even seawater at very low overpotentials at a turnover frequency rate in excess of 500 moles H.sub.2 per mole catalyst per second, with a turnover number (over a 20 hour period) of at least 19,000,000 moles H.sub.2 per mole of catalyst.

  16. Equilibrium fractionation of H and O isotopes in water from path integral molecular dynamics

    Science.gov (United States)

    Pinilla, Carlos; Blanchard, Marc; Balan, Etienne; Ferlat, Guillaume; Vuilleumier, Rodolphe; Mauri, Francesco

    2014-06-01

    The equilibrium fractionation factor between two phases is of importance for the understanding of many planetary and environmental processes. Although thermodynamic equilibrium can be achieved between minerals at high temperature, many natural processes involve reactions between liquids or aqueous solutions and solids. For crystals, the fractionation factor α can be theoretically determined using a statistical thermodynamic approach based on the vibrational properties of the phases. These calculations are mostly performed in the harmonic approximation, using empirical or ab-initio force fields. In the case of aperiodic and dynamic systems such as liquids or solutions, similar calculations can be done using finite-size molecular clusters or snapshots obtained from molecular dynamics (MD) runs. It is however difficult to assess the effect of these approximate models on the isotopic fractionation properties. In this work we present a systematic study of the calculation of the D/H and 18O/16O equilibrium fractionation factors in water for the liquid/vapour and ice/vapour phases using several levels of theory within the simulations. Namely, we use a thermodynamic integration approach based on Path Integral MD calculations (PIMD) and an empirical potential model of water. Compared with standard MD, PIMD takes into account quantum effects in the thermodynamic modeling of systems and the exact fractionation factor for a given potential can be obtained. We compare these exact results with those of modeling strategies usually used, which involve the mapping of the quantum system on its harmonic counterpart. The results show the importance of including configurational disorder for the estimation of isotope fractionation in liquid phases. In addition, the convergence of the fractionation factor as a function of parameters such as the size of the simulated system and multiple isotope substitution is analyzed, showing that isotope fractionation is essentially a local effect in

  17. Evaluation of pharmaceuticals and personal care products as water-soluble molecular markers of sewage.

    Science.gov (United States)

    Nakada, Norihide; Kiri, Kentaro; Shinohara, Hiroyuki; Harada, Arata; Kuroda, Keisuke; Takizawa, Satoshi; Takada, Hideshige

    2008-09-01

    We examined the utility of 13 pharmaceuticals and personal care products (PPCPs) as molecular markers of sewage contamination in riverine, groundwater, and coastal environments. The PPCPs were crotamiton, ibuprofen, naproxen, ketoprofen, fenoprofen, mefenamic acid, thymol, triclosan, propyphenazone, carbamazepine, diethyltoluamide, ethenzamide, and caffeine. Measurements in 37 Japanese rivers showed positive correlations of riverine flux of crotamiton (r2 = 0.85), carbamazepine (r2 = 0.84), ibuprofen (r2 = 0.73), and mefenamic acid (r2 = 0.67) with the population in the catchments. In three surveys in the Tamagawa estuary, crotamiton, carbamazepine, and mefenamic acid behaved conservatively across seasons within a salinity range of 0.4-29 per thousand, suggesting their utility as molecular markers in coastal environments. Removal of ketoprofen and naproxen in the estuary was ascribed to photodegradation. Ibuprofen and thymol were removed from estuarine waters in summer by microbial degradation. Triclosan was removed by a combination of microbial degradation, photodegradation, and adsorption. These results were consistent with those of river water incubated for 8 d at 25 degrees C in the dark in order to examine the effects of biodegradation and photodegradation. Crotamiton was detected in groundwater from the Tokyo metropolitan area (12 out of 14 samples), suggesting wastewater leakage from decrepit sewers. Carbamazepine, ketoprofen, and ibuprofen (5/14), caffeine (4/14), and diethyltoluamide (3/14) were also detected in the groundwater, whereas the other carboxylic and phenolic PPCPs were not detected and were thought to be removed during their passage through soil. All the data demonstrated the utility of crotamiton and carbamazepine as conservative markers in freshwater and coastal environments. We recommend combining these conservative markers with labile PPCPs to detect inputs of poorly treated sewage.

  18. Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

    Science.gov (United States)

    Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

    2008-04-01

    Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

  19. Influence of polymer molecular weight and concentration on coexistence curve of isobutyric acid + water.

    Science.gov (United States)

    Reddy, P Madhusudhana; Venkatesu, P; Bohidar, H B

    2011-10-27

    We report the influence of variation of molecular weights (MWs = 2, 4, 6, and 9 × 10(5) g mol(-1)) and concentration (C) of a long-chain polymer (polyethylene oxide, PEO) on an upper critical solution temperature (UCST) of isobutyric acid (I) + water (W) using density (ρ) measurements as a function of temperature. The ρ values in each coexisting phase of IW have been measured at three different PEO concentrations (C = 0.395, 0.796, and 1.605 mg/cm(3)) in the near critical composition of IW at temperatures below the system's upper critical point for each molecular weight (MW) of PEO. Further, to ascertain the PEO behavior in IW we have measured the polydispersity values for both coexisting liquid phases by using dynamic light scattering (DLS). The data show that the polymer was significantly affected in the critical region of IW and these various MWs and concentrations of PEO show significant modulation on the critical exponents (β), the critical temperatures (T(c)), and critical composition (ϕ(c)), which are depicting the shape of the coexistence curve. The values of β and T(c) increase with increasing PEO MW and concentrations. Besides, the ϕ(c) values slightly decrease with increasing the C values in the mixture of IW. However, the rate of decrease in ϕ(c) is insignificant. Our experimental results explicitly elucidate that most of polymer chain entangles in water rich phase, thereby the polymer monomers strongly interact with neighbor solvent particles and also intra chain interaction between polymer monomers.

