Some thermodynamical aspects of protein hydration water

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

Mallamace, Francesco, E-mail: francesco.mallamace@unime.it; Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139; Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215

2015-06-07

We study by means of nuclear magnetic resonance the self-diffusion of protein hydration water at different hydration levels across a large temperature range that includes the deeply supercooled regime. Starting with a single hydration shell (h = 0.3), we consider different hydrations up to h = 0.65. Our experimental evidence indicates that two phenomena play a significant role in the dynamics of protein hydration water: (i) the measured fragile-to-strong dynamic crossover temperature is unaffected by the hydration level and (ii) the first hydration shell remains liquid at all hydrations, even at the lowest temperature.

SoftWAXS: a computational tool for modeling wide-angle X-ray solution scattering from biomolecules.

PubMed

Bardhan, Jaydeep; Park, Sanghyun; Makowski, Lee

2009-10-01

This paper describes a computational approach to estimating wide-angle X-ray solution scattering (WAXS) from proteins, which has been implemented in a computer program called SoftWAXS. The accuracy and efficiency of SoftWAXS are analyzed for analytically solvable model problems as well as for proteins. Key features of the approach include a numerical procedure for performing the required spherical averaging and explicit representation of the solute-solvent boundary and the surface of the hydration layer. These features allow the Fourier transform of the excluded volume and hydration layer to be computed directly and with high accuracy. This approach will allow future investigation of different treatments of the electron density in the hydration shell. Numerical results illustrate the differences between this approach to modeling the excluded volume and a widely used model that treats the excluded-volume function as a sum of Gaussians representing the individual atomic excluded volumes. Comparison of the results obtained here with those from explicit-solvent molecular dynamics clarifies shortcomings inherent to the representation of solvent as a time-averaged electron-density profile. In addition, an assessment is made of how the calculated scattering patterns depend on input parameters such as the solute-atom radii, the width of the hydration shell and the hydration-layer contrast. These results suggest that obtaining predictive calculations of high-resolution WAXS patterns may require sophisticated treatments of solvent.

Aqueous solubility diagrams for cementitious waste stabilization systems. 3. Mechanism of zinc immobilizaton by calcium silicate hydrate.

PubMed

Tommaseo, C E; Kersten, M

2002-07-01

Zinc oxide was added during hydration of alite (C3S) as an analogue for solidification/stabilization by cement of metal-bearing hazardous waste. Curing of samples was stopped at various intervals between 8 h and 100 d, and the reaction products were analyzed by both X-ray diffraction (XRD) and X-ray absorption spectroscopy (EXAFS at Zn, Ca, and Si K-edges). Calcium zincate hydrate (CaZn2(OH)6 x 2H2O) initially formed together with calcium silicate hydrate (CSH) vanishes from X-ray diffractograms after 14 d, and no other crystalline Zn-bearing phase could be detected thereafter. EXAFS Zn K-edge data analysis reveals that Zn(O,OH)4 tetrahedra continue to determine the first shell coordination. However, a new Zn-Si bond appears in the second coordination shell as indicated by both Zn K-edge and Si K-edge EXAFS. Together with the Ca-Zn and Ca-Ca shells derived from the Ca K-edge EXAFS spectra, a structural model for the site occupation of Zn in CSH is proposed, whereby the Zn(O,OH)4 tetrahedra are bound in layer rather than interlayer positions substituting for the silicate bridging tetrahedra and/or at terminal silicate chain sites. This structural model enables ultimately the formulation of a thermodyamic Lippmann model to predict the aqueous solubility of Zn in solid solution with a CSH phase of a Ca/Si ratio fixed to unity.

Description of Hydration Water in Protein (Green Fluorescent Protein) Solution

DOE PAGES

Perticaroli, Stefania; Ehlers, Georg; Stanley, Christopher B.; ...

2016-10-26

The structurally and dynamically perturbed hydration shells that surround proteins and biomolecules have a substantial influence upon their function and stability. This makes the extent and degree of water perturbation of practical interest for general biological study and industrial formulation. Here, we present an experimental description of the dynamical perturbation of hydration water around green fluorescent protein in solution. Less than two shells (~5.5 Å) were perturbed, with dynamics a factor of 2–10 times slower than bulk water, depending on their distance from the protein surface and the probe length of the measurement. Furthermore, this dependence on probe length demonstratesmore » that hydration water undergoes subdiffusive motions (τ ∝ q –2.5 for the first hydration shell, τ ∝ q –2.3 for perturbed water in the second shell), an important difference with neat water, which demonstrates diffusive behavior (τ ∝ q –2). Our results help clarify the seemingly conflicting range of values reported for hydration water retardation as a logical consequence of the different length scales probed by the analytical techniques used.« less

Differences in Hydration Structure Around Hydrophobic and Hydrophilic Model Peptides Probed by THz Spectroscopy

NASA Astrophysics Data System (ADS)

Wirtz, Hanna; Schäfer, Sarah; Hoberg, Claudius; Havenith, Martina

2018-03-01

We have recorded the THz spectra of the peptides NALA and NAGA as well as the amino acid leucine as model systems for hydrophobic and hydrophilic hydration. The spectra were recorded as a function of temperature and concentration and were analyzed in terms of a principal component analysis approach. NAGA shows positive absorptions with an increasing effective absorption coefficient for increasing concentrations. We conclude that NAGA due to its polar and hydrophilic structure does not have a significant influence on the surrounding water network, but is instead integrated into the water network forming a supramolecular complex. In contrast, for NALA, one hydrogen atom is substituted by a hydrophobic iso-butyl chain. We observe for NALA a decrease in absorption below 1.5 THz and a nonlinearity with a turning point around 0.75 M. Our measurements indicate that the first hydration shell of NALA is still intact at 0.75 M (corresponding to 65 water molecules per NALA). However, for larger concentrations the hydration shells can overlap, which explains the nonlinearity. For leucine, the changes in the spectrum occur at smaller concentrations. This might indicate that leucine exhibits a long-range effect on the solvating water network.

Characteristics of gas hydrate-bearing sediments of the northern South China Sea: insight into past hydrate episodic dissociations and intensities of seepage

NASA Astrophysics Data System (ADS)

Chen, F.; Su, X.; Zhou, Y.; Zhang, G.; Zhuang, C.; Lu, H.

2016-12-01

In 2013 the second China's major gas hydrate expedition, GMGS2, cored and recovered abundant gas hydrates at five sites, which were located in the South China Sea.Site GMGS08 (95m long) contained two gas hydrate intervals and five authigenic carbonate intervals. We analyzed carbon and oxygen isotopes of authigenic carbonates and foraminifera shells in sediments recovered at this site, in order to understanding of features of hydrate-bearing sediments and timing of gas hydrate dissociation and methane seepage at this site. An age of younger than 0.27 Ma was estimated for the 95 m sedimentary sequences at Site GMGS08. A detailed age model was further established by employing of U/Th and AMS14C dating of authigenic carbonates and seep bivalve fragments. These carbonates are featured by 13C-depleted (with a range from -38.9‰ to 56.7‰ δ13C) and positive δ18O (from 2.94‰ to 5.66‰ δ18O) values. A further analysis indicated the formation of carbonates were correlated to methane seepages derived from gas hydrate dissociation. Subsequently, these five authigenic carbonates intervals were seen as five hydrate episodic dissociation events since last 0.27Ma at this site. The most significant event during the period of 0.11 Ma to 0.13 Ma were account for the formation of thick authigenic carbonate (with the lowest -56.8‰ δ13C value) platform on paleo-seafloor at this site. The upmost authigenic carbonates interval is just overlying on the top of the upper gas hydrate occurrence zone, and it represents the latest methane seepage event with an age of 26ka to 36ka. Well correlated to these five events, it existed five intervals with strongly 13C-depleted carbon (-15.85‰ PDB) of foraminifera shells both from benthic and planktonic. The anomalous δ13C depletion records of planktonic G. ruber shells should be caused by formation of secondary authigenic carbonates on the shells, which were derived from the anaerobic oxidation of methane (AOM). The analyses on carbonate samples indicated varied intensity of methane flux in each event. The most intensive methane venting flux occurred during the event of 0.11 Ma to 0.13 Ma, which is correlated to a warm and relative high sea level period of MIS stage 5. These records obtained at Site GMGS08 implied much complicated causes for formation of authigenic carbonates and gas hydrate episodic dissociation.

Hydration water and bulk water in proteins have distinct properties in radial distributions calculated from 105 atomic resolution crystal structures.

PubMed

Chen, Xianfeng; Weber, Irene; Harrison, Robert W

2008-09-25

Water plays a critical role in the structure and function of proteins, although the experimental properties of water around protein structures are not well understood. The water can be classified by the separation from the protein surface into bulk water and hydration water. Hydration water interacts closely with the protein and contributes to protein folding, stability, and dynamics, as well as interacting with the bulk water. Water potential functions are often parametrized to fit bulk water properties because of the limited experimental data for hydration water. Therefore, the structural and energetic properties of the hydration water were assessed for 105 atomic resolution (

Hydration energies and structures of alkaline earth metal ions, M2+(H2O)n, n = 5-7, M = Mg, Ca, Sr, and Ba.

PubMed

Rodriguez-Cruz, S E; Jockusch, R A; Williams, E R

1999-09-29

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M(2+)(H(2)O)(n) (M = Mg, Ca, and Sr for n = 5-7, and M = Ba for n = 4-7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (E(o)) are determined. These reactions should have a negligible reverse activation barrier; therefore, E(o) values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca(2+), Sr(2+), and Ba(2+) are consistent with structures in which all the water molecules are located in the first solvation shell.

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Structure and dynamics of the hydration shells of the Al3+ ion

NASA Astrophysics Data System (ADS)

Bylaska, Eric J.; Valiev, Marat; Rustad, James R.; Weare, John H.

2007-03-01

First principles simulations of the hydration shells surrounding Al3+ ions are reported for temperatures near 300°C. The predicted six water molecules in the octahedral first hydration shell were found to be trigonally coordinated via hydrogen bonds to 12s shell water molecules in agreement with the putative structure used to analyze the x-ray data, but in disagreement with the results reported from conventional molecular dynamics using two-and three-body potentials. Bond lengths and angles of the water molecules in the first and second hydration shells and the average radii of these shells also agreed very well with the results of the x-ray analysis. Water transfers into and out of the second solvation shell were observed to occur on a picosecond time scale via a dissociative mechanism. Beyond the second shell the bonding pattern substantially returned to the tetrahedral structure of bulk water. Most of the simulations were done with 64 solvating water molecules (20ps). Limited simulations with 128 water molecules (7ps) were also carried out. Results agreed as to the general structure of the solvation region and were essentially the same for the first and second shell. However, there were differences in hydrogen bonding and Al-O radial distribution function in the region just beyond the second shell. At the end of the second shell a nearly zero minimum in the Al-O radial distribution was found for the 128 water system. This minimum is less pronounced minimum found for the 64 water system, which may indicate that sizes larger than 64 may be required to reliably predict behavior in this region.

An experimental point of view on hydration/solvation in halophilic proteins

PubMed Central

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution PMID:24600446

Anisotropic mechanical behaviors and their structural dependences of crossed-lamellar structure in a bivalve shell.

PubMed

Jiao, D; Liu, Z Q; Qu, R T; Zhang, Z F

2016-02-01

Crossed-lamellar structure is one of the most common organizations found in mollusk shells and may serve as a natural mimetic model for designing bio-inspired synthetic materials. Nonetheless, the mechanical behaviors and corresponding mechanisms have rarely been investigated for individual macro-layer of such structure. The integrated effects of orientation and hydration also remain unclear. In this study, the mechanical behaviors and their structural dependences of pure crossed-lamellar structure in Saxidomus purpuratus shell were systematically examined by three-point bending and compression tests. Mechanical properties and fracture mechanisms were revealed to depend strongly on the orientation, hydration state and loading condition. Three basic cracking modes of inter-platelet, trans-platelet, and along the interfaces between first-order lamellae were identified, and the interfacial separation was enhanced by hydration. Macroscopic compressive fracture was accomplished through axial splitting during which multiple toughening mechanisms were activated. The competition among different cracking modes was quantitatively evaluated by analyzing their driving stresses and resistances from fundamental mechanics. This study helps to clarify the mechanical behaviors of naturally occurring crossed-lamellar structure, and accordingly, aids in designing new bio-inspired synthetic materials by mimicking it. Copyright © 2015 Elsevier B.V. All rights reserved.

An experimental point of view on hydration/solvation in halophilic proteins.

PubMed

Talon, Romain; Coquelle, Nicolas; Madern, Dominique; Girard, Eric

2014-01-01

Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution.

Equatorial and Apical Solvent Shells of the UO₂²⁺ Ion.

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

Nichols, Pat; Bylaska, Eric J.; Schenter, Gregory K.

2008-03-08

First principles molecular dynamics simulations of the hydration shells surrounding UO₂²⁺ ions are reported for temperatures near 300 K. Most of the simulations were done with 64 solvating water molecules (22 ps). Simulations with 122 water molecules (9 ps) were also carried out. The hydration structure predicted from the simulations was found to agree very well known results from X-ray data. The average U=O bond length was found to be 1.77Å . The first hydration shell contained five trigonally coordinated water molecules that were equatorially oriented about the O-U-O axis with the hydrogen atoms oriented away from the uranium atom.more » The five waters in the first shell were located at an average distance of 2.44Å (2.46Å - 122 water simulation). The second hydration shell was composed of distinct equatorial and apical regions resulting in a peak in the U-O radial distribution function at 4.59Å. The equatorial second shell contained 10 water molecules hydrogen-bonded to the five first shell molecules. Above and below the UO₂²⁺ ion, the water molecules were found to be significantly less structured. In these apical regions, water molecules were found to sporadically hydrogen bond to the oxygen atoms of the UO₂²⁺; oriented in such way as to have their protons pointed towards the cation. While the number of apical waters varied greatly, an average of 5-6 waters was found in this region. Many water transfers into and out of the equatorial and apical second solvation shells were observed to occur on a picosecond (ps) time scale via dissociative mechanisms. Beyond these shells, the bonding pattern substantially returned to the tetrahedral structure of bulk water.« less

Molecular mechanisms of decomposition of hydrated Na+Cl- ion pairs under planar nanopore conditions

NASA Astrophysics Data System (ADS)

Shevkunov, S. V.

2017-02-01

The decomposition of Na+Cl- ion pairs under the conditions of a nanoscopic planar pore with structureless walls in a material contact with water vapor at 298 K is simulated by Monte Carlo method. The transition from the state of a contact ion pair (CIP) to the state of solvent-separated ion pair (SSIP) is shown to occur as a result of an increase in the vapor pressure over a pore after exceeding the threshold number of molecules in a hydrate shell. It is found that the planar form of a molecular cluster under the conditions of a narrow pore does not level an abrupt structural transition and the formation of hydrogen bonds in the hydrate shell starts after three molecules are added. The hydrogen bond length under pore conditions is found to be resistant to variations in the hydrate shell size and coincides with that in water under normal conditions.

Importance of counteranions on the hydration structure of the curium ion

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

Atta Fynn, Raymond; Bylaska, Eric J.; De Jong, Wibe A.

2013-07-04

Using density functional theory based ab initio molecular dynamics and metadynamics we show that counter ions can trigger noticeable changes in the hydration shell structure of the curium ion. The free energies of curium-water coordination and the solvent hydrogen bond (HB) lifetimes in the absence and presence the counter anions predict that chloride and bromide counter anions strengthen the first shell and consequently the 8-fold coordination state is dominant by at least 98%. In contrast, the perchlorate counter anions are found to weaken the coordination shell and the HB network, with the 9-fold and 8-fold states existing in an 8:1more » ratio, which is in good agreement with reported 9:1 ratio seen in time resolved fluorescence spectroscopy experiments. To our knowledge this is the first time molecular simulations have shown that counter anions can directly affect the first hydration shell structure of a cation.« less

On the influence of hydrated ionic liquids on the dynamical structure of model proteins: a computational study.

PubMed

Haberler, Michael; Steinhauser, Othmar

2011-10-28

The solvation of the protein ubiquitin (PDB entry "1UBQ") in hydrated molecular ionic liquids was studied for varying water content or, equivalently, a diversity of ionic strengths. The cations and anions were 1-ethyl-3-methylimidazolium and trifluoromethanesulfonate, respectively. The protein's shape and stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations. The respective simulation trajectories covered 200 nanoseconds. Besides the characteristic point already found for the zinc finger motif at the transition from the pure aqueous environment to the ionic solution an even more pronounced state is found where several properties show extremal behaviour (maximum or minimum). This second characteristic point occurs at the transition from the ionic solution to the hydrated ionic melt where water changes its role from a solvent to a co-solvent. Most of the data analysis presented here is based on the Voronoi decomposition of space. This journal is © the Owner Societies 2011

Hydration Energies and Structures of Alkaline Earth Metal Ions, M2+ (H2O)n, n = 5–7, M = Mg, Ca, Sr, and Ba

PubMed Central

Rodriguez-Cruz, Sandra E.; Jockusch, Rebecca A.

2005-01-01

The evaporation of water from hydrated alkaline earth metal ions, produced by electrospray ionization, was studied in a Fourier transform mass spectrometer. Zero-pressure-limit dissociation rate constants for loss of a single water molecule from the hydrated divalent metal ions, M2+(H2O)n (M = Mg, Ca, and Sr for n = 5–7, and M = Ba for n = 4–7), are measured as a function of temperature using blackbody infrared radiative dissociation. From these values, zero-pressure-limit Arrhenius parameters are obtained. By modeling the dissociation kinetics using a master equation formalism, threshold dissociation energies (Eo) are determined. These reactions should have a negligible reverse activation barrier; therefore, Eo values should be approximately equal to the binding energy or hydration enthalpy at 0 K. For the hepta- and hexahydrated ions at low temperature, binding energies follow the trend expected on the basis of ionic radii: Mg > Ca > Sr > Ba. For the hexahydrated ions at high temperature, binding energies follow the order Ca > Mg > Sr > Ba. The same order is observed for the pentahydrated ions. Collisional dissociation experiments on the tetrahydrated species result in relative dissociation rates that directly correlate with the size of the metals. These results indicate the presence of two isomers for hexahydrated magnesium ions: a low-temperature isomer in which the six water molecules are located in the first solvation shell, and a high-temperature isomer with the most likely structure corresponding to four water molecules in the inner shell and two water molecules in the second shell. These results also indicate that the pentahydrated magnesium ions have a structure with four water molecules in the first solvation shell and one in the outer shell. The dissociation kinetics for the hexa- and pentahydrated clusters of Ca2+, Sr2+, and Ba2+ are consistent with structures in which all the water molecules are located in the first solvation shell. PMID:16429612

Ferroelectric hydration shells around proteins: electrostatics of the protein-water interface.

PubMed

LeBard, David N; Matyushov, Dmitry V

2010-07-22

Numerical simulations of hydrated proteins show that protein hydration shells are polarized into a ferroelectric layer with large values of the average dipole moment magnitude and the dipole moment variance. The emergence of the new polarized mesophase dramatically alters the statistics of electrostatic fluctuations at the protein-water interface. The linear response relation between the average electrostatic potential and its variance breaks down, with the breadth of the electrostatic fluctuations far exceeding the expectations of the linear response theories. The dynamics of these non-Gaussian electrostatic fluctuations are dominated by a slow (approximately = 1 ns) component that freezes in at the temperature of the dynamical transition of proteins. The ferroelectric shell propagates 3-5 water diameters into the bulk.

CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

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

Mei, Yuan; Liu, Weihua; Migdiov, A. A.

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

CuCl Complexation in the Vapor Phase: Insights from Ab Initio Molecular Dynamics Simulations

DOE PAGES

Mei, Yuan; Liu, Weihua; Migdiov, A. A.; ...

2018-05-02

We invesmore » tigated the hydration of the CuCl 0 complex in HCl-bearing water vapor at 350°C and a vapor-like fluid density between 0.02 and 0.09 g/cm 3 using ab initio molecular dynamics (MD) simulations. The simulations reveal that one water molecule is strongly bonded to Cu(I) (first coordination shell), forming a linear [H 2O-Cu-Cl] 0 moiety. The second hydration shell is highly dynamic in nature, and individual configurations have short life-spans in such low-density vapors, resulting in large fluctuations in instantaneous hydration numbers over a timescale of picoseconds. The average hydration number in the second shell (m) increased from ~0.5 to ~3.5 and the calculated number of hydrogen bonds per water molecule increased from 0.09 to 0.25 when fluid density (which is correlated to water activity) increased from 0.02 to 0.09 g/cm 3 ( f H 2O 1.72 to 2.05). These changes of hydration number are qualitatively consistent with previous solubility studies under similar conditions, although the absolute hydration numbers from MD were much lower than the values inferred by correlating experimental Cu fugacity with water fugacity. This could be due to the uncertainties in the MD simulations and uncertainty in the estimation of the fugacity coefficients for these highly nonideal “vapors” in the experiments. Finally, our study provides the first theoretical confirmation that beyond-first-shell hydrated metal complexes play an important role in metal transport in low-density hydrothermal fluids, even if it is highly disordered and dynamic in nature.« less

Polarization and charge transfer in the hydration of chloride ions

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

Zhao Zhen; Rogers, David M.; Beck, Thomas L.

2010-01-07

A theoretical study of the structural and electronic properties of the chloride ion and water molecules in the first hydration shell is presented. The calculations are performed on an ensemble of configurations obtained from molecular dynamics simulations of a single chloride ion in bulk water. The simulations utilize the polarizable AMOEBA force field for trajectory generation and MP2-level calculations are performed to examine the electronic structure properties of the ions and surrounding waters in the external field of more distant waters. The ChelpG method is employed to explore the effective charges and dipoles on the chloride ions and first-shell waters.more » The quantum theory of atoms in molecules (QTAIM) is further utilized to examine charge transfer from the anion to surrounding water molecules. The clusters extracted from the AMOEBA simulations exhibit high probabilities of anisotropic solvation for chloride ions in bulk water. From the QTAIM analysis, 0.2 elementary charges are transferred from the ion to the first-shell water molecules. The default AMOEBA model overestimates the average dipole moment magnitude of the ion compared to the quantum mechanical value. The average magnitude of the dipole moment of the water molecules in the first shell treated at the MP2-level, with the more distant waters handled with an AMOEBA effective charge model, is 2.67 D. This value is close to the AMOEBA result for first-shell waters (2.72 D) and is slightly reduced from the bulk AMOEBA value (2.78 D). The magnitude of the dipole moment of the water molecules in the first solvation shell is most strongly affected by the local water-water interactions and hydrogen bonds with the second solvation shell, rather than by interactions with the ion.« less

Methanogenic calcite, 13C-depleted bivalve shells, and gas hydrate from a mud volcano offshore southern California

USGS Publications Warehouse

Hein, J.R.; Normark, W.R.; McIntyre, B.R.; Lorenson, T.D.; Powell, C.L.

2006-01-01

Methane and hydrogen sulfide vent from a cold seep above a shallowly buried methane hydrate in a mud volcano located 24 km offshore southern California in?? 800 m of water. Bivalves, authigenic calcite, and methane hydrate were recovered in a 2.1 m piston core. Aragonite shells of two bivalve species are unusually depleted in 13C (to -91??? ??13C), the most 13C-depleted shells of marine macrofauna yet discovered. Carbon isotopes for both living and dead specimens indicate that they used, in part, carbon derived from anaerobically oxidized methane to construct their shells. The ??13C values are highly variable, but most are within the range -12??? to -91???. This variability may be diagnostic for identifying cold-seep-hydrate systems in the geologic record. Authigenic calcite is abundant in the cores down to ???1.5 m subbottom, the top of the methane hydrate. The calcite is depleted in 13C (??13C = -46??? to -58???), indicating that carbon produced by anaerobically oxidized methane is the main source of the calcite. Methane sources include a geologic hydrocarbon reservoir from Miocene source rocks, and biogenic and thermogenic degradation of organic matter in basin sediments. Oxygen isotopes indicate that most calcite formed out of isotopic equilibrium with ambient bottom water, under the influence of gas hydrate dissociation and strong methane flux. High metal content in the mud volcano sediment indicates leaching of basement rocks by fluid circulating along an underlying fault, which also allows for a high flux of fossil methane. ?? 2006 Geological Society of America.

Hydrate Formation in Gas-Rich Marine Sediments: A Grain-Scale Model

NASA Astrophysics Data System (ADS)

Holtzman, R.; Juanes, R.

2009-12-01

We present a grain-scale model of marine sediment, which couples solid- and multiphase fluid-mechanics together with hydrate kinetics. The model is applied to investigate the spatial distribution of the different methane phases - gas and hydrate - within the hydrate stability zone. Sediment samples are generated from three-dimensional packs of spherical grains, mapping the void space into a pore network by tessellation. Gas invasion into the water-saturated sample is simulated by invasion-percolation, coupled with a discrete element method that resolves the grain mechanics. The coupled model accounts for forces exerted by the fluids, including cohesion associated with gas-brine surface tension. Hydrate growth is represented by a hydrate film along the gas-brine interface, which increases sediment cohesion by cementing the grain contacts. Our model of hydrate growth includes the possible rupture of the hydrate layer, which leads to the creation of new gas-water interface. In previous work, we have shown that fine-grained sediments (FGS) exhibit greater tendency to fracture, whereas capillary invasion is the preferred mode of methane gas transport in coarse-grained sediments (CGS). The gas invasion pattern has profound consequences on the hydrate distribution: a larger area-to-volume ratio of the gas cluster leads to a larger drop in gas pressure inside the growing hydrate shell, causing it to rupture. Repeated cycles of imbibition and hydrate growth accompanied by trapping of gas allow us to determine the distribution of hydrate and gas within the sediment as a function of time. Our pore-scale model suggests that, even when film rupture takes place, the conversion of gas to hydrate is slow. This explains two common field observations: the coexistence of gas and hydrate within the hydrate stability zone in CGS, and the high methane fluxes through fracture conduits in FGS. These results demonstrate the importance of accounting for the strong coupling among multiphase flow, sediment mechanics, and hydrate formation. Our model explains the remarkable differences in hydrate distribution and saturation between fine- and coarse-grained sediments, and promotes the quantitative understanding of the role of methane hydrate in seafloor stability and the global carbon cycle, including the size of the hydrate energy resource, and estimates of methane fluxes into the ocean and the atmosphere.

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

NASA Astrophysics Data System (ADS)

Nakano, C. Masato; Ma, Heng; Wei, Tao

2015-04-01

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the other hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.

Unraveling halide hydration: A high dilution approach.

PubMed

Migliorati, Valentina; Sessa, Francesco; Aquilanti, Giuliana; D'Angelo, Paola

2014-07-28

The hydration properties of halide aqua ions have been investigated combining classical Molecular Dynamics (MD) with Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy. Three halide-water interaction potentials recently developed [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)], along with three plausible choices for the value of the absolute hydration free energy of the proton (ΔG [minus sign in circle symbol]hyd[H+]), have been checked for their capability to properly describe the structural properties of halide aqueous solutions, by comparing the MD structural results with EXAFS experimental data. A very good agreement between theory and experiment has been obtained with one parameter set, namely LE, thus strengthening preliminary evidences for a ΔG [minus sign in circle symbol]hyd[H] value of -1100 kJ mol(-1) [M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)]. The Cl(-), Br(-), and I(-) ions have been found to form an unstructured and disordered first hydration shell in aqueous solution, with a broad distribution of instantaneous coordination numbers. Conversely, the F(-) ion shows more ordered and defined first solvation shell, with only two statistically relevant coordination geometries (six and sevenfold complexes). Our thorough investigation on the effect of halide ions on the microscopic structure of water highlights that the perturbation induced by the Cl(-), Br(-), and I(-) ions does not extend beyond the ion first hydration shell, and the structure of water in the F(-) second shell is also substantially unaffected by the ion.

Neutron Scattering Studies of the Hydration Structure of Li +

DOE PAGES

Mason, P. E.; Ansell, S.; Neilson, G. W.; ...

2015-01-05

New results derived from the experimental method of neutron diffraction and isotopic substitution (NDIS) are presented for the hydration structure of the lithium cation (Li +) in aqueous solutions of lithium chloride in heavy water (D 2O) at concentrations of 6, 3 and 1 molal and at 1.5 molal lithium sulphate. By introducing new and more accurate data reduction procedures than in our earlier studies (Howell and Neilson, (1996)), we find in the first hydration shell of Li +,~4.3(2) water molecules at 6 molal, 4.9(3) at 3 molal, 4.8(3) at 1 molal in the LiCl solutions, and 5.0(3) water moleculesmore » in the case of Li 2SO 4 solution. The general form of the first hydration shell is similar in all four solutions, with the correlations for Li-O and Li-D sited at 1.96 (0.02) Å and 2.58 (0.02) Å, respectively. The results resemble those presented in 1996 in terms of ion-water distances and local coordination, but the hydration number is significantly lower for the case at 1 molal than the 6.5 (1.0) given at that time. Thus, experimental and theoretical results now agree that lithium is hydrated by a small number of waters (4-5) in the nearest coordination shell.« less

Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study.

PubMed

Pribil, Andreas B; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

2008-11-15

A simulation of phosphate in aqueous solution was carried out employing the new QMCF MD approach which offers the possibility to investigate composite systems with the accuracy of a QMMM method but without the time consuming creation of solute-solvent potential functions. The data of the simulations give a clear picture of the hydration shells of the phosphate anion. The first shell consists of 13 water molecules and each oxygen of the phosphate forms in average three hydrogens bonds to different solvent molecules. Several structural parameters such as radial distribution functions and coordination number distributions allow to fully characterize the embedding of the highly charged phosphate ion in the solvent water. The dynamics of the hydration structure of phosphate are described by mean residence times of the solvent molecules in the first hydration shell and the water exchange rate. 2008 Wiley Periodicals, Inc.

Solvation of Na^+ in water from first-principles molecular dynamics

NASA Astrophysics Data System (ADS)

White, J. A.; Schwegler, E.; Galli, G.; Gygi, F.

2000-03-01

We have carried out ab initio molecular dynamics (MD) simulations of the Na^+ ion in water with an MD cell containing a single alkali ion and 53 water molecules. The electron-electron and electron-ion interactions were modeled by density functional theory with a generalized gradient approximation for the exchange-correlation functional. The computed radial distribution functions, coordination numbers, and angular distributions are consistent with available experimental data. The first solvation shell contains 5.2±0.6 water molecules, with some waters occasionally exchanging with those of the second shell. The computed Na^+ hydration number is larger than that from calculations for water clusters surrounding an Na^+ ion, but is consistent with that derived from x-ray measurements. Our results also indicate that the first hydration shell is better defined for Na^+ than for K^+ [1], as indicated by the first minimum in the Na-O pair distribution function. [1] L.M. Ramaniah, M. Bernasconi, and M. Parrinello, J. Chem. Phys. 111, 1587 (1999). This work was performed for DOE under contract W-7405-ENG-48.

Study of lysozyme mobility and binding free energy during adsorption on a graphene surface

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

Nakano, C. Masato; Ma, Heng; Wei, Tao, E-mail: twei@lamar.edu

Understanding protein adsorption is a key to the development of biosensors and anti-biofouling materials. Hydration essentially controls the adsorption process on hydrophobic surfaces, but its effect is complicated by various factors. Here, we present an ideal model system to isolate hydration effects—lysozyme adsorption on a flat hydrophobic graphene surface. Our all-atom molecular dynamics and molecular-mechanics/Poisson-Boltzmann surface area computation study reveal that lysozyme on graphene displays much larger diffusivity than in bulk water. Protein's hydration free energy within the first hydration shell is dominated by the protein-water electrostatic interactions and acts as an energy barrier for protein adsorption. On the othermore » hand, the surface tension, especially that from the hydrophobic graphene, can effectively weaken the barrier to promote adsorption.« less

Fate of Methane Emitted from Dissociating Marine Hydrates: Modeling, Laboratory, and Field Constraints

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

Juanes, Ruben

The overall goals of this research are: (1) to determine the physical fate of single and multiple methane bubbles emitted to the water column by dissociating gas hydrates at seep sites deep within the hydrate stability zone or at the updip limit of gas hydrate stability, and (2) to quantitatively link theoretical and laboratory findings on methane transport to the analysis of real-world field-scale methane plume data placed within the context of the degrading methane hydrate province on the US Atlantic margin. The project is arranged to advance on three interrelated fronts (numerical modeling, laboratory experiments, and analysis of field-basedmore » plume data) simultaneously. The fundamental objectives of each component are the following: Numerical modeling: Constraining the conditions under which rising bubbles become armored with hydrate, the impact of hydrate armoring on the eventual fate of a bubble’s methane, and the role of multiple bubble interactions in survival of methane plumes to very shallow depths in the water column. Laboratory experiments: Exploring the parameter space (e.g., bubble size, gas saturation in the liquid phase, “proximity” to the stability boundary) for formation of a hydrate shell around a free bubble in water, the rise rate of such bubbles, and the bubble’s acoustic characteristics using field-scale frequencies. Field component: Extending the results of numerical modeling and laboratory experiments to the field-scale using brand new, existing, public-domain, state-of-the-art real world data on US Atlantic margin methane seeps, without acquiring new field data in the course of this particular project. This component quantitatively analyzes data on Atlantic margin methane plumes and place those new plumes and their corresponding seeps within the context of gas hydrate degradation processes on this margin.« less

Interruption of Hydrogen Bonding Networks of Water in Carbon Nanotubes Due to Strong Hydration Shell Formation.

PubMed

Oya, Yoshifumi; Hata, Kenji; Ohba, Tomonori

2017-10-24

We present the structures of NaCl aqueous solution in carbon nanotubes with diameters of 1, 2, and 3 nm based on an analysis performed using X-ray diffraction and canonical ensemble Monte Carlo simulations. Anomalously longer nearest-neighbor distances were observed in the electrolyte for the 1-nm-diameter carbon nanotubes; in contrast, in the 2 and 3 nm carbon nanotubes, the nearest-neighbor distances were shorter than those in the bulk electrolyte. We also observed similar properties for water in carbon nanotubes, which was expected because the main component of the electrolyte was water. However, the nearest-neighbor distances of the electrolyte were longer than those of water in all of the carbon nanotubes; the difference was especially pronounced in the 2-nm-diameter carbon nanotubes. Thus, small numbers of ions affected the entire structure of the electrolyte in the nanopores of the carbon nanotubes. The formation of strong hydration shells between ions and water molecules considerably interrupted the hydrogen bonding between water molecules in the nanopores of the carbon nanotubes. The hydration shell had a diameter of approximately 1 nm, and hydration shells were thus adopted for the nanopores of the 2-nm-diameter carbon nanotubes, providing an explanation for the large difference in the nearest-neighbor distances between the electrolyte and water in these nanopores.

Selective Permeability of Uranyl Peroxide Nanocages to Different Alkali Ions: Influences from Surface Pores and Hydration Shells

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

Gao, Yunyi; Haso, Fadi; Szymanowski, Jennifer E. S.

2015-11-16

The precise guidance to different ions across the biological channels is essential for many biological processes. An artificial nanopore system will facilitate the study of the ion-transport mechanism through nanosized channels and offer new views for designing nanodevices. Herein we reveal that a 2.5 nm-sized, fullerene-shaped molecular cluster Li48+mK12(OH)m[UO2(O2)(OH)]60-(H2O)n (m≈20 and n≈310) (U60) shows selective permeability to different alkali ions. The subnanometer pores on the water–ligand-rich surface of U60 are able to block Rb+ and Cs+ ions from passing through, while allowing Na+ and K+ ions, which possess larger hydrated sizes, to enter the interior space of U60. An interestinglymore » high entropy gain during the binding process between U60 and alkali ions suggests that the hydration shells of Na+/K+ and U60 are damaged during the interaction. The ion selectivity of U60 is greatly influenced by both the morphologies of the surface nanopores and the dynamics of the hydration shells.« less

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

PubMed

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

2009-06-02

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

Anomalously enhanced hydration of aqueous electrolyte solution in hydrophobic carbon nanotubes to maintain stability.

PubMed

Ohba, Tomonori

2014-02-24

An understanding of the structure and behavior of electrolyte solutions in nanoenvironements is crucial not only for a wide variety of applications, but also for the development of physical, chemical, and biological processes. We demonstrate the structure and stability of electrolyte in carbon nanotubes using hybrid reverse Monte Carlo simulations of X-ray diffraction patterns. Hydrogen bonds between water are adequately formed in carbon nanotubes, although some hydrogen bonds are restricted by the interfaces of carbon nanotubes. The hydrogen bonding network of water in electrolyte in the carbon nanotubes is further weakened. On the other hand, formation of the ion hydration shell is significantly enhanced in the electrolyte in the carbon nanotubes in comparison to ion hydration in bulk electrolyte. The significant hydrogen bond and hydration shell formation are a result of gaining stability in the hydrophobic nanoenvironment. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inner and Outer Coordination Shells of Mg(2+) in CorA Selectivity Filter from Molecular Dynamics Simulations.

PubMed

Kitjaruwankul, Sunan; Wapeesittipan, Pattama; Boonamnaj, Panisak; Sompornpisut, Pornthep

2016-01-28

Structural data of CorA Mg(2+) channels show that the five Gly-Met-Asn (GMN) motifs at the periplasmic loop of the pentamer structure form a molecular scaffold serving as a selectivity filter. Unfortunately, knowledge about the cation selectivity of Mg(2+) channels remains limited. Since Mg(2+) in aqueous solution has a strong first hydration shell and apparent second hydration sphere, the coordination structure of Mg(2+) in a CorA selectivity filter is expected to be different from that in bulk water. Hence, this study investigated the hydration structure and ligand coordination of Mg(2+) in a selectivity filter of CorA using molecular dynamics (MD) simulations. The simulations reveal that the inner-shell structure of Mg(2+) in the filter is not significantly different from that in aqueous solution. The major difference is the characteristic structural features of the outer shell. The GMN residues engage indirectly in the interactions with the metal ion as ligands in the second shell of Mg(2+). Loss of hydrogen bonds between inner- and outer-shell waters observed from Mg(2+) in bulk water is mostly compensated by interactions between waters in the first solvation shell and the GMN motif. Some water molecules in the second shell remain in the selectivity filter and become less mobile to support the metal binding. Removal of Mg(2+) from the divalent cation sensor sites of the protein had an impact on the structure and metal binding of the filter. From the results, it can be concluded that the GMN motif enhances the affinity of the metal binding site in the CorA selectivity filter by acting as an outer coordination ligand.

Molecular dynamics study of the solvation of calcium carbonate in water.

PubMed

Bruneval, Fabien; Donadio, Davide; Parrinello, Michele

2007-10-25

We performed molecular dynamics simulations of diluted solutions of calcium carbonate in water. To this end, we combined and tested previous polarizable models. The carbonate anion forms long-living hydrogen bonds with water and shows an amphiphilic character, in which the water molecules are expelled in a region close to its C(3) symmetry axis. The calcium cation forms a strongly bound ion pair with the carbonate. The first hydration shell around the CaCO(3) pair is found to be very similar to the location of the water molecules surrounding CaCO(3) in ikaite, the hydrated mineral.

Structure of aqueous cesium metaborate solutions by X-ray scattering and DFT calculation

NASA Astrophysics Data System (ADS)

Zhang, W. Q.; Fang, C. H.; Fang, Y.; Zhu, F. Y.; Zhou, Y. Q.; Liu, H. Y.; Li, W.

2018-05-01

In the present work, precise radial distribution function (RDF) of cesium metaborate solutions with salt-water molar ratio of 1:25, 1:30 and 1:35 in large scattering vector range (3.91-214.26 nm-1) were obtained by X-ray scattering. Polyborate species were given using Newton iteration method with measured pH and literature equilibrium constants. In model calculation, structural parameters such as the coordination number, interatomic distance and Debye-Waller factor were given through model calculation. The B-O(H2O) distance was determined to be ∼0.37 nm with the hydration number of ∼7.8 for B(OH)4-. The Cs-B distance of the contact ions CsB(OH)40 was measured to be ∼0.46 nm with interaction number of ∼0.77. The interaction distances and coordination number for the first shell and the second shell of Cs-O(W) are ∼0.325 nm, ∼0.517 nm and ∼8.0, ∼11, respectively. Five low-energy configurations of [Cs(H2O)8]+ were given with DFT calculation, including the first and the second hydration shell, and the most stable eight-coordinated one is close to the model calculation. Furthermore, the effect of concentration is discussed in the X-ray scattering analysis part, showing that hydration degree changes with the concentration. For the coordination number and distance of Cs-O(H2O) and H-bonding decrease with the increasing concentration. The coordination number of Cs-O(H2O) keep stable, and the coordination distance changes from 3.25 nm to 3.30 nm. For H-bonding, which the coordination number varies from 2.20 to 2.24, and the coordination distance varies from 2.76 nm to 2.78 nm with the decreasing concentration.

TMAO and urea in the hydration shell of the protein SNase.

PubMed

Smolin, Nikolai; Voloshin, Vladimir P; Anikeenko, Alexey V; Geiger, Alfons; Winter, Roland; Medvedev, Nikolai N

2017-03-01

We performed all-atom MD simulations of the protein SNase in aqueous solution and in the presence of two major osmolytes, trimethylamine-N-oxide (TMAO) and urea, as cosolvents at various concentrations and compositions and at different pressures and temperatures. The distributions of the cosolvent molecules and their orientation in the surroundings of the protein were analyzed in great detail. The distribution of urea is largely conserved near the protein. It varies little with pressure and temperature, and does practically not depend on the addition of TMAO. The slight decrease with temperature of the number of urea molecules that are in contact with the SNase molecule is consistent with the view that the interaction of the protein with urea is mainly of enthalpic nature. Most of the TMAO molecules tend to be oriented to the protein by its methyl groups, a small amount of these molecules contact the protein by its oxygen, forming hydrogen bonds with the protein, only. Unlike urea, the fraction of TMAO in the hydration shell of SNase slightly increases with temperature (a signature of a prevailing hydrophobic interaction between TMAO and SNase), and decreases significantly upon the addition of urea. This behavior reflects the diverse nature of the interaction of the two osmolytes with the protein. Using the Voronoi volume of the atoms of the solvent molecules (water, urea, TMAO), we compared the fraction of the volume occupied by a given type of solvent molecule in the hydration shell and in the bulk solvent. The volume fraction of urea in the hydration shell is more than two times larger than in the bulk, whereas the volume fraction of TMAO in the hydration shell is only slightly larger in the binary solvent (TMAO + water) and becomes even less than in the bulk in the ternary solvent (TMAO + water + urea). Thus, TMAO tends to be excluded from the hydration shell of the protein. The behavior of the two cosolvents in the vicinity of the protein does not change much with pressure (from 1 to 5000 bar) and temperature (from 280 to 330 K). This is also in line with the conception of the "osmophobic effect" of TMAO to protect proteins from denaturation also at harsh environmental conditions. We also calculated the volumetric parameters of SNase and found that the cosolvents have a small but significant effect on the apparent volume and its contributions, i.e. the intrinsic, molecular and thermal volumes.

Adaptive resolution simulation of a biomolecule and its hydration shell: Structural and dynamical properties

NASA Astrophysics Data System (ADS)

Fogarty, Aoife C.; Potestio, Raffaello; Kremer, Kurt

2015-05-01

A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.

Stabilizing effects of hydrated fullerenes C₆₀ in a wide range of concentrations on luciferase, alkaline phosphatase, and peroxidase in vitro.