  20. Solvent-free, molecular-level modeling of self-assembling amphiphiles in water

    Science.gov (United States)

    Dey, Somajit; Saha, Jayashree

    2017-02-01

    Aggregation mesophases of self-assembling amphiphiles in water are highly important in the context of biology (biomembranes), therapy (liposomes), industry (polymer surfactants), and condensed-matter physics (lyotropic liquid crystals). Besides helping to increase fundamental understanding of collective molecular behavior, simulations of these lyotropic phases are pivotal to technological and medical developments such as smart drug carriers for gene therapy. Implicit-solvent, coarse-grained, low resolution modeling with a simple pair potential is the key to realizing the larger length and time scales associated with such mesoscopic phenomena during a computer simulation. Modeling amphiphiles by directed, soft, ellipsoidal cores interacting via a computationally simple yet tunable anisotropic pair potential, we have come to such a single-site model amphiphile that can rapidly self-assemble to give diverse lyotropic phases (such as fluid bilayers, micelles, etc.) without requiring the explicit incorporation of solvent particles. The model directly represents a tunable packing parameter that manifests in the spontaneous curvature of the amphiphile aggregates. Besides the all-important hydrophobic interaction, the hydration force is also treated implicitly. Thanks to the efficient solvent-free molecular-level coarse graining, this model is suitable for generic mesoscale studies of phenomena such as self-assembly, amphiphile mixing, domain formation, fusion, elasticity, etc., in amphiphile aggregates.

  1. Vibrational energy transfer between carbon nanotubes and liquid water: a molecular dynamics study.

    Science.gov (United States)

    Nelson, Tammie R; Chaban, Vitaly V; Kalugin, Oleg N; Prezhdo, Oleg V

    2010-04-08

    The rates and magnitudes of vibrational energy transfer between single-wall carbon nanotubes (CNTs) and water are investigated by classical molecular dynamics. The interactions between the CNT and solvent confined inside of the tube, the CNT and solvent surrounding the tube, as well as the solvent inside and outside of the tube are considered for the (11,11), (15,15), and (19,19) armchair CNTs. The vibrational energy transfer exhibits two time scales, subpicosecond and picosecond, of roughly equal importance. Solvent molecules confined within CNTs are more strongly coupled to the tubes than the outside molecules. The energy exchange is facilitated by slow collective motions, including CNT radial breathing modes (RBM). The transfer rate between CNTs and the inside solvent shows strong dependence on the CNT diameter. In smaller tubes, the transfer is faster and the solvent coupling to RBMs is stronger. The magnitude of the CNT-outside solvent interaction scales with the CNT surface area, while that of the CNT-inside solvent exhibits scaling that is intermediate between the CNT volume and surface. The Coulomb interaction between the solvent molecules inside and outside of the CNTs is much weaker than the CNT-solvent interactions. The results indicate that the excitation energy supplied to CNTs in chemical and biological applications is rapidly deposited to the active molecular agents and should remain localized sufficiently long in order to perform the desired function.

  2. Prediction of soot-water partition coefficients for selected persistent organic pollutants from theoretical molecular descriptors

    Institute of Scientific and Technical Information of China (English)

    Qing Zhang; Jun Huang; Gang Yu

    2008-01-01

    Quantitative structure-property relationship (QSPR) models were developed for soot-water partition coefficient (KSC) values of selected persistent organic pollutants (POPs), I.e. 10 polychlorinated dibenzo-p-dioxins and dibenzofurans, nine polychlorinated biphe-nyls, four polycyclic aromatic hydrocarbons and two polybrominated diphenyl ethers, using partial least squares (PLS) regression. Quan-tum chemical descriptors computed by parameterized model revision 3 Hamiltonian method were used as predictor variables. The cross-validated Q2cum value for the optimal QSPR model is 0.844, indicating a good predictive capability for the logKsc values of these chem-icals. The QSPR results showed that average molecular polarizability (α), standard heat of formation (△Hf) and energy of the lowest unoccupied molecular orbital (ELUMO) have dominant effects on Ksc of POPs. The results suggested that logKSC values of POPs increase with the increase of α. Contrarily, logKSC values decrease with the increase of ELUMO and △Hf of POPs.

  3. Nuclear magnetic shielding constants of liquid water: Insights from hybrid quantum mechanics/molecular mechanics models

    Science.gov (United States)

    Kongsted, Jacob; Nielsen, Christian B.; Mikkelsen, Kurt V.; Christiansen, Ove; Ruud, Kenneth

    2007-01-01

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the O17 and H1 isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4ppm for the O17 shielding and 1ppm for the H1 shielding.

  4. Nuclear magnetic shielding constants of liquid water: insights from hybrid quantum mechanics/molecular mechanics models.

    Science.gov (United States)

    Kongsted, Jacob; Nielsen, Christian B; Mikkelsen, Kurt V; Christiansen, Ove; Ruud, Kenneth

    2007-01-21

    We present a gauge-origin independent method for the calculation of nuclear magnetic shielding tensors of molecules in a structured and polarizable environment. The method is based on a combination of density functional theory (DFT) or Hartree-Fock wave functions with molecular mechanics. The method is unique in the sense that it includes three important properties that need to be fulfilled in accurate calculations of nuclear magnetic shielding constants: (i) the model includes electron correlation effects, (ii) the model uses gauge-including atomic orbitals to give gauge-origin independent results, and (iii) the effect of the environment is treated self-consistently using a discrete reaction-field methodology. The authors present sample calculations of the isotropic nuclear magnetic shielding constants of liquid water based on a large number of solute-solvent configurations derived from molecular dynamics simulations employing potentials which treat solvent polarization either explicitly or implicitly. For both the (17)O and (1)H isotropic shielding constants the best predicted results compare fairly well with the experimental data, i.e., they reproduce the experimental solvent shifts to within 4 ppm for the (17)O shielding and 1 ppm for the (1)H shielding.

  5. Biodegradability and Molecular Composition of Dissolved Organic Nitrogen in Urban Stormwater Runoff and Outflow Water from a Stormwater Retention Pond.

    Science.gov (United States)

    Lusk, Mary G; Toor, Gurpal S

    2016-04-01

    Dissolved organic nitrogen (DON) can be a significant part of the reactive N in aquatic ecosystems and can accelerate eutrophication and harmful algal blooms. A bioassay method was coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) to determine the biodegradability and molecular composition of DON in the urban stormwater runoff and outflow water from an urban stormwater retention pond. The biodegradability of DON increased from 10% in the stormwater runoff to 40% in the pond outflow water and DON was less aromatic and had lower overall molecular weight in the pond outflow water than in the stormwater runoff. More than 1227 N-bearing organic formulas were identified with FT-ICR-MS in the stormwater runoff and pond outflow water, which were only 13% different in runoff and outflow water. These molecular formulas represented a wide range of biomolecules such as lipids, proteins, amino sugars, lignins, and tannins in DON from runoff and pond outflow water. This work implies that the urban infrastructure (i.e., stormwater retention ponds) has the potential to influence biogeochemical processes in downstream water bodies because retention ponds are often a junction between the natural and the built environment.

  6. Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation

    Science.gov (United States)

    Paluch, Andrew S.; Parameswaran, Sreeja; Liu, Shuai; Kolavennu, Anasuya; Mobley, David L.

    2015-01-01

    We present a general framework to predict the excess solubility of small molecular solids (such as pharmaceutical solids) in binary solvents via molecular simulation free energy calculations at infinite dilution with conventional molecular models. The present study used molecular dynamics with the General AMBER Force Field to predict the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol solvents. The simulations are able to predict the existence of solubility enhancement and the results are in good agreement with available experimental data. The accuracy of the predictions in addition to the generality of the method suggests that molecular simulations may be a valuable design tool for solvent selection in drug development processes.

  7. Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

    Energy Technology Data Exchange (ETDEWEB)

    Yang, J.; Martí, J., E-mail: jordi.marti@upc.edu [Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia (Spain); Calero, C. [Department of Physics and Nuclear Engineering, Technical University of Catalonia-Barcelona Tech, B4-B5 Northern Campus, Jordi Girona 1-3, 08034 Barcelona, Catalonia (Spain); Center for Polymer Studies, Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215 (United States)

    2014-03-14

    Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10{sup −5} cm{sup 2}/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10{sup −8} cm{sup 2}/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2–8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of

  8. What first principles molecular dynamics can tell us about EXAFS spectroscopy of radioactive heavy metal cations in water

    Energy Technology Data Exchange (ETDEWEB)

    Duvail, M.; Gaigeot, M.P.; Spezia, R. [Lab. Analyse et Modelisation pour la Biologie et l' Environnement, UMR 8587 CNRS, Univ. d' Evry Val d' Essonne, Evry (France); D' Angelo, P. [Dipt. di Chimica, Univ. di Roma La Sapienza (Italy); Vitorge, P. [Lab. Analyse et Modelisation pour la Biologie et l' Environnement, UMR 8587 CNRS, Univ. d' Evry Val d' Essonne, Evry (France); Lab. de Speciation des Radionucleides et Molecules, CEA Saclay, DEN/DPC/SECR, Gif-sur-Yvette (France)

    2009-07-01

    In this paper we show how molecular dynamics simulation can improve comprehension of structure and dynamics of water solvent around heavy cations. In particular, metal-water radial distribution function obtained from molecular dynamics can be used into EXAFS equation to improve the experimental signal fitting. Here we show results on structure and dynamics of Co{sup 2+}, that is a radiocontaminant cation in its isotopic form {sup 60}Co, and lanthanoids(III) that are the chemical analogues of actinides(III) in aqueous solution. (orig.)

  9. Molecular dynamics of phenol at the liquid-vapor interface of water

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1991-01-01

    Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

  10. A classical reactive potential for molecular clusters of sulphuric acid and water

    Energy Technology Data Exchange (ETDEWEB)

    Stinson, Jake L.; Kathmann, Shawn M.; Ford, Ian J.

    2015-10-12

    We present a two state empirical valence bond (EVB) potential describing interactions between sulphuric acid and water molecules and designed to model proton transfer between them within a classical dynamical framework. The potential has been developed in order to study the properties of molecular clusters of these species, which are thought to be relevant to atmospheric aerosol nucleation. The particle swarm optimisation method has been used to fit the parameters of the EVB model to density functional theory (DFT) calculations. Features of the parametrised model and DFT data are compared and found to be in satisfactory agreement. In particular, it is found that a single sulphuric acid molecule will donate a proton when clustered with four water molecules at 300 K and that this threshold is temperature dependent. SMK was supported in part by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences; JLS and IJF were supported by the IMPACT scheme at University College London (UCL). We acknowledge the UCL Legion High Performance Computing Facility, and associated support services together with the resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the U.S. Department of Energy under Contract No. DE-AC02- 05CH11231. JLS thanks Dr. Gregory Schenter, Dr. Theo Kurtén and Prof. Hanna Vehkamäki for important guidance and discussions.

  11. Molecular-scale Description of SPAN80 Desorption from the Squalane-Water Interface

    CERN Document Server

    Tan, L; Chaudhari, M I

    2016-01-01

    Extensive all-atom molecular dynamics calculations on the water-squalane interface for nine different loadings with sorbitan monooleate (SPAN80), at $T=300$K, are analyzed for the surface tension equation of state, desorption free energy profiles as they depend on loading, and to evaluate escape times for absorbed SPAN80 into the bulk phases. These results suggest that loading only weakly affects accommodation of a SPAN80 molecule by this squalane-water interface. Specifically, the surface tension equation of state is simple through the range of high tension to high loading studied, and the desorption free energy profiles are weakly dependent on loading here. The perpendicular motion of the centroid of the SPAN80 head-group ring is well-described by a diffusional model near the minimum of the desorption free energy profile. Lateral diffusional motion is weakly dependent on loading. Escape times evaluated on the basis of a diffusional model and the desorption free energies are $7\\times 10^{-2}$ s (into the squ...

  12. Water transport in bentonite: evaluation by molecular dynamics, homogenization analysis and similitude law

    Energy Technology Data Exchange (ETDEWEB)

    Yasuaki, Ichikawa; Somehai, Prayongphan [Nagoya Univ., Dpt. of Environmental Engineering and Architecture, Chikusa, Nagoya (Japan); Kazumi, Kitayama [NUMO, Minato, Tokyo (Japan); Katsuyuki, Kawamura [Tokyo Institute of Technology, Tokyo (Japan)

    2005-07-01

    The major scenario of transport of radioactive nuclides is due to groundwater flow in most HLW projects. The phenomena of water flow and diffusion of chemical species in a bentonite buffer and surrounding rock mass have been treated mainly based on the classical porous media theories under the Darcy law and Fick law. The classical theories involve the following difficulties: 1) True velocity field is hard to be identified, especially in microscale sense. Note that it essentially affects the transport of chemical species. 2) The classical theories are not applicable to the problems in which experimental data are not available. Thus, the very long time behavior cannot be proven. We commonly recognize that the water flow in bentonite and mud-stone is strongly retarded. It is highly doubtful whether the above classical theories are applicable for such very low permeable materials. In this work we first show that the velocity and diffusion fields in pure smectite bentonite can be calculated by a coupled molecular dynamics (MD) simulation and the homogenization analysis (HA). The true velocity field can be calculated by applying HA to the Navier-Stokes equation, and the local distribution of viscosity used in this HA is obtained by MD. The diffusion field is also calculated under the same procedure of MD/HA by using the local diffusion equation with diffusivity calculated by MD. (authors)