PubMed

Voeikov, Vladimir L; Yablonskaya, Olga I

2015-01-01

Hydrated fullerene (HyFnC60) is a highly hydrophilic supra-molecular complex consisting of unmodified С60 fullerene molecule enclosed into a hydrated shell. It has been shown in numerous experiments that aqueous solutions of HyFnC60 manifest a wide range of biological activities both in vivo and in vitro even at very low concentrations of HyFnC60. We used a spectrophotometric method and a method of biochemoluminescence to demonstrate that HyFnC60 in concentrations below 10(-9) M down to 10(-23) M stabilizes peroxidase, alkaline phosphatase, and bacterial luciferase against inactivation due to long-term incubation of the enzymes at room temperature and also against heat inactivation. In addition, HyFnC60 was able to "revive" heat inactivated enzymes. These effects cannot be explained by the direct action of the fullerene molecules upon the enzymes. We suggest that the effects of HyFnC60 on the enzymes are related to the ability of hydrated fullerene C60 molecules to organize thick aqueous shells around them. One of the specific properties of water phase in these shells is its ability to optimize redox reactions, which can support enzyme stability against factors deteriorating their structure.

Structure of cellulose microfibrils in mature cotton fibres.

PubMed

Martínez-Sanz, Marta; Pettolino, Filomena; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

2017-11-01

The structure of cellulose microfibrils in mature cotton fibres from three varieties - Gossypium hirsutum, G. barbadense and G. arboreum - has been investigated by a multi-technique approach combining small angle scattering techniques with spectroscopy and diffraction. Cellulose microfibrils present a Iβ-rich crystalline structure with limited surface disorder. Small angle scattering (SAXS and SANS) data have been successfully fitted using a core-shell model and the results obtained indicate that the cellulose microfibrils, formed by the association of 2-3 elementary fibrils, are composed of a ca. 2nm impermeable crystalline core, surrounded by a partially hydrated paracrystalline shell, with overall cross-sections of ca. 3.6-4.7nm. Different low levels of cell wall matrix components have a strong impact on the microfibril architecture and enable moisture penetration upon hydration. Furthermore, the higher amounts of non-cellulosic components in G. barbadense result in a less dense packing of cellulose microfibrils and increased solvent accessibility. Copyright © 2017 Elsevier Ltd. All rights reserved.

Protein hydration in solution: Experimental observation by x-ray and neutron scattering

PubMed Central

Svergun, D. I.; Richard, S.; Koch, M. H. J.; Sayers, Z.; Kuprin, S.; Zaccai, G.

1998-01-01

The structure of the protein–solvent interface is the subject of controversy in theoretical studies and requires direct experimental characterization. Three proteins with known atomic resolution crystal structure (lysozyme, Escherichia coli thioredoxin reductase, and protein R1 of E. coli ribonucleotide reductase) were investigated in parallel by x-ray and neutron scattering in H2O and D2O solutions. The analysis of the protein–solvent interface is based on the significantly different contrasts for the protein and for the hydration shell. The results point to the existence of a first hydration shell with an average density ≈10% larger than that of the bulk solvent in the conditions studied. Comparisons with the results of other studies suggest that this may be a general property of aqueous interfaces. PMID:9482874

Terahertz response of dipolar impurities in polar liquids: On anomalous dielectric absorption of protein solutions

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.

2010-02-01

A theory of radiation absorption by dielectric mixtures is presented. The coarse-grained formulation is based on the wave-vector-dependent correlation functions of molecular dipoles of the host polar liquid and a density structure factor of the solutes. A nonlinear dependence of the dielectric absorption coefficient on the solute concentration is predicted and originates from the mutual polarization of the liquid surrounding the solutes by the collective field of the solute dipoles aligned along the radiation field. The theory is applied to terahertz absorption of hydrated saccharides and proteins. While the theory gives an excellent account of the observations for saccharides, without additional assumptions and fitting parameters, experimental absorption coefficient of protein solutions significantly exceeds theoretical calculations with dipole moment of the bare protein assigned to the solute and shows a peak against the protein concentration. A substantial polarization of protein’s hydration shell, resulting in a net dipole moment, is required to explain the disagreement between theory and experiment. When the correlation function of the total dipole moment of the protein with its hydration shell from numerical simulations is used in the analytical model, an absorption peak, qualitatively similar to that seen in experiment, is obtained. The existence and position of the peak are sensitive to the specifics of the protein-protein interactions. Numerical testing of the theory requires the combination of dielectric and small-angle scattering measurements. The calculations confirm that “elastic ferroelectric bag” of water shells observed in previous numerical simulations is required to explain terahertz dielectric measurements.

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

Chatterjee, Anupam; Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076; Higham, Jonathan

A range of methods are presented to calculate a solute’s hydration shell from computer simulations of dilute solutions of monatomic ions and noble gas atoms. The methods are designed to be parameter-free and instantaneous so as to make them more general, accurate, and consequently applicable to disordered systems. One method is a modified nearest-neighbor method, another considers solute-water Lennard-Jones overlap followed by hydrogen-bond rearrangement, while three methods compare various combinations of water-solute and water-water forces. The methods are tested on a series of monatomic ions and solutes and compared with the values from cutoffs in the radial distribution function, themore » nearest-neighbor distribution functions, and the strongest-acceptor hydrogen bond definition for anions. The Lennard-Jones overlap method and one of the force-comparison methods are found to give a hydration shell for cations which is in reasonable agreement with that using a cutoff in the radial distribution function. Further modifications would be required, though, to make them capture the neighboring water molecules of noble-gas solutes if these weakly interacting molecules are considered to constitute the hydration shell.« less

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration.

PubMed

Hofer, Thomas S; Hünenberger, Philippe H

2018-06-14

The absolute intrinsic hydration free energy G H + ,wat ◦ of the proton, the surface electric potential jump χ wat ◦ upon entering bulk water, and the absolute redox potential V H + ,wat ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na + ) and potassium (K + ) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for G H + ,wat ◦ , χ wat ◦ , and V H + ,wat ◦ , reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na + and K + simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol -1 (K + minus Na + ), to be compared with the experimental value of 71.7 ± 2.8 kJ mol -1 . The calculated values of G H + ,wat ◦ , χ wat ◦ , and V H + ,wat ◦ (-1096.7 ± 6.1 kJ mol -1 , 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature (-1100 ± 5 kJ mol -1 , 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics.

Molecular dynamics of ion hydration in the presence of small carboxylated molecules and implications for calcification.

PubMed

Hamm, Laura M; Wallace, Adam F; Dove, Patricia M

2010-08-19

The aspartate-rich macromolecules found at nucleation sites of calcifying organisms are widely implicated in regulating biomineral formation. Anecdotal evidence suggests that their ability to influence the onset of nucleation and composition of calcified structures may arise from effects on ion hydration. This study investigates the interactions of acidic amino acids and dipeptides with hydrated cations using molecular dynamics. By monitoring the hydration states of Mg2+, Ca2+, and Sr2+ during their approach to negatively charged molecules, we show that carboxylate moieties of Asp promote dehydration of Ca2+ and Sr2+. A contact ion pair (CIP) is not required to disrupt cation hydration, and we demonstrate that reductions and rearrangements of first shell water can begin at ion-Asp separation distances as large as approximately 4.9 A for Ca2+ and approximately 5.1 A for Sr2+. CIP formation between Ca2+ and Sr2+ and carboxylate groups decreases the total first shell coordination number from an average of 8.0 and 8.4 in bulk water to 7.5 and 8.0, respectively. The energy barrier to physically replacing waters about Ca2+ with carboxylate oxygen atoms is small (approximately 2 kcal/mol) as compared to a somewhat larger barrier for Sr2+ (approximately 4 kcal/mol). This may be explained by differences in the strength of Coulombic interactions between the cations and the Asp, resulting in different paths of approach toward Asp for Ca2+ and Sr2+. In contrast, the primary solvation shell of Mg2+ remains largely unchanged during interactions with Asp until the abrupt physical replacement of water by carboxylate oxygen atoms, which comes at a high energetic cost. These insights support the claim that carboxylated biomolecules increase the growth rate of calcite by lowering the energy barrier to Ca2+ dehydration. The findings also suggest a physical basis for the idea that ion-specific behaviors of Ca2+ and Mg2+ in cellular systems arise from a critical balance between water binding in the ion hydration shells versus their interactions with ligands present in intracellular environments.

Water in the hydration shell of halide ions has significantly reduced Fermi resonance and moderately enhanced Raman cross section in the OH stretch regions.

PubMed

Ahmed, Mohammed; Singh, Ajay K; Mondal, Jahur A; Sarkar, Sisir K

2013-08-22

Water in the presence of electrolytes plays an important role in biological and industrial processes. The properties of water, such as the intermolecular coupling, Fermi resonance (FR), hydrogen-bonding, and Raman cross section were investigated by measuring the Raman spectra in the OD and OH stretch regions in presence of alkali halides (NaX; X = F, Cl, Br, I). It is observed that the changes in spectral characteristics by the addition of NaX in D2O are similar to those obtained by the addition of H2O in D2O. The spectral width decreases significantly by the addition of NaX in D2O (H2O) than that in the isotopically diluted water. Quantitative estimation, on the basis of integrated Raman intensity, revealed that the relative Raman cross section, σ(H)/σ(b) (σ(H) and σ(b) are the average Raman cross section of water in the first hydration shell of X(-) and in bulk, respectively), in D2O and H2O is higher than those in the respective isotopically diluted water. These results suggest that water in the hydration shell has reduced FR and intermolecular coupling compared to those in bulk. In the isotopically diluted water, the relative Raman cross section increases with increase in size of the halide ions (σ(H)/σ(b) = 0.6, 1.1, 1.5, and 1.9 for F(-), Cl(-), Br(-), and I(-), respectively), which is assignable to the enhancement of Raman cross section by charge transfer from halide ions to the hydrating water. Nevertheless, the experimentally determined σ(H)/σ(b) is lower than the calculated values obtained on the basis of the energy of the charge transfer state of water. The weak enhancement of σ(H)/σ(b) signifies that the charge transfer transition in the hydration shell of halide ions causes little change in the OD (OH) bond lengths of hydrating water.

Role of specific cations and water entropy on the stability of branched DNA motif structures.

PubMed

Pascal, Tod A; Goddard, William A; Maiti, Prabal K; Vaidehi, Nagarajan

2012-10-11

DNA three-way junctions (TWJs) are important intermediates in various cellular processes and are the simplest of a family of branched nucleic acids being considered as scaffolds for biomolecular nanotechnology. Branched nucleic acids are stabilized by divalent cations such as Mg(2+), presumably due to condensation and neutralization of the negatively charged DNA backbone. However, electrostatic screening effects point to more complex solvation dynamics and a large role of interfacial waters in thermodynamic stability. Here, we report extensive computer simulations in explicit water and salt on a model TWJ and use free energy calculations to quantify the role of ionic character and strength on stability. We find that enthalpic stabilization of the first and second hydration shells by Mg(2+) accounts for 1/3 and all of the free energy gain in 50% and pure MgCl(2) solutions, respectively. The more distorted DNA molecule is actually destabilized in pure MgCl(2) compared to pure NaCl. Notably, the first shell, interfacial waters have very low translational and rotational entropy (i.e., mobility) compared to the bulk, an entropic loss that is overcompensated by increased enthalpy from additional electrostatic interactions with Mg(2+). In contrast, the second hydration shell has anomalously high entropy as it is trapped between an immobile and bulklike layer. The nonmonotonic entropic signature and long-range perturbations of the hydration shells to Mg(2+) may have implications in the molecular recognition of these motifs. For example, we find that low salt stabilizes the parallel configuration of the three-way junction, whereas at normal salt we find antiparallel configurations deduced from the NMR. We use the 2PT analysis to follow the thermodynamics of this transition and find that the free energy barrier is dominated by entropic effects that result from the decreased surface area of the antiparallel form which has a smaller number of low entropy waters in the first monolayer.

Compressibility of the protein-water interface

NASA Astrophysics Data System (ADS)

Persson, Filip; Halle, Bertil

2018-06-01

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (˜0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ˜45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

Compressibility of the protein-water interface.

PubMed

Persson, Filip; Halle, Bertil

2018-06-07

The compressibility of a protein relates to its stability, flexibility, and hydrophobic interactions, but the measurement, interpretation, and computation of this important thermodynamic parameter present technical and conceptual challenges. Here, we present a theoretical analysis of protein compressibility and apply it to molecular dynamics simulations of four globular proteins. Using additively weighted Voronoi tessellation, we decompose the solution compressibility into contributions from the protein and its hydration shells. We find that positively cross-correlated protein-water volume fluctuations account for more than half of the protein compressibility that governs the protein's pressure response, while the self correlations correspond to small (∼0.7%) fluctuations of the protein volume. The self compressibility is nearly the same as for ice, whereas the total protein compressibility, including cross correlations, is ∼45% of the bulk-water value. Taking the inhomogeneous solvent density into account, we decompose the experimentally accessible protein partial compressibility into intrinsic, hydration, and molecular exchange contributions and show how they can be computed with good statistical accuracy despite the dominant bulk-water contribution. The exchange contribution describes how the protein solution responds to an applied pressure by redistributing water molecules from lower to higher density; it is negligibly small for native proteins, but potentially important for non-native states. Because the hydration shell is an open system, the conventional closed-system compressibility definitions yield a pseudo-compressibility. We define an intrinsic shell compressibility, unaffected by occupation number fluctuations, and show that it approaches the bulk-water value exponentially with a decay "length" of one shell, less than the bulk-water compressibility correlation length. In the first hydration shell, the intrinsic compressibility is 25%-30% lower than in bulk water, whereas its self part is 15%-20% lower. These large reductions are caused mainly by the proximity to the more rigid protein and are not a consequence of the perturbed water structure.

Preferential solvation, ion pairing, and dynamics of concentrated aqueous solutions of divalent metal nitrate salts

NASA Astrophysics Data System (ADS)

Yadav, Sushma; Chandra, Amalendu

2017-12-01

We have investigated the characteristics of preferential solvation of ions, structure of solvation shells, ion pairing, and dynamics of aqueous solutions of divalent alkaline-earth metal nitrate salts at varying concentration by means of molecular dynamics simulations. Hydration shell structures and the extent of preferential solvation of the metal and nitrate ions in the solutions are investigated through calculations of radial distribution functions, tetrahedral ordering, and also spatial distribution functions. The Mg2+ ions are found to form solvent separated ion-pairs while the Ca2+ and Sr2+ ions form contact ion pairs with the nitrate ions. These findings are further corroborated by excess coordination numbers calculated through Kirkwood-Buff G factors for different ion-ion and ion-water pairs. The ion-pairing propensity is found to be in the order of Mg(NO3) 2 < C a (NO3) 2 < S r (NO3) 2, and it follows the trend given by experimental activity coefficients. It is found that proper modeling of these solutions requires the inclusion of electronic polarization of the ions which is achieved in the current study through electronic continuum correction force fields. A detailed analysis of the effects of ion-pairs on the structure and dynamics of water around the hydrated ions is done through classification of water into different subspecies based on their locations around the cations or anions only or bridged between them. We have looked at the diffusion coefficients, relaxation of orientational correlation functions, and also the residence times of different subspecies of water to explore the dynamics of water in different structural environments in the solutions. The current results show that the water molecules are incorporated into fairly well-structured hydration shells of the ions, thus decreasing the single-particle diffusivities and increasing the orientational relaxation times of water with an increase in salt concentration. The different structural motifs also lead to the presence of substantial dynamical heterogeneity in these solutions of strongly interacting ions. The current study helps us to understand the molecular details of hydration structure, ion pairing, and dynamics of water in the solvation shells and also of ion diffusion in aqueous solutions of divalent metal nitrate salts.

How proteins modify water dynamics

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Much of biology happens at the protein-water interface, so all dynamical processes in this region are of fundamental importance. Local structural fluctuations in the hydration layer can be probed by 17O magnetic relaxation dispersion (MRD), which, at high frequencies, measures the integral of a biaxial rotational time correlation function (TCF)—the integral rotational correlation time. Numerous 17O MRD studies have demonstrated that this correlation time, when averaged over the first hydration shell, is longer than in bulk water by a factor 3-5. This rotational perturbation factor (RPF) has been corroborated by molecular dynamics simulations, which can also reveal the underlying molecular mechanisms. Here, we address several outstanding problems in this area by analyzing an extensive set of molecular dynamics data, including four globular proteins and three water models. The vexed issue of polarity versus topography as the primary determinant of hydration water dynamics is resolved by establishing a protein-invariant exponential dependence of the RPF on a simple confinement index. We conclude that the previously observed correlation of the RPF with surface polarity is a secondary effect of the correlation between polarity and confinement. Water rotation interpolates between a perturbed but bulk-like collective mechanism at low confinement and an exchange-mediated orientational randomization (EMOR) mechanism at high confinement. The EMOR process, which accounts for about half of the RPF, was not recognized in previous simulation studies, where only the early part of the TCF was examined. Based on the analysis of the experimentally relevant TCF over its full time course, we compare simulated and measured RPFs, finding a 30% discrepancy attributable to force field imperfections. We also compute the full 17O MRD profile, including the low-frequency dispersion produced by buried water molecules. Computing a local RPF for each hydration shell, we find that the perturbation decays exponentially with a decay "length" of 0.3 shells and that the second and higher shells account for a mere 3% of the total perturbation measured by 17O MRD. The only long-range effect is a weak water alignment in the electric field produced by an electroneutral protein (not screened by counterions), but this effect is negligibly small for 17O MRD. By contrast, we find that the 17O TCF is significantly more sensitive to the important short-range perturbations than the other two TCFs examined here.

Can xenon in water inhibit ice growth? Molecular dynamics of phase transitions in water-Xe system.

PubMed

Artyukhov, Vasilii I; Pulver, Alexander Yu; Peregudov, Alex; Artyuhov, Igor

2014-07-21

Motivated by recent experiments showing the promise of noble gases as cryoprotectants, we perform molecular dynamics modeling of phase transitions in water with xenon under cooling. We follow the structure and dynamics of xenon water solution as a function of temperature. Homogeneous nucleation of clathrate hydrate phase is observed and characterized. As the temperature is further reduced we observe hints of dissociation of clathrate due to stronger hydrophobic hydration, pointing towards a possible instability of clathrate at cryogenic temperatures and conversion to an amorphous phase comprised of "xenon + hydration shell" Xe·(H2O)21.5 clusters. Simulations of ice-xenon solution interface in equilibrium and during ice growth reveal the effects of xenon on the ice-liquid interface, where adsorbed xenon causes roughening of ice surface but does not preferentially form clathrate. These results provide evidence against the ice-blocker mechanism of xenon cryoprotection.

Studies of protein-protein and protein-water interactions by small angle x-ray scattering, terahertz spectroscopy, ASMOS, and computer simulation

NASA Astrophysics Data System (ADS)

Kim, Seung Joong

The protein folding problem has been one of the most challenging subjects in biological physics due to its complexity. Energy landscape theory based on statistical mechanics provides a thermodynamic interpretation of the protein folding process. We have been working to answer fundamental questions about protein-protein and protein-water interactions, which are very important for describing the energy landscape surface of proteins correctly. At first, we present a new method for computing protein-protein interaction potentials of solvated proteins directly from SAXS data. An ensemble of proteins was modeled by Metropolis Monte Carlo and Molecular Dynamics simulations, and the global X-ray scattering of the whole model ensemble was computed at each snapshot of the simulation. The interaction potential model was optimized and iterated by a Levenberg-Marquardt algorithm. Secondly, we report that terahertz spectroscopy directly probes hydration dynamics around proteins and determines the size of the dynamical hydration shell. We also present the sequence and pH-dependence of the hydration shell and the effect of the hydrophobicity. On the other hand, kinetic terahertz absorption (KITA) spectroscopy is introduced to study the refolding kinetics of ubiquitin and its mutants. KITA results are compared to small angle X-ray scattering, tryptophan fluorescence, and circular dichroism results. We propose that KITA monitors the rearrangement of hydrogen bonding during secondary structure formation. Finally, we present development of the automated single molecule operating system (ASMOS) for a high throughput single molecule detector, which levitates a single protein molecule in a 10 microm diameter droplet by the laser guidance. I also have performed supporting calculations and simulations with my own program codes.

Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration

NASA Astrophysics Data System (ADS)

Hofer, Thomas S.; Hünenberger, Philippe H.

2018-06-01

The absolute intrinsic hydration free energy GH+,w a t ◦ of the proton, the surface electric potential jump χwa t ◦ upon entering bulk water, and the absolute redox potential VH+,w a t ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy. However, this model describes the short-range solvation inaccurately and relies on the choice of arbitrary ion-size parameters. In the present study, both shortcomings are alleviated by performing first-principle calculations of the hydration free energies of the sodium (Na+) and potassium (K+) ions. The calculations rely on thermodynamic integration based on quantum-mechanical molecular-mechanical (QM/MM) molecular dynamics (MD) simulations involving the ion and 2000 water molecules. The ion and its first hydration shell are described using a correlated ab initio method, namely resolution-of-identity second-order Møller-Plesset perturbation (RIMP2). The next hydration shells are described using the extended simple point charge water model (SPC/E). The hydration free energy is first calculated at the MM level and subsequently increased by a quantization term accounting for the transformation to a QM/MM description. It is also corrected for finite-size, approximate-electrostatics, and potential-summation errors, as well as standard-state definition. These computationally intensive simulations provide accurate first-principle estimates for GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦, reported with statistical errors based on a confidence interval of 99%. The values obtained from the independent Na+ and K+ simulations are in excellent agreement. In particular, the difference between the two hydration free energies, which is not an elusive quantity, is 73.9 ± 5.4 kJ mol-1 (K+ minus Na+), to be compared with the experimental value of 71.7 ± 2.8 kJ mol-1. The calculated values of GH+,w a t ◦, χwa t ◦, and VH+,w a t ◦ (-1096.7 ± 6.1 kJ mol-1, 0.10 ± 0.10 V, and 4.32 ± 0.06 V, respectively, averaging over the two ions) are also in remarkable agreement with the values recommended by Reif and Hünenberger based on a thorough analysis of the experimental literature (-1100 ± 5 kJ mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V, respectively). The QM/MM MD simulations are also shown to provide an accurate description of the hydration structure, dynamics, and energetics.

Search for memory effects in methane hydrate: structure of water before hydrate formation and after hydrate decomposition.

PubMed

Buchanan, Piers; Soper, Alan K; Thompson, Helen; Westacott, Robin E; Creek, Jefferson L; Hobson, Greg; Koh, Carolyn A

2005-10-22

Neutron diffraction with HD isotope substitution has been used to study the formation and decomposition of the methane clathrate hydrate. Using this atomistic technique coupled with simultaneous gas consumption measurements, we have successfully tracked the formation of the sI methane hydrate from a water/gas mixture and then the subsequent decomposition of the hydrate from initiation to completion. These studies demonstrate that the application of neutron diffraction with simultaneous gas consumption measurements provides a powerful method for studying the clathrate hydrate crystal growth and decomposition. We have also used neutron diffraction to examine the water structure before the hydrate growth and after the hydrate decomposition. From the neutron-scattering curves and the empirical potential structure refinement analysis of the data, we find that there is no significant difference between the structure of water before the hydrate formation and the structure of water after the hydrate decomposition. Nor is there any significant change to the methane hydration shell. These results are discussed in the context of widely held views on the existence of memory effects after the hydrate decomposition.

Clathrate hydrate stability models for Titan: implications for a global subsurface ocean

NASA Astrophysics Data System (ADS)

Basu Sarkar, D.; Elwood Madden, M.

2013-12-01

Titan is the only planetary body in the solar system, apart from the Earth, with liquid at its surface. Titan's changing rotational period suggests that a global subsurface ocean decouples the icy crust from the interior. Several studies predict the existence of such an internal ocean below an Ice I layer, ranging in depth between a few tens of kilometers to a few hundreds of kilometers, depending on the composition of the icy crust and liquid-ocean. While the overall density of Titan is well constrained, the degree of differentiation within the interior is unclear. These uncertainties lead to poor understanding of the volatile content of the moon. However, unlike other similar large icy moons like Ganymede and Callisto, Titan has a thick nitrogen atmosphere, with methane as the second most abundant constituent - 5% near the surface. Titan's atmosphere, surface, and interior are likely home to various compounds such as C2H6, CO2, Ar, N2 and CH4, capable of forming clathrate hydrates. In addition, the moon has low temperature and low-to-high pressure conditions required for clathrate formation. Therefore the occurrence of extensive multicomponent hydrates may effect the composition of near-surface materials, the subsurface ocean, as well as the atmosphere. This work uses models of hydrate stability for a number of plausible hydrate formers including CH4, C2H6, CH4 + C2H6 and CH4 + NH3, and equilibrium geothermal gradients for probable near-surface materials to delineate the lateral and vertical extent of clathrate hydrate stability zones for Titan. By comparing geothermal gradients with clathrate stability fields for these systems we investigate possible compositions of Titan's global subsurface ocean. Preliminary model results indicate that ethane hydrates or compound hydrates of ethane and methane could be destabilized within the proposed depth range of the internal ocean, while methane/ammonia or pure methane hydrates may not be affected. Therefore, ethane or ethane-methane clathrates may be a major component of Titan's icy shell. Modeled geothermal gradients and stability fields of possible clathrate formers with three different scenarios for an internal ocean from the recent literature. Geothermal gradients obtained from thermal conductivity and density representing water ice and pure CH4-C2H6 hydrate. Clathrate stability field determined using HYDOFF and recent publications of NH3 clathrate stability.

Reconsideration on Hydration of Sodium Ion: From Micro-Hydration to Bulk Hydration

NASA Astrophysics Data System (ADS)

Yongquan, Zhou; Chunhui, Fang; Yan, Fang; Fayan, Zhu; Haiwen, Ge; Hongyan, Liu

2017-12-01

Micro hydration structures of the sodium ion, [Na(H2O) n ]+, n = 1-12, were probed by density functional theory (DFT) at B3LYP/aug-cc-pVDZ level in both gaseous and aqueous phase. The predicted equilibrium sodium-oxygen distance of 0.240 nm at the present level of theory. The four-, five- and six-coordinated cluster can transform from each other at the ambient condition. The analysis of the successive water binding energy and natural charge population (NBO) on Na+ clearly shows that the influence of Na+ on the surrounding water molecules goes beyond the first hydration shell with the hydration number of 6. The Car-Parrinello molecular dynamic simulation shows that only the first hydration sphere can be found, and the hydration number of Na+ is 5.2 and the hydration distance ( r Na-O) is 0.235 nm. All our simulations mentioned in the present paper show an excellent agreement with the diffraction result from X-ray scattering study.

Interfacial Properties and Mechanisms Dominating Gas Hydrate Cohesion and Adhesion in Liquid and Vapor Hydrocarbon Phases.

PubMed

Hu, Sijia; Koh, Carolyn A

2017-10-24

The interfacial properties and mechanisms of gas hydrate systems play a major role in controlling their interparticle and surface interactions, which is desirable for nearly all energy applications of clathrate hydrates. In particular, preventing gas hydrate interparticle agglomeration and/or particle-surface deposition is critical to the prevention of gas hydrate blockages during the exploration and transportation of oil and gas subsea flow lines. These agglomeration and deposition processes are dominated by particle-particle cohesive forces and particle-surface adhesive force. In this study, we present the first direct measurements on the cohesive and adhesive forces studies of the CH 4 /C 2 H 6 gas hydrate in a liquid hydrocarbon-dominated system utilizing a high-pressure micromechanical force (HP-MMF) apparatus. A CH 4 /C 2 H 6 gas mixture was used as the gas hydrate former in the model liquid hydrocarbon phase. For the cohesive force baseline test, it was found that the addition of liquid hydrocarbon changed the interfacial tension and contact angle of water in the liquid hydrocarbon compared to water in the gas phase, resulting in a force of 23.5 ± 2.5 mN m -1 at 3.45 MPa and 274 K for a 2 h annealing time period in which hydrate shell growth occurs. It was observed that the cohesive force was inversely proportional to the annealing time, whereas the force increased with increasing contact time. For a longer contact time (>12 h), the force could not be measured because the two hydrate particles adhered permanently to form one large particle. The particle-surface adhesive force in the model liquid hydrocarbon was measured to be 5.3 ± 1.1 mN m -1 under the same experimental condition. Finally, with a 1 h contact time, the hydrate particle and the carbon steel (CS) surface were sintered together and the force was higher than what could be measured by the current apparatus. A possible mechanism is presented in this article to describe the effect of contact time on the particle-particle cohesive force based on the capillary liquid bridge model. A model adapted from the capillary liquid bridge equation has been used to predict the particle-particle cohesive force as a function of contact time, showing close agreement with the experimental data. By comparing the cohesive forces results from gas hydrates for both gas and liquid bulk phases, the surface free energy of a hydrate particle was calculated and found to dominate the changes in the interaction forces with different continuous bulk phases.

Glacigenic sedimentation pulses triggered post-glacial gas hydrate dissociation.

PubMed

Karstens, Jens; Haflidason, Haflidi; Becker, Lukas W M; Berndt, Christian; Rüpke, Lars; Planke, Sverre; Liebetrau, Volker; Schmidt, Mark; Mienert, Jürgen

2018-02-12

Large amounts of methane are stored in continental margins as gas hydrates. They are stable under high pressure and low, but react sensitively to environmental changes. Bottom water temperature and sea level changes were considered as main contributors to gas hydrate dynamics after the last glaciation. However, here we show with numerical simulations that pulses of increased sedimentation dominantly controlled hydrate stability during the end of the last glaciation offshore mid-Norway. Sedimentation pulses triggered widespread gas hydrate dissociation and explains the formation of ubiquitous blowout pipes in water depths of 600 to 800 m. Maximum gas hydrate dissociation correlates spatially and temporally with the formation or reactivation of pockmarks, which is constrained by radiocarbon dating of Isorropodon nyeggaensis bivalve shells. Our results highlight that rapid changes of sedimentation can have a strong impact on gas hydrate systems affecting fluid flow and gas seepage activity, slope stability and the carbon cycle.

On the structure and dynamics of the hydrated sulfite ion in aqueous solution--an ab initio QMCF MD simulation and large angle X-ray scattering study.

PubMed

Eklund, Lars; Hofer, Thomas S; Pribil, Andreas B; Rode, Bernd M; Persson, Ingmar

2012-05-07

Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) formalism has been applied in conjunction to experimental large angle X-ray scattering to study the structure and dynamics of the hydrated sulfite ion in aqueous solution. The results show that there is a considerable effect of the lone electron-pair on sulfur concerning structure and dynamics in comparison with the sulfate ion with higher oxidation number and symmetry of the hydration shell. The S-O bond distance in the hydrated sulfite ion has been determined to 1.53(1) Å by both methods. The hydrogen bonds between the three water molecules bound to each sulfite oxygen are only slightly stronger than those in bulk water. The sulfite ion can therefore be regarded as a weak structure maker. The water exchange rate is somewhat slower for the sulfite ion than for the sulfate ion, τ(0.5) = 3.2 and 2.6 ps, respectively. An even more striking observation in the angular radial distribution (ARD) functions is that the for sulfite ion the water exchange takes place in close vicinity of the lone electron-pair directed at its sides, while in principle no water exchange did take place of the water molecules hydrogen bound to sulfite oxygens during the simulation time. This is also confirmed when detailed pathway analysis is conducted. The simulation showed that the water molecules hydrogen bound to the sulfite oxygens can move inside the hydration shell to the area outside the lone electron-pair and there be exchanged. On the other hand, for the hydrated sulfate ion in aqueous solution one can clearly see from the ARD that the distribution of exchange events is symmetrical around the entire hydration sphere.

Nucleation pathways of clathrate hydrates: effect of guest size and solubility.

PubMed

Jacobson, Liam C; Hujo, Waldemar; Molinero, Valeria

2010-11-04

Understanding the microscopic mechanism of nucleation of clathrate hydrates is important for their use in hydrogen storage, CO(2) sequestration, storage and transport of natural gas, and the prevention of the formation of hydrate plugs in oil and gas pipelines. These applications involve hydrate guests of varied sizes and solubility in water that form different hydrate crystal structures. Nevertheless, molecular studies of the mechanism of nucleation of hydrates have focused on the single class of small hydrophobic guests that stabilize the sI crystal. In this work, we use molecular dynamics simulations with a very efficient coarse-grained model to elucidate the mechanisms of nucleation of clathrate hydrates of four model guests that span a 2 orders of magnitude range in solubility in water and that encompass sizes which stabilize each one a different hydrate structure (sI and sII, with and without occupancy of the dodecahedral cages). We find that the overall mechanism of clathrate nucleation is similar for all guests and involves a first step of formation of blobs, dense clusters of solvent-separated guest molecules that are the birthplace of the clathrate cages. Blobs of hydrophobic guests are rarer and longer-lived than those for soluble guests. For each guest, we find multiple competing channels to form the critical nuclei, filled dodecahedral (5(12)) cages, empty 5(12) cages, and a variety of filled large (5(12)6(n) with n = 2, 3, and 4) clathrate cages. Formation of empty dodecahedra is an important nucleation channel for all but the smallest guest. The empty 5(12) cages are stabilized by the presence of guests from the blob in their first solvation shell. Under conditions of high supercooling, the structure of the critical and subcritical nuclei is mainly determined by the size of the guest and does not reflect the cage composition or ordering of the stable or metastable clathrate crystals.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture

NASA Astrophysics Data System (ADS)

Spickermann, C.; Thar, J.; Lehmann, S. B. C.; Zahn, S.; Hunger, J.; Buchner, R.; Hunt, P. A.; Welton, T.; Kirchner, B.

2008-09-01

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C2C1im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C2C1im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H2O )-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C2C1im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Why are ionic liquid ions mainly associated in water? A Car-Parrinello study of 1-ethyl-3-methyl-imidazolium chloride water mixture.

PubMed

Spickermann, C; Thar, J; Lehmann, S B C; Zahn, S; Hunger, J; Buchner, R; Hunt, P A; Welton, T; Kirchner, B

2008-09-14

In this study we present the results of a first principles molecular dynamics simulation of a single 1-ethyl-3-methyl-imidazolium chloride [C(2)C(1)im][Cl] ion pair dissolved in 60 water molecules. We observe a preference of the in plane chloride coordination with respect to the cation ring plane as compared to the energetic slightly more demanding on top coordination. Evaluation of the different radial distribution functions demonstrates that the structure of the hydration shell around the ion pair differs significantly from bulk water and that no true ion pair dissociation in terms of completely autonomous solvation shells takes place on the timescale of the simulation. In addition, dipole moment distributions of the solvent in distinct solvation shells around different functional parts of the [C(2)C(1)im][Cl] ion pair are calculated from maximally localized Wannier functions. The analysis of these distributions gives evidence for a depolarization of water molecules close to the hydrophobic parts of the cation as well as close to the anion. Examination of the angular distribution of different OH(H(2)O)-X angles in turn shows a linear coordination of chloride accompanied by a tangential orientation of water molecules around the hydrophobic groups, being a typical feature of hydrophobic hydration. Based on these orientational aspects, a structural model for the obvious preference of ion pair association is developed, which justifies the associating behavior of solvated [C(2)C(1)im][Cl] ions in terms of an energetically favorable interface between the solvation shells of the anion and the hydrophobic parts of the cation.

Scanning electron microscopy investigations of laboratory-grown gas clathrate hydrates formed from melting ice, and comparison to natural hydrates

USGS Publications Warehouse

Stern, L.A.; Kirby, S.H.; Circone, S.; Durham, W.B.

2004-01-01

Scanning electron microscopy (SEM) was used to investigate grain texture and pore structure development within various compositions of pure sI and sII gas hydrates synthesized in the laboratory, as well as in natural samples retrieved from marine (Gulf of Mexico) and permafrost (NW Canada) settings. Several samples of methane hydrate were also quenched after various extents of partial reaction for assessment of mid-synthesis textural progression. All laboratory-synthesized hydrates were grown under relatively high-temperature and high-pressure conditions from rounded ice grains with geometrically simple pore shapes, yet all resulting samples displayed extensive recrystallization with complex pore geometry. Growth fronts of mesoporous methane hydrate advancing into dense ice reactant were prevalent in those samples quenched after limited reaction below and at the ice point. As temperatures transgress the ice point, grain surfaces continue to develop a discrete "rind" of hydrate, typically 5 to 30 ??m thick. The cores then commonly melt, with rind microfracturing allowing migration of the melt to adjacent grain boundaries where it also forms hydrate. As the reaction continues under progressively warmer conditions, the hydrate product anneals to form dense and relatively pore-free regions of hydrate grains, in which grain size is typically several tens of micrometers. The prevalence of hollow, spheroidal shells of hydrate, coupled with extensive redistribution of reactant and product phases throughout reaction, implies that a diffusion-controlled shrinking-core model is an inappropriate description of sustained hydrate growth from melting ice. Completion of reaction at peak synthesis conditions then produces exceptional faceting and euhedral crystal growth along exposed pore walls. Further recrystallization or regrowth can then accompany even short-term exposure of synthetic hydrates to natural ocean-floor conditions, such that the final textures may closely mimic those observed in natural samples of marine origin. Of particular note, both the mesoporous and highly faceted textures seen at different stages during synthetic hydrate growth were notably absent from all examined hydrates recovered from a natural marine-environment setting.

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Hydration of copper(II): new insights from density functional theory and the COSMO solvation model.

PubMed

Bryantsev, Vyacheslav S; Diallo, Mamadou S; van Duin, Adri C T; Goddard, William A

2008-09-25

The hydrated structure of the Cu(II) ion has been a subject of ongoing debate in the literature. In this article, we use density functional theory (B3LYP) and the COSMO continuum solvent model to characterize the structure and stability of [Cu(H2O)n](2+) clusters as a function of coordination number (4, 5, and 6) and cluster size (n = 4-18). We find that the most thermodynamically favored Cu(II) complexes in the gas phase have a very open four-coordinate structure. They are formed from a stable square-planar [Cu(H2O)8](2+) core stabilized by an unpaired electron in the Cu(II) ion d(x(2)-y(2)) orbital. This is consistent with cluster geometries suggested by recent mass-spectrometric experiments. In the aqueous phase, we find that the more compact five-coordinate square-pyramidal geometry is more stable than either the four-coordinate or six-coordinate clusters in agreement with recent combined EXAFS and XANES studies of aqueous solutions of Cu(II). However, a small energetic difference (approximately 1.4 kcal/mol) between the five- and six-coordinate models with two full hydration shells around the metal ion suggests that both forms may coexist in solution.

Nuclear quantum effects in water exchange around lithium and fluoride ions

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

Wilkins, David M.; Manolopoulos, David E.; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the exchange processes are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium.« less

Ion Association in AlCl3 Aqueous Solutions from Constrained First-Principles Molecular Dynamics

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

Cauet, Emilie L.; Bogatko, Stuart A.; Bylaska, Eric J.

2012-10-15

Ab initio molecular dynamics was used to investigate the ion pairing behavior between Cl- and the Al3+ ion in an aqueous AlCl3 solution containing 63 water molecules. A series of constrained simulations was carried out at 300 K for up to 16 ps each, by fixing the inter-nuclear separation (rAl-Cl) between the Al3+ ion and one of the Cl- ions. The calculated potential of mean force of the Al3+-Cl- ion pair shows a pronounced minimum at rAl-Cl = 2.3 Å corresponding to a contact ion pair (CIP). Two local minima assigned to solvent separated ion pairs (SSIP) are identified atmore » rAl-Cl= 4.4 and 6.0 Å. The positions of the free energy minima coincide with the hydration shell intervals of the Al3+ cation suggesting that the Cl- ion is inclined to reside in regions of low concentration of waters, i.e. between the 1st and 2nd shells of Al3+ and between the 2nd shell and bulk. A detailed analysis of solvent structure around the Al3+ and Cl- ions as a function of rAl-Cl is presented. The results are compared to structure data from X-ray measurements and unconstrained AIMD simulations of single ions Al3+ and Cl- and AlCl3 solutions. The dipole moment of the water molecules inside the 1st and 2nd hydration shells of Al3+ and in the bulk region and those of the Clion were calculated as a function of rAl-Cl. Major changes in the electronic structure of the system result from the removal of Cl- from the 1st hydration shell of the Al3+ cation. Finally, two unconstrained AIMD simulations of aqueous AlCl3 solutions corresponding to CIP and SSIP configurations were performed (17 ps, 300 K). Only minor structural changes are observed in these systems, confirming their stability.« less

Hydrogen bond breaking in aqueous solutions near the critical point

USGS Publications Warehouse

Mayanovic, Robert A.; Anderson, Alan J.; Bassett, William A.; Chou, I.-Ming

2001-01-01

The nature of water-anion bonding is examined using X-ray absorption fine structure spectroscopy on a 1mZnBr2/6m NaBr aqueous solution, to near critical conditions. Analyses show that upon heating the solution from 25??C to 500??C, a 63% reduction of waters occurs in the solvation shell of ZnBr42-, which is the predominant complex at all pressure-temperature conditions investigated. A similar reduction in the hydration shell of waters in the Br- aqua ion was found. Our results indicate that the water-anion and water-water bond breaking mechanisms occurring at high temperatures are essentially the same. This is consistent with the hydration waters being weakly hydrogen bonded to halide anions in electrolyte solutions. ?? 2001 Elsevier Science B.V.

Theoretical modeling of magnesium ion imprints in the Raman scattering of water.

PubMed

Kapitán, Josef; Dracínský, Martin; Kaminský, Jakub; Benda, Ladislav; Bour, Petr

2010-03-18

Hydration envelopes of metallic ions significantly influence their chemical properties and biological functioning. Previous computational studies, nuclear magnetic resonance (NMR), and vibrational spectra indicated a strong affinity of the Mg(2+) cation to water. We find it interesting that, although monatomic ions do not vibrate themselves, they cause notable changes in the water Raman signal. Therefore, in this study, we used a combination of Raman spectroscopy and computer modeling to analyze the magnesium hydration shell and origin of the signal. In the measured spectra of several salts (LiCl, NaCl, KCl, MgCl(2), CaCl(2), MgBr(2), and MgI(2) water solutions), only the spectroscopic imprint of the hydrated Mg(2+) cation could clearly be identified as an exceptionally distinct peak at approximately 355 cm(-1). The assignment of this band to the Mg-O stretching motion could be confirmed on the basis of several models involving quantum chemical computations on metal/water clusters. Minor Raman spectral features could also be explained. Ab initio and Fourier transform (FT) techniques coupled with the Car-Parrinello molecular dynamics were adapted to provide the spectra from dynamical trajectories. The results suggest that even in concentrated solutions magnesium preferentially forms a [Mg(H(2)O)(6)](2+) complex of a nearly octahedral symmetry; nevertheless, the Raman signal is primarily associated with the relatively strong metal-H(2)O bond. Partially covalent character of the Mg-O bond was confirmed by a natural bond orbital analysis. Computations on hydrated chlorine anion did not provide a specific signal. The FT techniques gave good spectral profiles in the high-frequency region, whereas the lowest-wavenumber vibrations were better reproduced by the cluster models. Both dynamical and cluster computational models provided a useful link between spectral shapes and specific ion-water interactions.

Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

PubMed Central

Sutton, Rebecca; Sposito, Garrison

2002-01-01

Computer animation of center of mass coordinates obtained from 800 ps molecular dynamics simulations of Cs-smectite hydrates (1/3 and 2/3 water monolayers) provided information concerning the structure and dynamics of the interlayer region that could not be obtained through traditional simulation analysis methods. Cs+ formed inner sphere complexes with the mineral surface, and could be seen to jump from one attracting location near a layer charge site to the next, while water molecules were observed to migrate from the hydration shell of one ion to that of another. Neighboring ions maintained a partial hydration shell by sharing water molecules, such that a single water molecule hydrated two ions simultaneously for hundreds of picoseconds. Cs-montmorillonite hydrates featured the largest extent of this sharing interaction, because interlayer ions were able to inhabit positions near surface cavities as well as at their edges, close to oxygen triads. The greater positional freedom of Cs+ within the montmorillonite interlayer, a result of structural hydroxyl orientation and low tetrahedral charge, promoted the optimization of distances between cations and water molecules required for water sharing. Preference of Cs+ for locations near oxygen triads was observed within interlayer beidellite and hectorite. Water molecules also could be seen to interact directly with the mineral surface, entering its surface cavities to approach attracting charge sites and structural hydroxyls. With increasing water content, water molecules exhibited increased frequency and duration of both cavity habitation and water sharing interactions. Competition between Cs+ and water molecules for surface sites was evident. These important cooperative and competitive features of interlayer molecular behavior were uniquely revealed by animation of an otherwise highly complex simulation output.