  13. Hematite(001)-liquid water interface from hybrid density functional-based molecular dynamics

    Science.gov (United States)

    Falk von Rudorff, Guido; Jakobsen, Rasmus; Rosso, Kevin M.; Blumberger, Jochen

    2016-10-01

    The atom-scale characterisation of interfaces between transition metal oxides and liquid water is fundamental to our mechanistic understanding of diverse phenomena ranging from crystal growth to biogeochemical transformations to solar fuel production. Here we report on the results of large-scale hybrid density functional theory-based molecular dynamics simulations for the hematite(001)-liquid water interface. A specific focus is placed on understanding how different terminations of the same surface influence surface solvation. We find that the two dominant terminations for the hematite(001) surface exhibit strong differences both in terms of the active species formed on the surface and the strength of surface solvation. According to present simulations, we find that charged oxyanions (-O-) and doubly protonated oxygens (-OH2+ ) can be formed on the iron terminated layer via autoionization of neutral -OH groups. No such charged species are found for the oxygen terminated surface. In addition, the missing iron sublayer in the iron terminated surface strongly influences the solvation structure, which becomes less well ordered in the vicinity of the interface. These pronounced differences are likely to affect the reactivity of the two surface terminations, and in particular the energetics of excess charge carriers at the surface.

  14. Selective removal of diclofenac from contaminated water using molecularly imprinted polymer microspheres.

    Science.gov (United States)

    Dai, Chao-Meng; Geissen, Sven-Uwe; Zhang, Ya-Lei; Zhang, Yong-Jun; Zhou, Xue-Fei

    2011-06-01

    A molecularly imprinted polymer (MIP) was synthesized by precipitation polymerization using diclofenac (DFC) as a template. Binding characteristics of the MIP were evaluated using equilibrium binding experiments. Compared to the non-imprinted polymer (NIP), the MIP showed an outstanding affinity towards DFC in an aqueous solution with a binding site capacity (Q(max)) of 324.8 mg/g and a dissociation constant (K(d)) of 3.99 mg/L. The feasibility of removing DFC from natural water by the MIP was demonstrated by using river water spiked with DFC. Effects of pH and humic acid on the selectivity and adsorption capacity of MIP were evaluated in detail. MIP had better selectivity and higher adsorption efficiency for DFC as compared to that of powdered activated carbon (PAC). In addition, MIP reusability was demonstrated for at least 12 repeated cycles without significant loss in performance, which is a definite advantage over single-use activated carbon. Copyright © 2011. Published by Elsevier Ltd.

  15. Molecular dynamics simulations of wetting behavior of water droplets on polytetrafluorethylene surfaces.

    Science.gov (United States)

    Chen, Shuai; Wang, Jiadao; Ma, Tianbao; Chen, Darong

    2014-03-21

    Molecular dynamics simulations are performed to simulate the wetting behavior of nanosized water droplets on flat and pillar polytetrafluorethylene surfaces. The results show that the cutoff of the Lennard-Jones (LJ) potential has a large effect on the simulated value of the contact angle and some suggestions are given on how to choose an appropriate cutoff. On flat surfaces, the contact angle is independent of the size of the water droplet, which was determined by the energy parameters of the LJ potential. Furthermore, on pillar surfaces, two different equilibrium states are present: wetted contact and cross contact. For the wetted contact state, the contact angle increases with increasing droplet size and pillar size within a certain range. However, for the cross contact state, the contact angle and droplet size are uncorrelated, which results from the layering and structuring of molecules after their penetration into the hollows between pillars. However, additional simulations show that the final state depends on the initial geometry and the cross contact state is a metastable wetting state.

  16. Designing metal hydride complexes for water splitting reactions: a molecular electrostatic potential approach.

    Science.gov (United States)

    Sandhya, K S; Suresh, Cherumuttathu H

    2014-08-28

    The hydridic character of octahedral metal hydride complexes of groups VI, VII and VIII has been systematically studied using molecular electrostatic potential (MESP) topography. The absolute minimum of MESP at the hydride ligand (Vmin) and the MESP value at the hydride nucleus (VH) are found to be very good measures of the hydridic character of the hydride ligand. The increasing/decreasing electron donating feature of the ligand environment is clearly reflected in the increasing/decreasing negative character of Vmin and VH. The formation of an outer sphere metal hydride-water complex showing the HH dihydrogen interaction is supported by the location and the value of Vmin near the hydride ligand. A higher negative MESP suggested lower activation energy for H2 elimination. Thus, MESP features provided a way to fine-tune the ligand environment of a metal-hydride complex to achieve high hydridicity for the hydride ligand. The applicability of an MESP based hydridic descriptor in designing water splitting reactions is tested for group VI metal hydride model complexes of tungsten.

  17. Molecular dynamics of phenol at the liquid-vapor interface of water

    Science.gov (United States)

    Pohorille, Andrew; Benjamin, Ilan

    1991-01-01

    Results of molecular dynamics calculations on phenol at the water liquid-vapor interface are presented. The density profile of the center of mass of phenol exhibits a maximum 1 A from the Gibbs surface toward the vapor phase, indicating that the molecule is surface-active. Changes in the profile caused by the interface extend 6 A from the Gibbs surface into the liquid, significantly more than change in the density profile of water. The most probable orientation of the solute at the surface is such that its symmetry axis is perpendicular to the interface with the OH substituent pointing toward the liquid. An additional simulation with benzene shows that this molecule at the surface most often adopts orientations parallel to the interface. Deeper in the liquid all the solutes are preferentially ordered perpendicular to the surface. In the interfacial region the orientational preferences of the solute are primarily determined by cavity formation needed to accommodate the hydrophobic portion of the dissolved molecule.

  18. On the dissociative electron attachment as a potential source of molecular hydrogen in irradiated liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Cobut, V.; Jay-Gerin, J.-P.; Frongillo, Y. [Sherbrooke Univ., PQ (Canada). Faculte de Medecine; Patau, J.P. [Toulouse-3 Univ., 31 (France)

    1996-02-01

    In the radiolysis of liquid water, different mechanisms for the formation of molecular hydrogen (H{sub 2}) are involved at different times after the initial energy disposition. It has been suggested that the contributions of the e{sub aq}{sup -} + e{sub aq}{sup -}, H + e{sub aq}{sup -} and H + H reactions between hydrated electrons (e{sub aq}{sup -}) and hydrogen atoms in the spurs are not sufficient to account for all of the observed H{sub 2} yield (0.45 molecules/100 eV) on the microsecond time scale. Addressing the question of the origin of an unscavengeable H{sub 2} yield of 0.15 molecules/100 eV produced before spur expansion, we suggest that the dissociative capture of the so-called vibrationally-relaxing electrons by H{sub 2}O molecules is a possible pathway for the formation of part of the initial H{sub 2} yield. Comparison of recent dissociative-electron-attachment H{sup -}-anion yield-distribution measurements from amorphous H{sub 2}O films with the energy spectrum of vibrationally-relaxing electrons in irradiated liquid water, calculated by Monte Carlo simulations, plays in favor of this hypothesis. (author).