Flow strength of highly hydrated Mg- and Na-sulfate hydrate salts, pure and in mixtures with water ice, with application to Europa

USGS Publications Warehouse

Durham, W.B.; Stern, L.A.; Kubo, T.; Kirby, S.H.

2005-01-01

We selected two Europan-ice-shell candidate highly hydrated sulfate salts for a laboratory survey of ductile flow properties: MgSO4 ?? 7H2O (epsomite) and Na2SO4 ?? 10H2O (mirabilite), called MS7 and NS10, respectively. Polycrystalline samples in pure form and in mixtures with water ice I were tested using our cryogenic high-pressure creep apparatus at temperatures 232 ??? T ??? 294 K, confining pressures P = 50 and 100 MPa, and strain rates 4 ?? 10-8 ??? ???dot;e ??? 7 ?? 10-5 s-1. Grain size of NS10 samples was > 100 ??m. The flow strength ?? of pure MS7 was over 100 times that of polycrystalline ice I at comparable conditions; that of pure NS10 over 20 times that of ice. In terms of the creep law ???dot;e = A??n e-Q/RT, where R is the gas constant, we determine parameter values of A = 1012.1 MPa-ns-1, n = 5.4, and Q = 128 kJ/mol for pure NS10. Composites of ice I and NS10 of volume fraction ?? NS10 have flow strength ??c = [??NS10??NS10J + (1 - ?? NS10)??iceIJ]1/J where J ??? -0.5, making the effect on the flow of ice with low volume fractions of NS10 much like that of virtually undeformable hard rock inclusions. Being much stronger and denser than ice, massive sulfate inclusions in the warmer, ductile layer of the Europan ice shell are less likely to be entrained in convective ice flow and more likely to be drawn to the base of the ice shell by gravitational forces and eventually expelled. With only smaller, dispersed sulfate inclusions, at probable sulfate ?? < 0.2, the shell may be treated rheologically as pure, polycrystalline ice, with boundary conditions perhaps influenced by the high density and low thermal conductivity of the hydrated salts. Copyright 2005 by the American Geophysical Union.

Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly charged transition metal ions

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

Fulton, John L.; Bylaska, Eric J.; Bogatko, Stuart A.

DFT-MD simulations (PBE96 and PBE0) with MD-XAFS scattering calculations (FEFF9) show near quantitative agreement with new and existing XAFS measurements for a comprehensive series of transition metal ions which interact with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the U.S. DOE's Office ofmore » Biological and Environmental Research and located at Pacific Northwest National Laboratory.« less

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

PubMed Central

Chen, Hsieh; Cox, Jason R.; Ow, Hooisweng; Shi, Rena; Panagiotopoulos, Athanassios Z.

2016-01-01

Stabilizing colloids or nanoparticles in solution involves a fine balance between surface charges, steric repulsion of coating molecules, and hydration forces against van der Waals attractions. At high temperature and electrolyte concentrations, the colloidal stability of suspensions usually decreases rapidly. Here, we report a new experimental and simulation discovery that the polysaccharide (dextran) coated nanoparticles show ion-specific colloidal stability at high temperature, where we observed enhanced colloidal stability of nanoparticles in CaCl2 solution but rapid nanoparticle-nanoparticle aggregation in MgCl2 solution. The microscopic mechanism was unveiled in atomistic simulations. The presence of surface bound Ca2+ ions increases the carbohydrate hydration and induces strongly polarized repulsive water structures beyond at least three hydration shells which is farther-reaching than previously assumed. We believe leveraging the binding of strongly hydrated ions to macromolecular surfaces represents a new paradigm in achieving absolute hydration and colloidal stability for a variety of materials, particularly under extreme conditions. PMID:27334145

Hydration Repulsion between Carbohydrate Surfaces Mediated by Temperature and Specific Ions

NASA Astrophysics Data System (ADS)

Chen, Hsieh; Cox, Jason R.; Ow, Hooisweng; Shi, Rena; Panagiotopoulos, Athanassios Z.

2016-06-01

Stabilizing colloids or nanoparticles in solution involves a fine balance between surface charges, steric repulsion of coating molecules, and hydration forces against van der Waals attractions. At high temperature and electrolyte concentrations, the colloidal stability of suspensions usually decreases rapidly. Here, we report a new experimental and simulation discovery that the polysaccharide (dextran) coated nanoparticles show ion-specific colloidal stability at high temperature, where we observed enhanced colloidal stability of nanoparticles in CaCl2 solution but rapid nanoparticle-nanoparticle aggregation in MgCl2 solution. The microscopic mechanism was unveiled in atomistic simulations. The presence of surface bound Ca2+ ions increases the carbohydrate hydration and induces strongly polarized repulsive water structures beyond at least three hydration shells which is farther-reaching than previously assumed. We believe leveraging the binding of strongly hydrated ions to macromolecular surfaces represents a new paradigm in achieving absolute hydration and colloidal stability for a variety of materials, particularly under extreme conditions.

Electrostatics of the protein-water interface and the dynamical transition in proteins.

PubMed

Matyushov, Dmitry V; Morozov, Alexander Y

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Electrostatics of the protein-water interface and the dynamical transition in proteins

NASA Astrophysics Data System (ADS)

Matyushov, Dmitry V.; Morozov, Alexander Y.

2011-07-01

Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent experiments indicate a connection between the dynamical transition and the dielectric response of the hydrated protein. We analyze two mechanisms of the coupling between the protein atomic motions and the protein-water interface. The first mechanism considers viscoelastic changes in the global shape of the protein plasticized by its coupling to the hydration shell. The second mechanism involves modulations of the local motions of partial charges inside the protein by electrostatic fluctuations. The model is used to analyze mean-square displacements of iron of metmyoglobin reported by Mössbauer spectroscopy. We show that high displacement of heme iron at physiological temperatures is dominated by electrostatic fluctuations. Two onsets, one arising from the viscoelastic response and the second from electrostatic fluctuations, are seen in the temperature dependence of the mean-square displacements when the corresponding relaxation times enter the instrumental resolution window.

Laser interferometry of the hydrolytic changes in protein solutions: the refractive index and hydration shells.

PubMed

Sarimov, R M; Matveyeva, T A; Binhi, V N

2018-05-11

Using an original laser interferometer of enhanced sensitivity, an increase in the refractive index of a protein solution was observed during the reaction of proteolysis catalyzed by pepsin. The increase in the refractive index of the protein solution at a concentration of 4 mg/ml was [Formula: see text] for bovine serum albumin and [Formula: see text] for lysozyme. The observed effect disproves the existing idea that the refractive index of protein solutions is determined only by their amino acid composition and concentration. It is shown that the refractive index also depends on the state of protein fragmentation. A mathematical model of proteolysis and a real-time method for estimating the state of protein hydration based on the measurement of refractive index during the reaction are proposed. A good agreement between the experimental and calculated time dependences of the refractive index shows that the growth of the surface of protein fragments and the change in the number of hydration cavities during proteolysis can be responsible for the observed effect.

Integrated experimental and theoretical approach for the structural characterization of Hg2+ aqueous solutions

NASA Astrophysics Data System (ADS)

D'Angelo, Paola; Migliorati, Valentina; Mancini, Giordano; Barone, Vincenzo; Chillemi, Giovanni

2008-02-01

The structural and dynamic properties of the solvated Hg2+ ion in aqueous solution have been investigated by a combined experimental-theoretical approach employing x-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the x-ray absorption near-edge structure (XANES) spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. The XANES experimental data are accurately reproduced by a first-shell heptacoordinated cluster only if the second hydration shell is included in the calculations. These results confirm at the same time the existence of a sevenfold first hydration shell for the Hg2+ ion in aqueous solution and the reliability of the potentials used in the MD simulations. The combination of MD and XANES is found to be very helpful to get important new insights into the quantitative estimation of structural properties of disordered systems.

Hydration Dynamics of Hyaluronan and Dextran

PubMed Central

Hunger, Johannes; Bernecker, Anja; Bakker, Huib J.; Bonn, Mischa; Richter, Ralf P.

2012-01-01

Hyaluronan is a polysaccharide, which is ubiquitous in vertebrates and has been reported to be strongly hydrated in a biological environment. We study the hydration of hyaluronan in solution using the rotational dynamics of water as a probe. We measure these dynamics with polarization-resolved femtosecond-infrared and terahertz time-domain spectroscopies. Both experiments reveal that a subensemble of water molecules is slowed down in aqueous solutions of hyaluronan amounting to ∼15 water molecules per disaccharide unit. This quantity is consistent with what would be expected for the first hydration shell. Comparison of these results to the water dynamics in aqueous dextran solution, a structurally similar polysaccharide, yields remarkably similar results. This suggests that the observed interaction with water is a common feature for hydrophilic polysaccharides and is not specific to hyaluronan. PMID:22828349

Characterization via atomic force microscopy of discrete plasticity in collagen fibrils from mechanically overloaded tendons: Nano-scale structural changes mimic rope failure.

PubMed

Baldwin, Samuel J; Kreplak, Laurent; Lee, J Michael

2016-07-01

Tendons exposed to tensile overload show a structural alteration at the fibril scale termed discrete plasticity. Serial kinks appear along individual collagen fibrils that are susceptible to enzymatic digestion and are thermally unstable. Using atomic force microscopy we mapped the topography and mechanical properties in dehydrated and hydrated states of 25 control fibrils and 25 fibrils displaying periodic kinks, extracted from overloaded bovine tail tendons. Using the measured modulus of the hydrated fibrils as a probe of molecular density, we observed a non-linear negative correlation between molecular density and kink density of individual fibrils. This is accompanied by an increase in water uptake with kink density and a doubling of the coefficient of variation of the modulus between kinked, and control fibrils. The mechanical property maps of kinked collagen fibrils show radial heterogeneity that can be modeled as a high-density core surrounded by a low-density shell. The core of the fibril contains the kink structures characteristic of discrete plasticity; separated by inter-kink regions, which often retain the D-banding structure. We propose that the shell and kink structures mimic characteristic damage motifs observed in laid rope strands. Copyright © 2016 Elsevier Ltd. All rights reserved.

Deoxyribonucleoprotein structure and radiation injury - Cellular radiosensitivity is determined by LET-infinity-dependent DNA damage in hydrated deoxyribonucleoproteins and the extent of its repair

NASA Technical Reports Server (NTRS)

Lett, J. T.; Peters, E. L.

1992-01-01

Until recently, OH radicals formed in bulk nuclear water were believed to be the major causes of DNA damage that results in cell death, especially for sparsely ionizing radiations. That hypothesis has now been challenged, if not refuted. Lethal genomic DNA damage is determined mainly by energy deposition in deoxyribonucleoproteins, and their hydration shells, and charge (energy) transfer processes within those structures.

Dynamics of Hydration Water in Sugars and Peptides Solutions

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

Perticaroli, Stefania; Nakanishi, Masahiro; Pashkovski, Eugene

2013-01-01

We analyzed solute and solvent dynamics of sugars and peptides aqueous solutions using extended epolarized light scattering (EDLS) and broadband dielectric spectroscopies (BDS). Spectra measured with both techniques reveal the same mechanism of rotational diffusion of peptides molecules. In the case of sugars, this solute reorientational relaxation can be isolated by EDLS measurements, whereas its ontribution to the dielectric spectra is almost negligible. In the presented analysis, we characterize the hydration water in terms of hydration number and retardation ratio between relaxation times of hydration and bulk water. Both techniques provide similar estimates of . The retardation imposed on themore » hydration water by sugars is 3.3 1.3 and involves only water molecules hydrogen-bonded (HB) to solutes ( 3 water molecules per sugar OH-group). In contrast, polar peptides cause longer range erturbations beyond the first hydration shell, and between 2.8 and 8, increasing with the number of chemical groups engaged in HB formation. We demonstrate that chemical heterogeneity and specific HB interactions play a crucial role in hydration dynamics around polar solutes. The obtained results help to disentangle the role of excluded volume and enthalpic contributions in dynamics of hydration water at the interface with biological molecules.« less

Influence of drug binding on DNA hydration: acoustic and densimetric characterizations of netropsin binding to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes and the poly(dT).poly(dA).poly(dT) triplex at 25 degrees C.

PubMed

Chalikian, T V; Plum, G E; Sarvazyan, A P; Breslauer, K J

1994-07-26

We use high-precision acoustic and densimetric techniques to determine, at 25 degrees C, the changes in volume, delta V, and adiabatic compressibility, delta Ks, that accompany the binding of netropsin to the poly(dAdT).poly(dAdT) and poly(dA).poly(dT) duplexes, as well as to the poly(dT).poly(dA).poly(dT) triplex. We find that netropsin binding to the heteropolymeric poly(dAdT).poly(dAdT) duplex is accompanied by negative changes in volume, delta V, and small positive changes in compressibility, delta Ks. By contrast, netropsin binding to the homopolymeric poly(dA).poly(dT) duplex is accompanied by large positive changes in both volume, delta V, and compressibility, delta Ks. Furthermore, netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes changes in both volume and compressibility that are nearly twice as large as those observed when netropsin binds to the poly(dA).poly(dT) duplex. We interpret these macroscopic data in terms of binding-induced microscopic changes in the hydration of the DNA structures and the drug. Specifically, we find that netropsin binding induces the release of approximately 22 waters from the hydration shell of the poly(dAdT).poly(dAdT) heteropolymeric duplex, approximately 40 waters from the hydration shell of the poly(dA).poly(dT) homopolymeric duplex, and about 53 waters from the hydration shell of the poly(dA).poly(dT), induces the release of 18 more water molecules than netropsin binding to the heteropolymeric duplex, poly(dAdT).poly(dAdT). On the basis of apparent molar volume, phi V, and apparent molar adiabatic compressibility, phi Ks, values for the initial drug-free and final drug-bound states of the two all-AT duplexes, we propose that the larger dehydration of the poly(dA).poly(dT) duplex reflects, in part, the formation of a less hydrated poly(dA).poly(dT)-netropsin complex compared with the corresponding poly(dAdT).poly(dAdT)-netropsin complex. In conjunction with our previously published entropy data [Marky, L. A., & Breslauer, K. J. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363], we calculate that each water of hydration released to the bulk solvent by ligand binding contributes 1.6 cal K-1 mol-1 to the entropy of binding. This value corresponds to the average difference between the partial molar entropy of water in the bulk state and water in the hydration shells of the two all-AT duplexes. When netropsin binds to the poly(dT).poly(dA).poly(dT) triplex, the changes in both volume and compressibility suggest that the binding event induces more dehydration of the triplex than of the duplex state. Specifically, we calculate that netropsin binding to the poly(dT).poly(dA).poly(dT) triplex causes the release of 13 more waters than netropsin binding to the poly(dA).poly(dT) duplex.(ABSTRACT TRUNCATED AT 400 WORDS)

Methane hydrate formation and decomposition: structural studies via neutron diffraction and empirical potential structure refinement.

PubMed

Thompson, Helen; Soper, Alan K; Buchanan, Piers; Aldiwan, Nawaf; Creek, Jefferson L; Koh, Carolyn A

2006-04-28

Neutron diffraction studies with hydrogen/deuterium isotope substitution measurements are performed to investigate the water structure at the early, medium, and late periods of methane clathrate hydrate formation and decomposition. These measurements are coupled with simultaneous gas consumption measurements to track the formation of methane hydrate from a gas/water mixture, and then the complete decomposition of hydrate. Empirical potential structure refinement computer simulations are used to analyze the neutron diffraction data and extract from the data the water structure in the bulk methane hydrate solution. The results highlight the significant changes in the water structure of the remaining liquid at various stages of hydrate formation and decomposition, and give further insight into the way in which hydrates form. The results also have important implications on the memory effect, suggesting that the water structure in the presence of hydrate crystallites is significantly different at equivalent stages of forming compared to decomposing. These results are in sharp contrast to the previously reported cases when all remaining hydrate crystallites are absent from the solution. For these systems there is no detectable change in the water structure or the methane hydration shell before hydrate formation and after decomposition. Based on the new results presented in this paper, it is clear that the local water structure is affected by the presence of hydrate crystallites, which may in turn be responsible for the "history" or "memory" effect where the production of hydrate from a solution of formed and then subsequently melted hydrate is reportedly much quicker than producing hydrate from a fresh water/gas mixture.

The Role of Concentration and Solvent Character in the Molecular Organization of Humic Acids.

PubMed

Klučáková, Martina; Věžníková, Kateřina

2016-10-27

The molecular organization of humic acids in different aqueous solutions was studied over a wide concentration range (0.01-10 g·dm -3 ). Solutions of humic acids were prepared in three different media: NaOH, NaCl, and NaOH neutralized by HCl after dissolution of the humic sample. Potentiometry, conductometry, densitometry, and high resolution ultrasound spectrometry were used in order to investigate conformational changes in the humic systems. The molecular organization of humic acids in the studied systems could be divided into three concentration ranges. The rearrangements were observed at concentrations of ~0.02 g·dm -3 and ~1 g·dm -3 . The first "switch-over point" was connected with changes in the hydration shells of humic particles resulting in changes in their elasticity. The compressibility of water in the hydration shells is less than the compressibility of bulk water. The transfer of hydration water into bulk water increased the total compressibility of the solution, reducing the ultrasonic velocity. The aggregation of humic particles and the formation of rigid structures in systems with concentrations higher than 1 g·dm -3 was detected.

Hydration and dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions

NASA Astrophysics Data System (ADS)

Lyashchenko, A. K.; Balakaeva, I. V.; Simonova, Yu. A.; Timofeeva, L. M.

2017-10-01

Results from microwave measurements of the dielectrical properties of aqueous pyrrolidinium trifluoroacetate solutions at maximum water dispersion frequencies (13-25 GHz) and temperatures of 288, 298, and 308 K are given. The static dielectrical constants, times, and activation parameters of the dielectrical relaxation of solutions are calculated. The enthalpy and time of dielectrical relaxation activation are increased by deceleration of the motion of water molecules in the hydrate shells of ions. The changes in dielectrical parameters are in this case minimal in a series of aqueous solutions of diallylammonium salts with cations of different structures and degrees of substitution. It is shown that pyrrolidinium ions are characterized by weak hydrophobic hydration.

K/T spherules from Haiti and Wyoming: Origin, diagenesis, and similarity to some microtektites

NASA Technical Reports Server (NTRS)

Bohor, B. F.; Glass, B. P.; Betterton, W. J.

1993-01-01

Spherules with relict glass cores in the K/T boundary bed of Haiti allow for a comparison of these bodies with hollow goyazite shells in the K/T boundary claystone of Wyoming and with younger microtektites of the Ivory Coast strewn field. Samples of the Haitian beds from undisturbed sections at Beloc, as determined by Jehanno et al., contain both hollow shells and relict glass cores rimmed by palagonite that has been partially converted to smectite. These palagonite rims developed from hydration zones formed when hot, splash-form droplets of andesitic impact glass were deposited into water. Mutual collisions between these droplets in the ejecta curtain may have formed point-source stresses on their surfaces. Initiation of hydration would be facilitated at these surface stress points and propagated radially into the glass. The inner surface of these merged hemispherical fronts appears mammillary, which is reflected as scalloping in Haitian relict glass cores.

Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

PubMed

Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

2012-01-28

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. © 2012 American Institute of Physics

Nuclear quantum effects in water exchange around lithium and fluoride ions

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

Wilkins, David M.; Manolopoulos, David; Dang, Liem X.

2015-02-14

We employ classical and ring polymer molecular dynamics simulations to study the effect of nuclear quantum fluctuations on the structure and the water exchange dynamics of aqueous solutions of lithium and fluoride ions. While we obtain reasonably good agreement with experimental data for solutions of lithium by augmenting the Coulombic interactions between the ion and the water molecules with a standard Lennard-Jones ion-oxygen potential, the same is not true for solutions of fluoride, for which we find that a potential with a softer repulsive wall gives much better agreement. A small degree of destabilization of the first hydration shell ismore » found in quantum simulations of both ions when compared with classical simulations, with the shell becoming less sharply defined and the mean residence time of the water molecules in the shell decreasing. In line with these modest differences, we find that the mechanisms of the water exchange reactions are unaffected by quantization, so a classical description of these reactions gives qualitatively correct and quantitatively reasonable results. We also find that the quantum effects in solutions of lithium are larger than in solutions of fluoride. This is partly due to the stronger interaction of lithium with water molecules, partly due to the lighter mass of lithium, and partly due to competing quantum effects in the hydration of fluoride, which are absent in the hydration of lithium. LXD was supported by US Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.« less

Near-membrane electric field calcium ion dehydration.

PubMed

Barger, James P; Dillon, Patrick F

2016-12-01

The dehydration of ion-water complexes prior to ion channel transit has focused on channel protein-mediated dissociation of water. Ion dehydration by the membrane electric field has not previously been considered. Near membrane electric fields have previously been shown to cause the disassociation of non-covalently bound small molecule-small molecule, small molecule-protein, and protein-protein complexes. It is well known that cosmotropic, structure making ions such as calcium and sodium significantly bind multiple water ions in solution. It is also known that these ions are often not hydrated as they pass through membrane ion channels. Using capillary electrophoresis, the range of electric fields needed to strip water molecules from calcium ions has been measured. Ion migration velocity is a linear function of the electric field. At low electric fields, the migration rate of calcium ion was shown to be linearly related to the applied electric field. Using a form of the Stoke's equation applicable to ion migration, the hydrated calcium radius was found to be 0.334nm, corresponding to a water hydration shell of 5.09 water molecules. At higher electric fields, the slope of the calcium migration velocity as a function of the electric field increased, which was modeled as a decrease in the radius of the migrating ion as the water was removed. Using a tanh function to model the transition of the ion from a hydrated to a stripped state, the transition had a midpoint at 446V/cm, and was 88% complete at 587V/cm with a correlation coefficient of 0.9996. The migration velocity of the stripped calcium ion was found to be a function of both the decrease in radius and an increase in the effective, electronic viscosity of the dipole medium through which the dehydrated ion moved. The size of the electric field needed to dehydrate calcium occurs 6-7nm from the cell membrane. Calcium ions within this distance from the membrane will be devoid of water molecules when they reach the calcium selective channel pore entrances, all known to be approximately 1-2nm from the membrane. No matter what the calcium pore structure, calcium ions reaching the channel entrance will be devoid of a water shell. Copyright © 2016 Elsevier Ltd. All rights reserved.

New Model for Europa's Tidal Response Based after Laboratory Measurements

NASA Astrophysics Data System (ADS)

Castillo, J. C.; McCarthy, C.; Choukroun, M.; Rambaux, N.

2009-12-01

We explore the application of the Andrade model to the modeling of Europa’s tidal response at the orbital period and for different librations. Previous models have generally assumed that the satellite behaves as a Maxwell body. However, at the frequencies exciting Europa’s tides and librations, material anelasticity tends to dominate the satellite’s response for a wide range of temperatures, a feature that is not accounted for by the Maxwell model. Many experimental studies on the anelasticity of rocks, ice, and hydrates, suggest that the Andrade model usually provides a good fit to the dissipation spectra obtained for a wide range of frequencies, encompassing the tidal frequencies of most icy satellites. These data indicate that, at Europa’s orbital frequency, the Maxwell model overestimates water ice attenuation at temperature warmer than ~240 K, while it tends to significantly underestimate it at lower temperatures. Based on the available data we suggest an educated extrapolation of available data to Europa’s conditions. We compute the tidal response of a model of Europa differentiated in a rocky core and a water-rich shell. We assume various degrees of stratification of the core involving hydrated and anhydrous silicates, as well as an iron core. The water-rich shell of Europa is assumed to be fully frozen, or to have preserved a deep liquid layer. In both cases we consider a range of thermal structures, based on existing models. These structures take into account the presence of non-ice materials, especially hydrated salts. This new approach yields a greater tidal response (amplitude and phase lag) than previously expected. This is due to the fact that a greater volume of material dissipates tidal energy in comparison to models assuming a Maxwell body. Another feature of interest is that the tidal stress expected in Europa is at about the threshold between a linear and non-linear mechanical response of water ice as a function of stress. Increased stress at a time when Europa’s eccentricity was greater than its current value is likely to have resulted in significant dissipation increase. We will assess how this new approach affects our understanding of Europa, and we will quantify the tidal response of this satellite and the amount of tidal heating available to its evolution. Acknowledgements: Part of this work has been conducted at the Jet Propulsion Laboratory, California Institute of Technology, under contract with NASA. Government sponsorship acknowledged. Part of the experimental work was conducted at Brown University, funded by NASA. MC is supported by a NASA Postdoctoral Fellowship, administered by Oak Ridge Associated Universities.

Stepwise microhydration of aromatic amide cations: water solvation networks revealed by the infrared spectra of acetanilide+-(H2O)n clusters (n ≤ 3).

PubMed

Klyne, Johanna; Schmies, Matthias; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

2018-01-31

The structure and activity of peptides and proteins strongly rely on their charge state and the interaction with their hydration environment. Here, infrared photodissociation (IRPD) spectra of size-selected microhydrated clusters of cationic acetanilide (AA + , N-phenylacetamide), AA + -(H 2 O) n with n ≤ 3, are analysed by dispersion-corrected density functional theory calculations at the ωB97X-D/aug-cc-pVTZ level to determine the stepwise microhydration process of this aromatic peptide model. The IRPD spectra are recorded in the informative X-H stretch (ν OH , ν NH , ν CH , amide A, 2800-3800 cm -1 ) and fingerprint (amide I-II, 1000-1900 cm -1 ) ranges to probe the preferred hydration motifs and the cluster growth. In the most stable AA + -(H 2 O) n structures, the H 2 O ligands solvate the acidic NH proton of the amide by forming a hydrogen-bonded solvent network, which strongly benefits from cooperative effects arising from the excess positive charge. Comparison with neutral AA-H 2 O reveals the strong impact of ionization on the acidity of the NH proton and the topology of the interaction potential. Comparison with related hydrated formanilide clusters demonstrates the influence of methylation of the amide group (H → CH 3 ) on the shape of the intermolecular potential and the structure of the hydration shell.

Solution influence on biomolecular equilibria - Nucleic acid base associations

NASA Technical Reports Server (NTRS)

Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

1984-01-01

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

Hydration behavior of casein micelles in thin film geometry: a GISANS study?

PubMed

Metwalli, E; Moulin, J F; Gebhardt, R; Cubitt, R; Tolkach, A; Kulozik, U; Müller-Buschbaum, P

2009-04-07

The water content of casein micelle films in water vapor atmosphere is investigated using time-resolved grazing incidence small-angle neutron scattering (GISANS). Initial dry casein films are prepared with a spin-coating method. At 30 degrees C, the formation of a water-equilibrated casein protein film is reached after 11 min with a total content of 0.36 g of water/g of protein. With increasing water vapor temperature up to 70 degrees C, an increase in the water content is found. With GISANS, lateral structures on the nanometer scale are resolved during the swelling experiment at different temperatures and modeled using two types of spheres: micelles and mini-micelles. Upon water uptake, molecular assemblies in the size range of 15 nm (mini-micelles) are attributed to the formation of a high-contrast D2O outer shell on the small objects that already exist in the protein film. For large objects (>100 nm), the mean size increases at high D2O vapor temperature because of possible aggregation between hydrated micelles. These results are discussed and compared with various proposed models for casein micelle structures.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations.

PubMed

Černý, Jiří; Schneider, Bohdan; Biedermannová, Lada

2017-07-14

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures. The crystal-derived data include 3D maps of water distribution around amino-acids and probability of occurrence of each of the identified hydration sites. The quantum mechanics calculations validate and extend this primary description by optimizing the water position for each hydration site, by providing hydrogen atom positions and by quantifying the interaction energy that stabilizes the water molecule at the particular hydration site position. The calculations show that the majority of experimentally derived hydration sites are positioned near local energy minima for water, and the calculated interaction energies help to assess the preference of water for the individual hydration sites. We propose that the atlas can be used to validate water placement in electron density maps in crystallographic refinement, to locate water molecules mediating protein-ligand interactions in drug design, and to prepare and evaluate molecular dynamics simulations. WatAA: Atlas of Protein Hydration is freely available without login at .

Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

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

Biedermannová, Lada, E-mail: lada.biedermannova@ibt.cas.cz; Schneider, Bohdan

2015-10-27

The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. Themore » results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.« less

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

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

Xie, Wen Jun; Yang, Yi Isaac; Gao, Yi Qin, E-mail: gaoyq@pku.edu.cn

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 motionmore » 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.« less

Label-free detection and characterization of the binding of hemagglutinin protein and broadly neutralizing monoclonal antibodies using terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Sun, Yiwen; Zhong, Junlan; Zhang, Cunlin; Zuo, Jian; Pickwell-MacPherson, Emma

2015-03-01

Hemagglutinin (HA) is the main surface glycoprotein of the influenza A virus. The H9N2 subtype influenza A virus is recognized as the most possible pandemic strain as it has crossed the species barrier, infecting swine and humans. We use terahertz spectroscopy to study the hydration shell formation around H9 subtype influenza A virus's HA protein (H9 HA) as well as the detection of antigen binding of H9 HA with the broadly neutralizing monoclonal antibody. We observe a remarkable concentration dependent nonlinear response of the H9 HA, which reveals the formation process of the hydration shell around H9 HA molecules. Furthermore, we show that terahertz dielectric properties of the H9 HA are strongly affected by the presence of the monoclonal antibody F10 and that the terahertz dielectric loss tangent can be used to detect the antibody binding at lower concentrations than the standard ELISA test.

Cellulose Aggregation under Hydrothermal Pretreatment Conditions.

PubMed

Silveira, Rodrigo L; Stoyanov, Stanislav R; Kovalenko, Andriy; Skaf, Munir S

2016-08-08

Cellulose, the most abundant biopolymer on Earth, represents a resource for sustainable production of biofuels. Thermochemical treatments make lignocellulosic biomaterials more amenable to depolymerization by exposing cellulose microfibrils to enzymatic or chemical attacks. In such treatments, the solvent plays fundamental roles in biomass modification, but the molecular events underlying these changes are still poorly understood. Here, the 3D-RISM-KH molecular theory of solvation has been employed to analyze the role of water in cellulose aggregation under different thermodynamic conditions. The results show that, under ambient conditions, highly structured hydration shells around cellulose create repulsive forces that protect cellulose microfibrils from aggregating. Under hydrothermal pretreatment conditions, however, the hydration shells lose structure, and cellulose aggregation is favored. These effects are largely due to a decrease in cellulose-water interactions relative to those at ambient conditions, so that cellulose-cellulose attractive interactions become prevalent. Our results provide an explanation to the observed increase in the lateral size of cellulose crystallites when biomass is subject to pretreatments and deepen the current understanding of the mechanisms of biomass modification.

Dynamical properties of the hydration shell of fully deuterated myoglobin

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

Achterhold, Klaus; Parak, Fritz G.; Ostermann, Andreas

2011-10-15

Freeze-dried perdeuterated sperm whale myoglobin was kept in a water-saturated atmosphere in order to obtain a hydration degree of 335 {sup 1}H{sub 2}O molecules per one myoglobin molecule. Incoherent neutron scattering was performed at the neutron spectrometer TOFTOF at the FRM II in an angular range of q from 0.6 to 1.8 A{sup -1} and a temperature range from 4 to 297 K. We used neutrons with a wavelength of {lambda}{alpha}E 6 A and an energy resolution of about 65 {mu}eV corresponding to motions faster than 10 ps. At temperatures above 225 K, broad lines appear in the spectra causedmore » by quasielastic scattering. For an explanation of these lines, we assumed that there are only two types of protons, those that are part of the hydration water (72%) and those that belong to the protein (28%). The protons of the hydration water were analyzed with the diffusion model of Singwi and Sjoelander [Phys. Rev. 119, 863 (1960)]. In this model, a water molecule stays for a time {tau}{sub 0} in a bound state performing oscillatory motions. Thereafter, the molecule performs free diffusion for the time {tau}{sub 1} in a nonbound state followed again by the oscillatory motions for {tau}{sub 0} and so forth. We used the general formulation with no simplifications as {tau}{sub 0}>>{tau}{sub 1} or {tau}{sub 1}>>{tau}{sub 0}. At room temperature, we obtained {tau}{sub 0} {alpha}E 104 ps and {tau}{sub 1} {alpha}E 37 ps. For the protein bound hydrogen, the dynamics is described by a Brownian oscillator where the protons perform overdamped motions in limited space.« less

Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties

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

Liao, Sing; Green, Michael E.

2011-01-01

Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 watermore » molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if these potentials are used in Molecular Dynamics simulations.« less

Dynamics of water solutions of natural polysaccharides by fast field cycling nmr relaxometry

NASA Astrophysics Data System (ADS)

Prusova, Alena; Conte, Pellegrino; Kucerik, Jiri; de Pasquale, Claudio; Alonzo, Giuseppe

2010-05-01

Cryobiology studies the effect of low temperatures on living systems such as microorganisms and plants. In particular, plants growing in cold or frozen environments can survive such extreme conditions due to the cold hardening process. Hardening is a three step process during which, first, translocation of polysaccharides to the plant roots affects water structure in the cell-soil surface. For this reason, increase of cell-membrane permeability and resistance to temperatures from -5°C to -10°C is achieved. In a second step, chemical alteration of cell membrane arises and resistance to temperatures up to -20°C is obtained. The last hardening step consists in the vitrification of the plant tissues which allow plants to survive at temperatures as low as -50°C. Since polysaccharides play a very important role in the initial part of the cold hardening process, it is of paramount importance to study the effect of such natural biopolymers on water structure. Here, we present preliminary data obtained by fast field cycling NMR relaxometry on the effect of hyaluronan (an anionic, non-sulfated glycosaminoglycan) on water structure at different concentrations of the polysaccharide. Although hyaluronan is a polysaccharide found exceptionally in animal, human or bacterial bodies, in the present work it was used as a model "pilot" compound. In fact, it has an unique ability to hold water and it contains both polysaccharide and protein-like acetamido functionalities. For this reason, hyaluronan promotes the future research on other plant biopolymers such as, for instance, starch and other very specific proteins. Results revealed that different water-structure systems surround the molecule of hyaluronan in diluted and semidiluted systems. Namely, at the lowest hyaluronan concentration, three hydration shells can be recognized. The first hydration shell is made by bound water (BW) which is strongly fixed to the hyaluronan surface mainly through electrostatic interactions. A second hydration shell contains water molecules, also recognized as partly-bound (PBW), which are not directly interacting with the hyaluronan chains but with BW. Finally, water molecules, which dynamics is resembling that of the pure and undisturbed water, are indicated either as a bulk water or free water (FW). As hyaluronan concentration is increased the third FW hydration shell is lost and all water molecules are affected by the presence of hyaluronan molecules. This work showed the great potential of FFC-NMR relaxometry in revealing water nature in polysaccharide solutions and the possibility for future applications on complex biological systems. Acknowledgements A.P. gratefully acknowledges a bilateral Erasmus project between Brno University of Technology and University of Palermo which provided grant sustainment for working in Italy. Ministry of Education of the Czech Republic, project MSM 0021630501 is also acknwledged. This work was partially funded by Ce.R.T.A. s.c.r.l. (Centri Regionali per le Tecnologie Alimentari; Italy). Authors kindly acknowledge Dr. Vladimír Velebný (CPN company, Dolní Dobrouč, Czech Republic) for providing of hyaluronan sample.

Evaluation of the possible presence of clathrate hydrates in Europa's icy shell or seafloor

NASA Astrophysics Data System (ADS)

Prieto-Ballesteros, Olga; Kargel, Jeffrey S.; Fernández-Sampedro, Maite; Selsis, Franck; Martínez, Eduardo Sebastián; Hogenboom, David L.

2005-10-01

Several substances besides water ice have been detected on the surface of Europa by spectroscopic sensors, including CO 2, SO 2, and H 2S. These substances might occur as pure crystalline ices, as vitreous mixtures, or as clathrate hydrate phases, depending on the system conditions and the history of the material. Clathrate hydrates are crystalline compounds in which an expanded water ice lattice forms cages that contain gas molecules. The molecular gases that may constitute Europan clathrate hydrates may have two possible ultimate origins: they might be primordial condensates from the interstellar medium, solar nebula, or jovian subnebula, or they might be secondary products generated as a consequence of the geological evolution and complex chemical processing of the satellite. Primordial ices and volatile-bearing compounds would be difficult to preserve in pristine form in Europa without further processing because of its active geological history. But dissociated volatiles derived from differentiation of a chondritic rock or cometary precursor may have produced secondary clathrates that may be present now. We have evaluated the current stability of several types of clathrate hydrates in the crust and the ocean of Europa. The depth at which the clathrates of SO 2, CO 2, H 2S, and CH 4 are stable have been obtained using both the temperatures observed in the surface [Spencer, J.R., Tamppari, L.K., Martin, T.Z., Travis, L.D., 1999. Temperatures on Europa from Galileo photopolarimeter-radiometer: Nighttime thermal anomalies. Science 284, 1514-1516] and thermal models for the crust. In addition, their densities have been calculated in order to determine their buoyancy in the ocean, obtaining different results depending upon the salinity of the ocean and type of clathrate. For instance, assuming a eutectic composition of the system MgSO 4sbnd H 2O for the ocean, CO 2, H 2S, and CH 4 clathrates would float but SO 2 clathrate would sink to the seafloor; an ocean of much lower salinity would allow all these clathrates to sink, except that CH 4 clathrate would still float. Many geological processes may be driven or affected by the formation, presence, and destruction of clathrates in Europa such as explosive cryomagmatic activity [Stevenson, D.J., 1982. Volcanism and igneous processes in small icy satellites. Nature 298, 142-144], partial differentiation of the crust driven by its clathration, or the local retention of heat within or beneath clathrate-rich layers because of the low thermal conductivity of clathrate hydrates [Ross, R.G., Kargel, J.S., 1998. Thermal conductivity of Solar System ices, with special reference to martian polar caps. In: Schmitt, B., De Berg, C., Festou, M. (Eds.), Solar System Ices. Kluwer Academic, Dordrecht, pp. 33-62]. On the surface, destabilization of these minerals and compounds, triggered by fracture decompression or heating could result in formation of chaotic terrain morphologies, a mechanism that also has been proposed for some martian chaotic terrains [Tanaka, K.L., Kargel, J.S., MacKinnon, D.J., Hare, T.M., Hoffman, N., 2002. Catastrophic erosion of Hellas basin rim on Mars induced by magmatic intrusion into volatile-rich rocks. Geophys. Res. Lett. 29 (8); Kargel, J.S., Prieto-Ballesteros, O., Tanaka K.L., 2003. Is clathrate hydrate dissociation responsible for chaotic terrains on Earth, Mars, Europa, and Triton? Geophys. Res. 5. Abstract 14252]. Models of the evolution of the ice shell of Europa might take into account the presence of clathrate hydrates because if gases are vented from the silicate interior to the water ocean, they first would dissolve in the ocean and then, if the gas concentrations are sufficient, may crystallize. If any methane releases occur in Europa by hydrothermal or biological activity, they also might form clathrates. Then, from both geological and astrobiological perspectives, future missions to Europa should carry instrumentation capable of clathrate hydrate detection.

Global minimum-energy structure and spectroscopic properties of I2(*-) x n H2O clusters: a Monte Carlo simulated annealing study.

PubMed

Pathak, Arup Kumar; Mukherjee, Tulsi; Maity, Dilip Kumar

2010-01-18

The vibrational (IR and Raman) and photoelectron spectral properties of hydrated iodine-dimer radical-anion clusters, I(2)(*-) x n H(2)O (n=1-10), are presented. Several initial guess structures are considered for each size of cluster to locate the global minimum-energy structure by applying a Monte Carlo simulated annealing procedure including spin-orbit interaction. In the Raman spectrum, hydration reduces the intensity of the I-I stretching band but enhances the intensity of the O-H stretching band of water. Raman spectra of more highly hydrated clusters appear to be simpler than the corresponding IR spectra. Vibrational bands due to simultaneous stretching vibrations of O-H bonds in a cyclic water network are observed for I(2)(*-) x n H(2)O clusters with n > or = 3. The vertical detachment energy (VDE) profile shows stepwise saturation that indicates closing of the geometrical shell in the hydrated clusters on addition of every four water molecules. The calculated VDE of finite-size small hydrated clusters is extrapolated to evaluate the bulk VDE value of I(2)(*-) in aqueous solution as 7.6 eV at the CCSD(T) level of theory. Structure and spectroscopic properties of these hydrated clusters are compared with those of hydrated clusters of Cl(2)(*-) and Br(2)(*-).

Analysis of the detailed configuration of hydrated lanthanoid(III) ions in aqueous solution and crystalline salts by using K- and L(3)-edge XANES spectroscopy.

PubMed

D'Angelo, Paola; Zitolo, Andrea; Migliorati, Valentina; Persson, Ingmar

2010-01-11

The structural properties of the hydrated lanthanoid(III) ions in aqueous solution and in the isostructural trifluoromethanesulfonate salts have been investigated by a quantitative analysis of the X-ray absorption near-edge structure (XANES) spectra at the K- and L(3)-edges. The XANES analysis has provided a clear description of the variation of lanthanoid(III) hydration properties across the series. It was found that all of the lanthanoid(III) hydration complexes retain a tricapped trigonal prism (TTP) geometry, and along the series two of the capping water molecules become less and less strongly bound, before finally, on average, one of them leaves the hydration cluster. This gives rise to an eight-coordinated distorted bicapped trigonal prism with two different Ln--O capping distances for the smallest lanthanoid(III) ions. This systematic study has shown that for lanthanoid compounds more accurate structural information is obtained from the analysis of the L(3)-edge than from K-edge XANES data. Moreover, whereas the second hydration shells provide a detectable contribution to the L(3)-edge XANES spectra of the lighter lanthanoid ions, the K-edge spectra are insensitive to the more distant coordination spheres.

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Methane-derived authigenic carbonates from the northern Gulf of Mexico - MD02 Cruise

USGS Publications Warehouse

Chen, Y.; Matsumoto, R.; Paull, C.K.; Ussler, W.; Lorenson, T.; Hart, P.; Winters, W.

2007-01-01

Authigenic carbonates were sampled in piston cores collected from both the Tunica Mound and the Mississippi Canyon area on the continental slope of the northern Gulf of Mexico during a Marion Dufresne cruise in July 2002. The carbonates are present as hardgrounds, porous crusts, concretions or nodules and shell fragments with or without carbonate cements. Carbonates occurred at gas venting sites which are likely to overlie gas hydrates bearing sediments. Electron microprobe, X-ray diffraction (XRD) and thinsection investigations show that these carbonates are high-Mg calcite (6-21??mol% MgCO3), with significant presence of framboidal pyrite. All carbonates are depleted in 13C (??13C = - 61.9 to - 31.5??? PDB) indicating that the carbon is derived mainly from anaerobic methane oxidation (AMO). Age estimates based on 14C dating of shell fragments and on regional sedimentation rates indicate that these authigenic carbonates formed within the last 1000??yr in the Mississippi Canyon and within 5500??yr at the Tunica Mound. The oxygen isotopic composition of carbonates ranges from + 3.4 to + 5.9??? PDB. Oxygen isotopic compositions and Mg2+ contents of carbonates, and present in-situ temperatures of bottom seawater/sediments, show that some of these carbonates, especially from a core associated with underlying massive gas hydrates precipitated in or near equilibrium with bottom-water. On the other hand, those carbonates more enriched in 18O are interpreted to have precipitated from 18O-rich fluids which are thought to have been derived from the dissociation of gas hydrates. The dissociation of gas hydrates in the northern Gulf of Mexico within the last 5500??yr may be caused by nearby salt movement and related brines. ?? 2007 Elsevier B.V. All rights reserved.

Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters

NASA Astrophysics Data System (ADS)

León-Pimentel, C. I.; Amaro-Estrada, J. I.; Hernández-Cobos, J.; Saint-Martin, H.; Ramírez-Solís, A.

2018-04-01

The hydration features of [Mg(H2O)n ] 2 + and [Ca(H2O)n ] 2 + clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n ] 2 + clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

Photocatalytic activity of Ag/ZnO core-shell nanoparticles with shell thickness as controlling parameter under green environment

NASA Astrophysics Data System (ADS)

Rajbongshi, Himanshu; Bhattacharjee, Suparna; Datta, Pranayee

2017-02-01

Plasmonic Ag/ZnO core-shell nanoparticles have been synthesized via a simple two-step wet chemical method for application in Photocatalysis. The morphology, size, crystal structure, composition and optical properties of the nanoparticles are investigated by x-ray diffraction, transmission electron microscopy (TEM), FTIR spectroscopy, ultraviolet-visible (UV-Vis) absorption spectroscopy and photoluminescence (PL) spectroscopy. The shell thicknesses are varied by varying the concentration of zinc nitrate hexa-hydrate and triethanolamine. The ZnO shell coating over Ag core enhances the charge separation, whereas the larger shell thickness and increased refractive index of surrounding medium cause red shifts of surface Plasmon resonance (SPR) peak of Ag core. The photoluminescence (PL) spectra of Ag/ZnO core-shell show that the larger shell thickness quenches the near band edge UV emission of ZnO. The electrochemical impedance spectra (EIS) i.e. Nyquist plots also confirm the higher charge transfer efficiency of the Ag/ZnO core-shell nanoparticles. The Photocatalytic activities of Ag/ZnO core-shell nanoparticles are investigated by the degradation of methylene blue (MB) dye under direct sunlight irradiation. Compared to pure ZnO nanoparticles (NPs), Ag/ZnO core-shell NPs display efficient sunlight plasmonic photocatalytic activity because of the influence of SPR of Ag core and the electron sink effect. The photocatalytic activity of Ag/ZnO core-shell NPs is found to be enhanced with increase in shell thickness.

Resolving Nonadiabatic Dynamics of Hydrated Electrons Using Ultrafast Photoemission Anisotropy.

PubMed

Karashima, Shutaro; Yamamoto, Yo-Ichi; Suzuki, Toshinori

2016-04-01

We have studied ultrafast nonadiabatic dynamics of excess electrons trapped in the band gap of liquid water using time- and angle-resolved photoemission spectroscopy. Anisotropic photoemission from the first excited state was discovered, which enabled unambiguous identification of nonadiabatic transition to the ground state in 60 fs in H_{2}O and 100 fs in D_{2}O. The photoelectron kinetic energy distribution exhibited a rapid spectral shift in ca. 20 fs, which is ascribed to the librational response of a hydration shell to electronic excitation. Photoemission anisotropy indicates that the electron orbital in the excited state is depolarized in less than 40 fs.

Study of lithium cation in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-05-12

We present a potential model for Li(+)-water clusters based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM) that is to take ABEEM charges of the cation and all atoms, bonds, and lone pairs of water molecules into the intermolecular electrostatic interaction term in molecular mechanics. The model allows point charges on cationic site and seven sites of an ABEEM-7P water molecule to fluctuate responding to the cluster geometry. The water molecules in the first sphere of Li(+) are strongly structured and there is obvious charge transfer between the cation and the water molecules; therefore, the charge constraint on the ionic cluster includes the charged constraint on the Li(+) and the first-shell water molecules and the charge neutrality constraint on each water molecule in the external hydration shells. The newly constructed potential model based on ABEEM/MM is first applied to ionic clusters and reproduces gas-phase state properties of Li(+)(H(2)O)(n) (n = 1-6 and 8) including optimized geometries, ABEEM charges, binding energies, frequencies, and so on, which are in fair agreement with those measured by available experiments and calculated by ab initio methods. Prospects and benefits introduced by this potential model are pointed out.

Fabrication of Silica-Coated Hollow Carbon Nanospheres Encapsulating Fe3O4 Cluster for Magnetical and MR Imaging Guided NIR Light Triggering Hyperthermia and Ultrasound Imaging.

PubMed

Huang, Yun-Kai; Su, Chia-Hao; Chen, Jiu-Jeng; Chang, Chun-Ting; Tsai, Yu-Hsin; Syu, Sheng-Fu; Tseng, Tsu-Ting; Yeh, Chen-Sheng

2016-06-15

Iron oxide nanoparticles (IONPs)-carbon (C) hybrid zero-dimensional nanostructures normally can be categorized into core-shell and yolk-shell architectures. Although IONP-C is a promising theranostic nanoagent, the in vivo study has surprisingly been less described. In addition, little effort has strived toward the fabrication of yolk-shell compared to the core-shell structures. In this context, we synthesized a yolk-shell type of the silica-coated hollow carbon nanospheres encapsulating IONPs cluster, which can be dispersed in aqueous solution for systemic studies in vivo, via the preparation involving the mixed micellization, polymerization/hollowing, sol-gel (hydration-condensation), and pyrolysis processes. Through a surface modification of the polyethylenimine followed by the sol-gel process, the silica shell coating was able to escape from condensing and sintering courses resulting in aggregation, due to the annealing. Not limited to the well-known functionalities in magnetical targeting and magnetic resonance (MR) imaging for IONP-C hybrid structures, we expanded this yolk-shell NPs as a near-infrared (NIR) light-responsive echogenic nanoagent giving an enhanced ultrasound imaging. Overall, we fabricated the NIR sensitive yolk-shell IONP-C to activate ultrasound imaging and photothermal ablation under magnetically and MR imaging guided therapy.

Biomineral shell formation under ocean acidification: a shift from order to chaos.

PubMed

Fitzer, Susan C; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S; Kamenos, Nicholas A; Phoenix, Vernon R; Cusack, Maggie

2016-02-15

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Biomineral shell formation under ocean acidification: a shift from order to chaos

PubMed Central

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-01-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments. PMID:26876022

Biomineral shell formation under ocean acidification: a shift from order to chaos

NASA Astrophysics Data System (ADS)

Fitzer, Susan C.; Chung, Peter; Maccherozzi, Francesco; Dhesi, Sarnjeet S.; Kamenos, Nicholas A.; Phoenix, Vernon R.; Cusack, Maggie

2016-02-01

Biomineral production in marine organisms employs transient phases of amorphous calcium carbonate (ACC) in the construction of crystalline shells. Increasing seawater pCO2 leads to ocean acidification (OA) with a reduction in oceanic carbonate concentration which could have a negative impact on shell formation and therefore survival. We demonstrate significant changes in the hydrated and dehydrated forms of ACC in the aragonite and calcite layers of Mytilus edulis shells cultured under acidification conditions (1000 μatm pCO2) compared to present day conditions (380 μatm pCO2). In OA conditions, Mytilus edulis has more ACC at crystalisation sites. Here, we use the high-spatial resolution of synchrotron X-ray Photo Emission Electron Microscopy (XPEEM) combined with X-ray Absorption Spectroscopy (XAS) to investigate the influence of OA on the ACC formation in the shells of adult Mytilus edulis. Electron Backscatter Diffraction (EBSD) confirms that OA reduces crystallographic control of shell formation. The results demonstrate that OA induces more ACC formation and less crystallographic control in mussels suggesting that ACC is used as a repair mechanism to combat shell damage under OA. However, the resultant reduced crystallographic control in mussels raises concerns for shell protective function under predation and changing environments.

Structural and dynamical properties of the V(3+) ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation.

PubMed

Kritayakornupong, Chinapong

2009-12-01

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree-Fock level has been performed to investigate structural and dynamical parameters of the V(3+) ion in dilute aqueous solution. A distorted octahedral structure with the average V(3+)-O distance of 1.99 A is evaluated from the QM/MM simulation, which is in good agreement with the X-ray data. Several structural parameters such as angular distribution functions, theta- and tilt-angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V(3+). The Jahn-Teller distortions of the V(3+) ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. (c) 2009 Wiley Periodicals, Inc.

Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

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

Ohashi, Kazuhiko, E-mail: kazu@chem.kyushu-univ.jp; Sekiya, Hiroshi; Sasaki, Jun

2014-12-07

Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for nmore » = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.« less

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

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

The onset of calcium carbonate nucleation: a density functional theory molecular dynamics and hybrid microsolvation/continuum study.

PubMed

Di Tommaso, Devis; de Leeuw, Nora H

2008-06-12

Density functional theory (Perdew-Burke-Ernzerhof) based methods have been used to study the structure and hydration environment of the building blocks of CaCO 3 in aqueous solutions of calcium bicarbonate and calcium carbonate. Car-Parrinello molecular dynamics simulations of Ca(2+)/CO3(2-) and Ca (2+)/HCO3(-) in explicit water were performed to investigate the formation of CaCO3 and the hydration shell of the solvated hetero-ion pair. Our simulations show that the formation of the monomer of CaCO3 occurs with an associative mechanism and that the dominant building block of calcium (bi)carbonate in aqueous solution is Ca[eta(1)-(H)CO3](H2O)5, i.e., the preferred hydration number is five, while the (bi)carbonate is coordinated to the calcium in a monodentate mode. This result agrees with static calculations, where a hybrid approach using a combination of explicit solvent molecules and a polarizable continuum model has been applied to compute the solvation free energies of calcium bicarbonate species. Furthermore, the discrete-continuum calculations predict that the Ca(HCO3)2 and Ca(HCO3)3(-) species are stable in an aqueous environment preferentially as Ca(HCO3)2(H2O)4 and Ca(HCO3)3(H2O)2(-), respectively.

Deep Sea Shell Taphonomy: Interactive benthic experiments in hydrate environments of Barkley Canyon, Ocean Networks Canada.

NASA Astrophysics Data System (ADS)

Best, Mairi; Purser, Autun

2015-04-01

In order to quantify and track the rates and processes of modification of biogenic carbonate in gas hydrate environments, and their possible environmental/ecological correlates, ongoing observations of experimentally deployed specimens are being made using a remotely controlled crawler with camera and sensors. The crawler is connected to NEPTUNE Canada, an 800km, 5-node, regional cabled ocean network across the northern Juan de Fuca Plate, northeastern Pacific, part of Ocean Networks Canada. One of 15 study areas is an environment of exposed hydrate mounds along the wall of Barkley Canyon, at ˜865m water depth. This is the home of a benthic crawler developed by Jacobs University of Germany, who is affectionately known as Wally. Wally is equipped with a range of sensors including cameras, methane sensor, current meter, fluorometer, turbidity meter, CTD, and a sediment microprofiler with probes for oxygen, methane, sulphide, pH, temperature, and conductivity. In conjunction with this sensor suite, a series of experiments have been designed to assess the cycling of biogenic carbon and carbonate in this complex environment. The biota range from microbes, to molluscs, to large fish, and therefore the carbon inputs include both a range of organic carbon compounds as well as the complex materials that are "biogenic carbonate". Controlled experimental specimens were deployed of biogenic carbonate (Mytilus edulis fresh shells) and cellulose (pieces of untreated pine lumber) that had been previously well characterized (photographed, weighed, and numbered, matching valves and lumber kept as controls). Deployment at the sediment/water interface was in such a way to maximize natural burial exhumation cycles but to minimize specimen interaction. 10 replicate specimens of each material were deployed in two treatments: 1) adjacent to a natural life and death assemblage of chemosynthetic bivalves and exposed hydrate on a hydrate mound and 2) on the muddy seafloor at a distance from the mound. On retrieval, the specimens are being further studied for net material loss, surface alteration, microbial recruitment, endo- and epibionts, and microstructural and chemical modification. Understanding the production and cycling of carbon across the sediment/water interface in this environment will help elucidate the formation and evolution of these hydrate deposits, their distribution through time, and the ecological and taphonomic feedbacks they generate.

The mechanism of vapor phase hydration of calcium oxide: implications for CO2 capture.

PubMed

Kudłacz, Krzysztof; Rodriguez-Navarro, Carlos

2014-10-21

Lime-based sorbents are used for fuel- and flue-gas capture, thereby representing an economic and effective way to reduce CO2 emissions. Their use involves cyclic carbonation/calcination which results in a significant conversion reduction with increasing number of cycles. To reactivate spent CaO, vapor phase hydration is typically performed. However, little is known about the ultimate mechanism of such a hydration process. Here, we show that the vapor phase hydration of CaO formed after calcination of calcite (CaCO3) single crystals is a pseudomorphic, topotactic process, which progresses via an intermediate disordered phase prior to the final formation of oriented Ca(OH)2 nanocrystals. The strong structural control during this solid-state phase transition implies that the microstructural features of the CaO parent phase predetermine the final structural and physicochemical (reactivity and attrition) features of the product hydroxide. The higher molar volume of the product can create an impervious shell around unreacted CaO, thereby limiting the efficiency of the reactivation process. However, in the case of compact, sintered CaO structures, volume expansion cannot be accommodated in the reduced pore volume, and stress generation leads to pervasive cracking. This favors complete hydration but also detrimental attrition. Implications of these results in carbon capture and storage (CCS) are discussed.

The spatial range of protein hydration

NASA Astrophysics Data System (ADS)

Persson, Filip; Söderhjelm, Pär; Halle, Bertil

2018-06-01

Proteins interact with their aqueous surroundings, thereby modifying the physical properties of the solvent. The extent of this perturbation has been investigated by numerous methods in the past half-century, but a consensus has still not emerged regarding the spatial range of the perturbation. To a large extent, the disparate views found in the current literature can be traced to the lack of a rigorous definition of the perturbation range. Stating that a particular solvent property differs from its bulk value at a certain distance from the protein is not particularly helpful since such findings depend on the sensitivity and precision of the technique used to probe the system. What is needed is a well-defined decay length, an intrinsic property of the protein in a dilute aqueous solution, that specifies the length scale on which a given physical property approaches its bulk-water value. Based on molecular dynamics simulations of four small globular proteins, we present such an analysis of the structural and dynamic properties of the hydrogen-bonded solvent network. The results demonstrate unequivocally that the solvent perturbation is short-ranged, with all investigated properties having exponential decay lengths of less than one hydration shell. The short range of the perturbation is a consequence of the high energy density of bulk water, rendering this solvent highly resistant to structural perturbations. The electric field from the protein, which under certain conditions can be long-ranged, induces a weak alignment of water dipoles, which, however, is merely the linear dielectric response of bulk water and, therefore, should not be thought of as a structural perturbation. By decomposing the first hydration shell into polarity-based subsets, we find that the hydration structure of the nonpolar parts of the protein surface is similar to that of small nonpolar solutes. For all four examined proteins, the mean number of water-water hydrogen bonds in the nonpolar subset is within 1% of the value in bulk water, suggesting that the fragmentation and topography of the nonpolar protein-water interface has evolved to minimize the propensity for protein aggregation by reducing the unfavorable free energy of hydrophobic hydration.

A novel dressing for the combined delivery of platelet lysate and vancomycin hydrochloride to chronic skin ulcers: Hyaluronic acid particles in alginate matrices.

PubMed

Rossi, S; Mori, M; Vigani, B; Bonferoni, M C; Sandri, G; Riva, F; Caramella, C; Ferrari, F

2018-06-15

The aim of the present work was to develop a medication allowing for the combined delivery of platelet lysate (PL) and an anti-infective model drug, vancomycin hydrochloride (VCM), to chronic skin ulcers. A simple method was set up for the preparation of hyaluronic acid (HA) core-shell particles, loaded with PL and coated with calcium alginate, embedded in a VCM containing alginate matrix. Two different CaCl 2 concentrations were investigated to allow for HA/PL core-shell particle formation. The resulting dressings were characterized for mechanical and hydration properties and tested in vitro (on fibroblasts) and ex-vivo (on skin biopsies) for biological activity. They were found of sufficient mechanical strength to withstand packaging and handling stress and able to absorb a high amount of wound exudate and to form a protective gel on the lesion area. The CaCl 2 concentration used for shell formation did not affect VCM release from the alginate matrix, but strongly modified the release of PGFAB (chosen as representative of growth factors present in PL) from HA particles. In vitro and ex vivo tests provided sufficient proof of concept of the ability of dressings to improve skin ulcers healing. Copyright © 2018 Elsevier B.V. All rights reserved.

Enhancing capacitance behaviour of CoOOH nanostructures using transition metal dopants by ambient oxidation.

PubMed

Chen, Yanhui; Zhou, Junfeng; Maguire, Pierce; O'Connell, Robert; Schmitt, Wolfgang; Li, Yonghe; Yan, Zhengguang; Zhang, Yuefei; Zhang, Hongzhou

2016-02-08

Cobalt hydrate and doped binary Co0.9M0.1OOH (M = Ni, Mn, Fe) nanorings of 100-300 nm were fabricated in solution through a facile ambient oxidation method. A transformation from Co0.9Ni0.1(OH)2 nanodiscs to hollow Co0.9Ni0.1OOH nanorings was observed with prolonged reaction time. Core-shell nanodiscs have elemental segregation with a Co(OH)2 core and Ni(OH)2 shell. Co0.9Ni0.1OOH nanorings displayed a higher electrochemical capacitance than Mn and Fe doped nanorings materials or materials with disc-like geometries.

Porous silicon and diatoms micro-shells: an example of inverse biomimetic

NASA Astrophysics Data System (ADS)

De Tommasi, Edoardo; Rea, Ilaria; Rendina, Ivo; De Stefano, Luca

2011-05-01

Porous silicon (PSi) is by far a very useful technological platform for optical monitoring of chemical and biological substances and due to its peculiar physical and morphological properties it is worldwide used in sensing experiments. On the other hand, we have discovered a natural material, the micro-shells of marine diatoms, ubiquitous unicellular algae, which are made of hydrated amorphous silica, but, most of all, show geometrical structures made of complex patterns of pores which are surprisingly similar to those of porous silicon. Moreover, under laser irradiation, this material is photoluminescent and the photoluminescence is very sensitive to the surrounding atmosphere, which means that the material can act as a transducer. Starting from our experience on PSi devices, we explore the optical and photonic properties of marine diatoms micro-shells in a sort of inverse biomimicry.

The hydration structure of the heavy-alkalines Rb+ and Cs+ through molecular dynamics and X-ray absorption spectroscopy: surface clusters and eccentricity.

PubMed

Caralampio, Daniel Z; Martínez, José M; Pappalardo, Rafael R; Marcos, Enrique Sánchez

2017-11-01

Physicochemical properties of the two heaviest stable alkaline cations, Rb + and Cs + , in water have been examined from classical molecular dynamics (MD) simulations. Alkaline cation-water intermolecular potentials have been built from ab initio interaction energies of [M(H 2 O) n ] + clusters. Unlike in the case of other monatomic metal cations, the sampling needed the inclusion of surface clusters to properly describe the interactions. The first coordination shell is found at an average M-O distance of 2.87 Å and 3.12 Å for Rb + and Cs + , respectively, with coordination numbers of 8 and 10. Structural, dynamical and energetic properties are discussed on the basis of the delicate compromise among the ion-water and water-water interactions which contribute almost on the same foot to the definition of the solvent structure around the ions. A significant asymmetry is detected in the Rb + and Cs + first hydration shell. Reorientational times of first-shell water molecules for Cs + support a clear structure-breaking nature for this cation, whereas the Rb + values do not differ from pure water behavior. Experimental EXAFS and XANES spectra have been compared to simulated ones, obtained by means of application of the FEFF code to a set of statistically significant structures taken from the MD simulations. Due to the presence of multi-excitations in the absorption spectra, theoretical-experimental agreement for the EXAFS spectra is reached when the multi-excitations are removed from the experimental spectra.

The importance of dehydration in determining ion transport in narrow pores.

PubMed

Richards, Laura A; Schäfer, Andrea I; Richards, Bryce S; Corry, Ben

2012-06-11

The transport of hydrated ions through narrow pores is important for a number of processes such as the desalination and filtration of water and the conductance of ions through biological channels. Here, molecular dynamics simulations are used to systematically examine the transport of anionic drinking water contaminants (fluoride, chloride, nitrate, and nitrite) through pores ranging in effective radius from 2.8 to 6.5 Å to elucidate the role of hydration in excluding these species during nanofiltration. Bulk hydration properties (hydrated size and coordination number) are determined for comparison with the situations inside the pores. Free energy profiles for ion transport through the pores show energy barriers depend on pore size, ion type, and membrane surface charge and that the selectivity sequence can change depending on the pore size. Ion coordination numbers along the trajectory showed that partial dehydration of the transported ion is the main contribution to the energy barriers. Ion transport is greatly hindered when the effective pore radius is smaller than the hydrated radius, as the ion has to lose some associated water molecules to enter the pore. Small energy barriers are still observed when pore sizes are larger than the hydrated radius due to re-orientation of the hydration shell or the loss of more distant water. These results demonstrate the importance of ion dehydration in transport through narrow pores, which increases the current level of mechanistic understanding of membrane-based desalination and transport in biological channels. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Dynamics Studies of Overbased Detergents on a Water Surface.

PubMed

Bodnarchuk, M S; Dini, D; Heyes, D M; Breakspear, A; Chahine, S

2017-07-25

Molecular dynamics (MD) simulations are reported of model overbased detergent nanoparticles on a model water surface which mimic their behavior on a Langmuir trough or large water droplet in engine oil. The simulations predict that the structure of the nanoparticle on a water surface is different to when it is immersed in a bulk hydrophobic solvent. The surfactant tails are partly directed out of the water, while the carbonate core maximizes its extent of contact with the water. Umbrella sampling calculations of the potential of mean force between two particles showed that they are associated with varying degrees with a maximum binding free energy of ca. 10 k B T for the salicylate stabilized particle, ca. 8 k B T for a sulfurized alkyl phenate stabilized particle, and ca. 5 k B T for a sulfonate stabilized particle. The differences in the strength of attraction depend on the proximity of nearest approach and the energy penalty associated with the disruption of the hydration shell of water molecules around the calcium carbonate core when the two particles approach. This is greatest for the sulfonate particle, which partially loses the surfactant ions to the solution, and least for the salicylate, which forms the weakest water "cage". The particles are separated by a water hydration layer, even at the point of closest approach.

Damage to cellular DNA from particulate radiations, the efficacy of its processing and the radiosensitivity of mammalian cells. Emphasis on DNA double strand breaks and chromatin breaks

NASA Technical Reports Server (NTRS)

Lett, J. T.

1992-01-01

For several years, it has been evident that cellular radiation biology is in a necessary period of consolidation and transition (Lett 1987, 1990; Lett et al. 1986, 1987). Both changes are moving apace, and have been stimulated by studies with heavy charged particles. From the standpoint of radiation chemistry, there is now a consensus of opinion that the DNA hydration shell must be distinguished from bulk water in the cell nucleus and treated as an integral part of DNA (chromatin) (Lett 1987). Concomitantly, sentiment is strengthening for the abandonment of the classical notions of "direct" and "indirect" action (Fielden and O'Neill 1991; O'Neill 1991; O'Neill et al. 1991; Schulte-Frohlinde and Bothe 1991 and references therein). A layer of water molecules outside, or in the outer edge of, the DNA (chromatin) hydration shell influences cellular radiosensitivity in ways not fully understood. Charge and energy transfer processes facilitated by, or involving, DNA hydration must be considered in rigorous theories of radiation action on cells. The induction and processing of double stand breaks (DSBs) in DNA (chromatin) seem to be the predominant determinants of the radiotoxicity of normally radioresistant mammalian cells, the survival curves of which reflect the patterns of damage induced and the damage present after processing ceases, and can be modelled in formal terms by the use of reaction (enzyme) kinetics. Incongruities such as sublethal damage are neither scientifically sound nor relevant to cellular radiation biology (Calkins 1991; Lett 1990; Lett et al. 1987a). Increases in linear energy transfer (LET infinity) up to 100-200 keV micron-1 cause increases in the extents of neighboring chemical and physical damage in DNA denoted by the general term DSB. Those changes are accompanied by decreasing abilities of cells normally radioresistant to sparsely ionizing radiations to process DSBs in DNA and chromatin and to recover from radiation exposure, so they make significant contributions to the relative biological effectiveness (RBE) of a given radiation.(ABSTRACT TRUNCATED AT 400 WORDS).

Solvent Electrostatic Response: From Simple Solutes to Proteins

NASA Astrophysics Data System (ADS)

Dinpajooh, Mohammadhasan

How water behaves at interfaces is relevant to many scientific and technological applications; however, many subtle phenomena are unknown in aqueous solutions. In this work, interfacial structural transition in hydration shells of a polarizable solute at critical polarizabilities is discovered. The transition is manifested in maximum water response, the reorientation of the water dipoles at the interface, and an increase in the density of dangling OH bonds. This work also addresses the role of polarizability of the active site of proteins in biological catalytic reactions. For proteins, the hydration shell becomes very heterogeneous and involves a relatively large number of water molecules. The molecular dynamics simulations show that the polarizability, along with the atomic charge distribution, needs to be a part of the picture describing how enzymes work. Non Gaussian dynamics in time-resolved linear and nonlinear (correlation) 2D spectra are also analyzed. Additionally, a theoretical formalism is presented to show that when preferential orientations of water dipoles exist at the interface, electrophoretic charges can be produced without free charge carriers, i.e., neutral solutes can move in a constant electric field due to the divergence of polarization at the interface. Furthermore, the concept of interface susceptibility is introduced. It involves the fluctuations of the surface charge density caused by thermal motion and its correlation over the characteristic correlation length with the fluctuations of the solvent charge density. Solvation free energy and interface dielectric constant are formulated accordingly. Unlike previous approaches, the solvation free energy scales quite well in a broad range of ion sizes, namely in the range of 2-14 A. Interface dielectric constant is defined such that the boundary conditions in the Laplace equation describing a micro- or mesoscopic interface are satisfied. The effective dielectric constant of interfacial water is found to be significantly lower than its bulk value. Molecular dynamics simulation results show that the interface dielectric constant for a TIP3P water model changes from nine to four when the effective solute radius is increased from 5 Ato 18 A. The small value of the interface dielectric constant of water has potentially dramatic consequences for hydration.

Water adsorption on TiO2 surfaces probed by soft X-ray spectroscopies: bulk materials vs. isolated nanoparticles

PubMed Central

Benkoula, Safia; Sublemontier, Olivier; Patanen, Minna; Nicolas, Christophe; Sirotti, Fausto; Naitabdi, Ahmed; Gaie-Levrel, François; Antonsson, Egill; Aureau, Damien; Ouf, François-Xavier; Wada, Shin-Ichi; Etcheberry, Arnaud; Ueda, Kiyoshi; Miron, Catalin

2015-01-01

We describe an experimental method to probe the adsorption of water at the surface of isolated, substrate-free TiO2 nanoparticles (NPs) based on soft X-ray spectroscopy in the gas phase using synchrotron radiation. To understand the interfacial properties between water and TiO2 surface, a water shell was adsorbed at the surface of TiO2 NPs. We used two different ways to control the hydration level of the NPs: in the first scheme, initially solvated NPs were dried and in the second one, dry NPs generated thanks to a commercial aerosol generator were exposed to water vapor. XPS was used to identify the signature of the water layer shell on the surface of the free TiO2 NPs and made it possible to follow the evolution of their hydration state. The results obtained allow the establishment of a qualitative determination of isolated NPs’ surface states, as well as to unravel water adsorption mechanisms. This method appears to be a unique approach to investigate the interface between an isolated nano-object and a solvent over-layer, paving the way towards new investigation methods in heterogeneous catalysis on nanomaterials. PMID:26462615

Hydrogen bonding in hydrates with one acetic acid molecule.

PubMed

Pu, Liang; Sun, Yueming; Zhang, Zhibing

2010-10-14

Hydrogen bonding (H-bond) interaction significantly influences the separation of acetic acid (HAc) from the HAc/H(2)O mixtures, especially the dilute solution, in distillation processes. It has been examined from the HAc mono-, di-, tri-, and tetrahydrates by analyzing the structures, binding energies, and infrared vibrational frequencies from quantum chemical calculations. For the first coordinate shell the 6-membered head-on ring is surely the most favorable structure because it has (1) the most favorable H-bonding parameters, (2) almost the largest binding energy per H-bond, (3) the biggest wavenumber shifts, and (4) the highest ring distribution (the AIMD simulations). Moreover, the comparison of the calculations with the experiments (the X-ray scattering data and IR frequencies) suggests that the possible structures in dilute aqueous solution are those involving two or more coordinate shells. The H-bonding in these water-surrounded HAc hydrates are the origin of the low-efficiency problem of isolating HAc from the dilute HAc/H(2)O mixtures. It is apparently a tougher work to break the H-bonds among HAc and the surrounded H(2)O molecules with respect to the case of more concentrated solutions, where the dominant structures are HAc or H(2)O aggregates.

Cations Form Sequence Selective Motifs within DNA Grooves via a Combination of Cation-Pi and Ion-Dipole/Hydrogen Bond Interactions

PubMed Central

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl+) and the polarized first hydration shell waters of divalent cations (Mg2+, Ca2+) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves. PMID:23940752

Cations form sequence selective motifs within DNA grooves via a combination of cation-pi and ion-dipole/hydrogen bond interactions.

PubMed

Stewart, Mikaela; Dunlap, Tori; Dourlain, Elizabeth; Grant, Bryce; McFail-Isom, Lori

2013-01-01

The fine conformational subtleties of DNA structure modulate many fundamental cellular processes including gene activation/repression, cellular division, and DNA repair. Most of these cellular processes rely on the conformational heterogeneity of specific DNA sequences. Factors including those structural characteristics inherent in the particular base sequence as well as those induced through interaction with solvent components combine to produce fine DNA structural variation including helical flexibility and conformation. Cation-pi interactions between solvent cations or their first hydration shell waters and the faces of DNA bases form sequence selectively and contribute to DNA structural heterogeneity. In this paper, we detect and characterize the binding patterns found in cation-pi interactions between solvent cations and DNA bases in a set of high resolution x-ray crystal structures. Specifically, we found that monovalent cations (Tl⁺) and the polarized first hydration shell waters of divalent cations (Mg²⁺, Ca²⁺) form cation-pi interactions with DNA bases stabilizing unstacked conformations. When these cation-pi interactions are combined with electrostatic interactions a pattern of specific binding motifs is formed within the grooves.

States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

PubMed

Serwer, Philip; Wright, Elena T; Demeler, Borries; Jiang, Wen

2018-04-01

Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

Hydrate-melt electrolytes for high-energy-density aqueous batteries

NASA Astrophysics Data System (ADS)

Yamada, Yuki; Usui, Kenji; Sodeyama, Keitaro; Ko, Seongjae; Tateyama, Yoshitaka; Yamada, Atsuo

2016-10-01

Aqueous Li-ion batteries are attracting increasing attention because they are potentially low in cost, safe and environmentally friendly. However, their low energy density (<100 Wh kg-1 based on total electrode weight), which results from the narrow operating potential window of water and the limited selection of suitable negative electrodes, is problematic for their future widespread application. Here, we explore optimized eutectic systems of several organic Li salts and show that a room-temperature hydrate melt of Li salts can be used as a stable aqueous electrolyte in which all water molecules participate in Li+ hydration shells while retaining fluidity. This hydrate-melt electrolyte enables a reversible reaction at a commercial Li4Ti5O12 negative electrode with a low reaction potential (1.55 V versus Li+/Li) and a high capacity (175 mAh g-1). The resultant aqueous Li-ion batteries with high energy density (>130 Wh kg-1) and high voltage (˜2.3-3.1 V) represent significant progress towards performance comparable to that of commercial non-aqueous batteries (with energy densities of ˜150-400 Wh kg-1 and voltages of ˜2.4-3.8 V).

Molecular-dynamics simulations of alkaline-earth metal cations in water by atom-bond electronegativity equalization method fused into molecular mechanics.

PubMed

Yang, Zhong-Zhi; Li, Xin

2005-09-01

Intermolecular potential for alkaline-earth metal (Be(2+), Mg(2+), and Ca(2+)) cations in water has been derived using the atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM), and it is consistent with what was previously applied to the hydration study of the monovalent cations. Parameters for the effective interaction between a cation and a water molecule were determined, reproducing the ab initio results. The static, dynamic, and thermodynamic properties of Be(2+)(aq), Mg(2+)(aq), and Ca(2+)(aq) were studied using these potential parameters. Be(2+) requires a more complicated form of the potential function than Mg(2+) and Ca(2+) in order to obtain better fits. Strong influences of the twofold charged cations on the structures of the hydration shells and some other properties of aqueous ionic solutions are discussed and compared with the results of a previous study of monovalent cations in water. At the same time, comparative study of the hydration properties of each cation is also discussed. This work demonstrates that ABEEM/MM provides a useful tool in the exploration of the hydration of double-charged cations in water.

Hydration of Li+ -ion in atom-bond electronegativity equalization method-7P water: a molecular dynamics simulation study.

PubMed

Li, Xin; Yang, Zhong-Zhi

2005-02-22

We have carried out molecular dynamics simulations of a Li(+) ion in water over a wide range of temperature (from 248 to 368 K). The simulations make use of the atom-bond electronegativity equalization method-7P water model, a seven-site flexible model with fluctuating charges, which has accurately reproduced many bulk water properties. The recently constructed Li(+)-water interaction potential through fitting to the experimental and ab initio gas-phase binding energies and to the measured structures for Li(+)-water clusters is adopted in the simulations. ABEEM was proposed and developed in terms of partitioning the electron density into atom and bond regions and using the electronegativity equalization method (EEM) and the density functional theory (DFT). Based on a combination of the atom-bond electronegativity equalization method and molecular mechanics (ABEEM/MM), a new set of water-water and Li(+)-water potentials, successfully applied to ionic clusters Li(+)(H(2)O)(n)(n=1-6,8), are further investigated in an aqueous solution of Li(+) in the present paper. Two points must be emphasized in the simulations: first, the model allows for the charges on the interacting sites fluctuating as a function of time; second, the ABEEM-7P model has applied the parameter k(lp,H)(R(lp,H)) to explicitly describe the short-range interaction of hydrogen bond in the hydrogen bond interaction region, and has a new description for the hydrogen bond. The static, dynamic, and thermodynamic properties have been studied in detail. In addition, at different temperatures, the structural properties such as radial distribution functions, and the dynamical properties such as diffusion coefficients and residence times of the water molecules in the first hydration shell of Li(+), are also simulated well. These simulation results show that the ABEEM/MM-based water-water and Li(+)-water potentials appear to be robust giving the overall characteristic hydration properties in excellent agreement with experiments and other molecular dynamics simulations on similar system.

Development of hydrate risk quantification in oil and gas production

NASA Astrophysics Data System (ADS)

Chaudhari, Piyush N.

Subsea flowlines that transport hydrocarbons from wellhead to the processing facility face issues from solid deposits such as hydrates, waxes, asphaltenes, etc. The solid deposits not only affect the production but also pose a safety concern; thus, flow assurance is significantly important in designing and operating subsea oil and gas production. In most subsea oil and gas operations, gas hydrates form at high pressure and low temperature conditions, causing the risk of plugging flowlines, with a undesirable impact on production. Over the years, the oil and gas industry has shifted their perspective from hydrate avoidance to hydrate management given several parameters such as production facility, production chemistry, economic and environmental concerns. Thus, understanding the level of hydrate risk associated with subsea flowlines is an important in developing efficient hydrate management techniques. In the past, hydrate formation models were developed for various flow-systems (e.g., oil dominated, water dominated, and gas dominated) present in the oil and gas production. The objective of this research is to extend the application of the present hydrate prediction models for assessing the hydrate risk associated with subsea flowlines that are prone to hydrate formation. It involves a novel approach for developing quantitative hydrate risk models based on the conceptual models built from the qualitative knowledge obtained from experimental studies. A comprehensive hydrate risk model, that ranks the hydrate risk associated with the subsea production system as a function of time, hydrates, and several other parameters, which account for inertial, viscous, interfacial forces acting on the flow-system, is developed for oil dominated and condensate systems. The hydrate plugging risk for water dominated systems is successfully modeled using The Colorado School of Mines Hydrate Flow Assurance Tool (CSMHyFAST). It is found that CSMHyFAST can be used as a screening tool in order to reduce the parametric study that may require a long duration of time using The Colorado School of Mines Hydrate Kinetic Model (CSMHyK). The evolution of the hydrate plugging risk along flowline-riser systems is modeled for steady state and transient operations considering the effect of several critical parameters such as oil-hydrate slip, duration of shut-in, and water droplet size on a subsea tieback system. This research presents a novel platform for quantification of the hydrate plugging risk, which in-turn will play an important role in improving and optimizing current hydrate management strategies. The predictive strength of the hydrate risk quantification and hydrate prediction models will have a significant impact on flow assurance engineering and design with respect to building safe and efficient hydrate management techniques for future deep-water developments.

Proton transfer reactions and dynamics in CH(3)OH-H(3)O(+)-H(2)O complexes.

PubMed

Sagarik, Kritsana; Chaiwongwattana, Sermsiri; Vchirawongkwin, Viwat; Prueksaaroon, Supakit

2010-01-28

Proton transfer reactions and dynamics in hydrated complexes formed from CH(3)OH, H(3)O(+) and H(2)O were studied using theoretical methods. The investigations began with searching for equilibrium structures at low hydration levels using the DFT method, from which active H-bonds in the gas phase and continuum aqueous solution were characterized and analyzed. Based on the asymmetric stretching coordinates (Deltad(DA)), four H-bond complexes were identified as potential transition states, in which the most active unit is represented by an excess proton nearly equally shared between CH(3)OH and H(2)O. These cannot be definitive due to the lack of asymmetric O-H stretching frequencies (nu(OH)) which are spectral signatures of transferring protons. Born-Oppenheimer molecular dynamics (BOMD) simulations revealed that, when the thermal energy fluctuations and dynamics were included in the model calculations, the spectral signatures at nu(OH) approximately 1000 cm(-1) appeared. In continuum aqueous solution, the H-bond complex with incomplete water coordination at charged species turned out to be the only active transition state. Based on the assumption that the thermal energy fluctuations and dynamics could temporarily break the H-bonds linking the transition state complex and water molecules in the second hydration shell, elementary reactions of proton transfer were proposed. The present study showed that, due to the coupling among various vibrational modes, the discussions on proton transfer reactions cannot be made based solely on static proton transfer potentials. Inclusion of thermal energy fluctuations and dynamics in the model calculations, as in the case of BOMD simulations, together with systematic IR spectral analyses, have been proved to be the most appropriate theoretical approaches.

A Study of the Hydration of the Alkali Metal Ions in Aqueous Solution

PubMed Central

2011-01-01

The hydration of the alkali metal ions in aqueous solution has been studied by large angle X-ray scattering (LAXS) and double difference infrared spectroscopy (DDIR). The structures of the dimethyl sulfoxide solvated alkali metal ions in solution have been determined to support the studies in aqueous solution. The results of the LAXS and DDIR measurements show that the sodium, potassium, rubidium and cesium ions all are weakly hydrated with only a single shell of water molecules. The smaller lithium ion is more strongly hydrated, most probably with a second hydration shell present. The influence of the rubidium and cesium ions on the water structure was found to be very weak, and it was not possible to quantify this effect in a reliable way due to insufficient separation of the O–D stretching bands of partially deuterated water bound to these metal ions and the O–D stretching bands of the bulk water. Aqueous solutions of sodium, potassium and cesium iodide and cesium and lithium hydroxide have been studied by LAXS and M–O bond distances have been determined fairly accurately except for lithium. However, the number of water molecules binding to the alkali metal ions is very difficult to determine from the LAXS measurements as the number of distances and the temperature factor are strongly correlated. A thorough analysis of M–O bond distances in solid alkali metal compounds with ligands binding through oxygen has been made from available structure databases. There is relatively strong correlation between M–O bond distances and coordination numbers also for the alkali metal ions even though the M–O interactions are weak and the number of complexes of potassium, rubidium and cesium with well-defined coordination geometry is very small. The mean M–O bond distance in the hydrated sodium, potassium, rubidium and cesium ions in aqueous solution have been determined to be 2.43(2), 2.81(1), 2.98(1) and 3.07(1) Å, which corresponds to six-, seven-, eight- and eight-coordination. These coordination numbers are supported by the linear relationship of the hydration enthalpies and the M–O bond distances. This correlation indicates that the hydrated lithium ion is four-coordinate in aqueous solution. New ionic radii are proposed for four- and six-coordinate lithium(I), 0.60 and 0.79 Å, respectively, as well as for five- and six-coordinate sodium(I), 1.02 and 1.07 Å, respectively. The ionic radii for six- and seven-coordinate K+, 1.38 and 1.46 Å, respectively, and eight-coordinate Rb+ and Cs+, 1.64 and 1.73 Å, respectively, are confirmed from previous studies. The M–O bond distances in dimethyl sulfoxide solvated sodium, potassium, rubidium and cesium ions in solution are very similar to those observed in aqueous solution. PMID:22168370

Enhancing capacitance behaviour of CoOOH nanostructures using transition metal dopants by ambient oxidation

PubMed Central

Chen, Yanhui; Zhou, Junfeng; Maguire, Pierce; O’Connell, Robert; Schmitt, Wolfgang; Li, Yonghe; Yan, Zhengguang; Zhang, Yuefei; Zhang, Hongzhou

2016-01-01

Cobalt hydrate and doped binary Co0.9M0.1OOH (M = Ni, Mn, Fe) nanorings of 100–300 nm were fabricated in solution through a facile ambient oxidation method. A transformation from Co0.9Ni0.1(OH)2 nanodiscs to hollow Co0.9Ni0.1OOH nanorings was observed with prolonged reaction time. Core-shell nanodiscs have elemental segregation with a Co(OH)2 core and Ni(OH)2 shell. Co0.9Ni0.1OOH nanorings displayed a higher electrochemical capacitance than Mn and Fe doped nanorings materials or materials with disc-like geometries. PMID:26853105

Authigenic carbonates from newly discovered active cold seeps on the northwestern slope of the South China Sea: Constraints on fluid sources, formation environments, and seepage dynamics

NASA Astrophysics Data System (ADS)

Liang, Qianyong; Hu, Yu; Feng, Dong; Peckmann, Jörn; Chen, Linying; Yang, Shengxiong; Liang, Jinqiang; Tao, Jun; Chen, Duofu

2017-06-01

Authigenic carbonates recovered from two newly discovered active cold seeps on the northwestern slope of the South China Sea have been studied using petrography, mineralogy, stable carbon and oxygen isotopic, as well as trace element compositions, together with AMS 14C ages of shells of seep-dwelling bivalves to unravel fluid sources, formation conditions, and seepage dynamics. The two seeps (ROV1 and ROV2), referred to as 'Haima seeps' herein, are approximately 7 kilometers apart, and are typified by abundant carbonate rocks represented bycrusts and nodules. Aragonite and high-Mg calcite are the main carbonate minerals. Based on low δ13Ccarbonate values ranging from -43.0‰ to -27.5‰ (V-PDB) methane is apparently the predominant carbon source of seep carbonates. The corresponding δ18O values, varying from 2.5‰ to 5.8‰ (V-PDB), mostly are higher than calculated values representing precipitation in equilibrium with seawater (2.5‰ to 3.8‰), which probably reflects past destabilization of locally abundant gas hydrates. In addition, we found that carbonates with bivalve shells are generally aragonite-dominated, and bear no barium enrichment but uranium enrichments, reflecting shallow formation depths close to the seafloor. In contrast, carbonate crusts without bivalve shells and nodules contain more calcite, and are characterized by major molybdenum enrichment and different degrees of barium enrichment, agreeing with precipitation at greater depth under strictly anoxic conditions. AMS 14C ages suggest that a major episode of carbonate precipitation occurred between 6.1 ka and 5.1 ka BP at the Haima seeps, followed by a possibly subordinate episode from approximately 3.9 ka to 2.9 ka BP. The common occurrence of dead bivalves at both sites indicates that chemosynthesis-based communities flourished to a greater extent in the past, probably reflecting a decline of seepage activity in recent times. Overall, these results confirm that authigenic carbonates from gas hydrate-bearing areas can provide insight into long-term seepage dynamics and the genesis and fate of marine gas hydrate reservoirs.