  19. 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.

  20. Water interactions with condensed organic phases: a combined experimental and theoretical study of molecular-level processes

    Science.gov (United States)

    Johansson, Sofia M.; Kong, Xiangrui; Thomson, Erik S.; Papagiannakopoulos, Panos; Pettersson, Jan B. C.; Lovrić, Josip; Toubin, Céline

    2016-04-01

    Water uptake on aerosol particles modifies their chemistry and microphysics with important implications for air quality and climate. A large fraction of the atmospheric aerosol consists of organic aerosol particles or inorganic particles with condensed organic components. Here, we combine laboratory studies using the environmental molecular beam (EMB) method1 with molecular dynamics (MD) simulations to characterize water interactions with organic surfaces in detail. The over-arching aim is to characterize the mechanisms that govern water uptake, in order to guide the development of physics-based models to be used in atmospheric modelling. The EMB method enables molecular level studies of interactions between gases and volatile surfaces at near ambient pressure,1 and the technique may provide information about collision dynamics, surface and bulk accommodation, desorption and diffusion kinetics. Molecular dynamics simulations provide complementary information about the collision dynamics and initial interactions between gas molecules and the condensed phase. Here, we focus on water interactions with condensed alcohol phases that serve as highly simplified proxies for systems in the environment. Gas-surface collisions are in general found to be highly inelastic and result in efficient surface accommodation of water molecules. As a consequence, surface accommodation of water can be safely assumed to be close to unity under typical ambient conditions. Bulk accommodation is inefficient on solid alcohol and the condensed materials appear to produce hydrophobic surface structures, with limited opportunities for adsorbed water to form hydrogen bonds with surface molecules. Accommodation is significantly more efficient on the dynamic liquid alcohol surfaces. The results for n-butanol (BuOH) are particularly intriguing where substantial changes in water accommodation taking place over a 10 K interval below and above the BuOH melting point.2 The governing mechanisms for the

  1. Isolation and molecular identification of biodegrading Mycobacteria from water supplies of Iranian hospitals.

    Directory of Open Access Journals (Sweden)

    Davood Azadi

    2014-08-01

    Full Text Available Some microorganisms, mainly members of two genera including Pseudomonas and Mycobacterium, were found to be capable of transforming and degrading of polluting agents. We herein report the isolation of a few mycobacteria with the ability to biodegrade organic and inorganic compounds from water supplies of Iranian hospitals.The water samples were collected from hospital water supplies. Isolation processes were done according to standard methods. The colonies were subcultured on Löwenstein-Jensen medium to obtain a pure culture. The identification and characterization of the isolates were based on conventional and molecular methods including direct sequence analysis of almost full length of 16S rRNA gene.The almost complete 16S rRNA gene sequences of the studied strains revealed that the isolates WP16, AW18-1 and AW18-3 were identified as M. fredriksbergense, AW18-2 as M. austroafricanum, AW27-2 as M. obuenseand AW27-6 as M. phocaicum.The relationship between our isolates and standard strains of Mycobacterium was supported by a phylogenetic tree of 16S rRNA gene.In the current study we were able to isolate and characterize six mycobacteria with capability of transforming and degrading polluting agents from Iranian hospital environments. This is indeed the first report on isolation and characterization of mycobacteria with degrading capability of polluting agents from Iranian hospitals. It can be considered as a pioneer study to open up a new horizon in the study of microbial diversity in Iran with an objective-based and applied approach to tackle environmental challenges.

  2. Molecularly imprinted polymer dedicated to the extraction of glyphosate in natural waters.

    Science.gov (United States)

    Puzio, K; Claude, B; Amalric, L; Berho, C; Grellet, E; Bayoudh, S; Nehmé, R; Morin, Ph

    2014-09-26

    Three molecularly imprinted polymers (MIPs) have been synthesized in order to bind efficiently glyphosate (GLY) in natural waters (mineral and underground). Since the target analyte is polar and hydrophilic, electrostatic interactions and hydrogen bonds have been favored with two templates (phenylphosphonic acid and diethyl(α-aminobenzyl)-phosphonic acid) and two functional monomers (1-allyl-2-thiourea and methacrylic acid). MIPs have been assessed by comparison of the recoveries obtained with MIP and NIP (non imprinted polymer) by solid-phase extraction (SPE). The selectivity of MIP versus NIP was satisfactory for the three imprinted polymers with a very straightforward protocol: conditioning of 250 mg of MIP or NIP packed in 3-mL polypropylene cartridges with 3 mL Milli-Q water, loading of Milli-Q water (15 mL) spiked with 5 mg L(-1) of GLY and its metabolite, aminomethylphosphonic acid (AMPA) and elution by 3 mL NH4OH (10mM) or 3 mL HCl (100mM). SPE fractions were directly analyzed by capillary electrophoresis (CE). Thus, the recoveries of both analytes were greater than 80% for all MIPs and less than 25% for most NIPs. Moreover, the MIP prepared with 1-allyl-2-thiourea as functional monomer and phenylphosphonic acid as template displayed a capacity of 0.033 μmol/mg for GLY. However, the substitution of Milli-Q water by mineral water caused the decrease of MIP recoveries, for that, a pretreatment of the sample by ionic exchange resins was set up and succeeded in improving recoveries (about 50% for GLY and 25% for AMPA). Then, groundwaters were spiked with low concentrations of GLY and AMPA (0.5 μgL(-1)) and directly percolated through MIP cartridges. The extractions were carried out by triplicate and the elution fractions were analyzed by UPLC-MS/MS. The results showed no retention of AMPA but a total retention of GLY by MIP. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers.

    Energy Technology Data Exchange (ETDEWEB)

    Chandross, Michael Evan; Grest, Gary Stephen; Lane, J. Matthew D.; Lorenz, Christian Douglas (King' s College London, London, UK); Stevens, Mark Jackson

    2008-12-01

    We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

  4. Molecular Simulations of the Vapor-Liquid Phase Interfaces of Pure Water Modeled with the SPC/E and the TIP4P/2005 Molecular Models

    Science.gov (United States)

    Vinš, Václav; Celný, David; Planková, Barbora; Němec, Tomáš; Duška, Michal; Hrubý, Jan

    2016-03-01

    In our previous study [Planková et al., EPJWeb. Conf. 92, 02071 (2015)], several molecular simulations of vapor-liquid phase interfaces for pure water were performed using the DL_POLY Classic software. The TIP4P/2005 molecular model was successfully used for the modeling of the density profile and the thickness of phase interfaces together with the temperature dependence of the surface tension. In the current study, the extended simple point charge (SPC/E) model for water was employed for the investigation of vapor-liquid phase interfaces over a wide temperature range from 250 K to 600 K. The TIP4P/2005 model was also used with the temperature step of 25 K to obtain more consistent data compared to our previous study. Results of the new simulations are in a good agreement with most of the literature data. TIP4P/2005 provides better results for the saturated liquid density with its maximum close to 275 K, while SPC/E predicts slightly better saturated vapor density. Both models give qualitatively correct representation for the surface tension of water. The maximum absolute deviation from the IAPWS standard for the surface tension of ordinary water is 10.4 mN · m-1 and 4.1 mN · m-1 over the temperature range from 275 K to 600 K in case of SPC/E and TIP4P/2005, respectively.

  5. Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

    KAUST Repository

    Turgman-Cohen, Salomon

    2013-10-08

    We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

  6. A numerical method for reorientation of rotating tidally deformed viscoelastic bodies

    Science.gov (United States)

    Hu, H.; Wal, W.; Vermeersen, L. L. A.

    2017-01-01

    Existing approaches for simulating the true polar wander (TPW) of a viscoelastic body can be divided into three categories: (i) a linear dynamic approach which uses the linearized Liouville equation (e.g., Wu and Peltier (1984) and Mitrovica et al. (2005)); (ii) a nonlinear dynamic approach which is based on the quasi-fluid approximation (e.g., Sabadini and Peltier (1981), Ricard et al. (1993), and Cambiotti et al. (2011)); and (iii) a long-term limit approach which only considers the fluid limit of a reorientation (e.g., Matsuyama and Nimmo (2007)). Several limitations of these approaches have not been studied: the range for which the linear approach is accurate, the validity of the quasi-fluid approximation, and the dynamic solution for TPW of a tidally deformed rotating body. We establish a numerical procedure which is able to determine the large-angle reorientation of a viscoelastic celestial body that can be both centrifugally and tidally deformed. We show that the linear approach leads to significant errors for loadings near the poles or the equator. Second, we show that slow relaxation modes can have a significant effect on large-angle TPW of Earth or other planets. Finally, we show that reorientation of a tidally deformed body driven by a positive mass anomaly near the poles has a preference for rotating around the tidal axis instead of toward it. At a tidally deformed body which does not have a remnant bulge, positive mass anomalies are more likely to be found near the equator and the plane perpendicular to the tidal axis, while negative mass anomalies tend to be near the great circle that contains the tidal and rotational axes.

  7. Reorientation of Magnetic Graphene Oxide Nanosheets in Crosslinked Quaternized Polyvinyl Alcohol as Effective Solid Electrolyte

    Directory of Open Access Journals (Sweden)

    Jia-Shuin Lin

    2016-11-01

    Full Text Available This work aims to clarify the effect of magnetic graphene oxide (GO reorientation in a polymer matrix on the ionic conduction and methanol barrier properties of nanocomposite membrane electrolytes. Magnetic iron oxide (Fe3O4 nanoparticles were prepared and dispersed on GO nanosheets (GO-Fe3O4. The magnetic GO-Fe3O4 was imbedded into a quaternized polyvinyl alcohol (QPVA matrix and crosslinked (CL- with glutaraldehyde (GA to obtain a polymeric nanocomposite. A magnetic field was applied in the through-plane direction during the drying and film formation steps. The CL-QPVA/GO-Fe3O4 nanocomposite membranes were doped with an alkali to obtain hydroxide-conducting electrolytes for direct methanol alkaline fuel cell (DMAFC applications. The magnetic field-reoriented CL-QPVA/GO-Fe3O4 electrolyte demonstrated higher conductivity and lower methanol permeability than the unoriented CL-QPVA/GO-Fe3O4 membrane or the CL-QPVA film. The reoriented CL-QPVA/GO-Fe3O4 nanocomposite was used as the electrolyte in a DMAFC and resulted in a maximum power density of 55.4 mW·cm−2 at 60 °C, which is 73.7% higher than that of the composite without the magnetic field treatment (31.9 mW·cm−2. In contrast, the DMAFC using the CL-QPVA electrolyte generated only 22.4 mW·cm−2. This research proved the surprising benefits of magnetic-field-assisted orientation of GO-Fe3O4 in facilitating the ion conduction of a polymeric electrolyte.

  8. Environment size and the use of feature and geometric cues for reorientation.

    Science.gov (United States)

    Sturz, Bradley R; Kelly, Debbie M

    2013-02-01

    We tested associative-based accounts of orientation by investigating the influence of environment size on the use of feature and geometric cues for reorientation. Two groups of participants were trained in dynamic three-dimensional virtual rectangular environments that differed in size to find a distinctly colored bin located at one of the four corners. Subsequently, we probed the reliance on feature and geometric cues for reorientation during test trials by presenting six trial types: Small Geometry Only, Large Geometry Only, Small Cue Conflict, Large Cue Conflict, Small Distal, and Large Distal. During Geometry Only test trials, all bins were black; thus, all distinctive featural information was removed leaving only geometric cues. For Cue Conflict test trials, all colored bins were shifted counter-clockwise one corner; thus, the geometric cues from the trained corner and the trained color were in direct conflict. During Distal test trials, the bin in the geometrically incorrect corner farthest from the trained corner was colored the same as during training; the remaining three bins were black. Thus, only this distant feature cue could be used to determine the location of the goal bin. Results suggested that geometric cues were used across changes in environment size, featural cues exerted greater influence when in conflict with geometric cues, and the far featural cue was used to disambiguate the correct from the rotationally equivalent location. In short, both feature and geometric cues were used for reorientation, and environment size influenced the relative use of feature and geometric cues. Collectively, our results provide evidence against associative-based accounts of orientation. Copyright © 2012 Elsevier B.V. All rights reserved.