Assessment of waste oyster shells and coal mine drainage sludge for the stabilization of As-, Pb-, and Cu-contaminated soil.

PubMed

Moon, Deok Hyun; Cheong, Kyung Hoon; Koutsospyros, Agamemnon; Chang, Yoon-Young; Hyun, Seunghun; Ok, Yong Sik; Park, Jeong-Hun

2016-02-01

A novel treatment mix was designed for the simultaneous immobilization of As, Cu, and Pb in contaminated soils using natural (waste oyster shells (WOS)) and industrial (coal mine drainage sludge (CMDS)) waste materials. The treatments were conducted using the standard U.S. sieve size no. 20 (0.85 mm) calcined oyster shells (COS) and CMDS materials with a curing time of 1 and 28 days. The As immobilization treatments were evaluated using the 1-N HCl extraction fluid, whereas the Pb and Cu immobilization treatments were evaluated using the 0.1-N HCl extraction fluid based on the Korean leaching standards. The treatment results showed that the immobilization of As, Cu, and Pb was best achieved using a combination mix of 10 wt% COS and 10 wt% CMDS. This treatment mix was highly effective leading to superior leachability reductions for all three target contaminants (>93 % for As and >99 % for Cu and Pb) for a curing period of 28 days. The X-ray absorption near-edge structure (XANES) results showed that As was present in the form of As(V) in the control sample and that no changes in As speciation were observed following the COS-CMDS treatments. The scanning electron microscopy (SEM)-energy dispersive X-ray spectroscopy (EDX) sample treated with 10 wt% COS and 10 wt% CMDS indicated that As immobilization may be associated with the formation of Ca-As and Fe-As precipitates while Pb and Cu immobilization was most probably linked to calcium silicate hydrates (CSHs) and calcium aluminum hydrates (CAHs).

Reduced Point Charge Models of Proteins: Effect of Protein-Water Interactions in Molecular Dynamics Simulations of Ubiquitin Systems.

PubMed

Leherte, Laurence; Vercauteren, Daniel P

2017-10-26

We investigate the influence of various solvent models on the structural stability and protein-water interface of three ubiquitin complexes (PDB access codes: 1Q0W , 2MBB , 2G3Q ) modeled using the Amber99sb force field (FF) and two different point charge distributions. A previously developed reduced point charge model (RPCM), wherein each amino acid residue is described by a limited number of point charges, is tested and compared to its all-atom (AA) version. The complexes are solvated in TIP4P-Ew or TIP3P type water molecules, involving either the scaling of the Lennard-Jones protein-O water interaction parameters, or the coarse-grain (CG) SIRAH water description. The best agreements between the RPCM and AA models were obtained for structural, protein-water, and ligand-ubiquitin properties when using the TIP4P-Ew water FF with a scaling factor γ of 0.7. At the RPCM level, a decrease in γ, or the inclusion of SIRAH particles, allows weakening of the protein-water interactions. It results in a slight collapse of the protein structure and a less compact hydration shell and, thus, in a decrease in the number of protein-water and water-water H-bonds. The dynamics of the surface protein atoms and of the water shell molecules are also slightly refrained, which allow the generation of stable RPCM trajectories.

Deconstructing Free Energies in the Law of Matching Water Affinities.

PubMed

Shi, Yu; Beck, Thomas

2017-03-09

The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

Unraveling the role of water in the stereoselective step of aqueous proline-catalyzed aldol reactions.

PubMed

Ribas-Arino, Jordi; Carvajal, Maria Angels; Chaumont, Alain; Masia, Marco

2012-12-03

A multiscale computational study was performed with the aim of tracing the source of stereoselectivity and disclosing the role of water in the stereoselective step of propionaldehyde aldol self-condensation catalyzed by proline amide in water, a reaction that serves as a model for aqueous organocatalytic aldol condensations. Solvent mixing and hydration behavior were assessed by classical molecular dynamics simulations, which show that the reaction between propanal and the corresponding enamine takes place in a fully hydrated environment. First-principles molecular dynamics simulations were used to study the free-energy profile of four possible reaction paths, each of which yields a different stereoisomer, and high-level static first-principles calculations were employed to characterize the transition states for microsolvated species. The first solvation shell of the oxygen atom of the electrophilic aldehyde at the transition states contains two water molecules, each of which donates one hydrogen bond to the nascent alkoxide and thereby largely stabilizes its excess electron density. The stereoselectivity originates in an extra hydrogen bond donated by the amido group of proline amide in two reaction paths. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Geomechanical Modeling of Gas Hydrate Bearing Sediments

NASA Astrophysics Data System (ADS)

Sanchez, M. J.; Gai, X., Sr.

2015-12-01

This contribution focuses on an advance geomechanical model for methane hydrate-bearing soils based on concepts of elasto-plasticity for strain hardening/softening soils and incorporates bonding and damage effects. The core of the proposed model includes: a hierarchical single surface critical state framework, sub-loading concepts for modeling the plastic strains generally observed inside the yield surface and a hydrate enhancement factor to account for the cementing effects provided by the presence of hydrates in sediments. The proposed framework has been validated against recently published experiments involving both, synthetic and natural hydrate soils, as well as different sediments types (i.e., different hydrate saturations, and different hydrates morphologies) and confinement conditions. The performance of the model in these different case studies was very satisfactory.

Removal of Heavy Metal Ions with Acid Activated Carbons Derived from Oil Palm and Coconut Shells

PubMed Central

Rahman, Mokhlesur M.; Adil, Mohd; Yusof, Alias M.; Kamaruzzaman, Yunus B.; Ansary, Rezaul H.

2014-01-01

In this work, batch adsorption experiments were carried out to investigate the suitability of prepared acid activated carbons in removing heavy metal ions such as nickel(II), lead(II) and chromium(VI). Acid activated carbons were obtained from oil palm and coconut shells using phosphoric acid under similar activation process while the differences lie either in impregnation condition or in both pretreatment and impregnation conditions. Prepared activated carbons were modified by dispersing hydrated iron oxide. The adsorption equilibrium data for nickel(II) and lead(II) were obtained from adsorption by the prepared and commercial activated carbons. Langmuir and Freundlich models fit the data well. Prepared activated carbons showed higher adsorption capacity for nickel(II) and lead(II). The removal of chromium(VI) was studied by the prepared acid activated, modified and commercial activated carbons at different pH. The isotherms studies reveal that the prepared activated carbon performs better in low concentration region while the commercial ones in the high concentration region. Thus, a complete adsorption is expected in low concentration by the prepared activated carbon. The kinetics data for Ni(II), Pb(II) and Cr(VI) by the best selected activated carbon fitted very well to the pseudo-second-order kinetic model. PMID:28788640

Surfactant Effect on Hydrate Crystallization at the Oil-Water Interface.

PubMed

Dann, Kevin; Rosenfeld, Liat

2018-05-29

Gas hydrates pose economic and environmental risks to the oil and gas industry when plug formation occurs in pipelines. A novel approach was applied to understand cyclopentane clathrate hydrate formation in the presence of nonionic surfactant to achieve hydrate inhibition at low percent weight compared to thermodynamic inhibitors. The hydrate-inhibiting performance of low (CMC) concentrations of Span 20, Span 80, Pluronic L31, and Tween 65 at 2 °C on a manually nucleated 2 μL droplet showed a morphological shift in crystallization from planar shell growth to conical growth. Monitoring the internal pressure of the water droplet undergoing hydrate crystallization provides information on the change in interfacial tension during the crystallization process. The results of this study will provide information on the surfactant effect on hydrate crystallization and inhibition. At low surfactant concentrations (below CMC), a planar hydrate crystal was formed. Decreasing interfacial tension was observed, which can be related to the shrinking area of the water-cyclopentane interface. At high surfactant concentration, the crystal morphology was shifted to conical. Interfacial tension measurements reveal oscillations of the interfacial tension during the crystallization process. The oscillations of the interfacial tension result from the fact that once the crystal has reached a critical size a portion of the cone breaks free from the droplet surface, which results in a sudden increase in the available surface for the surfactant molecules. Hence, a temporary increase in the interfacial tension can be observed. The oscillatory behavior of the interfacial tension is a result of the growth and release of the hydrate cones from the surface of the droplet. We have found that the most efficient surfactant in hydrate inhibition would be the one with HLB closest to 10 (equal hydrophilic-hydrophobic parts). In this way, the surfactant molecules will stay at the interface as they observe equal affinities for both the oil and water phases. Surfactant molecules that have the strongest affinity to the interface will be able to inhibit the growth of the crystal as they will force the cones to break and will not allow them to grow.

Water permeability in hydrate-bearing sediments: A pore-scale study

NASA Astrophysics Data System (ADS)

Dai, Sheng; Seol, Yongkoo

2014-06-01

Permeability is a critical parameter governing methane flux and fluid flow in hydrate-bearing sediments; however, limited valid data are available due to experimental challenges. Here we investigate the relationship between apparent water permeability (k') and hydrate saturation (Sh), accounting for hydrate pore-scale growth habit and meso-scale heterogeneity. Results from capillary tube models rely on cross-sectional tube shapes and hydrate pore habits, thus are appropriate only for sediments with uniform hydrate distribution and known hydrate pore character. Given our pore network modeling results showing that accumulating hydrate in sediments decreases sediment porosity and increases hydraulic tortuosity, we propose a modified Kozeny-Carman model to characterize water permeability in hydrate-bearing sediments. This model agrees well with experimental results and can be easily implemented in reservoir simulators with no empirical variables other than Sh. Results are also relevant to flow through other natural sediments that undergo diagenesis, salt precipitation, or bio-clogging.

Economic geology of natural gas hydrate

USGS Publications Warehouse

Max, M.D.; Johnson, A.H.; Dillon, William P.

2006-01-01

This is the first book that attempts to broadly integrate the most recent knowledge in the fields of hydrate nucleation and growth in permafrost regions and marine sediments. Gas hydrate reactant supply, growth models, and implications for pore fill by natural gas hydrate are discussed for both seawater precursors in marine sediments and for permafrost hydrate. These models for forming hydrate concentrations that will constitute targets for exploration are discussed, along with exploration methods. Thermodynamic models for the controlled conversion of hydrate to natural gas, which can be recovered using conventional industry practices, suggest that a number of different types of hydrate occurrence are likely to be practical sources of hydrate natural gas. Current progress in the various aspects of commercial development of hydrate gas deposits are discussed, along with the principal extractive issues that have yet to be resolved.

Methane Hydrate Recovered From A Mud Volcano in Santa Monica Basin, Offshore Southern California

NASA Astrophysics Data System (ADS)

Normark, W. R.; Hein, J. R.; Powell, C. L.; Lorenson, T. D.; Lee, H. J.; Edwards, B. D.

2003-12-01

In July 2003, a short (2.1 m) piston core from the summit of a mud volcano recovered methane hydrate at a water depth of 813 m in Santa Monica Basin. The discovery core penetrated into in the hydrate as evidenced by chunks of ice and violent degassing of the core section between 162 and 212 cm depth. The core consists of shell hash and carbonate clasts (to 7-cm long) in silty mud. The methanogenic carbonates are of two types: massive, recrystallized nodular masses with an outer mm-thick sugary patina and a bivalve coquina with carbonate cement. Living clams including the genus Vesicomya, commonly found at cold-seep sites elsewhere, were recovered from the top of the core. Further sampling attempts using piston, gravity, and box corers, all of which were obtained within 15 m of the discovery core, recovered olive-brown silty mud with variable amounts of whole and fragmented bivalve shells and methanogenic carbonate fragments characteristic of cold-seep environments. Gases collected in cores adjacent to the discovery core contain elevated amounts of methane and trace amounts of heavier hydrocarbon gases, indicating some component from thermogenic sources. Hydrogen sulfide was also detected in these sediment samples. Vertical channels in one core may have served as fluid pathways. The existence of hydrate at such a shallow depth in the sediment was unexpected, however, the presence of Vesicomya and hydrogen sulfide indicate that the mud volcano is a site of active methane venting. The mud volcano, which is about 24 km west-southwest of Redondo Beach, is about 300 m in diameter at the base. No internal structure is resolved on either high resolution deep-tow boomer or single-channel air-gun profiles, most likely as a result of the gas content and sediment deformation. The diapiric structure has ascended through well-bedded sediment on the lower slope of the basin, producing as much as 30 m of bathymetric relief. It is located in an area where strike-slip motion along the San Pedro Basin fault zone to the south is replaced by convergent motion to the north. The source horizon for the gas in the hydrate is unknown but appears to be collecting in beds as shallow as 200 m below the regional seafloor based on the presence of a strong and irregular reflection interval.

Gas Hydrate Estimation Using Rock Physics Modeling and Seismic Inversion

NASA Astrophysics Data System (ADS)

Dai, J.; Dutta, N.; Xu, H.

2006-05-01

ABSTRACT We conducted a theoretical study of the effects of gas hydrate saturation on the acoustic properties (P- and S- wave velocities, and bulk density) of host rocks, using wireline log data from the Mallik wells in the Mackenzie Delta in Northern Canada. We evaluated a number of gas hydrate rock physics models that correspond to different rock textures. Our study shows that, among the existing rock physics models, the one that treats gas hydrate as part of the solid matrix best fits the measured data. This model was also tested on gas hydrate hole 995B of ODP leg 164 drilling at Blake Ridge, which shows adequate match. Based on the understanding of rock models of gas hydrates and properties of shallow sediments, we define a procedure that quantifies gas hydrate using rock physics modeling and seismic inversion. The method allows us to estimate gas hydrate directly from seismic information only. This paper will show examples of gas hydrates quantification from both 1D profile and 3D volume in the deepwater of Gulf of Mexico.

Revisiting a many-body model for water based on a single polarizable site: from gas phase clusters to liquid and air/liquid water systems.

PubMed

Réal, Florent; Vallet, Valérie; Flament, Jean-Pierre; Masella, Michel

2013-09-21

We present a revised version of the water many-body model TCPE [M. Masella and J.-P. Flament, J. Chem. Phys. 107, 9105 (1997)], which is based on a static three charge sites and a single polarizable site to model the molecular electrostatic properties of water, and on an anisotropic short range many-body energy term specially designed to accurately model hydrogen bonding in water. The parameters of the revised model, denoted TCPE/2013, are here developed to reproduce the ab initio energetic and geometrical properties of small water clusters (up to hexamers) and the repulsive water interactions occurring in cation first hydration shells. The model parameters have also been refined to reproduce two liquid water properties at ambient conditions, the density and the vaporization enthalpy. Thanks to its computational efficiency, the new model range of applicability was validated by performing simulations of liquid water over a wide range of temperatures and pressures, as well as by investigating water liquid/vapor interfaces over a large range of temperatures. It is shown to reproduce several important water properties at an accurate enough level of precision, such as the existence liquid water density maxima up to a pressure of 1000 atm, the water boiling temperature, the properties of the water critical point (temperature, pressure, and density), and the existence of a "singularity" temperature at about 225 K in the supercooled regime. This model appears thus to be particularly well-suited for characterizing ion hydration properties under different temperature and pressure conditions, as well as in different phases and interfaces.

Simulation of water solutions of Ni 2+ at infinite dilution

NASA Astrophysics Data System (ADS)

Natália, M.; Cordeiro, D. S.; Ignaczak, Anna; Gomes, José A. N. F.

1993-10-01

A new ab initio pair potential is developed to describe the nickel—water interactions in Ni(II) aqueous solutions. Results of Monte Carlo simulations for the Ni(II)(H 2O) 200 system are presented for this pair potential with and without three-body classical polarization terms (the water—water interaction is described by the ab initio MCY potential). The structure of the solution around Ni(II) is discussed in terms of radial distribution functions, coordination numbers and thermal ellipsoids. The results show that the three-body terms have a non-negligible effect on the simulated solution. In fact, the experimental coordination number of six is reproduced with the full potential while a higher value is predicted when the simple pairwise-additive potential is used. The equilibrium NiO distance for the first hydration shell is also dependent on the use of the three-body terms. Comparison of our distribution functions with those obtained by neutron-diffraction experiments shows a reasonable quantitative agreement. Statistical pattern recognition analysis has also been applied to our simulations in order to better understand the local thermal motion of the water molecules around the metal ion. In this way, thermal ellipsoids have been computed (and graphically displayed) for each atom of the water molecules belonging to the Ni(II) first hydration shell. This analysis revealed that the twisting and bending motions are greater than the radial motion, and that the hydrogens have a higher mobility than the oxygens. In addition, a thermodynamic perturbation method has been incorporated in our Monte Carlo procedure in order to compute the free energy of hydration for the Ni(II) ion. Agreement between these results and the experimental ones is also sufficiently reasonable to demonstrate the feasibility of this new potential for the nickel—water interactions.

Hydrate-CASM for modeling Methane Hydrate-Bearing Sediments

NASA Astrophysics Data System (ADS)

De La Fuente Ruiz, M.; Vaunat, J.; Marin Moreno, H.

2017-12-01

A clear understanding of the geomechanical behavior of methane hydrate-bearing sediments (MHBS) is crucial to assess the stability of the seafloor and submarine infrastructures to human and natural loading changes. Here we present the Hydrate-CASM, a new elastoplastic constitutive model to predict the geomechanical behavior of MHBS. Our model employs the critical state model CASM (Clay and Sand Model) because of its flexibility in describing the shape of the yield surface and its proven ability to predict the mechanical behavior of sands, the most commercially viable hydrate reservoirs. The model considers MHBS as a deformable elastoplastic continuum, and hydrate-related changes in the stress-strain behavior are predicted by a densification mechanism. The densification attributes the mechanical contribution of hydrate to; a reduction of the available void ratio; a decrease of the swelling line slope; and an increase of the volumetric yield stress. It is described by experimentally derived physical parameters except from the swelling slope coefficient that requires empirical calibration. The Hydrate-CASM is validated against published triaxial laboratory tests performed at different confinement stresses, hydrate saturations, and hydrate morphologies. During the validation, we focused on capturing the mechanical behavior of the host sediment and consider perturbations of the sediment's mechanical properties that could result from the sample preparation. Our model successfully captures the experimentally observed influence of hydrate saturation in the magnitude and trend of the stiffness, shear strength, and dilatancy of MHBS. Hence, we propose that hydrate-related densification changes might be a major factor controlling the geomechanical response of MHBS.

Molecular Friction-Induced Electroosmotic Phenomena in Thin Neutral Nanotubes.

PubMed

Vuković, Lela; Vokac, Elizabeth; Král, Petr

2014-06-19

We reveal by classical molecular dynamics simulations electroosmotic flows in thin neutral carbon (CNT) and boron nitride (BNT) nanotubes filled with ionic solutions of hydrated monovalent atomic ions. We observe that in (12,12) BNTs filled with single ions in an electric field, the net water velocity increases in the order of Na(+) < K(+) < Cl(-), showing that different ions have different power to drag water in thin nanotubes. However, the effect gradually disappears in wider nanotubes. In (12,12) BNTs containing neutral ionic solutions in electric fields, we observe net water velocities going in the direction of Na(+) for (Na(+), Cl(-)) and in the direction of Cl(-) for (K(+), Cl(-)). We hypothesize that the electroosmotic flows are caused by different strengths of friction between ions with different hydration shells and the nanotube walls.

Gas Hydrate Stability at Low Temperatures and High Pressures with Applications to Mars and Europa

NASA Technical Reports Server (NTRS)

Marion, G. M.; Kargel, J. S.; Catling, D. C.

2004-01-01

Gas hydrates are implicated in the geochemical evolution of both Mars and Europa [1- 3]. Most models developed for gas hydrate chemistry are based on the statistical thermodynamic model of van der Waals and Platteeuw [4] with subsequent modifications [5-8]. None of these models are, however, state-of-the-art with respect to gas hydrate/electrolyte interactions, which is particularly important for planetary applications where solution chemistry may be very different from terrestrial seawater. The objectives of this work were to add gas (carbon dioxide and methane) hydrate chemistries into an electrolyte model parameterized for low temperatures and high pressures (the FREZCHEM model) and use the model to examine controls on gas hydrate chemistries for Mars and Europa.

Gas hydrate saturations estimated from pore-and fracture-filling gas hydrate reservoirs in the Qilian Mountain permafrost, China.

PubMed

Xiao, Kun; Zou, Changchun; Lu, Zhenquan; Deng, Juzhi

2017-11-24

Accurate calculation of gas hydrate saturation is an important aspect of gas hydrate resource evaluation. The effective medium theory (EMT model), the velocity model based on two-phase medium theory (TPT model), and the two component laminated media model (TCLM model), are adopted to investigate the characteristics of acoustic velocity and gas hydrate saturation of pore- and fracture-filling reservoirs in the Qilian Mountain permafrost, China. The compressional wave (P-wave) velocity simulated by the EMT model is more consistent with actual log data than the TPT model in the pore-filling reservoir. The range of the gas hydrate saturation of the typical pore-filling reservoir in hole DKXX-13 is 13.0~85.0%, and the average value of the gas hydrate saturation is 61.9%, which is in accordance with the results by the standard Archie equation and actual core test. The P-wave phase velocity simulated by the TCLM model can be transformed directly into the P-wave transverse velocity in a fracture-filling reservoir. The range of the gas hydrate saturation of the typical fracture-filling reservoir in hole DKXX-19 is 14.1~89.9%, and the average value of the gas hydrate saturation is 69.4%, which is in accordance with actual core test results.

Surfactants at Single-Walled Carbon Nanotube-Water Interface: Physics of Surfactants, Counter-Ions, and Hydration Shell

NASA Astrophysics Data System (ADS)

Khare, Ketan S.; Phelan, Frederick R., Jr.

Specialized applications of single-walled carbon nanotubes (SWCNTs) require an efficient and reliable method to sort these materials into monodisperse fractions with respect to their defining metrics (chirality, length, etc.) while retaining their physical and chemical integrity. A popular method to achieve this goal is to use surfactants that individually disperse SWCNTs in water and then to separate the resulting colloidal mixture into fractions that are enriched in monodisperse SWCNTs. Recently, experiments at NIST have shown that subtle point mutations of chemical groups in bile salt surfactants have a large impact on the hydrodynamic properties of SWCNT-surfactant complexes during ultracentrifugation. These results provide strong motivation for understanding the rich physics underlying the assembly of surfactants around SWCNTs, the structure and dynamics of counter ions around the resulting complex, and propagation of these effects into the first hydration shell. Here, all-atom molecular dynamics simulations are used to investigate the thermodynamics of SWCNT-bile salt surfactant complexes in water with an emphasis on the buoyant characteristics of the SWCNT-surfactant complexes. Simulation results will be presented along with a comparison with experimental data. Official contribution of the National Institute of Standards and Technology; not subject to copyright in the United States.

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

PubMed Central

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

2015-01-01

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

O-H anharmonic vibrational motions in Cl(-)···(CH3OH)(1-2) ionic clusters. Combined IRPD experiments and AIMD simulations.

PubMed

Beck, Jordan P; Cimas, Alvaro; Lisy, James M; Gaigeot, Marie-Pierre

2014-02-05

The structures of Cl(-)-(Methanol)1,2 clusters have been unraveled combining Infrared Predissociation (IR-PD) experiments and DFT-based molecular dynamics simulations (DFT-MD) at 100 K. The dynamical IR spectra extracted from DFT-MD provide the initial 600 cm(-1) large anharmonic red-shift of the O-H stretch from uncomplexed methanol (3682 cm(-1)) to Cl(-)-(Methanol)1 complex (3085 cm(-1)) as observed in the IR-PD experiment, as well as the subtle supplementary blue- and red-shifts of the O-H stretch in Cl(-)-(Methanol)2 depending on the structure. The anharmonic vibrational calculations remarkably provide the 100 cm(-1) O-H blue-shift when the two methanol molecules are simultaneously organized in the anion first hydration shell (conformer 2A), while they provide the 240 cm(-1) O-H red-shift when the second methanol is in the second hydration shell of Cl(-) (conformer 2B). RRKM calculations have also shown that 2A/2B conformers interconvert on a nanosecond time-scale at the estimated 100 K temperature of the clusters formed by evaporative cooling of argon prior to the IR-PD process. Copyright © 2013 Elsevier B.V. All rights reserved.

High-Order Ca(II)-Chloro Complexes in Mixed CaCl2-LiCl Aqueous Solution: Insights from Density Functional Theory and Molecular Dynamics Simulations.

PubMed

Wang, Yu-Lin; Wang, Ying; Yi, Hai-Bo

2016-07-21

In this study, the structural characteristics of high-coordinated Ca-Cl complexes present in mixed CaCl2-LiCl aqueous solution were investigated using density functional theory (DFT) and molecular dynamics (MD) simulations. The DFT results show that [CaClx](2-x) (x = 4-6) clusters are quite unstable in the gas phase, but these clusters become metastable when hydration is considered. The MD simulations show that high-coordinated Ca-chloro complexes are possible transient species that exist for up to nanoseconds in concentrated (11.10 mol·kg(-1)) Cl(-) solution at 273 and 298 K. As the temperature increases to 423 K, these high-coordinated structures tend to disassociate and convert into smaller clusters and single free ions. The presence of high-order Ca-Cl species in concentrated LiCl solution can be attributed to their enhanced hydration shell and the inadequate hydration of ions. The probability of the [CaClx](2-x)aq (x = 4-6) species being present in concentrated LiCl solution decreases greatly with increasing temperature, which also indicates that the formation of the high-coordinated Ca-Cl structure is related to its hydration characteristics.

Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

NASA Astrophysics Data System (ADS)

Coridan, Robert H.; Schmidt, Nathan W.; Lai, Ghee Hwee; Abbamonte, Peter; Wong, Gerard C. L.

2012-03-01

Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å).

Dynamics of Uncrystallized Water, Ice, and Hydrated Protein in Partially Crystallized Gelatin-Water Mixtures Studied by Broadband Dielectric Spectroscopy.

PubMed

Sasaki, Kaito; Panagopoulou, Anna; Kita, Rio; Shinyashiki, Naoki; Yagihara, Shin; Kyritsis, Apostolos; Pissis, Polycarpos

2017-01-12

The glass transition of partially crystallized gelatin-water mixtures was investigated using broadband dielectric spectroscopy (BDS) over a wide range of frequencies (10 mHz to 10 MHz), temperatures (113-298 K), and concentrations (10-45 wt %). Three dielectric relaxation processes (processes I, II, and III) were clearly observed. Processes I, II, and III originate from uncrystallized water (UCW) in the hydration shells of gelatin, ice, and hydrated gelatin, respectively. A dynamic crossover, called the Arrhenius to non-Arrhenius transition of UCW, was observed at the glass transition temperature of the relaxation process of hydrated gelatin for all mixtures. The amount of UCW increases with increasing gelatin content. However, above 35 wt % gelatin, the amount of UCW became more dependent on the gelatin concentration. This increase in UCW causes a decrease in the glass transition temperature of the cooperative motion of gelatin and UCW, which appears to result from a change in the aggregation structure of gelatin in the mixture at a gelatin concentration of approximately 35 wt %. The temperature dependence of the relaxation time of process II has nearly the same activation energy as pure ice made by slow crystallization of ice Ih. This implies that process II originates from the dynamics of slowly crystallized ice Ih.

Study of transmittance and reflectance spectra of the cornea and the sclera in the THz frequency range

NASA Astrophysics Data System (ADS)

Iomdina, Elena N.; Goltsman, Gregory N.; Seliverstov, Sergey V.; Sianosyan, Alisa A.; Teplyakova, Kseniya O.; Rusova, Anastasia A.

2016-09-01

An adequate water balance (hydration extent) is one of the basic factors of normal eye function, including its external shells: the cornea and the sclera. Adequate control of corneal and scleral hydration is very important for early diagnosis of a variety of eye diseases, stating indications for and contraindications against keratorefractive surgeries and the choice of contact lens correction solutions. THz systems of creating images in reflected beams are likely to become ideal instruments of noninvasive control of corneal and scleral hydration degrees. This paper reports on the results of a study involving transmittance and reflectance spectra for the cornea and the sclera of rabbit and human eyes, as well as those of the rabbit eye, in the frequency range of 0.13 to 0.32 THz. The dependence of the reflectance coefficient of these tissues on water mass percentage content was determined. The experiments were performed on three corneas, three rabbit scleras, two rabbit eyes, and three human scleras. The preliminary results demonstrate that the proposed technique, based on the use of a continuous THz radiation, may be utilized to create a device for noninvasive control of corneal and scleral hydration, which has clear potential of broad practical application.

Modeling dynamic accumulation of gas hydrates in Shenhu area, northern South China Sea

NASA Astrophysics Data System (ADS)

Su, Z.; Cao, Y.; Wu, N.

2013-12-01

The accumulation of the hydrates in Shenhu area on northern continental slope of the South China Sea (SCS) could not be well quantified by the numerical models. The formation mechanism of the hydrate deposits remains an open question. Here, a conceptual model was applied for illustrating the formation pattern of hydrate accumulation in Shenhu area based on the studies of sedimentary and tectonic geologies. Our results indicated that the present hydrate deposits were a development of 'ancient hydrates' in the faulted sediment. The dynamic accumulation of the hydrates was further quantified by using a numerical model with two controlling parameters of seafloor sedimentation rate and water flow rate. The model results were testified with the hydrate saturations derived from the chloride abnormalities at site SH2 in Shenhu area. It suggested that the hydrate accumulation in Shenhu area had experienced two typical stages. In the first stage, the gas hydrates grew in the fractured sediment ~1.5 Ma. High permeability of the fractured sediment permitted rapid water flow that carrying methane gas toward the seafloor. Massive gas transformed to gas hydrate in the gas hydrate stability zone (GHSZ) at water flow rate of 50m/kyr within 40kyrs. The 'ancient hydrate' filled 20% volume of the sediment pores in the stage. The second stage was initiated after ending of the last faulting activity. The water flow rate dropped to 0.7m/kyr due to quick burial of fine-grained sediments. Inadequate gas supply could merely sustain hydrate growth slowly at the base of GHSZ, and ultimately yielded the current hydrate deposits in Shenhu area after a subsequent evolution of 1.5 Myrs.

Two-state protein model with water interactions: Influence of temperature on the intrinsic viscosity of myoglobin

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

Bakk, Audun

2001-06-01

We describe a single-domain protein as a two-state system with water interactions. Around the unfolded apolar parts of the protein we incorporate the hydration effect by introducing hydrogen bonds between the water molecules in order to mimic the {open_quotes}icelike{close_quotes} shell structure. Intrinsic viscosity, proportional to the effective hydrodynamic volume, for sperm whale metmyoglobin is assigned from experimental data in the folded and in the denaturated state. By weighing statistically the two states against the degree of folding, we express the total intrinsic viscosity. The temperature dependence of the intrinsic viscosity, for different chemical potentials, is in good correspondence with experimentalmore » data [P. L. Privalov , J. Mol. Biol. >190, 487 (1986)]. Cold and warm unfolding, common to small globular proteins, is also a result of the model.« less

Multi-scale model for the hierarchical architecture of native cellulose hydrogels.

PubMed

Martínez-Sanz, Marta; Mikkelsen, Deirdre; Flanagan, Bernadine; Gidley, Michael J; Gilbert, Elliot P

2016-08-20

The structure of protiated and deuterated cellulose hydrogels has been investigated using a multi-technique approach combining small-angle scattering with diffraction, spectroscopy and microscopy. A model for the multi-scale structure of native cellulose hydrogels is proposed which highlights the essential role of water at different structural levels characterised by: (i) the existence of cellulose microfibrils containing an impermeable crystalline core surrounded by a partially hydrated paracrystalline shell, (ii) the creation of a strong network of cellulose microfibrils held together by hydrogen bonding to form cellulose ribbons and (iii) the differential behaviour of tightly bound water held within the ribbons compared to bulk solvent. Deuterium labelling provides an effective platform on which to further investigate the role of different plant cell wall polysaccharides in cellulose composite formation through the production of selectively deuterated cellulose composite hydrogels. Copyright © 2016 Elsevier Ltd. All rights reserved.

Models for Gas Hydrate-Bearing Sediments Inferred from Hydraulic Permeability and Elastic Velocities

USGS Publications Warehouse

Lee, Myung W.

2008-01-01

Elastic velocities and hydraulic permeability of gas hydrate-bearing sediments strongly depend on how gas hydrate accumulates in pore spaces and various gas hydrate accumulation models are proposed to predict physical property changes due to gas hydrate concentrations. Elastic velocities and permeability predicted from a cementation model differ noticeably from those from a pore-filling model. A nuclear magnetic resonance (NMR) log provides in-situ water-filled porosity and hydraulic permeability of gas hydrate-bearing sediments. To test the two competing models, the NMR log along with conventional logs such as velocity and resistivity logs acquired at the Mallik 5L-38 well, Mackenzie Delta, Canada, were analyzed. When the clay content is less than about 12 percent, the NMR porosity is 'accurate' and the gas hydrate concentrations from the NMR log are comparable to those estimated from an electrical resistivity log. The variation of elastic velocities and relative permeability with respect to the gas hydrate concentration indicates that the dominant effect of gas hydrate in the pore space is the pore-filling characteristic.

Theoretical study of gas hydrate decomposition kinetics: model predictions.

PubMed

Windmeier, Christoph; Oellrich, Lothar R

2013-11-27

In order to provide an estimate of intrinsic gas hydrate dissolution and dissociation kinetics, the Consecutive Desorption and Melting Model (CDM) was developed in a previous publication (Windmeier, C.; Oellrich, L. R. J. Phys. Chem. A 2013, 117, 10151-10161). In this work, an extensive summary of required model data is given. Obtained model predictions are discussed with respect to their temperature dependence as well as their significance for technically relevant areas of gas hydrate decomposition. As a result, an expression for determination of the intrinsic gas hydrate decomposition kinetics for various hydrate formers is given together with an estimate for the maximum possible rates of gas hydrate decomposition.

Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

PubMed

Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

2017-06-13

We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

Estimation of potential distribution of gas hydrate in the northern South China Sea

NASA Astrophysics Data System (ADS)

Wang, Chunjuan; Du, Dewen; Zhu, Zhiwei; Liu, Yonggang; Yan, Shijuan; Yang, Gang

2010-05-01

Gas hydrate research has significant importance for securing world energy resources, and has the potential to produce considerable economic benefits. Previous studies have shown that the South China Sea is an area that harbors gas hydrates. However, there is a lack of systematic investigations and understanding on the distribution of gas hydrate throughout the region. In this paper, we applied mineral resource quantitative assessment techniques to forecast and estimate the potential distribution of gas hydrate resources in the northern South China Sea. However, current hydrate samples from the South China Sea are too few to produce models of occurrences. Thus, according to similarity and contrast principles of mineral outputs, we can use a similar hydrate-mining environment with sufficient gas hydrate data as a testing ground for modeling northern South China Sea gas hydrate conditions. We selected the Gulf of Mexico, which has extensively studied gas hydrates, to develop predictive models of gas hydrate distributions, and to test errors in the model. Then, we compared the existing northern South China Sea hydrate-mining data with the Gulf of Mexico characteristics, and collated the relevant data into the model. Subsequently, we applied the model to the northern South China Sea to obtain the potential gas hydrate distribution of the area, and to identify significant exploration targets. Finally, we evaluated the reliability of the predicted results. The south seabed area of Taiwan Bank is recommended as a priority exploration target. The Zhujiang Mouth, Southeast Hainan, and Southwest Taiwan Basins, including the South Bijia Basin, also are recommended as exploration target areas. In addition, the method in this paper can provide a useful predictive approach for gas hydrate resource assessment, which gives a scientific basis for construction and implementation of long-term planning for gas hydrate exploration and general exploitation of the seabed of China.

Water Mediated Ligand Functional Group Cooperativity: The Contribution of a Methyl Group to Binding Affinity is Enhanced by a COO− Group Through Changes in the Structure and Thermo dynamics of the Hydration Waters of Ligand-Thermolysin Complexes

PubMed Central

Nasief, Nader N; Tan, Hongwei; Kong, Jing; Hangauer, David

2012-01-01

Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2′ pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO− reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2′ pocket, and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding. PMID:22894131

Hydration properties of adenosine phosphate series as studied by microwave dielectric spectroscopy.

PubMed

Mogami, George; Wazawa, Tetsuichi; Morimoto, Nobuyuki; Kodama, Takao; Suzuki, Makoto

2011-02-01

Hydration properties of adenine nucleotides and orthophosphate (Pi) in aqueous solutions adjusted to pH=8 with NaOH were studied by high-resolution microwave dielectric relaxation (DR) spectroscopy at 20 °C. The dielectric spectra were analyzed using a mixture theory combined with a least-squares Debye decomposition method. Solutions of Pi and adenine nucleotides showed qualitatively similar dielectric properties described by two Debye components. One component was characterized by a relaxation frequency (f(c)=18.8-19.7 GHz) significantly higher than that of bulk water (17 GHz) and the other by a much lower f(c) (6.4-7.6 GHz), which are referred to here as hyper-mobile water and constrained water, respectively. By contrast, a hydration shell of only the latter type was found for adenosine (f(c)~6.7 GHz). The present results indicate that phosphoryl groups are mostly responsible for affecting the structure of the water surrounding the adenine nucleotides by forming one constrained water layer and an additional three or four layers of hyper-mobile water. Copyright © 2010 Elsevier B.V. All rights reserved.

Function and biotechnology of extremophilic enzymes in low water activity

PubMed Central

2012-01-01

Enzymes from extremophilic microorganisms usually catalyze chemical reactions in non-standard conditions. Such conditions promote aggregation, precipitation, and denaturation, reducing the activity of most non-extremophilic enzymes, frequently due to the absence of sufficient hydration. Some extremophilic enzymes maintain a tight hydration shell and remain active in solution even when liquid water is limiting, e.g. in the presence of high ionic concentrations, or at cold temperature when water is close to the freezing point. Extremophilic enzymes are able to compete for hydration via alterations especially to their surface through greater surface charges and increased molecular motion. These properties have enabled some extremophilic enzymes to function in the presence of non-aqueous organic solvents, with potential for design of useful catalysts. In this review, we summarize the current state of knowledge of extremophilic enzymes functioning in high salinity and cold temperatures, focusing on their strategy for function at low water activity. We discuss how the understanding of extremophilic enzyme function is leading to the design of a new generation of enzyme catalysts and their applications to biotechnology. PMID:22480329

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution.

PubMed

Lanaro, G; Patey, G N

2018-01-14

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (∼49 kJ mol -1 ) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li + and F - ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

The influence of ion hydration on nucleation and growth of LiF crystals in aqueous solution

NASA Astrophysics Data System (ADS)

Lanaro, G.; Patey, G. N.

2018-01-01

Molecular dynamics (MD) simulations are employed to investigate crystal nucleation and growth in oversaturated aqueous LiF solutions. Results obtained for a range of temperatures provide evidence that the rate of crystal growth is determined by a substantial energy barrier (˜49 kJ mol-1) related to the loss of water from the ion hydration shells. Employing direct MD simulations, we do not observe spontaneous nucleation of LiF crystals at 300 K, but nucleation is easily observable in NVT simulations at 500 K. This contrasts with the NaCl case, where crystal nucleation is directly observed in similar simulations at 300 K. Based on these observations, together with a detailed analysis of ion clustering in metastable LiF solutions, we argue that the ion dehydration barrier also plays a key role in crystal nucleation. The hydration of the relatively small Li+ and F- ions strongly influences the probability of forming large, crystal-like ion clusters, which are a necessary precursor to nucleation. This important factor is not accounted for in classical nucleation theory.

Evaluation of Gas Hydrate at Alaminos Canyon 810, Northern Gulf of Mexico Slope

NASA Astrophysics Data System (ADS)

Yang, C.; Cook, A.; Sawyer, D.; Hillman, J. I. T.

2016-12-01

We characterize the gas hydrate reservoir in Alaminos Canyon Block 810 (AC810) on the northern Gulf of Mexico slope, approximately 400 km southeast of Houston, Texas, USA. Three-dimensional seismic data shows a bottom-simulating-reflection (BSR), over 30 km2, which suggests that a significant gas hydrate accumulation may occur at AC810. Furthermore, logging while drilling (LWD) data acquired from a Statoil well located that penetrated the BSR near the crest of the regional anticline indicates two possible gas hydrate units (Hydrate Unit A and Hydrate Unit B). LWD data in this interval are limited to gamma ray and resistivity only. Resistivity curve separations are observed in Hydrate Unit A (131 to 253 mbsf) suggesting hydrate-filled fractures in marine mud. A spiky high resistivity response in Hydrate Unit B (308 to 354 mbsf) could either be a marine mud or a sand-prone interval. The abrupt decrease (from 7 to 1 Ωm) in resistivity logs at 357 mbsf generally corresponds with the interpreted base of hydrate stability, as the BSR is observed near 350 mbsf on the seismic data. To further investigate the formation characteristics, we generate synthetic traces using general velocity and density trends for marine sediments to match the seismic trace extracted at the Statoil well. We consider models with 1) free gas and 2) water only below the base of hydrate stability. In our free gas-below models, we find the velocity of Hydrate Unit A and Hydrate Unit B is generally low and does not deviate significantly from the general velocity trends, suggesting that gas hydrate is present in a marine mud. In the water-below model, the compressional velocity of Hydrate Unit B ranges from 2450 m/s to 3150 m/s. This velocity is similar to the velocity of high hydrate saturation in sand; typically greater than 2500 m/s. This may indicate that Hydrate Unit B is sand with high hydrate saturation; however, to achieve a suitable match between the water-below synthetic seismogram and the trace, a high velocity layer was required below the base of hydrate stability, which is not indicated by the well logs. Our models indicate that at AC810, Hydrate Unit A probably contains hydrate filled fractures in a marine mud. For Hydrate Unit B, our models suggest hydrate may occur in a sand-prone interval, but is more likely to be gas hydrate filled fractures in marine mud.

Gas hydrate concentration and characteristics within Hydrate Ridge inferred from multicomponent seismic reflection data

NASA Astrophysics Data System (ADS)

Kumar, Dhananjay; Sen, Mrinal K.; Bangs, Nathan L.

2007-12-01

A seismic experiment composed of streamer and ocean bottom seismometer (OBS) surveys was conducted in the summer of 2002 at southern Hydrate Ridge, offshore Oregon, to map the gas hydrate distribution within the hydrate stability zone. Gas hydrate concentrations within the reservoir can be estimated with P wave velocity (Vp); however, we can further constrain gas hydrate concentrations using S wave velocity (Vs), and use Vs through its relationship to Vp (Vp/Vs) to reveal additional details such as gas hydrate form within the matrix (i.e., hydrate cements the grains, becomes part of the matrix frame or floats in pore space). Both Vp and Vs can be derived simultaneously by inverting multicomponent seismic data. In this study, we use OBS data to estimate seismic velocities where both gas hydrate and free gas are present in the shallow sediments. Once Vp and Vs are estimated, they are simultaneously matched with modeled velocities to estimate the gas hydrate concentration. We model Vp using an equation based on a modification of Wood's equation that incorporates an appropriate rock physics model and Vs using an empirical relation. The gas hydrate concentration is estimated to be up to 7% of the rock volume, or 12% of the pore space. However, Vp and Vs do not always fit the model simultaneously. Vp can vary substantially more than Vs. Thus we conclude that a model, in which higher concentrations of hydrate do not affect shear stiffness, is more appropriate. Results suggest gas hydrates form within the pore space of the sediments and become part of the rock framework in our survey area.

Complex Resistivity experiment of Methane Hydrate in Porous Media

NASA Astrophysics Data System (ADS)

Chen, Q.; Wang, C.