  9. Resting-state functional connectivity of ventral parietal regions associated with attention reorienting and episodic recollection

    Directory of Open Access Journals (Sweden)

    Sander M Daselaar

    2013-02-01

    Full Text Available In functional neuroimaging studies, ventral parietal cortex (VPC is recruited by very different cognitive tasks. Explaining the contributions VPC to these tasks has become a topic of intense study and lively debate. Perception studies frequently find VPC activations during tasks involving attention-reorienting, and memory studies frequently find them during tasks involving episodic recollection. According to the Attention to Memory (AtoM model, both phenomena can be explained by the same VPC function: bottom-up attention. Yet, a recent functional MRI (fMRI meta-analysis suggested that attention-reorienting activations are more frequent in anterior VPC, whereas recollection activations are more frequent in posterior VPC. Also, there is evidence that anterior and posterior VPC regions have different functional connectivity patterns. To investigate these issues, we conducted a resting-state functional connectivity analysis using as seeds the center-of-mass of attention-reorienting and recollection activations in the meta-analysis, which were located in the supramarginal gyrus (SMG, around the temporo-parietal junction—TPJ and in the angular gyrus (AG, respectively. The SMG seed showed stronger connectivity with ventrolateral prefrontal cortex (VLPFC and occipito-temporal cortex, whereas the AG seed showed stronger connectivity with the hippocampus and default network regions. To investigate whether these connectivity differences were graded or sharp, VLPFC and hippocampal connectivity was measured in VPC regions traversing through the SMG and AG seeds. The results showed a graded pattern: VLPFC connectivity gradually decreases from SMG to AG, whereas hippocampal connectivity gradually increases from SMG to AG. Importantly, both gradients showed an abrupt break when extended beyond VPC borders. This finding suggests that functional differences between SMG and AG are more subtle than previously thought. These connectivity differences can be

  10. Reorientation and faulting of Pluto due to volatile loading within Sputnik Planitia

    Science.gov (United States)

    Keane, James T.; Matsuyama, Isamu; Kamata, Shunichi; Steckloff, Jordan K.

    2016-12-01

    Pluto is an astoundingly diverse, geologically dynamic world. The dominant feature is Sputnik Planitia—a tear-drop-shaped topographic depression approximately 1,000 kilometres in diameter possibly representing an ancient impact basin. The interior of Sputnik Planitia is characterized by a smooth, craterless plain three to four kilometres beneath the surrounding rugged uplands, and represents the surface of a massive unit of actively convecting volatile ices (N2, CH4 and CO) several kilometres thick. This large feature is very near the Pluto-Charon tidal axis. Here we report that the location of Sputnik Planitia is the natural consequence of the sequestration of volatile ices within the basin and the resulting reorientation (true polar wander) of Pluto. Loading of volatile ices within a basin the size of Sputnik Planitia can substantially alter Pluto’s inertia tensor, resulting in a reorientation of the dwarf planet of around 60 degrees with respect to the rotational and tidal axes. The combination of this reorientation, loading and global expansion due to the freezing of a possible subsurface ocean generates stresses within the planet’s lithosphere, resulting in a global network of extensional faults that closely replicate the observed fault networks on Pluto. Sputnik Planitia probably formed northwest of its present location, and was loaded with volatiles over million-year timescales as a result of volatile transport cycles on Pluto. Pluto’s past, present and future orientation is controlled by feedbacks between volatile sublimation and condensation, changing insolation conditions and Pluto’s interior structure.

  11. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin

    Science.gov (United States)

    Khan, Naima A.; Engle, Mark A.; Dungan, Barry; Holguin, F. Omar; Xu, Pei; Carroll, Kenneth C.

    2016-01-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production.

  12. Volatile-organic molecular characterization of shale-oil produced water from the Permian Basin.

    Science.gov (United States)

    Khan, Naima A; Engle, Mark; Dungan, Barry; Holguin, F Omar; Xu, Pei; Carroll, Kenneth C

    2016-04-01

    Growth in unconventional oil and gas has spurred concerns on environmental impact and interest in beneficial uses of produced water (PW), especially in arid regions such as the Permian Basin, the largest U.S. tight-oil producer. To evaluate environmental impact, treatment, and reuse potential, there is a need to characterize the compositional variability of PW. Although hydraulic fracturing has caused a significant increase in shale-oil production, there are no high-resolution organic composition data for the shale-oil PW from the Permian Basin or other shale-oil plays (Eagle Ford, Bakken, etc.). PW was collected from shale-oil wells in the Midland sub-basin of the Permian Basin. Molecular characterization was conducted using high-resolution solid phase micro extraction gas chromatography time-of-flight mass spectrometry. Approximately 1400 compounds were identified, and 327 compounds had a >70% library match. PW contained alkane, cyclohexane, cyclopentane, BTEX (benzene, toluene, ethylbenzene, and xylene), alkyl benzenes, propyl-benzene, and naphthalene. PW also contained heteroatomic compounds containing nitrogen, oxygen, and sulfur. 3D van Krevelen and double bond equivalence versus carbon number analyses were used to evaluate molecular variability. Source composition, as well as solubility, controlled the distribution of volatile compounds found in shale-oil PW. The salinity also increased with depth, ranging from 105 to 162 g/L total dissolved solids. These data fill a gap for shale-oil PW composition, the associated petroleomics plots provide a fingerprinting framework, and the results for the Permian shale-oil PW suggest that partial treatment of suspended solids and organics would support some beneficial uses such as onsite reuse and bio-energy production.

  13. A common column density threshold for scattering at 3.6 mum and water-ice in molecular clouds

    CERN Document Server

    Andersen, M; Steinacker, J; Tothill, N

    2014-01-01

    Context: Observations of scattered light in the 1-5 $\\mu$m range have revealed dust grains in molecular cores with sizes larger than commonly inferred for the diffuse interstellar medium. It is currently unclear whether these grains are grown within the molecular cores or are an ubiquitous component of the interstellar medium. Aims: We investigate whether the large grains necessary for efficient scattering at 1-5 mum are associated with the abundance of water-ice within molecular clouds and cores. Methods: We combined water-ice abundance measurements for sight lines through the Lupus IV molecular cloud complex with measurements of the scattered light at 3.6 mum for the same sight lines. Results: We find that there is a similar threshold for the cores in emission in scattered light at 3.6 mum (tau_9.7=0.15pm0.05, A_K=0.4pm0.2 as water-ice (tau_9.7=0.11pm0.01, A_K=0.19pm0.04) and that the scattering efficiency increases as the relative water-ice abundance increases. The ice layer increases the average grain siz...

  14. Slosh wave excitation due to cryogenic liquid reorientation in space-based propulsion system

    Science.gov (United States)

    Hung, R. J.; Shyu, K. L.; Lee, C. C.

    1991-01-01

    The objective of the cryogenic fluid management of the spacecraft propulsion system is to develop the technology necessary for acquistion or positioning of liquid and vapor within a tank in reduced gravity to enable liquid outflow or vapor venting. In this study slosh wave excitation induced by the resettling flow field activated by 1.0 Hz medium frequency impulsive reverse gravity acceleration during the course of liquid fluid reorientation with the initiation of geyser for liquid filled levels of 30, 50, and 80 percent have been studied. Characteristics of slosh waves with various frequencies excited are discussed.

  15. Dynamic Isovector Reorientation of Deuteron as a Probe to Nuclear Symmetry Energy.

    Science.gov (United States)

    Ou, Li; Xiao, Zhigang; Yi, Han; Wang, Ning; Liu, Min; Tian, Junlong

    2015-11-20

    We present the calculations on a novel reorientation effect of deuteron attributed to isovector interaction in the nuclear field of heavy target nuclei. The correlation angle determined by the relative momentum vector of the proton and the neutron originating from the breakup deuteron, which is experimentally detectable, exhibits significant dependence on the isovector nuclear potential but is robust against the variation of the isoscaler sector. In terms of sensitivity and cleanness, the breakup reactions induced by the polarized deuteron beam at about 100 MeV/u provide a more stringent constraint to the symmetry energy at subsaturation densities.

  16. Influence of family, religion, and social conformity on client participation in sexual reorientation therapy.

    Science.gov (United States)

    Maccio, Elaine M

    2010-01-01

    This study examined the likelihood of participating in sexual reorientation therapy (SRT) based on actual or expected family reactions to the disclosure of one's same-sex sexuality, religious fundamentalism, social conformity, and several demographic variables. A sample of 52 SRT participants and 211 SRT nonparticipants who had ever identified as gay, lesbian, or bisexual completed a survey either online or in hardcopy format. Actual or expected negative family reactions, high religious fundamentalism, and identifying as spiritual significantly increased one's odds of participating in SRT. The findings are essential for preparing practitioners in any clinical practice setting to work with clients struggling with their sexuality.

  17. Nd-induced Mn spin-reorientation transition in NdMnAsO

    OpenAIRE

    Marcinkova, A.; Hansen, T.C.; Curfs, C.; Margadonna, S.; Bos, J. -W. G.

    2010-01-01

    A combination of synchrotron x-ray, neutron powder-diffraction, magnetization, heat-capacity, and electrical-resistivity measurements reveals that NdMnAsO is an antiferromagnetic semiconductor with large Neel temperature [T-N=359(2) K]. At room temperature the magnetic propagation vector k=0 and the Mn moments are directed along the crystallographic c axis [m(Mn)=2.41(6) mu(B)]. Upon cooling a spin-reorientation (SR) transition of the Mn moments into the ab plane occurs (T-SR=23 K). This coin...

  18. Piezoluminescence at the air-water interface through dynamic molecular recognition driven by lateral pressure application.

    Science.gov (United States)

    Ariga, Katsuhiko; Nakanishi, Takashi; Terasaka, Yukiko; Tsuji, Hiromitsu; Sakai, Daisuke; Kikuchi, Jun-ichi

    2005-02-01

    The steroid cyclophanes with a cyclic core consisting of a 1,6,20,25-tetraaza[6.1.6.1]paracyclophane connected to four steroid moieties (cholic acid or cholanic acid) through a flexible l-lysine spacer were spread on water as Langmuir monolayers. The pi-A isotherm of the cholic-type steroid cyclophane includes a transition to the condensed phase with a limiting area of approximately 2 nm(2). This value is close to the cross-sectional area of the steroid cyclophane with a standing-up conformation of the cholic acid moieties, strongly suggesting that the cavity converts from a two-dimensional cavity to a three-dimensional cavity upon compressing the monolayer. Surface-reflective fluorescence spectroscopy of the monolayer using an aqueous fluorescent probe (6-(p-toluidino)naphthalene-2-sulfonate (TNS)) showed an abrupt increase in the TNS fluorescence intensity at a molecular area of 2 nm(2). Efficient binding of the guest probe would occur upon the completion of the three-dimensional cavity. Repeated compression and expansion induces periodic changes in the fluorescence intensity. This indicates a piezoluminescence effect through the catch and release of the TNS guest upon dynamic cavity formation. Analyses of the binding behavior of TNS to the steroid cyclophane resulted in binding constants in the range of approximately (5-9) x 10(4) M(-1) which are similar to that observed in lipid bilayer media (K = 5.1 x 10(4) M(-1)). The fluorescence intensity within the condensed phase was significantly increased with increasing pressure, suggesting that suppression of the molecular motion of the bound TNS may retard the nonemission process. Similar monolayer experiments were carried out with the monolayer of the cholanic-type steroid cyclophane that cannot form an open conformation on water. Both the phase transition in the pi-A isotherm and the change in the fluorescence intensity were negligible, confirming that the dynamic characteristic of the cavity is indispensable for

  19. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

  20. Molecular origin of drug release by water boiling inside carbon nanotubes from reactive molecular dynamics simulation and DFT perspectives.

    Science.gov (United States)

    Ganji, M Darvish; Mirzaei, Sh; Dalirandeh, Z

    2017-07-05

    Owing to their nanosized hollow cylindrical structure, CNTs hold the promise to be utilized as desired materials for encapsulating molecules which demonstrate wide inferences in drug delivery. Here we evaluate the possibility of drug release from the CNTs with various types and edge chemistry by reactive MD simulation to explain the scientifically reliable relations for proposed process. It was shown that heating of CNTs (up to 750 K) cannot be used for release of incorporated drug (phenylalanine) into water and even carbonated water solvent with very low boiling temperature. This is due to the strong physisorption (π-stacking interaction) between the aromatic of encapsulated drug and CNT sidewall which causes the drug to bind the nanotube sidewall. We have further investigated the interaction nature and release mechanism of water and drug confined/released within/from the CNTs by DFT calculations and the results confirmed our MD simulation findings. The accuracy of DFT method was also validated against the experimental and theoretical values at MP2/CCSD level. Therefore, we find that boiling of water/carbonated water confined within the CNTs could not be a suitable technique for efficient drug release. Our atomistic simulations provide a well-grounded understanding for the release of drug molecules confined within CNTs.