2017-12-01

Electric logging plays an important role in gas hydrate exploration and saturation estimation. However, due to the lack of specialized model, some classical models of petroleum industry were used to calculate the hydrate reserves such as Archie's law. But the widely used resistivity model is unable to characterize the electrical properties of hydrate bearing sediments comprehensively, while the complex resistivity method can reveal more details about the electric properties of gas hydrate porous media. In this paper, a series of electrochemical impedance spectroscope tests were carried out during methane hydrate formation and dissociation process in porous media with 3.5% brine. The hydrate saturation was controlled by decrease the pressure at certain temperature. At each saturation, complex resistivities with frequency of 0.1 Hz 1 MHz were acquired and the frequency dispersion characteristics were analyzed. Conclusion as below: 1. It exhibited remarkable frequency dispersion characteristics in hydrate porous media, especially when the frequency was below 10Hz. At certain hydrate saturation, the resistivity amplitude/real part/imaginary part decreased with frequency, but the resistivity variation trends were complicated with frequency: between 0.1- 2.3Hz, the resistivity amplitude and real part were decreased as hydrate saturation increasing; however when the frequency become higher, the resistivity were increased with hydrate saturation. 2. In the hydrate porous media test, the resistivity amplitude/real part/imaginary part didn't show a linear variation with hydrate saturation in the double logarithmic coordinate, so the Archie's law cannot get constant a, m parameters. Moreover, different frequency lead to different resistivity value at certain saturation, Archie's law parameters must be readjusted to certain logging method. 3. In this study the impedance spectroscopy of porous medium containing hydrate can be fitted through an equivalent circuit model with a resistor and capacitor in series, and the resultant complex resistivity model can be used to calculate the gas hydrate saturation which may provide a new way to predict hydrate reserves.

The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

PubMed

Dureckova, Hana; Woo, Tom K; Udachin, Konstantin A; Ripmeester, John A; Alavi, Saman

2017-10-13

Clathrate hydrate phases of Cl 2 and Br 2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl 2 and Br 2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl 2 and Br 2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Elastic velocity models for gas-hydrate-bearing sediments-a comparison

NASA Astrophysics Data System (ADS)

Chand, Shyam; Minshull, Tim A.; Gei, Davide; Carcione, José M.

2004-11-01

The presence of gas hydrate in oceanic sediments is mostly identified by bottom-simulating reflectors (BSRs), reflection events with reversed polarity following the trend of the seafloor. Attempts to quantify the amount of gas hydrate present in oceanic sediments have been based mainly on the presence or absence of a BSR and its relative amplitude. Recent studies have shown that a BSR is not a necessary criterion for the presence of gas hydrates, but rather its presence depends on the type of sediments and the in situ conditions. The influence of hydrate on the physical properties of sediments overlying the BSR is determined by the elastic properties of their constituents and on sediment microstructure. In this context several approaches have been developed to predict the physical properties of sediments, and thereby quantify the amount of gas/gas hydrate present from observed deviations of these properties from those predicted for sediments without gas hydrate. We tested four models: the empirical weighted equation (WE); the three-phase effective-medium theory (TPEM); the three-phase Biot theory (TPB) and the differential effective-medium theory (DEM). We compared these models for a range of variables (porosity and clay content) using standard values for physical parameters. The comparison shows that all the models predict sediment properties comparable to field values except for the WE model at lower porosities and the TPB model at higher porosities. The models differ in the variation of velocity with porosity and clay content. The variation of velocity with hydrate saturation is also different, although the range is similar. We have used these models to predict velocities for field data sets from sediment sections with and without gas hydrates. The first is from the Mallik 2L-38 well, Mackenzie Delta, Canada, and the second is from Ocean Drilling Program (ODP) Leg 164 on Blake Ridge. Both data sets have Vp and Vs information along with the composition and porosity of the matrix. Models are considered successful if predictions from both Vp and Vs match hydrate saturations inferred from other data. Three of the models predict consistent hydrate saturations of 60-80 per cent from both Vp and Vs from log and vertical seismic profiling data for the Mallik 2L-38 well data set, but the TPEM model predicts 20 per cent higher saturations, as does the DEM model with a clay-water starting medium. For the clay-rich sediments of Blake Ridge, the DEM, TPEM and WE models predict 10-20 per cent hydrate saturation from Vp data, comparable to that inferred from resistivity data. The hydrate saturation predicted by the TPB model from Vp is higher. Using Vs data, the DEM and TPEM models predict very low or zero hydrate saturation while the TPB and WE models predict hydrate saturation very much higher than those predicted from Vp data. Low hydrate saturations are observed to have little effect on Vs. The hydrate phase appears to be connected within the sediment microstructure even at low saturations.

The analysis of magnesium oxide hydration in three-phase reaction system

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

Tang, Xiaojia; Guo, Lin; Chen, Chen

In order to investigate the magnesium oxide hydration process in gas–liquid–solid (three-phase) reaction system, magnesium hydroxide was prepared by magnesium oxide hydration in liquid–solid (two-phase) and three-phase reaction systems. A semi-empirical model and the classical shrinking core model were used to fit the experimental data. The fitting result shows that both models describe well the hydration process of three-phase system, while only the semi-empirical model right for the hydration process of two-phase system. The characterization of the hydration product using X-Ray diffraction (XRD) and scanning electron microscope (SEM) was performed. The XRD and SEM show hydration process in the two-phasemore » system follows common dissolution/precipitation mechanism. While in the three-phase system, the hydration process undergo MgO dissolution, Mg(OH){sub 2} precipitation, Mg(OH){sub 2} peeling off from MgO particle and leaving behind fresh MgO surface. - Graphical abstract: There was existence of a peeling-off process in the gas–liquid–solid (three-phase) MgO hydration system. - Highlights: • Magnesium oxide hydration in gas–liquid–solid system was investigated. • The experimental data in three-phase system could be fitted well by two models. • The morphology analysis suggested that there was existence of a peel-off process.« less

An Analytical Solution and Numerical Modeling Study of Gas Hydrate Saturation Effects on Porosity and Permeability of Porous Media

NASA Astrophysics Data System (ADS)

Zerpa, L.; Gao, F.; Wang, S.

2017-12-01

There are two major types of natural gas hydrate distributions in porous media: pore filling and contact cementing. The difference between these two distribution types is related to hydrate nucleation and growth processes. In the pore filling distribution, hydrate nucleates from a gas-dissolved aqueous phase at the grain boundary and grows away from grain contacts and surfaces into the pore space. In the contact cementing distribution, hydrate nucleates and grows at the gas-water interface and at intergranular contacts. Previous attempts to correlate changes on porosity and permeability during hydrate formation/dissociation were based on the length difference between the pore body and pore throat, and only considered contact cementing hydrate distribution. This work consists of a study of mathematical models of permeability and porosity as a function of gas hydrate saturation during formation and dissociation of gas hydrates in porous media. In this work, first we derive the permeability equation for the pore filling hydrate deposition as a function of hydrate saturation. Then, a more comprehensive model considering both types of gas hydrate deposition is developed to represent changes in permeability and porosity during hydrate formation and dissociation. This resulted in a model that combines pore filling and contact cementing deposition types in the same reservoir. Finally, the TOUGH+Hydrate numerical reservoir simulator was modified to include these models to analyze the response of production and saturation during a depressurization process, considering different combinations of pore filling and contact cementing hydrate distributions. The empirical exponent used in the permeability adjustment factor model influences both production profile and saturation results. This empirical factor describes the permeability dependence to changes in porosity caused by solid phase formation in the porous medium. The use of the permeability exponent decreases the permeability of the system for a given hydrate saturation, which affects the hydraulic performance of the system. However, from published experimental work, there is only a rough estimation of this permeability exponent. This factor could be represented with an empirical equation if more laboratory and field data becomes available.

Synthesis of hydroxyapatite nanoparticles from egg shells by sol-gel method

NASA Astrophysics Data System (ADS)

Azis, Y.; Adrian, M.; Alfarisi, C. D.; Khairat; Sri, R. M.

2018-04-01

Hydroxyapatite, [Ca10(PO4)6(OH)2, (HAp)] is widely used in medical fields especially as a bone and teeth substitute. Hydroxyapatite nanoparticles have been succesfully synthesized from egg shells as a source of calcium by using sol-gel method. The egg shells were calcined, hydrated (slaking) and undergone carbonation to form Precipitated Calcium Carbonate (PCC).Then the PCC was added (NH4)2HPO4 to form HAp with variation the mole ratio Ca and P (1.57; 1.67 and 1.77), aging time (24, 48, and 72 hr) and under basic condition pH (9, 10 and 11). The formation of hydroxyapatite biomaterial was characterized using XRD, FTIR, SEM-EDX. The XRD patterns showed that the products were hydroxyapatite crystals. The best result was obtained at 24 hr aging time, pH 9 with hexagonal structure of hydroxyapatite. Particle size of HAp was 35-54 nm and the morphology of hydroxyapatite observed using SEM, it showed that the uniformity crystal of hydroxyapatite.

Physical properties and rock physics models of sediment containing natural and laboratory-formed methane gas hydrate

USGS Publications Warehouse

Winters, W.J.; Pecher, I.A.; Waite, W.F.; Mason, D.H.

2004-01-01

This paper presents results of shear strength and acoustic velocity (p-wave) measurements performed on: (1) samples containing natural gas hydrate from the Mallik 2L-38 well, Mackenzie Delta, Northwest Territories; (2) reconstituted Ottawa sand samples containing methane gas hydrate formed in the laboratory; and (3) ice-bearing sands. These measurements show that hydrate increases shear strength and p-wave velocity in natural and reconstituted samples. The proportion of this increase depends on (1) the amount and distribution of hydrate present, (2) differences, in sediment properties, and (3) differences in test conditions. Stress-strain curves from the Mallik samples suggest that natural gas hydrate does not cement sediment grains. However, stress-strain curves from the Ottawa sand (containing laboratory-formed gas hydrate) do imply cementation is present. Acoustically, rock physics modeling shows that gas hydrate does not cement grains of natural Mackenzie Delta sediment. Natural gas hydrates are best modeled as part of the sediment frame. This finding is in contrast with direct observations and results of Ottawa sand containing laboratory-formed hydrate, which was found to cement grains (Waite et al. 2004). It therefore appears that the microscopic distribution of gas hydrates in sediment, and hence the effect of gas hydrate on sediment physical properties, differs between natural deposits and laboratory-formed samples. This difference may possibly be caused by the location of water molecules that are available to form hydrate. Models that use laboratory-derived properties to predict behavior of natural gas hydrate must account for these differences.

Quasielastic small-angle neutron scattering from heavy water solutions of cyclodextrins

NASA Astrophysics Data System (ADS)

Kusmin, André; Lechner, Ruep E.; Saenger, Wolfram

2011-01-01

We present a model for quasielastic neutron scattering (QENS) by an aqueous solution of compact and inflexible molecules. This model accounts for time-dependent spatial pair correlations between the atoms of the same as well as of distinct molecules and includes all coherent and incoherent neutron scattering contributions. The extension of the static theory of the excluded volume effect [A. K. Soper, J. Phys.: Condens. Matter 9, 2399 (1997)] to the time-dependent (dynamic) case allows us to obtain simplified model expressions for QENS spectra in the low Q region in the uniform fluid approximation. The resulting expressions describe the quasielastic small-angle neutron scattering (QESANS) spectra of D _2O solutions of native and methylated cyclodextrins well, yielding in particular translational and rotational diffusion coefficients of these compounds in aqueous solution. Finally, we discuss the full potential of the QESANS analysis (that is, beyond the uniform fluid approximation), in particular, the information on solute-solvent interactions (e.g., hydration shell properties) that such an analysis can provide, in principle.

Methane hydrate formation in partially water-saturated Ottawa sand

USGS Publications Warehouse

Waite, W.F.; Winters, W.J.; Mason, D.H.

2004-01-01

Bulk properties of gas hydrate-bearing sediment strongly depend on whether hydrate forms primarily in the pore fluid, becomes a load-bearing member of the sediment matrix, or cements sediment grains. Our compressional wave speed measurements through partially water-saturated, methane hydrate-bearing Ottawa sands suggest hydrate surrounds and cements sediment grains. The three Ottawa sand packs tested in the Gas Hydrate And Sediment Test Laboratory Instrument (GHASTLI) contain 38(1)% porosity, initially with distilled water saturating 58, 31, and 16% of that pore space, respectively. From the volume of methane gas produced during hydrate dissociation, we calculated the hydrate concentration in the pore space to be 70, 37, and 20% respectively. Based on these hydrate concentrations and our measured compressional wave speeds, we used a rock physics model to differentiate between potential pore-space hydrate distributions. Model results suggest methane hydrate cements unconsolidated sediment when forming in systems containing an abundant gas phase.

On the Theory of Accumulation of Hydrocarbons in a Dome Used to Eliminate a Technogenic Spill at the Bottom of the Ocean

NASA Astrophysics Data System (ADS)

Gimaltdinov, I. K.; Kil'dibaeva, S. R.

2018-01-01

Consideration is given to the operation of a dome separator installed at the bottom of the World Ocean and intended to eliminate the effects of technogenic spill of hydrocarbons. It is assumed that oil and gas (methane) escape from the damaged well on the ocean floor. Under the conditions of stable existence of a hydrate, a hydration sheath is formed on the surface of methane bubbles. To collect the entering hydrocarbons, a dome from a soft polyurethane shell is installed above the spill site, inside which the hydrocarbons are accumulated. In the regime of steady-state operation of the dome, provision is made for pumping out of hydrocarbons for transportation and further utilization. In the work, temperature fields of the hydrocarbon layers accumulated in the dome are investigated.

3D pore-type digital rock modeling of natural gas hydrate for permafrost and numerical simulation of electrical properties

NASA Astrophysics Data System (ADS)

Dong, Huaimin; Sun, Jianmeng; Lin, Zhenzhou; Fang, Hui; Li, Yafen; Cui, Likai; Yan, Weichao

2018-02-01

Natural gas hydrate is being considered as an alternative energy source for sustainable development and has become a focus of research throughout the world. In this paper, based on CT scanning images of hydrate reservoir rocks, combined with the microscopic distribution of hydrate, a diffusion limited aggregation (DLA) model was used to construct 3D hydrate digital rocks of different distribution types, and the finite-element method was used to simulate their electrical characteristics in order to study the influence of different hydrate distribution types, hydrate saturation and formation of water salinity on electrical properties. The results show that the hydrate digital rocks constructed using the DLA model can be used to characterize the microscopic distribution of different types of hydrates. Under the same conditions, the resistivity of the adhesive hydrate digital rock is higher than the cemented and scattered type digital rocks, and the resistivity of the scattered hydrate digital rock is the smallest among the three types. Besides, the difference in the resistivity of the different types of hydrate digital rocks increases with an increase in hydrate saturation, especially when the saturation is larger than 55%, and the rate of increase of each of the hydrate types is quite different. Similarly, the resistivity of the three hydrate types decreases with an increase in the formation of water salinity. The single distribution hydrate digital rock constructed, combined with the law of microscopic distribution and influence of saturation on the electrical properties, can effectively improve the accuracy of logging identification of hydrate reservoirs and is of great significance for the estimation of hydrate reserves.

Glacial Cycles Influence Marine Methane Hydrate Formation

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A. E.; Daigle, H.; Oryan, B.

2018-01-01

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sediments with greater organic carbon content deposited during the penultimate glacial cycle ( 120-240 ka). The model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.

Elastic-wave velocity in marine sediments with gas hydrates: Effective medium modeling

USGS Publications Warehouse

Helgerud, M.B.; Dvorkin, J.; Nur, A.; Sakai, A.; Collett, T.

1999-01-01

We offer a first-principle-based effective medium model for elastic-wave velocity in unconsolidated, high porosity, ocean bottom sediments containing gas hydrate. The dry sediment frame elastic constants depend on porosity, elastic moduli of the solid phase, and effective pressure. Elastic moduli of saturated sediment are calculated from those of the dry frame using Gassmann's equation. To model the effect of gas hydrate on sediment elastic moduli we use two separate assumptions: (a) hydrate modifies the pore fluid elastic properties without affecting the frame; (b) hydrate becomes a component of the solid phase, modifying the elasticity of the frame. The goal of the modeling is to predict the amount of hydrate in sediments from sonic or seismic velocity data. We apply the model to sonic and VSP data from ODP Hole 995 and obtain hydrate concentration estimates from assumption (b) consistent with estimates obtained from resistivity, chlorinity and evolved gas data. Copyright 1999 by the American Geophysical Union.

Optimization of linear and branched alkane interactions with water to simulate hydrophobic hydration

NASA Astrophysics Data System (ADS)

Ashbaugh, Henry S.; Liu, Lixin; Surampudi, Lalitanand N.

2011-08-01

Previous studies of simple gas hydration have demonstrated that the accuracy of molecular simulations at capturing the thermodynamic signatures of hydrophobic hydration is linked both to the fidelity of the water model at replicating the experimental liquid density at ambient pressure and an accounting of polarization interactions between the solute and water. We extend those studies to examine alkane hydration using the transferable potentials for phase equilibria united-atom model for linear and branched alkanes, developed to reproduce alkane phase behavior, and the TIP4P/2005 model for water, which provides one of the best descriptions of liquid water for the available fixed-point charge models. Alkane site/water oxygen Lennard-Jones cross interactions were optimized to reproduce the experimental alkane hydration free energies over a range of temperatures. The optimized model reproduces the hydration free energies of the fitted alkanes with a root mean square difference between simulation and experiment of 0.06 kcal/mol over a wide temperature range, compared to 0.44 kcal/mol for the parent model. The optimized model accurately reproduces the temperature dependence of hydrophobic hydration, as characterized by the hydration enthalpies, entropies, and heat capacities, as well as the pressure response, as characterized by partial molar volumes.

Natural Gas Hydrates Estimation Using Seismic Inversion and Rock Physics

NASA Astrophysics Data System (ADS)

Dutta, N.; Dai, J.; Kleinberg, R.; Xu, H.

2005-05-01

Gas hydrate drilling worldwide indicates that the formation of gas hydrates in shallow sediments tends to increase P- and S-wave velocities of the hosting rocks. Rock physics models of gas hydrates provide the links between velocity anomalies and gas hydrate concentration. In this abstract, we evaluate the numerical predictions of some of the major rock physics models of gas hydrates and validate those with well log data from the Mallik and Blake Ridge wells. We find that a model in which the gas hydrate is a part of the rock framework produces results that are consistent with well log data. To enhance the accuracy of seismic estimation, we adopt a five-step, integrated workflow that enables us to identify and quantify gas hydrates in the deepwater Gulf of Mexico (GOM). It includes: 1) Reprocessing conventional 3D seismic data at high resolution using an amplitude-preserving flow with prestack time migration, 2) A detailed stratigraphic evaluation to identify potential hydrate zones, 3) Seismic attribute analysis to further delineate anomalous zones, 4) Full waveform prestack inversion to characterize acoustic properties of gas hydrates in 1D (Mallick, 1995; Mallick, 1999) and map in 3D using hybrid inversion techniques (Dutta, 2002; Mallick and Dutta, 2002), and 5) Quantitative estimation of gas hydrate saturation using rock property models. We illustrate the procedure using 3D seismic data, and estimate gas hydrate saturation in the study area in the GOM.

Structural Basis for the Inhibition of Gas Hydrates by α-Helical Antifreeze Proteins

PubMed Central

Sun, Tianjun; Davies, Peter L.; Walker, Virginia K.

2015-01-01

Kinetic hydrate inhibitors (KHIs) are used commercially to inhibit gas hydrate formation and growth in pipelines. However, improvement of these polymers has been constrained by the lack of verified molecular models. Since antifreeze proteins (AFPs) act as KHIs, we have used their solved x-ray crystallographic structures in molecular modeling to explore gas hydrate inhibition. The internal clathrate water network of the fish AFP Maxi, which extends to the protein’s outer surface, is remarkably similar to the {100} planes of structure type II (sII) gas hydrate. The crystal structure of this water web has facilitated the construction of in silico models for Maxi and type I AFP binding to sII hydrates. Here, we have substantiated our models with experimental evidence of Maxi binding to the tetrahydrofuran sII model hydrate. Both in silico and experimental evidence support the absorbance-inhibition mechanism proposed for KHI binding to gas hydrates. Based on the Maxi crystal structure we suggest that the inhibitor adsorbs to the gas hydrate lattice through the same anchored clathrate water mechanism used to bind ice. These results will facilitate the rational design of a next generation of effective green KHIs for the petroleum industry to ensure safe and efficient hydrocarbon flow. PMID:26488661

Modeling of acoustic wave dissipation in gas hydrate-bearing sediments

NASA Astrophysics Data System (ADS)

Guerin, Gilles; Goldberg, David

2005-07-01

Recent sonic and seismic data in gas hydrate-bearing sediments have indicated strong waveform attenuation associated with a velocity increase, in apparent contradiction with conventional wave propagation theory. Understanding the reasons for such energy dissipation could help constrain the distribution and the amounts of gas hydrate worldwide from the identification of low amplitudes in seismic surveys. A review of existing models for wave propagation in frozen porous media, all based on Biot's theory, shows that previous formulations fail to predict any significant attenuation with increasing hydrate content. By adding physically based components to these models, such as cementation by elastic shear coupling, friction between the solid phases, and squirt flow, we are able to predict an attenuation increase associated with gas hydrate formation. The results of the model agree well with the sonic logging data recorded in the Mallik 5L-38 Gas Hydrate Research Well. Cementation between gas hydrate and the sediment grains is responsible for the increase in shear velocity. The primary mode of energy dissipation is found to be friction between gas hydrate and the sediment matrix, combined with an absence of inertial coupling between gas hydrate and the pore fluid. These results predict similar attenuation increase in hydrate-bearing formations over most of the sonic and seismic frequency range.

Modeling of Hydration, Compressive Strength, and Carbonation of Portland-Limestone Cement (PLC) Concrete.

PubMed

Wang, Xiao-Yong

2017-01-26

Limestone is widely used in the construction industry to produce Portland limestone cement (PLC) concrete. Systematic evaluations of hydration kinetics, compressive strength development, and carbonation resistance are crucial for the rational use of limestone. This study presents a hydration-based model for evaluating the influences of limestone on the strength and carbonation of concrete. First, the hydration model analyzes the dilution effect and the nucleation effect of limestone during the hydration of cement. The degree of cement hydration is calculated by considering concrete mixing proportions, binder properties, and curing conditions. Second, by using the gel-space ratio, the compressive strength of PLC concrete is evaluated. The interactions among water-to-binder ratio, limestone replacement ratio, and strength development are highlighted. Third, the carbonate material contents and porosity are calculated from the hydration model and are used as input parameters for the carbonation model. By considering concrete microstructures and environmental conditions, the carbon dioxide diffusivity and carbonation depth of PLC concrete are evaluated. The proposed model has been determined to be valid for concrete with various water-to-binder ratios, limestone contents, and curing periods.

Modeling of Hydration, Compressive Strength, and Carbonation of Portland-Limestone Cement (PLC) Concrete

PubMed Central

Wang, Xiao-Yong

2017-01-01

Limestone is widely used in the construction industry to produce Portland limestone cement (PLC) concrete. Systematic evaluations of hydration kinetics, compressive strength development, and carbonation resistance are crucial for the rational use of limestone. This study presents a hydration-based model for evaluating the influences of limestone on the strength and carbonation of concrete. First, the hydration model analyzes the dilution effect and the nucleation effect of limestone during the hydration of cement. The degree of cement hydration is calculated by considering concrete mixing proportions, binder properties, and curing conditions. Second, by using the gel–space ratio, the compressive strength of PLC concrete is evaluated. The interactions among water-to-binder ratio, limestone replacement ratio, and strength development are highlighted. Third, the carbonate material contents and porosity are calculated from the hydration model and are used as input parameters for the carbonation model. By considering concrete microstructures and environmental conditions, the carbon dioxide diffusivity and carbonation depth of PLC concrete are evaluated. The proposed model has been determined to be valid for concrete with various water-to-binder ratios, limestone contents, and curing periods. PMID:28772472

Study on small-strain behaviours of methane hydrate sandy sediments using discrete element method

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

Yu Yanxin; Cheng Yipik; Xu Xiaomin

Methane hydrate bearing soil has attracted increasing interest as a potential energy resource where methane gas can be extracted from dissociating hydrate-bearing sediments. Seismic testing techniques have been applied extensively and in various ways, to detect the presence of hydrates, due to the fact that hydrates increase the stiffness of hydrate-bearing sediments. With the recognition of the limitations of laboratory and field tests, wave propagation modelling using Discrete Element Method (DEM) was conducted in this study in order to provide some particle-scale insights on the hydrate-bearing sandy sediment models with pore-filling and cementation hydrate distributions. The relationship between shear wavemore » velocity and hydrate saturation was established by both DEM simulations and analytical solutions. Obvious differences were observed in the dependence of wave velocity on hydrate saturation for these two cases. From the shear wave velocity measurement and particle-scale analysis, it was found that the small-strain mechanical properties of hydrate-bearing sandy sediments are governed by both the hydrate distribution patterns and hydrate saturation.« less

The water retention curve and relative permeability for gas production from hydrate-bearing sediments: pore-network model simulation

NASA Astrophysics Data System (ADS)

Mahabadi, Nariman; Dai, Sheng; Seol, Yongkoo; Sup Yun, Tae; Jang, Jaewon

2016-08-01

The water retention curve and relative permeability are critical to predict gas and water production from hydrate-bearing sediments. However, values for key parameters that characterize gas and water flows during hydrate dissociation have not been identified due to experimental challenges. This study utilizes the combined techniques of micro-focus X-ray computed tomography (CT) and pore-network model simulation to identify proper values for those key parameters, such as gas entry pressure, residual water saturation, and curve fitting values. Hydrates with various saturation and morphology are realized in the pore-network that was extracted from micron-resolution CT images of sediments recovered from the hydrate deposit at the Mallik site, and then the processes of gas invasion, hydrate dissociation, gas expansion, and gas and water permeability are simulated. Results show that greater hydrate saturation in sediments lead to higher gas entry pressure, higher residual water saturation, and steeper water retention curve. An increase in hydrate saturation decreases gas permeability but has marginal effects on water permeability in sediments with uniformly distributed hydrate. Hydrate morphology has more significant impacts than hydrate saturation on relative permeability. Sediments with heterogeneously distributed hydrate tend to result in lower residual water saturation and higher gas and water permeability. In this sense, the Brooks-Corey model that uses two fitting parameters individually for gas and water permeability properly capture the effect of hydrate saturation and morphology on gas and water flows in hydrate-bearing sediments.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

NASA Astrophysics Data System (ADS)

Li, Tanping; Cui, Yaowen; Mathaga, John; Kumar, Revati; Kuroda, Daniel G.

2015-06-01

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm-1 region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ˜0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters.

Hydration and vibrational dynamics of betaine (N,N,N-trimethylglycine)

PubMed Central

Li, Tanping; Cui, Yaowen; Mathaga, John; Kumar, Revati; Kuroda, Daniel G.

2015-01-01

Zwitterions are naturally occurring molecules that have a positive and a negative charge group in its structure and are of great importance in many areas of science. Here, the vibrational and hydration dynamics of the zwitterionic system betaine (N,N,N-trimethylglycine) is reported. The linear infrared spectrum of aqueous betaine exhibits an asymmetric band in the 1550-1700 cm−1 region of the spectrum. This band is attributed to the carboxylate asymmetric stretch of betaine. The potential of mean force computed from ab initio molecular dynamic simulations confirms that the two observed transitions of the linear spectrum are related to two different betaine conformers present in solution. A model of the experimental data using non-linear response theory agrees very well with a vibrational model comprising of two vibrational transitions. In addition, our modeling shows that spectral parameters such as the slope of the zeroth contour plot and central line slope are both sensitive to the presence of overlapping transitions. The vibrational dynamics of the system reveals an ultrafast decay of the vibrational population relaxation as well as the correlation of frequency-frequency correlation function (FFCF). A decay of ∼0.5 ps is observed for the FFCF correlation time and is attributed to the frequency fluctuations caused by the motions of water molecules in the solvation shell. The comparison of the experimental observations with simulations of the FFCF from ab initio molecular dynamics and a density functional theory frequency map shows a very good agreement corroborating the correct characterization and assignment of the derived parameters. PMID:26049458

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

PubMed

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

2015-12-02

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

The importance of dissolved salts to the in vivo efficacy of antifreeze proteins.

PubMed

Evans, Robert P; Hobbs, Rod S; Goddard, Sally V; Fletcher, Garth L

2007-11-01

Antifreeze proteins (AFP) and antifreeze glycoproteins (AFGP) lower the freezing point of marine fish plasma non-colligatively by specifically adsorbing to certain surfaces of ice crystals, modifying their structure and inhibiting further growth. While the freezing point is lowered, the melting point is unaltered and the difference between the two is termed thermal hysteresis (TH). In pure water, the level of TH is directly related to the intrinsic activity of the specific AF(G)P in solution and to their concentration. Results of this study indicate that when AF(G)P are dissolved in salt solutions, such as NaCl, encompassing the range they could encounter in nature, there is a synergistic enhancement of basal TH that is positively related to the salt concentration. This enhancement is likely a result of the hydration shell surrounding the dissolved ions and, as a consequence, reducing freezable water. A secondary reason for the enhancement is that the salt could be influencing the hydration shell surrounding the AF(G)P, increasing their solubility and thus the protein surface area available to adsorb to the ice/water interface. The former hypothesis for the salt enhanced TH has implications for the in vivo function of AF(G)P, particularly at the seawater/external epithelia (gills, skin, stomach) interface. The latter hypothesis is likely only relevant to in vitro situations where freeze dried protein is dissolved in low salt solutions.

Neutron Nucleic Acid Crystallography.

PubMed

Chatake, Toshiyuki

2016-01-01

The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

Sulfate content of Europa's ocean and shell: evolutionary considerations and some geological and astrobiological implications.

PubMed

McKinnon, William B; Zolensky, Michael E

2003-01-01

Recent models for the origin of Jupiter indicate that the Galilean satellites were mostly derived from largely unprocessed solar nebula solids and planetesimals. In the jovian subnebula the solids that built Europa were first heated and then cooled, but the major effect was most likely partial or total devolatilization, and less likely to have been wholesale thermochemical reprocessing of rock + metal compositions (e.g., oxidation of Fe and hydration of silicates). Ocean formation and substantial alteration of interior rock by accreted water and ice would occur during and after accretion, but none of the formation models predicts or implies accretion of sulfates. Europa's primordial ocean was most likely sulfidic. After accretion and later radiogenic and tidal heating, the primordial ocean would have interacted hydrothermally with subjacent rock. It has been hypothesized that sulfides could be converted to sulfates if sufficient hydrogen was lost to space, but pressure effects and the impermeability of serpentinite imply that extraction of sulfate from thoroughly altered Europa-rock would have been inefficient (if indeed Mg sulfates formed at all). Permissive physical limits on the extent of alteration limit the sulfate concentration of Europa's evolved ocean to 10% by weight MgSO(4) or equivalent. Later oxidation of the deep interior of Europa may have also occurred because of water released by the breakdown of hydrated silicates, ultimately yielding S magma and/or SO(2) gas. Geological and astrobiological implications are considered.

Nonequilibrium Thermodynamics of Hydrate Growth on a Gas-Liquid Interface

NASA Astrophysics Data System (ADS)

Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

2018-04-01

We develop a continuum-scale phase-field model to study gas-liquid-hydrate systems far from thermodynamic equilibrium. We design a Gibbs free energy functional for methane-water mixtures that recovers the isobaric temperature-composition phase diagram under thermodynamic equilibrium conditions. The proposed free energy is incorporated into a phase-field model to study the dynamics of hydrate formation on a gas-liquid interface. We elucidate the role of initial aqueous concentration in determining the direction of hydrate growth at the interface, in agreement with experimental observations. Our model also reveals two stages of hydrate growth at an interface—controlled by a crossover in how methane is supplied from the gas and liquid phases—which could explain the persistence of gas conduits in hydrate-bearing sediments and other nonequilibrium phenomena commonly observed in natural methane hydrate systems.

Nonequilibrium Thermodynamics of Hydrate Growth on a Gas-Liquid Interface.

PubMed

Fu, Xiaojing; Cueto-Felgueroso, Luis; Juanes, Ruben

2018-04-06

We develop a continuum-scale phase-field model to study gas-liquid-hydrate systems far from thermodynamic equilibrium. We design a Gibbs free energy functional for methane-water mixtures that recovers the isobaric temperature-composition phase diagram under thermodynamic equilibrium conditions. The proposed free energy is incorporated into a phase-field model to study the dynamics of hydrate formation on a gas-liquid interface. We elucidate the role of initial aqueous concentration in determining the direction of hydrate growth at the interface, in agreement with experimental observations. Our model also reveals two stages of hydrate growth at an interface-controlled by a crossover in how methane is supplied from the gas and liquid phases-which could explain the persistence of gas conduits in hydrate-bearing sediments and other nonequilibrium phenomena commonly observed in natural methane hydrate systems.

An effective medium inversion algorithm for gas hydrate quantification and its application to laboratory and borehole measurements of gas hydrate-bearing sediments

NASA Astrophysics Data System (ADS)

Chand, Shyam; Minshull, Tim A.; Priest, Jeff A.; Best, Angus I.; Clayton, Christopher R. I.; Waite, William F.

2006-08-01

The presence of gas hydrate in marine sediments alters their physical properties. In some circumstances, gas hydrate may cement sediment grains together and dramatically increase the seismic P- and S-wave velocities of the composite medium. Hydrate may also form a load-bearing structure within the sediment microstructure, but with different seismic wave attenuation characteristics, changing the attenuation behaviour of the composite. Here we introduce an inversion algorithm based on effective medium modelling to infer hydrate saturations from velocity and attenuation measurements on hydrate-bearing sediments. The velocity increase is modelled as extra binding developed by gas hydrate that strengthens the sediment microstructure. The attenuation increase is modelled through a difference in fluid flow properties caused by different permeabilities in the sediment and hydrate microstructures. We relate velocity and attenuation increases in hydrate-bearing sediments to their hydrate content, using an effective medium inversion algorithm based on the self-consistent approximation (SCA), differential effective medium (DEM) theory, and Biot and squirt flow mechanisms of fluid flow. The inversion algorithm is able to convert observations in compressional and shear wave velocities and attenuations to hydrate saturation in the sediment pore space. We applied our algorithm to a data set from the Mallik 2L-38 well, Mackenzie delta, Canada, and to data from laboratory measurements on gas-rich and water-saturated sand samples. Predictions using our algorithm match the borehole data and water-saturated laboratory data if the proportion of hydrate contributing to the load-bearing structure increases with hydrate saturation. The predictions match the gas-rich laboratory data if that proportion decreases with hydrate saturation. We attribute this difference to differences in hydrate formation mechanisms between the two environments.

An effective medium inversion algorithm for gas hydrate quantification and its application to laboratory and borehole measurements of gas hydrate-bearing sediments

USGS Publications Warehouse

Chand, S.; Minshull, T.A.; Priest, J.A.; Best, A.I.; Clayton, C.R.I.; Waite, W.F.

2006-01-01

The presence of gas hydrate in marine sediments alters their physical properties. In some circumstances, gas hydrate may cement sediment grains together and dramatically increase the seismic P- and S-wave velocities of the composite medium. Hydrate may also form a load-bearing structure within the sediment microstructure, but with different seismic wave attenuation characteristics, changing the attenuation behaviour of the composite. Here we introduce an inversion algorithm based on effective medium modelling to infer hydrate saturations from velocity and attenuation measurements on hydrate-bearing sediments. The velocity increase is modelled as extra binding developed by gas hydrate that strengthens the sediment microstructure. The attenuation increase is modelled through a difference in fluid flow properties caused by different permeabilities in the sediment and hydrate microstructures. We relate velocity and attenuation increases in hydrate-bearing sediments to their hydrate content, using an effective medium inversion algorithm based on the self-consistent approximation (SCA), differential effective medium (DEM) theory, and Biot and squirt flow mechanisms of fluid flow. The inversion algorithm is able to convert observations in compressional and shear wave velocities and attenuations to hydrate saturation in the sediment pore space. We applied our algorithm to a data set from the Mallik 2L–38 well, Mackenzie delta, Canada, and to data from laboratory measurements on gas-rich and water-saturated sand samples. Predictions using our algorithm match the borehole data and water-saturated laboratory data if the proportion of hydrate contributing to the load-bearing structure increases with hydrate saturation. The predictions match the gas-rich laboratory data if that proportion decreases with hydrate saturation. We attribute this difference to differences in hydrate formation mechanisms between the two environments.

Theoretical modeling insights into elastic wave attenuation mechanisms in marine sediments with pore-filling methane hydrate

NASA Astrophysics Data System (ADS)

Marín-Moreno, H.; Sahoo, S. K.; Best, A. I.

2017-03-01

The majority of presently exploitable marine methane hydrate reservoirs are likely to host hydrate in disseminated form in coarse grain sediments. For hydrate concentrations below 25-40%, disseminated or pore-filling hydrate does not increase elastic frame moduli, thus making impotent traditional seismic velocity-based methods. Here, we present a theoretical model to calculate frequency-dependent P and S wave velocity and attenuation of an effective porous medium composed of solid mineral grains, methane hydrate, methane gas, and water. The model considers elastic wave energy losses caused by local viscous flow both (i) between fluid inclusions in hydrate and pores and (ii) between different aspect ratio pores (created when hydrate grows); the inertial motion of the frame with respect to the pore fluid (Biot's type fluid flow); and gas bubble damping. The sole presence of pore-filling hydrate in the sediment reduces the available porosity and intrinsic permeability of the sediment affecting Biot's type attenuation at high frequencies. Our model shows that attenuation maxima due to fluid inclusions in hydrate are possible over the entire frequency range of interest to exploration seismology (1-106 Hz), depending on the aspect ratio of the inclusions, whereas maxima due to different aspect ratio pores occur only at sonic to ultrasound frequencies (104-106 Hz). This frequency response imposes further constraints on possible hydrate saturations able to reproduce broadband elastic measurements of velocity and attenuation. Our results provide a physical basis for detecting the presence and amount of pore-filling hydrate in seafloor sediments using conventional seismic surveys.

Stress and Dilatancy Relation of Methane Hydrate Bearing Sand with Various Fines Content

NASA Astrophysics Data System (ADS)

Hyodo, M.

2016-12-01

This study presents an experimental and numerical study on the shear behaviour of methane hydrate bearing sand with variable confining pressures and methane hydrate saturations. A representative grading curve of Nankai Trough is selected as the grain size distribution of host sand to artificially produce the methane hydrate bearing sand. A shear strength estimation equation for methane hydrate bearing sand from test results is established. A simple constitutive model has been proposed to predict the stress-strain response of methane hydrate bearing sand based on a few well-known relationships. Experimental results indicate that the inclination of stress-dilatancy curve becomes steeper with a rise in methane hydrate saturation. A revised stress-dilatancy equation has been integrated with this simple model to consider the variance in the inclination of stress-dilatancy curve. The mean stress Pcr at critical state when the peak stress ratio reduces to the residual stress ratio increases with the level of methane hydrate saturation. The dilatancy parameter a tends to increase with the methane hydrate saturation. The shear deformability parameter A exhibits a decreasing tendency with the rise in methane hydrate saturation at each confining pressure. This model is capable of reasonably predicting the strength and stiffness enhancement and the dilation behaviour as methane hydrate saturation increases. The volumetric variation from contraction to expansion of MH bearing sand at a lower confining pressure and only pure volumetric contraction a higher confining pressure can be represented by this simple model.

Thermodynamic and structural signatures of water-driven methane-methane attraction in coarse-grained mW water.

PubMed

Song, Bin; Molinero, Valeria

2013-08-07

Hydrophobic interactions are responsible for water-driven processes such as protein folding and self-assembly of biomolecules. Microscopic theories and molecular simulations have been used to study association of a pair of methanes in water, the paradigmatic example of hydrophobic attraction, and determined that entropy is the driving force for the association of the methane pair, while the enthalpy disfavors it. An open question is to which extent coarse-grained water models can still produce correct thermodynamic and structural signatures of hydrophobic interaction. In this work, we investigate the hydrophobic interaction between a methane pair in water at temperatures from 260 to 340 K through molecular dynamics simulations with the coarse-grained monatomic water model mW. We find that the coarse-grained model correctly represents the free energy of association of the methane pair, the temperature dependence of free energy, and the positive change in entropy and enthalpy upon association. We investigate the relationship between thermodynamic signatures and structural order of water through the analysis of the spatial distribution of the density, energy, and tetrahedral order parameter Qt of water. The simulations reveal an enhancement of tetrahedral order in the region between the first and second hydration shells of the methane molecules. The increase in tetrahedral order, however, is far from what would be expected for a clathrate-like or ice-like shell around the solutes. This work shows that the mW water model reproduces the key signatures of hydrophobic interaction without long ranged electrostatics or the need to be re-parameterized for different thermodynamic states. These characteristics, and its hundred-fold increase in efficiency with respect to atomistic models, make mW a promising water model for studying water-driven hydrophobic processes in more complex systems.

Pore-Scale Determination of Gas Relative Permeability in Hydrate-Bearing Sediments Using X-Ray Computed Micro-Tomography and Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Chen, Xiongyu; Verma, Rahul; Espinoza, D. Nicolas; Prodanović, Maša.

2018-01-01

This work uses X-ray computed micro-tomography (μCT) to monitor xenon hydrate growth in a sandpack under the excess gas condition. The μCT images give pore-scale hydrate distribution and pore habit in space and time. We use the lattice Boltzmann method to calculate gas relative permeability (krg) as a function of hydrate saturation (Shyd) in the pore structure of the experimental hydrate-bearing sand retrieved from μCT data. The results suggest the krg - Shyd data fit well a new model krg = (1-Shyd)·exp(-4.95·Shyd) rather than the simple Corey model. In addition, we calculate krg-Shyd curves using digital models of hydrate-bearing sand based on idealized grain-attaching, coarse pore-filling, and dispersed pore-filling hydrate habits. Our pore-scale measurements and modeling show that the krg-Shyd curves are similar regardless of whether hydrate crystals develop grain-attaching or coarse pore-filling habits. The dispersed pore filling habit exhibits much lower gas relative permeability than the other two, but it is not observed in the experiment and not compatible with Ostwald ripening mechanisms. We find that a single grain-shape factor can be used in the Carman-Kozeny equation to calculate krg-Shyd data with known porosity and average grain diameter, suggesting it is a useful model for hydrate-bearing sand.

Glacial cycles influence marine methane hydrate formation

DOE PAGES

Malinverno, A.; Cook, A. E.; Daigle, H.; ...

2018-01-12

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sedimentsmore » with greater organic carbon content deposited during the penultimate glacial cycle (~120-240 ka). As a result, the model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.« less

Glacial cycles influence marine methane hydrate formation

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

Malinverno, A.; Cook, A. E.; Daigle, H.

Methane hydrates in fine-grained continental slope sediments often occupy isolated depth intervals surrounded by hydrate-free sediments. As they are not connected to deep gas sources, these hydrate deposits have been interpreted as sourced by in situ microbial methane. We investigate here the hypothesis that these isolated hydrate accumulations form preferentially in sediments deposited during Pleistocene glacial lowstands that contain relatively large amounts of labile particulate organic carbon, leading to enhanced microbial methanogenesis. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent organic carbon deposition controlled by glacioeustatic sea level variations. In the model, hydrate forms in sedimentsmore » with greater organic carbon content deposited during the penultimate glacial cycle (~120-240 ka). As a result, the model predictions match hydrate-bearing intervals detected in three sites drilled on the northern Gulf of Mexico continental slope, supporting the hypothesis of hydrate formation driven by enhanced organic carbon burial during glacial lowstands.« less

Anisotropic Velocities of Gas Hydrate-Bearing Sediments in Fractured Reservoirs

USGS Publications Warehouse

Lee, Myung W.

2009-01-01

During the Indian National Gas Hydrate Program Expedition 01 (NGHP-01), one of the richest marine gas hydrate accumulations was discovered at drill site NGHP-01-10 in the Krishna-Godavari Basin, offshore of southeast India. The occurrence of concentrated gas hydrate at this site is primarily controlled by the presence of fractures. Gas hydrate saturations estimated from P- and S-wave velocities, assuming that gas hydrate-bearing sediments (GHBS) are isotropic, are much higher than those estimated from the pressure cores. To reconcile this difference, an anisotropic GHBS model is developed and applied to estimate gas hydrate saturations. Gas hydrate saturations estimated from the P-wave velocities, assuming high-angle fractures, agree well with saturations estimated from the cores. An anisotropic GHBS model assuming two-component laminated media - one component is fracture filled with 100-percent gas hydrate, and the other component is the isotropic water-saturated sediment - adequately predicts anisotropic velocities at the research site.

Elevated gas hydrate saturation within silt and silty clay sediments in the Shenhu area, South China Sea

USGS Publications Warehouse

Wang, Xiujuan; Hutchinson, Deborah R.; Wu, Shiguo; Yang, Shengxiong; Guo, Yiqun

2011-01-01

Gas hydrate saturations were estimated using five different methods in silt and silty clay foraminiferous sediments from drill hole SH2 in the South China Sea. Gas hydrate saturations derived from observed pore water chloride values in core samples range from 10 to 45% of the pore space at 190–221 m below seafloor (mbsf). Gas hydrate saturations estimated from resistivity (Rt) using wireline logging results are similar and range from 10 to 40.5% in the pore space. Gas hydrate saturations were also estimated by P wave velocity obtained during wireline logging by using a simplified three-phase equation (STPE) and effective medium theory (EMT) models. Gas hydrate saturations obtained from the STPE velocity model (41.0% maximum) are slightly higher than those calculated with the EMT velocity model (38.5% maximum). Methane analysis from a 69 cm long depressurized core from the hydrate-bearing sediment zone indicates that gas hydrate saturation is about 27.08% of the pore space at 197.5 mbsf. Results from the five methods show similar values and nearly identical trends in gas hydrate saturations above the base of the gas hydrate stability zone at depths of 190 to 221 mbsf. Gas hydrate occurs within units of clayey slit and silt containing abundant calcareous nannofossils and foraminifer, which increase the porosities of the fine-grained sediments and provide space for enhanced gas hydrate formation. In addition, gas chimneys, faults, and fractures identified from three-dimensional (3-D) and high-resolution two-dimensional (2-D) seismic data provide pathways for fluids migrating into the gas hydrate stability zone which transport methane for the formation of gas hydrate. Sedimentation and local canyon migration may contribute to higher gas hydrate saturations near the base of the stability zone.

Competing Insertion and External Binding Motifs in Hydrated Neurotransmitters: Infrared Spectra of Protonated Phenylethylamine Monohydrate.

PubMed

Bouchet, Aude; Schütz, Markus; Dopfer, Otto

2016-01-18

Hydration has a drastic impact on the structure and function of flexible biomolecules, such as aromatic ethylamino neurotransmitters. The structure of monohydrated protonated phenylethylamine (H(+) PEA-H2 O) is investigated by infrared photodissociation (IRPD) spectroscopy of cold cluster ions by using rare-gas (Rg=Ne and Ar) tagging and dispersion-corrected density functional theory calculations at the B3LYP-D3/aug-cc-pVTZ level. Monohydration of this prototypical neurotransmitter gives an insight into the first step of the formation of its solvation shell, especially regarding the competition between intra- and intermolecular interactions. The spectra of Rg-tagged H(+) PEA-H2 O reveal the presence of a stable insertion structure in which the water molecule is located between the positively charged ammonium group and the phenyl ring of H(+) PEA, acting both as a hydrogen bond acceptor (NH(+) ⋅⋅⋅O) and donor (OH⋅⋅⋅π). Two other nearly equivalent isomers, in which water is externally H bonded to one of the free NH groups, are also identified. The balance between insertion and external hydration strongly depends on temperature. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Seismic modeling of multidimensional heterogeneity scales of Mallik gas hydrate reservoirs, Northwest Territories of Canada

NASA Astrophysics Data System (ADS)

Huang, Jun-Wei; Bellefleur, Gilles; Milkereit, Bernd

2009-07-01

In hydrate-bearing sediments, the velocity and attenuation of compressional and shear waves depend primarily on the spatial distribution of hydrates in the pore space of the subsurface lithologies. Recent characterizations of gas hydrate accumulations based on seismic velocity and attenuation generally assume homogeneous sedimentary layers and neglect effects from large- and small-scale heterogeneities of hydrate-bearing sediments. We present an algorithm, based on stochastic medium theory, to construct heterogeneous multivariable models that mimic heterogeneities of hydrate-bearing sediments at the level of detail provided by borehole logging data. Using this algorithm, we model some key petrophysical properties of gas hydrates within heterogeneous sediments near the Mallik well site, Northwest Territories, Canada. The modeled density, and P and S wave velocities used in combination with a modified Biot-Gassmann theory provide a first-order estimate of the in situ volume of gas hydrate near the Mallik 5L-38 borehole. Our results suggest a range of 528 to 768 × 106 m3/km2 of natural gas trapped within hydrates, nearly an order of magnitude lower than earlier estimates which did not include effects of small-scale heterogeneities. Further, the petrophysical models are combined with a 3-D finite difference modeling algorithm to study seismic attenuation due to scattering and leaky mode propagation. Simulations of a near-offset vertical seismic profile and cross-borehole numerical surveys demonstrate that attenuation of seismic energy may not be directly related to the intrinsic attenuation of hydrate-bearing sediments but, instead, may be largely attributed to scattering from small-scale heterogeneities and highly attenuate leaky mode propagation of seismic waves through larger-scale heterogeneities in sediments.

Scalable Graphene-Based Membranes for Ionic Sieving with Ultrahigh Charge Selectivity.

PubMed

Hong, Seunghyun; Constans, Charlotte; Surmani Martins, Marcos Vinicius; Seow, Yong Chin; Guevara Carrió, Juan Alfredo; Garaj, Slaven

2017-02-08

Nanostructured graphene-oxide (GO) laminate membranes, exhibiting ultrahigh water flux, are excellent candidates for next generation nanofiltration and desalination membranes, provided the ionic rejection could be further increased without compromising the water flux. Using microscopic drift-diffusion experiments, we demonstrated the ultrahigh charge selectivity for GO membranes, with more than order of magnitude difference in the permeabilities of cationic and anionic species of equivalent hydration radii. Measuring diffusion of a wide range of ions of different size and charge, we were able to clearly disentangle different physical mechanisms contributing to the ionic sieving in GO membranes: electrostatic repulsion between ions and charged chemical groups; and the compression of the ionic hydration shell within the membrane's nanochannels, following the activated behavior. The charge-selectivity allows us to rationally design membranes with increased ionic rejection and opens up the field of ion exchange and electrodialysis to the GO membranes.

Acoustic Velocity Log Numerical Simulation and Saturation Estimation of Gas Hydrate Reservoir in Shenhu Area, South China Sea

PubMed Central

Xiao, Kun; Zou, Changchun; Xiang, Biao; Liu, Jieqiong

2013-01-01

Gas hydrate model and free gas model are established, and two-phase theory (TPT) for numerical simulation of elastic wave velocity is adopted to investigate the unconsolidated deep-water sedimentary strata in Shenhu area, South China Sea. The relationships between compression wave (P wave) velocity and gas hydrate saturation, free gas saturation, and sediment porosity at site SH2 are studied, respectively, and gas hydrate saturation of research area is estimated by gas hydrate model. In depth of 50 to 245 m below seafloor (mbsf), as sediment porosity decreases, P wave velocity increases gradually; as gas hydrate saturation increases, P wave velocity increases gradually; as free gas saturation increases, P wave velocity decreases. This rule is almost consistent with the previous research result. In depth of 195 to 220 mbsf, the actual measurement of P wave velocity increases significantly relative to the P wave velocity of saturated water modeling, and this layer is determined to be rich in gas hydrate. The average value of gas hydrate saturation estimated from the TPT model is 23.2%, and the maximum saturation is 31.5%, which is basically in accordance with simplified three-phase equation (STPE), effective medium theory (EMT), resistivity log (Rt), and chloride anomaly method. PMID:23935407

HYDRATE v1.5 OPTION OF TOUGH+ v1.5

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

Moridis, George

HYDRATE v1.5 is a numerical code that for the simulation of the behavior of hydrate-bearing geologic systems, and represents the third update of the code since its first release [Moridis et al., 2008]. It is an option of TOUGH+ v1.5 [Moridis and Pruess, 2014], a successor to the TOUGH2 [Pruess et al., 1999, 2012] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. HYDRATE v1.5 needs the TOUGH+ v1.5 core code in order to compile and execute. It is written in standard FORTRAN 95/2003, and can be run on any computational platformmore » (workstation, PC, Macintosh) for which such compilers are available. By solving the coupled equations of mass and heat balance, the fully operational TOUGH+HYDRATE code can model the non-isothermal gas release, phase behavior and flow of fluids and heat under conditions typical of common natural CH 4-hydrate deposits (i.e., in the permafrost and in deep ocean sediments) in complex geological media at any scale (from laboratory to reservoir) at which Darcy's law is valid. TOUGH+HYDRATE v1.5 includes both an equilibrium and a kinetic model of hydrate formation and dissociation. The model accounts for heat and up to four mass components, i.e., water, CH 4, hydrate, and water-soluble inhibitors such as salts or alcohols. These are partitioned among four possible phases (gas phase, liquid phase, ice phase and hydrate phase). Hydrate dissociation or formation, phase changes and the corresponding thermal effects are fully described, as are the effects of inhibitors. The model can describe all possible hydrate dissociation mechanisms, i.e., depressurization, thermal stimulation, salting-out effects and inhibitor-induced effects.« less

Experimental and modeling study on decomposition kinetics of methane hydrates in different media.

PubMed

Liang, Minyan; Chen, Guangjin; Sun, Changyu; Yan, Lijun; Liu, Jiang; Ma, Qinglan

2005-10-13

The decomposition kinetic behaviors of methane hydrates formed in 5 cm3 porous wet activated carbon were studied experimentally in a closed system in the temperature range of 275.8-264.4 K. The decomposition rates of methane hydrates formed from 5 cm3 of pure free water and an aqueous solution of 650 g x m(-3) sodium dodecyl sulfate (SDS) were also measured for comparison. The decomposition rates of methane hydrates in seven different cases were compared. The results showed that the methane hydrates dissociate more rapidly in porous activated carbon than in free systems. A mathematical model was developed for describing the decomposition kinetic behavior of methane hydrates below ice point based on an ice-shielding mechanism in which a porous ice layer was assumed to be formed during the decomposition of hydrate, and the diffusion of methane molecules through it was assumed to be one of the control steps. The parameters of the model were determined by correlating the decomposition rate data, and the activation energies were further determined with respect to three different media. The model was found to well describe the decomposition kinetic behavior of methane hydrate in different media.

Theoretical study of gas hydrate decomposition kinetics--model development.

PubMed

Windmeier, Christoph; Oellrich, Lothar R

2013-10-10

In order to provide an estimate of the order of magnitude of intrinsic gas hydrate dissolution and dissociation kinetics, the "Consecutive Desorption and Melting Model" (CDM) is developed by applying only theoretical considerations. The process of gas hydrate decomposition is assumed to comprise two consecutive and repetitive quasi chemical reaction steps. These are desorption of the guest molecule followed by local solid body melting. The individual kinetic steps are modeled according to the "Statistical Rate Theory of Interfacial Transport" and the Wilson-Frenkel approach. All missing required model parameters are directly linked to geometric considerations and a thermodynamic gas hydrate equilibrium model.

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.

PubMed

Damjanović, Ana; Brooks, Bernard R; García-Moreno, Bertrand

2011-04-28

Molecular dynamics simulations were used to examine the effects of ionization of internal groups on the structures of eighteen variants of staphylococcal nuclease (SNase) with internal Lys, Asp, or Glu. In most cases the RMSD values of internal ionizable side chains were larger when the ionizable moieties were charged than when they were neutral. Calculations of solvent-accessible surface area showed that the internal ionizable side chains were buried in the protein interior when they were neutral and moved toward crevices and toward the protein-water interface when they were charged. The only exceptions are Lys-36, Lys-62, and Lys-103, which remained buried even after charging. With the exception of Lys-38, the number of internal water molecules surrounding the ionizable group increased upon charging: the average number of water oxygen atoms within the first hydration shell increased by 1.7 for Lys residues, by 5.2 for Asp residues, and by 3.2 for Glu residues. The polarity of the microenvironment of the ionizable group also increased when the groups were charged: the average number of polar atoms of any kind within the first hydration shell increased by 2.7 for Lys residues, by 4.8 for Asp residues, and by 4.0 for Glu residues. An unexpected correlation was observed between the absolute value of the shifts in pK(a) values measured experimentally, and several parameters of structural relaxation: the net difference in the polarity of the microenvironment of the charged and neutral forms of the ionizable groups, the net difference in hydration of the charged and neutral forms of the ionizable groups, and the difference in RMSD values of the charged and neutral forms of the ionizable groups. The effects of ionization of internal groups on the conformation of the backbone were noticeable but mostly small and localized to the area immediately next to the internal ionizable moiety. Some variants did exhibit local unfolding.

Selective tuning of the self-assembly and gelation of a hydrophilic poloxamine by cyclodextrins.

PubMed

González-Gaitano, Gustavo; da Silva, Marcelo A; Radulescu, Aurel; Dreiss, Cécile A

2015-05-26

Complexes formed between cyclodextrins (CDs) and polymers - pseudopolyrotaxanes (PPRs) - are the starting point of a multitude of supramolecular structures, which are proposed for a wide range of biomedical and technological applications. In this work, we investigate the complexation of a range of cyclodextrins with Tetronic T1307, a four-arm block copolymer of poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide) with a pH-responsive central ethylene diamine spacer, and its impact on micellization and the sol-gel transition. At low concentrations, small-angle neutron scattering (SANS) combined with dynamic light scattering (DLS) measurements show the presence of spherical micelles with a highly hydrated shell and a dehydrated core. Increasing the temperature leads to more compact micelles and larger aggregation numbers, whereas acidic conditions induce a shrinking of the micelles, with fewer unimers per micelle and a more hydrated corona. At high concentrations, T1307 undergoes a sol-gel transition, which is suppressed at pH below the pKa,1 (4.6). SANS data analysis reveals that the gels result from a random packing of the micelles, which have an increasing aggregation number and increasingly dehydrated shell and hydrated core with the temperature. Native CDs (α, β, γ-CD) can complex T1307, resulting in the precipitation of a PPR. Instead, modified CDs compete with micellization to an extent that is critically dependent on the nature of the substitution. (1)H and ROESY NMR combined with SANS demonstrate that dimethylated β-CD can thread onto the polymer, preferentially binding to the PO units, thus hindering self-aggregation by solubilizing the hydrophobic block. The various CDs are able to modulate the onset of gelation and the extent of the gel phase, and the effect correlates with the ability of the CDs to disrupt the micelles, with the exception of a sulfated sodium salt of β-CD, which, while not affecting the CMT, is able to fully suppress the gel phase.

Region-specific role of water in collagen unwinding and assembly.

PubMed

Ravikumar, Krishnakumar M; Hwang, Wonmuk

2008-09-01

Conformational stability of the collagen triple helix affects its turnover and determines tissue homeostasis. Although it is known that the presence of imino acids (prolines or hydroxyprolines) confer stability to the molecule, little is known regarding the stability of the imino-poor region lacking imino acids, which plays a key role in collagen cleavage. In particular, there have been continuing debates about the role of water in collagen stability. We addressed these issues using molecular dynamics simulations on 30-residue long collagen triple helices, including a structure that has a biologically relevant 9-residue imino-poor region from type III collagen (PDB ID: 1BKV). A torsional map approach was used to characterize the conformational motion of the molecule that differ between imino-rich and imino-poor regions. At temperatures 300 K and above, unwinding initiates at a common cleavage site, the glycine-isoleucine bond in the imino-poor region. This provides a linkage between previous observations that unwinding of the imino-poor region is a requirement for collagenase cleavage, and that isolated collagen molecules are unstable at body temperature. We found that unwinding of the imino-poor region is controlled by dynamic water bridges between backbone atoms with average lifetimes on the order of a few picoseconds, as the degree of unwinding strongly correlated with the loss of water bridges, and unwinding could be either prevented or enhanced, respectively by enforcing or forbidding water bridge formation. While individual water bridges were short-lived in the imino-poor region, the hydration shell surrounding the entire molecule was stable even at 330 K. The diameter of the hydrated collagen including the first hydration shell was about 14 A, in good agreement with the experimentally measured inter-collagen distances. These results elucidate the general role of water in collagen turnover: water not only affects collagen cleavage by controlling its torsional motion, but it also forms a larger-scale lubrication layer mediating collagen self-assembly. 2008 Wiley-Liss, Inc.

Reconstruction of SAXS Profiles from Protein Structures

PubMed Central

Putnam, Daniel K.; Lowe, Edward W.

2013-01-01

Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration. PMID:24688746

Microstructural characteristics of natural gas hydrates hosted in various sand sediments.

PubMed

Zhao, Jiafei; Yang, Lei; Liu, Yu; Song, Yongchen

2015-09-21

Natural gas hydrates have aroused worldwide interest due to their energy potential and possible impact on climate. The occurrence of natural gas hydrates hosted in the pores of sediments governs the seismic exploration, resource assessment, stability of deposits, and gas production from natural gas hydrate reserves. In order to investigate the microstructure of natural gas hydrates occurring in pores, natural gas hydrate-bearing sediments were visualized using microfocus X-ray computed tomography (CT). Various types of sands with different grain sizes and wettability were used to study the effect of porous materials on the occurrence of natural gas hydrates. Spatial distributions of methane gas, natural gas hydrates, water, and sands were directly identified. This work indicates that natural gas hydrates tend to reside mainly within pore spaces and do not come in contact with adjacent sands. Such an occurring model of natural gas hydrates is termed the floating model. Furthermore, natural gas hydrates were observed to nucleate at gas-water interfaces as lens-shaped clusters. Smaller sand grain sizes contribute to higher hydrate saturation. The wetting behavior of various sands had little effect on the occurrence of natural gas hydrates within pores. Additionally, geometric properties of the sediments were collected through CT image reconstructions. These findings will be instructive for understanding the microstructure of natural gas hydrates within major global reserves and for future resource utilization of natural gas hydrates.

Polymeric microcapsules with switchable mechanical properties for self-healing concrete: synthesis, characterisation and proof of concept

NASA Astrophysics Data System (ADS)

Kanellopoulos, A.; Giannaros, P.; Palmer, D.; Kerr, A.; Al-Tabbaa, A.

2017-04-01

Microcapsules, with sodium silicate solution as core, were produced using complex coacervation in a double, oil-in-water-in oil, emulsion system. The shell material was a gelatin-acacia gum crosslinked coacervate and the produced microcapsules had diameters ranging from 300 to 700 μm. The shell material designed with switchable mechanical properties. When it is hydrated exhibits soft and ‘rubbery’ behaviour and, when dried, transitions to a stiff and ‘glassy’ material. The microcapsules survived drying and rehydrating cycles and preserved their structural integrity when exposed to highly alkaline solutions that mimic the pH environment of concrete. Microscopy revealed that the shell thickness of the microcapsules varies across their perimeter from 5 to 20 μm. Thermal analysis showed that the produced microcapsules were very stable up to 190 °C. Proof of concept investigation has demonstrated that the microcapsules successfully survive and function when exposed to a cement-based matrix. Observations showed that the microcapsules survive mixing with cement and rupture successfully upon crack formation releasing the encapsulated sodium silicate solution.

Functional importance of short-range binding and long-range solvent interactions in helical antifreeze peptides.

PubMed

Ebbinghaus, Simon; Meister, Konrad; Prigozhin, Maxim B; Devries, Arthur L; Havenith, Martina; Dzubiella, Joachim; Gruebele, Martin

2012-07-18

Short-range ice binding and long-range solvent perturbation both have been implicated in the activity of antifreeze proteins and antifreeze glycoproteins. We study these two mechanisms for activity of winter flounder antifreeze peptide. Four mutants are characterized by freezing point hysteresis (activity), circular dichroism (secondary structure), Förster resonance energy transfer (end-to-end rigidity), molecular dynamics simulation (structure), and terahertz spectroscopy (long-range solvent perturbation). Our results show that the short-range model is sufficient to explain the activity of our mutants, but the long-range model provides a necessary condition for activity: the most active peptides in our data set all have an extended dynamical hydration shell. It appears that antifreeze proteins and antifreeze glycoproteins have reached different evolutionary solutions to the antifreeze problem, utilizing either a few precisely positioned OH groups or a large quantity of OH groups for ice binding, assisted by long-range solvent perturbation. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

New in Situ Measurements of the Viscosity of Gas Clathrate Hydrate Slurries Formed from Model Water-in-Oil Emulsions.

PubMed

Majid, Ahmad A A; Wu, David T; Koh, Carolyn A

2017-10-24

In situ rheological measurements for clathrate hydrate slurries were performed using a high pressure rheometer to determine the effect of hydrate particles on the viscosity and transportability of these slurries. These measurements were conducted using a well-characterized model water-in-oil emulsion ( Delgado-Linares et al. Model Water in-Oil Emulsions for Gas Hydrate Studies in Oil Continuous Systems . Energy Fuels 2013 , 27 , 4564 - 4573 ). The emulsion consists of a model liquid hydrocarbon, water, and a surfactant mixture of sorbitane monooleate 80 (Span 80) and sodium di-2-ethylhexylsulfosuccinate (Aerosol OT, AOT). This emulsion was used as an analog to water-in-crude oil (w/o) emulsions and provides reproducible results. The flow properties of the model w/o emulsion prior to hydrate formation were investigated in terms of several parameters including water percentage, temperature and pressure. A general equation that describes the viscosity of the emulsion as a function of the aforementioned parameters was developed. This general equation was able to predict the viscosity of a saturated emulsion at various temperatures and water percentages to within ±13% error. The general equation was then used to analyze the effect of hydrate formation on the transportability of gas hydrate slurries. As for hydrate slurries investigation, measurements were performed using methane gas as the hydrate former and a straight vane impeller as a stirring system. Tests were conducted at constant temperature and pressure (1 °C and 1500 psig of methane) and water percentages ranging from 5 to 30 vol %. Results of this work were analyzed and presented in terms of relative values, i.e., viscosities of the slurries relative to the viscosities of the continuous phase at similar temperature and pressure. In this work, a correlation to predict the relative viscosity of a hydrate slurry at various hydrate volume fractions was developed. Analysis of the developed correlation showed that the model was able to predict the relative viscosity of a hydrate slurry to within ±17% error.

Competitive Sorption of CO2 and H2O in 2:1 Layer Phyllosilicates

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

Schaef, Herbert T.; Loring, John S.; Glezakou, Vassiliki Alexandra

The salting out effect, where increasing the ionic strength of aqueous solutions decreases the solubility of dissolved gases is a well-known phenomenon. Less explored is the opposite process where an initially anhydrous system containing a volatile, relatively non-polar component and inorganic ions is systematically hydrated. Expandable clays such as montmorillonite are ideal systems for exploring this scenario as they have readily accessible exchange sites containing cations that can be systematically dehydrated or hydrated, from near anhydrous to almost bulk-like water conditions. This phenomenon has new significance with the simultaneous implementation of geological sequestration and secondary utilization of CO2 to bothmore » mitigate climate warming and enhance extraction of methane from hydrated clay-rich formations. Here, the partitioning of CO2 and H2O between Na-, Ca-, and Mg-exchanged montmorillonite and variably hydrated supercritical CO2 (scCO2) was investigated using in situ X-ray diffraction, infrared (IR)spectroscopic titrations, and quartz crystal microbalance (QCM) measurements. Density functional theory calculations provided mechanistic insights. Structural volumetric changes were correlated to quantified changes in sorbed H2O and CO2 concentrations as a function of %H2O saturated in scCO2. Intercalation of CO2 is favored at low H2O/CO2 ratios in the interlayer region, where CO2 can solvate the interlayer cation. As the clay becomes more hydrated and the H2O/CO2 ratio increases, H2O displaces CO2 from the solvation shell of the cation and CO2 tends to segregate. This transition decreases both the entropic and enthalpic driving force for CO2 intercalation, consistent with experimentally observed loss of intercalated CO2.« less

Preliminary Experimental Examination Of Controls On Methane Expulsion During Melting Of Natural Gas Hydrate Systems

NASA Astrophysics Data System (ADS)

Kneafsey, T. J.; Flemings, P. B.; Bryant, S. L.; You, K.; Polito, P. J.

2013-12-01

Global climate change will cause warming of the oceans and land. This will affect the occurrence, behavior, and location of subseafloor and subterranean methane hydrate deposits. We suggest that in many natural systems local salinity, elevated by hydrate formation or freshened by hydrate dissociation, may control gas transport through the hydrate stability zone. We are performing experiments and modeling the experiments to explore this behavior for different warming scenarios. Initially, we are exploring hydrate association/dissociation in saline systems with constant water mass. We compare experiments run with saline (3.5 wt. %) water vs. distilled water in a sand mixture at an initial water saturation of ~0.5. We increase the pore fluid (methane) pressure to 1050 psig. We then stepwise cool the sample into the hydrate stability field (~3 degrees C), allowing methane gas to enter as hydrate forms. We measure resistivity and the mass of methane consumed. We are currently running these experiments and we predict our results from equilibrium thermodynamics. In the fresh water case, the modeled final hydrate saturation is 63% and all water is consumed. In the saline case, the modeled final hydrate saturation is 47%, the salinity is 12.4 wt. %, and final water saturation is 13%. The fresh water system is water-limited: all the water is converted to hydrate. In the saline system, pore water salinity is elevated and salt is excluded from the hydrate structure during hydrate formation until the salinity drives the system to three phase equilibrium (liquid, gas, hydrate) and no further hydrate forms. In our laboratory we can impose temperature gradients within the column, and we will use this to investigate equilibrium conditions in large samples subjected to temperature gradients and changing temperature. In these tests, we will quantify the hydrate saturation and salinity over our meter-long sample using spatially distributed temperature sensors, spatially distributed resistivity probes, compressional wave velocities, and X-ray computed tomography scanning. Modeling of hydrate formation and dissociation for these conditions indicates that the transport of bulk fluid phases (gas and water) plays a crucial role in the overall behavior, and we will explore open-system boundary conditions in the experiments to test this prediction.

Controls on the physical properties of gas-hydrate-bearing sediments because of the interaction between gas hydrate and porous media

USGS Publications Warehouse

Lee, Myung W.; Collett, Timothy S.

2005-01-01

Physical properties of gas-hydrate-bearing sediments depend on the pore-scale interaction between gas hydrate and porous media as well as the amount of gas hydrate present. Well log measurements such as proton nuclear magnetic resonance (NMR) relaxation and electromagnetic propagation tool (EPT) techniques depend primarily on the bulk volume of gas hydrate in the pore space irrespective of the pore-scale interaction. However, elastic velocities or permeability depend on how gas hydrate is distributed in the pore space as well as the amount of gas hydrate. Gas-hydrate saturations estimated from NMR and EPT measurements are free of adjustable parameters; thus, the estimations are unbiased estimates of gas hydrate if the measurement is accurate. However, the amount of gas hydrate estimated from elastic velocities or electrical resistivities depends on many adjustable parameters and models related to the interaction of gas hydrate and porous media, so these estimates are model dependent and biased. NMR, EPT, elastic-wave velocity, electrical resistivity, and permeability measurements acquired in the Mallik 5L-38 well in the Mackenzie Delta, Canada, show that all of the well log evaluation techniques considered provide comparable gas-hydrate saturations in clean (low shale content) sandstone intervals with high gas-hydrate saturations. However, in shaly intervals, estimates from log measurement depending on the pore-scale interaction between gas hydrate and host sediments are higher than those estimates from measurements depending on the bulk volume of gas hydrate.

The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates

NASA Astrophysics Data System (ADS)

Powers, Anna; Scribano, Yohann; Lauvergnat, David; Mebe, Elsy; Benoit, David M.; Bačić, Zlatko

2018-04-01

We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v =0 and v =1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2-H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v =0 or v =1 , is derived from the high-quality ab initio full-dimensional (9D) PES of the H2-H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

Modeling the interactions of phthalocyanines in water: from the Cu(II)-tetrasulphonate to the metal-free phthalocyanine.

PubMed

Martín, Elisa I; Martínez, Jose M; Sánchez Marcos, Enrique

2011-01-14

A quantum and statistical study on the effects of the ions Cu(2+) and SO(3)(-) in the solvent structure around the metal-free phthalocyanine (H(2)Pc) is presented. We developed an ab initio interaction potential for the system CuPc-H(2)O based on quantum chemical calculations and studied its transferability to the H(2)Pc-H(2)O and [CuPc(SO(3))(4)](4-)-H(2)O interactions. The use of the molecular dynamics technique allows the determination of energetic and structural properties of CuPc, H(2)Pc, and [CuPc(SO(3))(4)](4-) in water and the understanding of the keys for the different behaviors of the three phthalocyanine (Pc) derivatives in water. The inclusion of the Cu(2+) cation in the Pc structure reinforces the appearance of two axial water molecules and second-shell water molecules in the solvent structure, whereas the presence of SO(3)(-) anions implies a well defined hydration shell of about eight water molecules around them making the macrocycle soluble in water. Debye-Waller factors for axial water molecules have been obtained in order to examine the potential sensitivity of the extended x-ray absorption fine structure technique to detect the axial water molecules.

Key Role of Nitrate in Phase Transitions of Urban Particles: Implications of Important Reactive Surfaces for Secondary Aerosol Formation

NASA Astrophysics Data System (ADS)

Sun, Jiaxing; Liu, Lei; Xu, Liang; Wang, Yuanyuan; Wu, Zhijun; Hu, Min; Shi, Zongbo; Li, Yongjie; Zhang, Xiaoye; Chen, Jianmin; Li, Weijun

2018-01-01

Ammonium sulfate (AS) and ammonium nitrate (AN) are key components of urban fine particles. Both field and model studies showed that heterogeneous reactions of SO2, NO2, and NH3 on wet aerosols accelerated the haze formation in northern China. However, little is known on phase transitions of AS-AN containing haze particles. Here hygroscopic properties of laboratory-generated AS-AN particles and individual particles collected during haze events in an urban site were investigated using an individual particle hygroscopicity system. AS-AN particles showed a two-stage deliquescence at mutual deliquescence relative humidity (MDRH) and full deliquescence relative humidity (DRH) and three physical states: solid before MDRH, solid-aqueous between MDRH and DRH, and aqueous after DRH. During hydration, urban haze particles displayed a solid core and aqueous shell at RH = 60-80% and aqueous phase at RH > 80%. Most particles were in aqueous phase at RH > 50% during dehydration. Our results show that AS content in individual particles determines their DRH and AN content determines their MDRH. AN content increase can reduce MDRH, which indicates occurrence of aqueous shell at lower RH. The humidity-dependent phase transitions of nitrate-abundant urban particles are important to provide reactive surfaces of secondary aerosol formation in the polluted air.

Water retention curve for hydrate-bearing sediments

NASA Astrophysics Data System (ADS)

Dai, Sheng; Santamarina, J. Carlos

2013-11-01

water retention curve plays a central role in numerical algorithms that model hydrate dissociation in sediments. The determination of the water retention curve for hydrate-bearing sediments faces experimental difficulties, and most studies assume constant water retention curves regardless of hydrate saturation. This study employs network model simulation to investigate the water retention curve for hydrate-bearing sediments. Results show that (1) hydrate in pores shifts the curve to higher capillary pressures and the air entry pressure increases as a power function of hydrate saturation; (2) the air entry pressure is lower in sediments with patchy rather than distributed hydrate, with higher pore size variation and pore connectivity or with lower specimen slenderness along the flow direction; and (3) smaller specimens render higher variance in computed water retention curves, especially at high water saturation Sw > 0.7. Results are relevant to other sediment pore processes such as bioclogging and mineral precipitation.

A Circuit Model of Real Time Human Body Hydration.

PubMed

Asogwa, Clement Ogugua; Teshome, Assefa K; Collins, Stephen F; Lai, Daniel T H

2016-06-01

Changes in human body hydration leading to excess fluid losses or overload affects the body fluid's ability to provide the necessary support for healthy living. We propose a time-dependent circuit model of real-time human body hydration, which models the human body tissue as a signal transmission medium. The circuit model predicts the attenuation of a propagating electrical signal. Hydration rates are modeled by a time constant τ, which characterizes the individual specific metabolic function of the body part measured. We define a surrogate human body anthropometric parameter θ by the muscle-fat ratio and comparing it with the body mass index (BMI), we find theoretically, the rate of hydration varying from 1.73 dB/min, for high θ and low τ to 0.05 dB/min for low θ and high τ. We compare these theoretical values with empirical measurements and show that real-time changes in human body hydration can be observed by measuring signal attenuation. We took empirical measurements using a vector network analyzer and obtained different hydration rates for various BMI, ranging from 0.6 dB/min for 22.7 [Formula: see text] down to 0.04 dB/min for 41.2 [Formula: see text]. We conclude that the galvanic coupling circuit model can predict changes in the volume of the body fluid, which are essential in diagnosing and monitoring treatment of body fluid disorder. Individuals with high BMI would have higher time-dependent biological characteristic, lower metabolic rate, and lower rate of hydration.

Nanotribology of charged polymer brushes

NASA Astrophysics Data System (ADS)

Klein, Jacob

Polymers at surfaces, whose modern understanding may be traced back to early work by Sam Edwards1, have become a paradigm for modification of surface properties, both as steric stabilizers and as remarkable boundary lubricants2. Charged polymer brushes are of particular interest, with both technological implications and especially biological relevance where most macromolecules are charged. In the context of biolubrication, relevant in areas from dry eye syndrome to osteoarthritis, charged polymer surface phases and their complexes with other macromolecules may play a central role. The hydration lubrication paradigm, where tenaciously-held yet fluid hydration shells surrounding ions or zwitterions serve as highly-efficient friction-reducing elements, has been invoked to understand the excellent lubrication provided both by ionized3 and by zwitterionic4 brushes. In this talk we describe recent advances in our understanding of the nanotribology of such charged brush systems. We consider interactions between charged end-grafted polymers, and how one may disentangle the steric from the electrostatic surface forces5. We examine the limits of lubrication by ionized brushes, both synthetic and of biological origins, and how highly-hydrated zwitterionic chains may provide extremely effective boundary lubrication6. Finally we describe how the lubrication of articular cartilage in the major joints, a tribosystem presenting some of the greatest challenges and opportunities, may be understood in terms of a supramolecular synergy between charged surface-attached polymers and zwitterionic groups7. Work supported by European Research Council (HydrationLube), Israel Science Foundation (ISF), Petroleum Research Fund of the American Chemical Society, ISF-NSF China Joint Program.

Seismic imaging of gas hydrate reservoir heterogeneities

NASA Astrophysics Data System (ADS)

Huang, Jun-Wei

Natural gas hydrate, a type of inclusion compound or clathrate, are composed of gas molecules trapped within a cage of water molecules. The presence of gas hydrate has been confirmed by core samples recovered from boreholes. Interests in the distribution of natural gas hydrate stem from its potential as a future energy source, geohazard to drilling activities and their possible impact on climate change. However the current geophysical investigations of gas hydrate reservoirs are still too limited to fully resolve the location and the total amount of gas hydrate due to its complex nature of distribution. The goal of this thesis is twofold, i.e., to model (1) the heterogeneous gas hydrate reservoirs and (2) seismic wave propagation in the presence of heterogeneities in order to address the fundamental questions: where are the location and occurrence of gas hydrate and how much is stored in the sediments. Seismic scattering studies predict that certain heterogeneity scales and velocity contrasts will generate strong scattering and wave mode conversion. Vertical Seismic Profile (VSP) techniques can be used to calibrate seismic characterization of gas hydrate expressions on surface seismograms. To further explore the potential of VSP in detecting the heterogeneities, a wave equation based approach for P- and S-wave separation is developed. Tests on synthetic data as well as applications to field data suggest alternative acquisition geometries for VSP to enable wave mode separation. A new reservoir modeling technique based on random medium theory is developed to construct heterogeneous multi-variable models that mimic heterogeneities of hydrate-bearing sediments at the level of detail provided by borehole logging data. Using this new technique, I modeled the density, and P- and S-wave velocities in combination with a modified Biot-Gassmann theory and provided a first order estimate of the in situ volume of gas hydrate near the Mallik 5L-38 borehole. Our results suggest a range of 528 to 768x10 6 m3/km2 of natural gas trapped within hydrate, nearly an order of magnitude lower than earlier estimates which excluded effects of small-scale heterogeneities. Further, the petrophysical models are combined with a 3-D Finite Difference method to study seismic attenuation. Thus a framework is built to further tune the models of gas hydrate reservoirs with constraints from well logs other disciplinary data.

Theoretical and computational studies of renewable energy materials: Room temperature ionic liquids and proton exchange membranes

NASA Astrophysics Data System (ADS)

Feng, Shulu

2011-12-01

Two kinds of renewable energy materials, room temperature ionic liquids (RTILs) and proton exchange membranes (PEMs), especially Nafion, are studied by computational and theoretical approaches. The ultimate purpose of the present research is to design novel materials to meet the future energy demands. To elucidate the effect of alkyl side chain length and anion on the structure and dynamics of the mixtures, molecular dynamics (MD) simulations of three RTILs/water mixtures at various water mole fractions: 1-butyl-3-methylimidazolium (BMIM+)/BF4-, 1-octyl-3-methylimidazolium (OMIM+)/BF4-, and OMIM +/Cl- are performed. Replacing the BMIM + cation with OMIM+ results in stronger aggregation of the cations as well as a slower diffusion of the anions, and replacing the BF4- anion with Cl- alters the water distribution at low water mole fractions and slows diffusion of the mixtures. Potential experimental manifestations of these behaviors in both cases are provided. Proton solvation properties and transport mechanisms are studied in hydrated Nafion, by using the self-consistent multistate empirical valence bond (SCI-MS-EVB) method. It is found that by stabilizing a more Zundel-like (H5O 2+) structure in the first solvation shells, the solvation of excess protons, as well as the proton hydration structure are both influenced by the sulfonate groups. Hydrate proton-related hydrogen bond networks are observed to be more stable than those with water alone. In order to characterize the nature of the proton transport (PT), diffusive motion, Arrhenius activation energies, and transport pathways are calculated and analyzed. Analysis of diffusive motion suggests that (1) a proton-hopping mechanism dominates the proton transport for the studied water loading levels and (2) there is an obvious degree of anti-correlation between the proton hopping and the vehicular transport. The activation energy drops rapidly with an increasing water content when the water loading level is smaller than ˜ 10 H2O/SO 3-, which is consistent with experimental observations. The sulfonate groups are also found to have influence on the proton hopping directions. The temperature and water content effects on the PT pathways are also investigated. The morphological effects on proton solvation and transport in hydrated Nafion are investigated, by using the SCI-MS-EVB method. Two of the most significant morphological models of Nafion, the lamellar model and the cylinder model, are selected. The two models exhibit distinct PT patterns, which result in different proton diffusion rates. In both models, the interaction between protons and the sulfonate groups are proven to be the key to determining PT behavior. The proton solvation structure change as a function of the distance between protons and sulfonate groups has been analyzed. It is found that the increase of water cylinder radius or water layer height leads to the presence of more protons around the sulfonate groups. Furthermore, at a lower hydration level, the increased amount of protons around the sulfonate groups consists of more Zundel-like structures, which is influenced by the distinct morphological structures of Nafion.

Permeability and porosity of hydrate-bearing sediments in the northern Gulf of Mexico

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

Daigle, Hugh; Cook, Ann; Malinverno, Alberto

Hydrate-bearing sands are being actively explored because they contain the highest concentrations of hydrate and are the most economically recoverable hydrate resource. However, relatively little is known about the mechanisms or timescales of hydrate formation, which are related to methane supply, fluid flux, and host sediment properties such as permeability. We used logging-while-drilling data from locations in the northern Gulf of Mexico to develop an effective medium theory-based model for predicting permeability based on clay-sized sediment fraction. The model considers permeability varying between sand and clay endpoint permeabilities that are defined from laboratory data. We verified the model using permeabilitymore » measurements on core samples from three boreholes, and then used the model to predict permeability in two wells drilled in Walker Ridge Block 313 during the Gulf of Mexico Gas Hydrate Joint Industry Project Leg II expedition in 2009. We found that the cleanest sands (clay-sized fraction <0.05) had intrinsic (hydrate-free) permeability contrasts of 5-6 orders of magnitude with the surrounding clays, which is sufficient to provide focused hydrate formation due to advection of methane from a deep source or diffusion of microbial methane from nearby clay layers. In sands where the clay-sized fraction exceeds 0.05, the permeability reduces significantly and focused flow is less pronounced. In these cases, diffusion of dissolved microbial methane is most likely the preferred mode of methane supply for hydrate formation. In conclusion, our results provide important constraints on methane supply mechanisms in the Walker Ridge area and have global implications for evaluating rates of methane migration and hydrate formation in hydrate-bearing sands.« less

Permeability and porosity of hydrate-bearing sediments in the northern Gulf of Mexico

DOE PAGES

Daigle, Hugh; Cook, Ann; Malinverno, Alberto

2015-10-14

Hydrate-bearing sands are being actively explored because they contain the highest concentrations of hydrate and are the most economically recoverable hydrate resource. However, relatively little is known about the mechanisms or timescales of hydrate formation, which are related to methane supply, fluid flux, and host sediment properties such as permeability. We used logging-while-drilling data from locations in the northern Gulf of Mexico to develop an effective medium theory-based model for predicting permeability based on clay-sized sediment fraction. The model considers permeability varying between sand and clay endpoint permeabilities that are defined from laboratory data. We verified the model using permeabilitymore » measurements on core samples from three boreholes, and then used the model to predict permeability in two wells drilled in Walker Ridge Block 313 during the Gulf of Mexico Gas Hydrate Joint Industry Project Leg II expedition in 2009. We found that the cleanest sands (clay-sized fraction <0.05) had intrinsic (hydrate-free) permeability contrasts of 5-6 orders of magnitude with the surrounding clays, which is sufficient to provide focused hydrate formation due to advection of methane from a deep source or diffusion of microbial methane from nearby clay layers. In sands where the clay-sized fraction exceeds 0.05, the permeability reduces significantly and focused flow is less pronounced. In these cases, diffusion of dissolved microbial methane is most likely the preferred mode of methane supply for hydrate formation. In conclusion, our results provide important constraints on methane supply mechanisms in the Walker Ridge area and have global implications for evaluating rates of methane migration and hydrate formation in hydrate-bearing sands.« less

Gas hydrate property measurements in porous sediments with resonant ultrasound spectroscopy

NASA Astrophysics Data System (ADS)

McGrail, B. P.; Ahmed, S.; Schaef, H. T.; Owen, A. T.; Martin, P. F.; Zhu, T.

2007-05-01

Resonant ultrasound spectroscopy was used to characterize a natural geological core sample obtained from the Mallik 5L-38 gas hydrate research well at high pressure and subambient temperatures. Using deuterated methane gas to form gas hydrate in the core sample, it was discovered that resonance amplitudes are correlated with the fraction of the pore space occupied by the gas hydrate crystals. A pore water freezing model was developed that utilizes the known pore size distribution and pore water chemistry to predict gas hydrate saturation as a function of pressure and temperature. The model showed good agreement with the experimental measurements and demonstrated that pore water chemistry is the most important factor controlling equilibrium gas hydrate saturations in these sediments when gas hydrates are formed artificially in laboratory pressure vessels. With further development, the resonant ultrasound technique can provide a rapid, nondestructive, field portable means of measuring the equilibrium P-T properties and dissociation kinetics of gas hydrates in porous media, determining gas hydrate saturations, and may provide new insights into the nature of gas hydrate formation mechanisms in geologic materials.

Signature of Europa's Ocean Density on Gravity Data

NASA Astrophysics Data System (ADS)

Castillo, J. C.; Rambaux, N.

2015-12-01

Observations by the Galileo mission at Europa and Cassini-Huygens mission at Europa, Ganymede, Callisto, Enceladus, and Titan have found deep oceans at these objects with evidence for the presence of salts. Salt compounds are the products of aqueous alteration of the rock phase under hydrothermal conditions and have been predicted theoretically for these objects per analogy with carbonaceous chondrite parent bodies. Evidence for salt enrichment comes from magnetometer measurements (Galilean satellites), direct detection in the case of Enceladus, and inversion of the gravity data obtained at Titan. While there is direct detection for the presence of chlorides in icy grains ejected from Enceladus, the chemistry of the oceans detected so far, or even their densities, remain mostly unconstrained. However the increased ocean density impacts the interpretation of the tidal Love number k2and this may introduce confusion in the inference of the icy shell thickness from that parameter. We will present estimates of k2for a range of assumptions on Europa's hydrospheric structure that build on geophysical observations obtained by the Galileo mission combined with new models of Europa's interior. These models keep track of the compositions of the hydrated core and oceanic composition in a self-consistent manner. We will also estimate the electrical conductivity corresponding to the modeled oceanic composition. Finally we will explore how combining electromagnetic, topographic, and gravity data can decouple the signatures of the shell thickness and ocean composition on these geophysical observations. Acknowledgement: This work is being carried out at the Jet Propulsion Laboratory, California Institute of Technology, under contract to NASA. Government sponsorship acknowledged.

Response of the oceanic methane hydrate inventory to future climate change (AR5 RCP 4.5 - 8.5)

NASA Astrophysics Data System (ADS)

Hunter, S. J.; Goldobin, D.; Haywood, A. M.; Ridgwell, A. J.; Rees, J.

2012-12-01

We present results from a study designed to look at the change in global methane hydrate volume in response to AR5 Representative Concentration Pathways (Fifth Assessment Report RCP). We use bottom water conditions derived from 12 climate models within the CMIP5 multi-model ensemble along with a series of linear sea-level models to define boundary conditions. We model the change in global hydrate stability zone volume and hydrate inventory from the pre-industrial era and forward model through the RCP scenarios (to 2100 and 2300) to 5 kyr into the future. We find that thermal effects (i.e. warming induced hydrate dissociation) are dominant even when accompanied by extreme rates of sea level rise (i.e. 15 and 20 mm yr-1). Over the coming century dissociation is focussed within the top 100 m of Arctic and Subarctic sediments, beneath < ˜500 m water depth. Assuming a simple model of hydrate fill fraction (with a nominal 1% average hydrate-fill fraction) estimated globally integrated hydrate dissociation rates at ˜2100 are 120, 140 and 180 Tg CH4 yr-1 for RCP 4.5, 6.0 and 8.5 and at year ˜2300 are 150 and 600 Tg CH4 yr-1 under ECP 4.5 and 8.5 respectively. Under the unmitigated business-as-usual scenario (RCP 8.5) globally-integrated CH4 fluxes from hydrate dissociation could exceed estimates of natural sea-floor levels by 2100. Subsequent oxidation of resulting CH4 within the water column would significantly reduce atmospheric release rates to between ˜0.7 and ˜1.4 Tg CH4 yr-1 at ˜2100.

Elevated gas hydrate saturation within silt and silty clay sediments in the Shenhu area, South China Sea

USGS Publications Warehouse

Wang, X.; Hutchinson, D.R.; Wu, S.; Yang, S.; Guo, Y.

2011-01-01

Gas hydrate saturations were estimated using five different methods in silt and silty clay foraminiferous sediments from drill hole SH2 in the South China Sea. Gas hydrate saturations derived from observed pore water chloride values in core samples range from 10 to 45% of the pore space at 190-221 m below seafloor (mbsf). Gas hydrate saturations estimated from resistivity (Rt) using wireline logging results are similar and range from 10 to 40.5% in the pore space. Gas hydrate saturations were also estimated by P wave velocity obtained during wireline logging by using a simplified three-phase equation (STPE) and effective medium theory (EMT) models. Gas hydrate saturations obtained from the STPE velocity model (41.0% maximum) are slightly higher than those calculated with the EMT velocity model (38.5% maximum). Methane analysis from a 69 cm long depressurized core from the hydrate-bearing sediment zone indicates that gas hydrate saturation is about 27.08% of the pore space at 197.5 mbsf. Results from the five methods show similar values and nearly identical trends in gas hydrate saturations above the base of the gas hydrate stability zone at depths of 190 to 221 mbsf. Gas hydrate occurs within units of clayey slit and silt containing abundant calcareous nannofossils and foraminifer, which increase the porosities of the fine-grained sediments and provide space for enhanced gas hydrate formation. In addition, gas chimneys, faults, and fractures identified from three-dimensional (3-D) and high-resolution two-dimensional (2-D) seismic data provide pathways for fluids migrating into the gas hydrate stability zone which transport methane for the formation of gas hydrate. Sedimentation and local canyon migration may contribute to higher gas hydrate saturations near the base of the stability zone. Copyright 2011 by the American Geophysical Union.

Hydration of calcium sulfoaluminate cements - Experimental findings and thermodynamic modelling

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

Winnefeld, Frank, E-mail: Frank.Winnefeld@empa.c; Lothenbach, Barbara

Calcium sulfoaluminate cements (CSA) are a promising low-CO{sub 2} alternative to ordinary Portland cements and are as well of interest concerning their use as binder for waste encapsulation. In this study, the hydration of two CSA cements has been investigated experimentally and by thermodynamic modelling between 1 h and 28 days at w/c ratios of 0.72 and 0.80, respectively. The main hydration product of CSA is ettringite, which precipitates together with amorphous Al(OH){sub 3} until the calcium sulfate is consumed after around 1-2 days of hydration. Afterwards, monosulfate is formed. In the presence of belite, straetlingite occurs as an additionalmore » hydration product. The pore solution analysis reveals that straetlingite can bind a part of the potassium ions, which are released by the clinker minerals. The microstructure of both cements is quite dense even after 16 h of hydration, with not much pore space available at a sample age of 28 days. The pore solution of both cements is dominated during the first hours of hydration by potassium, sodium, calcium, aluminium and sulfate; the pH is around 10-11. When the calcium sulfate is depleted, the sulfate concentration drops by a factor of 10. This increases pH to around 12.5-12.8. Based on the experimental data, a thermodynamic hydration model for CSA cements based on cement composition, hydration kinetics of clinker phases and calculations of thermodynamic equilibria by geochemical speciation has been established. The modelled phase development with ongoing hydration agrees well with the experimental findings.« less

Gas hydrate volume estimations on the South Shetland continental margin, Antarctic Peninsula

USGS Publications Warehouse

Jin, Y.K.; Lee, M.W.; Kim, Y.; Nam, S.H.; Kim, K.J.

2003-01-01

Multi-channel seismic data acquired on the South Shetland margin, northern Antarctic Peninsula, show that Bottom Simulating Reflectors (BSRs) are widespread in the area, implying large volumes of gas hydrates. In order to estimate the volume of gas hydrate in the area, interval velocities were determined using a 1-D velocity inversion method and porosities were deduced from their relationship with sub-bottom depth for terrigenous sediments. Because data such as well logs are not available, we made two baseline models for the velocities and porosities of non-gas hydrate-bearing sediments in the area, considering the velocity jump observed at the shallow sub-bottom depth due to joint contributions of gas hydrate and a shallow unconformity. The difference between the results of the two models is not significant. The parameters used to estimate the total volume of gas hydrate in the study area were 145 km of total length of BSRs identified on seismic profiles, 350 m thickness and 15 km width of gas hydrate-bearing sediments, and 6.3% of the average volume gas hydrate concentration (based on the second baseline model). Assuming that gas hydrates exist only where BSRs are observed, the total volume of gas hydrates along the seismic profiles in the area is about 4.8 ?? 1010 m3 (7.7 ?? 1012 m3 volume of methane at standard temperature and pressure).

Hydration behaviour of food grains and modelling their moisture pick up as per Peleg's equation: Part I. Cereals.

PubMed

Vasudeva, Singh; Vishwanathan, K H; Aswathanarayana, K N; Indhudhara Swamy, Y M

2010-01-01

Cereals and millets generally hydrate at a moderate rate and their hydration behaviour differs in native and in processed state. The study was on the hydration of paddy, milled rice, parboiled rice, wheat, millets and equilibrium moisture content (EMC) on soaking at room temperature. Paddy hydrated very slowly, hydration rate was slow in brown rice but fast in milled rice and highest in waxy rice. In most of the rice varieties, maximum absorption occurred at the end of 30 min. In wheat hydration rate was slow and its EMC was highest (43%). Maize grits of big size hydrated slowly compared to small grits. In coarse cereals EMC varied from 28 to 38%. Foxtail millet hydration was slow whereas that of finger millet was fast. The data were tested on the Peleg's equation, which gave a reasonable fit to experimental data. Peleg's constants k1 and k2 were calculated for the above grains and their hydration behaviour has been predicted. The model fitted very well to milled rice hydration data where the coefficient of variance ranged from 0.9982 to 0.9995. With exception in some millet the hydration data fitted well with the Peleg's equation. Generalized equations have been formulated for prediction of moisture content of cereals and millets.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding.

PubMed

Stadler, Andreas M; Demmel, Franz; Ollivier, Jacques; Seydel, Tilo

2016-08-03

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions. Here, we report an experimental study on the conformational dynamics of different folded conformational states of apo- and holomyoglobin in solution. Global protein diffusion and internal molecular motions were probed by neutron time-of-flight and neutron backscattering spectroscopy on the picosecond and nanosecond time scales. Global protein diffusion was found to depend on the α-helical content of the protein suggesting that charges on the macromolecule increase the short-time diffusion of protein. With regard to the molten globules, a gel-like phase due to protein entanglement and interactions with neighbouring macromolecules was visible due to a reduction of the global diffusion coefficients on the nanosecond time scale. Diffusion coefficients, residence and relaxation times of internal protein dynamics and root mean square displacements of localised internal motions were determined for the investigated structural states. The difference in conformational entropy ΔSconf of the protein between the unfolded and the partially or fully folded conformations was extracted from the measured root mean square displacements. Using thermodynamic parameters from the literature and the experimentally determined ΔSconf values we could identify the entropic contribution of the hydration shell ΔShydr of the different folded states. Our results point out the relevance of conformational entropy of the protein and the hydration shell for stability and folding of myoglobin.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Observations of different core water cluster ions Y-(H2O)n (Y = O2, HOx, NOx, COx) and magic number in atmospheric pressure negative corona discharge mass spectrometry.

PubMed

Sekimoto, Kanako; Takayama, Mitsuo

2011-01-01

Reliable mass spectrometry data from large water clusters Y(-)(H(2)O)(n) with various negative core ions Y(-) such as O(2)(-), HO(-), HO(2)(-), NO(2)(-), NO(3)(-), NO(3)(-)(HNO(3))(2), CO(3)(-) and HCO(4)(-) have been obtained using atmospheric pressure negative corona discharge mass spectrometry. All the core Y(-) ions observed were ionic species that play a central role in tropospheric ion chemistry. These mass spectra exhibited discontinuities in ion peak intensity at certain size clusters Y(-)(H(2)O)(m) indicating specific thermochemical stability. Thus, Y(-)(H(2)O)(m) may correspond to the magic number or first hydrated shell in the cluster series Y(-)(H(2)O)(n). The high intensity discontinuity at HO(-)(H(2)O)(3) observed was the first mass spectrometric evidence for the specific stability of HO(-)(H(2)O)(3) as the first hydrated shell which Eigen postulated in 1964. The negative ion water clusters Y(-)(H(2)O)(n) observed in the mass spectra are most likely to be formed via core ion formation in the ambient discharge area (760 torr) and the growth of water clusters by adiabatic expansion in the vacuum region of the mass spectrometers (≈1 torr). The detailed mechanism of the formation of the different core water cluster ions Y(-)(H(2)O)(n) is described. Copyright © 2010 John Wiley & Sons, Ltd.

Application of conditional simulation of heterogeneous rock properties to seismic scattering and attenuation analysis in gas hydrate reservoirs

NASA Astrophysics Data System (ADS)

Huang, Jun-Wei; Bellefleur, Gilles; Milkereit, Bernd

2012-02-01

We present a conditional simulation algorithm to parameterize three-dimensional heterogeneities and construct heterogeneous petrophysical reservoir models. The models match the data at borehole locations, simulate heterogeneities at the same resolution as borehole logging data elsewhere in the model space, and simultaneously honor the correlations among multiple rock properties. The model provides a heterogeneous environment in which a variety of geophysical experiments can be simulated. This includes the estimation of petrophysical properties and the study of geophysical response to the heterogeneities. As an example, we model the elastic properties of a gas hydrate accumulation located at Mallik, Northwest Territories, Canada. The modeled properties include compressional and shear-wave velocities that primarily depend on the saturation of hydrate in the pore space of the subsurface lithologies. We introduce the conditional heterogeneous petrophysical models into a finite difference modeling program to study seismic scattering and attenuation due to multi-scale heterogeneity. Similarities between resonance scattering analysis of synthetic and field Vertical Seismic Profile data reveal heterogeneity with a horizontal-scale of approximately 50 m in the shallow part of the gas hydrate interval. A cross-borehole numerical experiment demonstrates that apparent seismic energy loss can occur in a pure elastic medium without any intrinsic attenuation of hydrate-bearing sediments. This apparent attenuation is largely attributed to attenuative leaky mode propagation of seismic waves through large-scale gas hydrate occurrence as well as scattering from patchy distribution of gas hydrate.

Hydration of nonelectrolytes in binary aqueous solutions

NASA Astrophysics Data System (ADS)

Rudakov, A. M.; Sergievskii, V. V.

2010-10-01

Literature data on the thermodynamic properties of binary aqueous solutions of nonelectrolytes that show negative deviations from Raoult's law due largely to the contribution of the hydration of the solute are briefly surveyed. Attention is focused on simulating the thermodynamic properties of solutions using equations of the cluster model. It is shown that the model is based on the assumption that there exists a distribution of stoichiometric hydrates over hydration numbers. In terms of the theory of ideal associated solutions, the equations for activity coefficients, osmotic coefficients, vapor pressure, and excess thermodynamic functions (volume, Gibbs energy, enthalpy, entropy) are obtained in analytical form. Basic parameters in the equations are the hydration numbers of the nonelectrolyte (the mathematical expectation of the distribution of hydrates) and the dispersions of the distribution. It is concluded that the model equations adequately describe the thermodynamic properties of a wide range of nonelectrolytes partly or completely soluble in water.

A New Critical State Model for Geomechanical Behavior of Methane Hydrate-Bearing Sands

NASA Astrophysics Data System (ADS)

Lin, J. S.; Xing, P.; Rutqvist, J.; Seol, Y.; Choi, J. H.

2014-12-01

Methane hydrate bearing sands behave like sands once the hydrate has dissociated, but could exhibit a substantial increase in the shear strength, stiffness and dilatancy as the degree of hydrate saturation increases. A new critical state model was developed that incorporates the spatially mobilized plane (SMP) concept, which has been proven effective in modeling mechanical behavior of sands. While this new model was built on the basic constructs of the critical state model, important enhancements were introduced. The model adopted the t-stress concept, which defined the normal and shear stress on the SMP, in describing the plastic behavior of the soil. In this connection the versatile Matsuoka-Nakai yield criterion was also employed, which defined the general three dimensional yield behavior. The resulting constitutive law was associated in the t-stress space, but became non-associated in the conventional p-q stress space as it should be for sands. The model also introduced a generalized degree of hydrate saturation concept that was modified from the pioneering work of the Cambridge group. The model gives stress change when the sands are subjected to straining, and/or to hydrate saturation changes. The performance of the model has been found satisfactory using data from laboratory triaxial tests on reconstituted samples and core samples taken from Nankai Trough, Japan. The model has been implemented into FLAC3D. A coupling example with the multiphase flow code, TOUGH+, is presented which simulates the mechanical behavior of a sample when the surrounding temperature has been raised, and the hydrate undergoes state change and no longer resides in the stability zone.

Temperature and pressure correlation for volume of gas hydrates with crystal structures sI and sII

NASA Astrophysics Data System (ADS)

Vinš, Václav; Jäger, Andreas; Hielscher, Sebastian; Span, Roland; Hrubý, Jan; Breitkopf, Cornelia

The temperature and pressure correlations for the volume of gas hydrates forming crystal structures sI and sII developed in previous study [Fluid Phase Equilib. 427 (2016) 268-281], focused on the modeling of pure gas hydrates relevant in CCS (carbon capture and storage), were revised and modified for the modeling of mixed hydrates in this study. A universal reference state at temperature of 273.15 K and pressure of 1 Pa is used in the new correlation. Coefficients for the thermal expansion together with the reference lattice parameter were simultaneously correlated to both the temperature data and the pressure data for the lattice parameter. A two-stage Levenberg Marquardt algorithm was employed for the parameter optimization. The pressure dependence described in terms of the bulk modulus remained unchanged compared to the original study. A constant value for the bulk modulus B0 = 10 GPa was employed for all selected hydrate formers. The new correlation is in good agreement with the experimental data over wide temperature and pressure ranges from 0 K to 293 K and from 0 to 2000 MPa, respectively. Compared to the original correlation used for the modeling of pure gas hydrates the new correlation provides significantly better agreement with the experimental data for sI hydrates. The results of the new correlation are comparable to the results of the old correlation in case of sII hydrates. In addition, the new correlation is suitable for modeling of mixed hydrates.

Beaufort Sea deep-water gas hydrate recovery from a seafloor mound in a region of widespread BSR occurrence

USGS Publications Warehouse

Hart, Patrick E.; Pohlman, John W.; Lorenson, T.D.; Edwards, Brian D.

2011-01-01

Gas hydrate was recovered from the Alaskan Beaufort Sea slope north of Camden Bay in August 2010 during a U.S. Coast Guard Cutter Healy expedition (USCG cruise ID HLY1002) under the direction of the U.S. Geological Survey (USGS). Interpretation of multichannel seismic (MCS) reflection data collected in 1977 by the USGS across the Beaufort Sea continental margin identified a regional bottom simulating reflection (BSR), indicating that a large segment of the Beaufort Sea slope is underlain by gas hydrate. During HLY1002, gas hydrate was sampled by serendipity with a piston core targeting a steep-sided bathymetric high originally thought to be an outcrop of older, exposed strata. The feature cored is an approximately 1100m diameter, 130 m high conical mound, referred to here as the Canning Seafloor Mound (CSM), which overlies the crest of a buried anticline in a region of sub-parallel compressional folds beneath the eastern Beaufort outer slope. An MCS profile shows a prominent BSR upslope and downslope from the mound. The absence of a BSR beneath the CSM and occurrence of gas hydrate near the summit indicates that free gas has migrated via deep-rooted thrust faults or by structural focusing up the flanks of the anticline to the seafloor. Gas hydrate recovered from near the CSM summit at a subbottom depth of about 5.7 meters in a water depth of 2538 m was of nodular and vein-filling morphology. Although the hydrate was not preserved, residual gas from the core liner contained >95% methane by volume when corrected for atmospheric contamination. The presence of trace C4+hydrocarbons (<0.1% by volume) confirms at least a minor thermogenic component. Authigenic carbonates and mollusk shells found throughout the core indicate sustained methane-rich fluid advection and possible sediment extrusion contributing to the development of the mound. Blister-like inflation of the seafloor caused by formation and accumulation of shallow hydrate lenses is also a likely factor in CSM growth. Pore water analysis shows the sulfate-methane transition to be very shallow (0-1 mbsf), also supporting an active high-flux interpretation. Pore water with chloride concentrations as low as 160 mM suggest fluid migration pathways may extend to the mound from buried non-marine sediments containing low-salinity fluids.

Methane hydrate induced permeability modification for multiphase flow in unsaturated porous media

NASA Astrophysics Data System (ADS)

Seol, Yongkoo; Kneafsey, Timothy J.

2011-08-01

An experimental study was performed using X-ray computed tomography (CT) scanning to capture three-dimensional (3-D) methane hydrate distributions and potential discrete flow pathways in a sand pack sample. A numerical study was also performed to develop and analyze empirical relations that describe the impacts of hydrate accumulation habits within pore space (e.g., pore filling or grain cementing) on multiphase fluid migration. In the experimental study, water was injected into a hydrate-bearing sand sample that was monitored using an X-ray CT scanner. The CT images were converted into numerical grid elements, providing intrinsic sample data including porosity and phase saturations. The impacts of hydrate accumulation were examined by adapting empirical relations into the flow simulations as additional relations governing the evolution of absolute permeability of hydrate bearing sediment with hydrate deposition. The impacts of pore space hydrate accumulation habits on fluid migration were examined by comparing numerical predictions with experimentally measured water saturation distributions and breakthrough curves. A model case with 3-D heterogeneous initial conditions (hydrate saturation, porosity, and water saturation) and pore body-preferred hydrate accumulations best captured water migration behavior through the hydrate-bearing sample observed in the experiment. In the best matching model, absolute permeability in the hydrate bearing sample does not decrease significantly with increasing hydrate saturation until hydrate saturation reaches about 40%, after which it drops rapidly, and complete blockage of flow through the sample can occur as hydrate accumulations approach 70%. The result highlights the importance of permeability modification due to hydrate accumulation habits when predicting multiphase flow through high-saturation, reservoir quality hydrate-bearing sediments.

Dependence of the form factor of ganglioside micelles on a conformational change with temperature

NASA Astrophysics Data System (ADS)

Corti, Mario; Boretta, Marco; Cantù, Laura; Del Favero, Elena; Lesieur, Pierre

1996-09-01

The gangliosides GM2, GM1 and GD1b, biological amphiphiles with a double tail hydrophobic part and an oligosaccharide chain headgroup, form micelles in solution. Light scattering experiments have shown that ganglioside micelles which have gone through a temperature cycle have a smaller molecular mass and hydrodynamic radius than those which have been kept at room temperature. This fact has been interpreted with the hypothesis that, with temperature, the ganglioside molecules undergo a conformational change which affects their micellar properties appreciably. Careful small angle X-ray experiments, aimed to confirm the light scattering data and to evidence differences in the micellar internal structure are presented. Ganglioside micelles are quite inhomogeneous particles with respect to X-ray scattering, since there is a large contrast variation between the inner lipid part and the external hydrated sugar layer. Experimental form factors are fitted with a double-shell oblate-ellipsoid model.

Stable prenucleation mineral clusters are liquid-like ionic polymers

PubMed Central

Demichelis, Raffaella; Raiteri, Paolo; Gale, Julian D.; Quigley, David; Gebauer, Denis

2011-01-01

Calcium carbonate is an abundant substance that can be created in several mineral forms by the reaction of dissolved carbon dioxide in water with calcium ions. Through biomineralization, organisms can harness and control this process to form various functional materials that can act as anything from shells through to lenses. The early stages of calcium carbonate formation have recently attracted attention as stable prenucleation clusters have been observed, contrary to classical models. Here we show, using computer simulations combined with the analysis of experimental data, that these mineral clusters are made of an ionic polymer, composed of alternating calcium and carbonate ions, with a dynamic topology consisting of chains, branches and rings. The existence of a disordered, flexible and strongly hydrated precursor provides a basis for explaining the formation of other liquid-like amorphous states of calcium carbonate, in addition to the non-classical behaviour during growth of amorphous calcium carbonate. PMID:22186886

Modeling of Hydrate Formation Mode in Raw Natural Gas Air Coolers

NASA Astrophysics Data System (ADS)

Scherbinin, S. V.; Prakhova, M. Yu; Krasnov, A. N.; Khoroshavina, E. A.

2018-05-01

Air cooling units (ACU) are used at all the gas fields for cooling natural gas after compressing. When using ACUs on raw (wet) gas in a low temperature condition, there is a danger of hydrate plug formation in the heat exchanging tubes of the ACU. To predict possible hydrate formation, a mathematical model of the air cooler thermal behavior used in the control system shall adequately calculate not only gas temperature at the cooler's outlet, but also a dew point value, a temperature at which condensation, as well as the gas hydrate formation point, onsets. This paper proposes a mathematical model allowing one to determine the pressure in the air cooler which makes hydrate formation for a given gas composition possible.

Methane Hydrate Formation in Thick Sand Reservoirs: Long-range Gas Transport or Short-range Methane Diffusion?

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2016-12-01

We developed two 2-D numerical models to simulate hydrate formation by long range methane gas transport and short-range methane diffusion. We interpret that methane hydrates in thick sands are most likely formed by long range gas transport where methane gas is transported upward into the hydrate stability zone (HSZ) under buoyancy and locally forms hydrate to its stability limit. In short-range methane diffusion, methane is generated locally by biodegradation of organic matter in mud and diffused into bounding sands where it forms hydrate. We could not simulate enough methane transport by diffusion to account for its observed concentration in thick sands. In our models, we include the capillary effect on dissolved methane solubility and on the hydrate phase boundary, sedimentation and different compaction in sand and mud, fracture generation as well as the fully coupled multiphase flow and multicomponent transport. We apply our models to a 12 meter-thick hydrate-bearing sand layer at Walker Ridge 313, Northern Gulf of Mexico. With the long-range gas transport, hydrate saturation is greater than 90% and salinity is increased from seawater to about 8 wt.% through the entire sand. With short-range diffusion, hydrate saturation is more than 90% at the sand base and is less than 10% in the overlying section; salinity is close to seawater when sand is deposited to 800 meter below seafloor by short-range methane diffusion. With short-range diffusion, the amount of hydrate formed is much less than that interpreted from the well log data. Two transient gas layers separated by a hydrate layer are formed from short-range diffusion caused by capillary effect. This could be interpreted as a double bottom simulating reflector. This study provides further insights into different hydrate formation mechanisms, and could serve as a base to confirm the hydrate formation mechanism in fields.

Fractional order creep model for dam concrete considering degree of hydration

NASA Astrophysics Data System (ADS)

Huang, Yaoying; Xiao, Lei; Bao, Tengfei; Liu, Yu

2018-05-01

Concrete is a material that is an intermediate between an ideal solid and an ideal fluid. The creep of concrete is related not only to the loading age and duration, but also to its temperature and temperature history. Fractional order calculus is a powerful tool for solving physical mechanics modeling problems. Using a software element based on the generalized Kelvin model, a fractional order creep model of concrete considering the loading age and duration is established. Then, the hydration rate of cement is considered in terms of the degree of hydration, and the fractional order creep model of concrete considering the degree of hydration is established. Moreover, uniaxial tensile creep tests of dam concrete under different curing temperatures were conducted, and the results were combined with the creep test data and complex optimization method to optimize the parameters of a new creep model. The results show that the fractional tensile creep model based on hydration degree can better describe the tensile creep properties of concrete, and this model involves fewer parameters than the 8-parameter model.

Biocatalytic CO2 sequestration based on shell regeneration

NASA Astrophysics Data System (ADS)

Lee, S.

2012-04-01

Carbon dioxide, CO2, is one of the green gases, being uniformly distributed over the earth's surface. Recently, a variety of methods exists or has been proposed for pre- or post-emission capture and sequestration of CO2. However, CCS (carbon capture & storage) do not quarntee permanent treatment of CO2 and could ingenerate environment risks. Some organisms convert CO2 into exoskeleton (e.g., mollusks) or energy sources (e.g., plants) during metabolism under atmospheric conditions. One of representative biomaterials in ocean is bivalve shell to be composed of CaCO3. Calcium carbonate is not only abundant material in the world but also thermodynamically stable mineral in the capture of CO2. Bivalve has produced CaCO3 under seawater condition, in other word, near atmospheric conditions (1 atm. and around 20-25 oC). At the inorganic point, the synthesis of CaCO3 is as followed. Ca2+ + CO32- -> CaCO3 The bivalve shell plays an important role to protect bivalve's internal organs from prodetor. What will be happened if the shell is damaged and a hole is made? Bivalve must cover the hole to prevent the oxidation of internal organs as fast as possible. From in vitro crystallization test of a notched shell, rapid CaCO3 production was identified at the damaged area. The biocatalyst related to shell regeneration was purified and named as SPSR (Soluble Protein related to Shell Regeneration) that is obtained from the oyster, Crassostrea gigas. And in vitro CaCO3 crystallization test was used to calculate the crystal growth rate of SPSR on CaCO3 crystallization. The characteristics of SPRR are discussed at the point of CO2 hydration and rapid CaCO3 synthesis. To develop the bioinspired process based on shell regeneration concept, the analysis of protein structure has been studied and the immobilization has been carried out for easy recovery of SPSR.

Sensitivity Studies on Productivity Performance from 3D Heterogeneous Reservoir Model Based on the L-Pad Gas Hydrate Accumulation in Prudhoe Bay Unit, North Slope Alaska

NASA Astrophysics Data System (ADS)

Myshakin, E. M.; Ajayi, T.; Seol, Y.; Boswell, R.

2016-12-01

Three-dimensional reservoir model of the "L-Pad" hydrate deposit located in the Prudhoe Bay region of the Alaska's North Slope was created including four stratigraphic units; silty shale overburden, hydrate-bearing D sand, inter-reservoir silty shale, hydrate-bearing C sand, and silty shale underburden. The model incorporates the actual geological settings, accounts for the presence of faults, reservoir dip, the hydrate-water contact in the C sand. Geostatistical porosity distributions in D and C sands conditioned to log data from 78 wells drilled in the vicinity of the Prudhoe Bay "L-pad" were developed providing vertical and lateral 3D heterogeneity in porosity and porosity-dependent hydrate saturation and intrinsic permeability. Gas production potential was estimated using a conventional vertical wellbore completion and a deviated toe-down wellbore perforated through both sand units to induce hydrate depressurization at a constant bottom-hole pressure. The results have shown the greater performance of the deviated well design over the vertical one. The scenarios involving simultaneous and sequential hydrate dissociation in sand units were explored and the effect of the underlying aquifer in the C sand was estimated. Sensitivity analysis has demonstrated that hydraulic communication with over- and underlying shale units affects production in the beginning of depressurization due to competitive water influx into producing mobile flow and could suppress efficient hydrate decomposition resulting in production lag. Another important factor greatly influencing the productivity performance is the effective permeability of hydrate-bearing sediment controlled by the relative permeability function. The results call for the necessity of thorough fundamental studies to understand multi-phase flow in hydrate-bearing sediments with different hydrate precipitation habits.

TOUGH+HYDRATE v1.2 User's Manual: A Code for the Simulation of System Behavior in Hydrate-Bearing Geologic Media

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

Moridis, George J.; Kowalsky, Michael B.; Pruess, Karsten

TOUGH+HYDRATE v1.2 is a code for the simulation of the behavior of hydratebearing geologic systems, and represents the second update of the code since its first release [Moridis et al., 2008]. By solving the coupled equations of mass and heat balance, TOUGH+HYDRATE can model the non-isothermal gas release, phase behavior and flow of fluids and heat under conditions typical of common natural CH4-hydrate deposits (i.e., in the permafrost and in deep ocean sediments) in complex geological media at any scale (from laboratory to reservoir) at which Darcy’s law is valid. TOUGH+HYDRATE v1.2 includes both an equilibrium and a kinetic modelmore » of hydrate formation and dissociation. The model accounts for heat and up to four mass components, i.e., water, CH4, hydrate, and water-soluble inhibitors such as salts or alcohols. These are partitioned among four possible phases (gas phase, liquid phase, ice phase and hydrate phase). Hydrate dissociation or formation, phase changes and the corresponding thermal effects are fully described, as are the effects of inhibitors. The model can describe all possible hydrate dissociation mechanisms, i.e., depressurization, thermal stimulation, salting-out effects and inhibitor-induced effects. TOUGH+HYDRATE is a member of TOUGH+, the successor to the TOUGH2 [Pruess et al., 1991] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. It is written in standard FORTRAN 95/2003, and can be run on any computational platform (workstation, PC, Macintosh) for which such compilers are available.« less

Simulation and Characterization of Methane Hydrate Formation

NASA Astrophysics Data System (ADS)

Dhakal, S.; Gupta, I.

2017-12-01

The ever rising global energy demand dictates human endeavor to explore and exploit new and innovative energy sources. As conventional oil and gas reserves deplete, we are constantly looking for newer sources for sustainable energy. Gas hydrates have long been discussed as the next big energy resource to the earth. Its global occurrence and vast quantity of natural gas stored is one of the main reasons for such interest in its study and exploration. Gas hydrates are solid crystalline substances with trapped molecules of gas inside cage-like crystals of water molecules. Gases such as methane, ethane, propane and carbon dioxide can form hydrates but in natural state, methane hydrates are the most common. Subsurface geological conditions with high pressure and low temperature favor the formation and stability of gas hydrates. While the occurrence and potential of gas hydrates as energy source has long been studied, there are still gaps in knowledge, especially in the quantitative research of gas hydrate formation and reservoir characterization. This study is focused on exploring and understanding the geological setting in which gas hydrates are formed and the subsequent changes in rock characteristics as they are deposited. It involves the numerical simulation of methane gas flow through fault to form hydrates. The models are representative of the subsurface geologic setting of Gulf of Mexico with a fault through layers of shale and sandstone. Hydrate formation simulated is of thermogenic origin. The simulations are conducted using TOUGH+HYDRATE, a numerical code developed at the Lawrence Berkley National Laboratory for modeling multiphase flow through porous medium. Simulation results predict that as the gas hydrates form in the pores of the model, the porosity, permeability and other rock properties are altered. Preliminary simulation results have shown that hydrates begin to form in the fault zone and gradually in the sandstone layers. The increase in hydrate saturation is followed by decrease in the porosity and permeability of the reservoir rock. Sensitivities on flow rates of gas and water are simulated, using different reservoir properties, fault angles and grid sizes to study the properties of hydrate formation and accumulation in the subsurface.

Dynamical transition, hydrophobic interface, and the temperature dependence of electrostatic fluctuations in proteins.

PubMed

Lebard, David N; Matyushov, Dmitry V

2008-12-01

Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of electrostatic fluctuations, expressed in terms of the reorganization energy of changing the redox state of the protein, is related to the formation of the hydrophobic protein-water interface, allowing large-amplitude collective fluctuations of the water density in the protein's first solvation shell. On top of the monotonic increase of the reorganization energy with increasing temperature, we have observed a spike at approximately 220 K also accompanied by a significant slowing of the exponential collective Stokes shift dynamics. In contrast to the local density fluctuations of the hydration-shell waters, these spikes might be related to the global property of the water solvent crossing the Widom line or undergoing a weak first-order transition.

3-D basin-scale reconstruction of natural gas hydrate system of the Green Canyon, Gulf of Mexico

NASA Astrophysics Data System (ADS)

Burwicz, Ewa; Reichel, Thomas; Wallmann, Klaus; Rottke, Wolf; Haeckel, Matthias; Hensen, Christian

2017-05-01

Our study presents a basin-scale 3-D modeling solution, quantifying and exploring gas hydrate accumulations in the marine environment around the Green Canyon (GC955) area, Gulf of Mexico. It is the first modeling study that considers the full complexity of gas hydrate formation in a natural geological system. Overall, it comprises a comprehensive basin reconstruction, accounting for depositional and transient thermal history of the basin, source rock maturation, petroleum components generation, expulsion and migration, salt tectonics, and associated multistage fault development. The resulting 3-D gas hydrate distribution in the Green Canyon area is consistent with independent borehole observations. An important mechanism identified in this study and leading to high gas hydrate saturation (>80 vol %) at the base of the gas hydrate stability zone (GHSZ) is the recycling of gas hydrate and free gas enhanced by high Neogene sedimentation rates in the region. Our model predicts the rapid development of secondary intrasalt minibasins situated on top of the allochthonous salt deposits which leads to significant sediment subsidence and an ensuing dislocation of the lower GHSZ boundary. Consequently, large amounts of gas hydrates located in the deepest parts of the basin dissociate and the released free methane gas migrates upward to recharge the GHSZ. In total, we have predicted the gas hydrate budget for the Green Canyon area that amounts to ˜3256 Mt of gas hydrate, which is equivalent to ˜340 Mt of carbon (˜7 × 1011 m3 of CH4 at STP conditions), and consists mostly of biogenic hydrates.

A method to predict equilibrium conditions of gas hydrate formation in porous media

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

Clarke, M.A.; Pooladi-Darvish, M.; Bishnoi, P.R.

1999-06-01

In the petroleum industry, it is desirable to avoid the formation of gas hydrates. When gas hydrates form, they tend to agglomerate and block pipelines and process equipment. However, naturally occurring gas hydrates that form in the permafrost region or in deep oceans represent a vast untouched natural gas reserve. Although the exact amount of gas in the hydrate form is not known, it is believed to be comparable to the known amount of gas in the free state. Numerous methods for the recovery of natural gas from hydrate fields have been proposed. These techniques include thermal decomposition, depressurization, andmore » chemical injection. To fully exploit hydrate reserves, it will be necessary to know the decomposition/formation conditions of the gas hydrate in porous media. A predictive model has been developed to determine the incipient hydrate formation conditions in porous media. The only additional information that is needed to determine the incipient hydrate formation conditions is the pore radius, surface energy per unit area, and wetting angle. It was found that the model performed well in predicting the experimental data of Handa and Stupin.« less

Sivelestat sodium hydrate improves post-traumatic knee osteoarthritis through nuclear factor-κB in a rat model.

PubMed

Yu, Xiaofeng; Zhao, Lijun; Yu, Zhiping; Yu, Changzheng; Bi, Jianfei; Sun, Binglong; Cong, Haibo

2017-08-01

As a specific inhibitor of neutrophil elastase, sivelestat sodium hydrate has primarily been used in the treatment of acute lung injury caused by various factors since its approval in 2002. Sivelestat sodium hydrate also improves post-traumatic knee osteoarthritis (KOA), although its underlying mechanisms of action have yet to be elucidated. The aim of the current study was to determine if sivelestat sodium hydrate improves post-traumatic KOA through nuclear factor (NF)-κB in a rat model. Treatment with sivelestat sodium hydrate significantly inhibited the induction of structural changes and significantly increased the vertical episode count and ipsilateral static weight bearing of the joint in KOA rats (all P<0.01). Sivelestat sodium hydrate significantly inhibited tumor necrosis factor-α and interleukin-6 production, serum nitrite levels, inducible nitric oxide synthase protein expression and high mobility group box 1 (HMGB1) secretion in KOA rats compared with the model group (all P<0.01). Sivelestat sodium hydrate also significantly suppressed p50/p65 DNA binding activity and NF-κB and phosphorylated inhibitor of κB protein expression in the joints of KOA rats compared with the model group (all P<0.01). These results suggest that sivelestat sodium hydrate improves post-traumatic KOA through HMGB1 and NF-κB in rats.

Sivelestat sodium hydrate improves post-traumatic knee osteoarthritis through nuclear factor-κB in a rat model

PubMed Central

Yu, Xiaofeng; Zhao, Lijun; Yu, Zhiping; Yu, Changzheng; Bi, Jianfei; Sun, Binglong; Cong, Haibo

2017-01-01

As a specific inhibitor of neutrophil elastase, sivelestat sodium hydrate has primarily been used in the treatment of acute lung injury caused by various factors since its approval in 2002. Sivelestat sodium hydrate also improves post-traumatic knee osteoarthritis (KOA), although its underlying mechanisms of action have yet to be elucidated. The aim of the current study was to determine if sivelestat sodium hydrate improves post-traumatic KOA through nuclear factor (NF)-κB in a rat model. Treatment with sivelestat sodium hydrate significantly inhibited the induction of structural changes and significantly increased the vertical episode count and ipsilateral static weight bearing of the joint in KOA rats (all P<0.01). Sivelestat sodium hydrate significantly inhibited tumor necrosis factor-α and interleukin-6 production, serum nitrite levels, inducible nitric oxide synthase protein expression and high mobility group box 1 (HMGB1) secretion in KOA rats compared with the model group (all P<0.01). Sivelestat sodium hydrate also significantly suppressed p50/p65 DNA binding activity and NF-κB and phosphorylated inhibitor of κB protein expression in the joints of KOA rats compared with the model group (all P<0.01). These results suggest that sivelestat sodium hydrate improves post-traumatic KOA through HMGB1 and NF-κB in rats. PMID:28810618

Strength and acoustic properties of Ottawa sand containing laboratory-formed methane gas hydrate

USGS Publications Warehouse

Winters, William J.; Waite, William F.; Mason, David H.

2004-01-01

Although gas hydrate occurs in a wide variety of sediment types and is present and even pervasive at some locations on continental margins, little is known about how it forms naturally. Physical properties of the resultant gas hydrate-sediment mixtures, data needed for input into models that predict location and quantity of in situ hydrate are also lacking. Not only do properties of the host materials influence the type and quantity of hydrate formed and whether a particular deposit may be an economic resource or a geohazard, the properties of the natural sediment are also subsequently changed by the formation of gas hydrate in the pore space. The magnitude of the change is primarily related to the amount and the weighted inter-particle distribution of the hydrate deposits in relation to the actual sediment grains. Our goal is to understand the interaction between natural sediments and gas hydrate formation in order to quantify physical properties that are useful to predictive models.

Characterization of a stratigraphically constrained gas hydrate system along the western continental margin of Svalbard from ocean bottom seismometer data

NASA Astrophysics Data System (ADS)

Chabert, Anne; Minshull, Tim A.; Westbrook, Graham K.; Berndt, Christian; Thatcher, Kate E.; Sarkar, Sudipta

2011-12-01

The ongoing warming of bottom water in the Arctic region is anticipated to destabilize some of the gas hydrate present in shallow seafloor sediment, potentially causing the release of methane from dissociating hydrate into the ocean and the atmosphere. Ocean-bottom seismometer (OBS) experiments were conducted along the continental margin of western Svalbard to quantify the amount of methane present as hydrate or gas beneath the seabed. P- and S-wave velocities were modeled for five sites along the continental margin, using ray-trace forward modeling. Two southern sites were located in the vicinity of a 30 km long zone where methane gas bubbles escaping from the seafloor were observed during the cruise. The three remaining sites were located along an E-W orientated line in the north of the margin. At the deepest northern site, Vp anomalies indicate the presence of hydrate in the sediment immediately overlying a zone containing free gas up to 100-m thick. The acoustic impedance contrast between the two zones forms a bottom-simulating reflector (BSR) at approximately 195 m below the seabed. The two other sites within the gas hydrate stability zone (GHSZ) do not show the clear presence of a BSR or of gas hydrate. However, anomalously low Vp, indicating the presence of free gas, was modeled for both sites. The hydrate content was estimated from Vp and Vs, using effective-medium theory. At the deepest northern site, modeling suggests a pore-space hydrate concentration of 7-12%, if hydrate forms as part of a connected framework, and about 22% if it is pore-filling. At the two other northern sites, located between the deepest site and the landward limit of the GHSZ, we suggest that hydrate is present in the sediment as inclusions. Hydrate may be present in small quantities at these two sites (4-5%) of the pore space. The variation in lithology for the three sites indicated by high-resolution seismic profiles may control the distribution, concentration and formation of hydrate and free gas.

Analysis of past recurrent methane seep activity using radiocarbon dating of Calyptogena spp. shells in the eastern Nankai subduction zone, Japan

NASA Astrophysics Data System (ADS)

Yagasaki, Kazuhiro; Ashi, Juichiro; Yokoyama, Yusuke; Miyairi, Yosuke; Kuramoto, Shin'ichi

2016-04-01

Fault activity around subduction zones have been widely studied and monitored through drilling of oceanic plates, studying piston cores, use of monitoring equipment or through visual analysis using submersible vehicles. Yet the understanding of how small scale faults near shallow regions of the seabed behave in relation to cold seep vent activity is still vague, especially determining when they were active in the past. In tectonically active margins such as the Nankai and Tokai regions off Japan, dense methane hydrate reservoirs have been identified. Cold seeps releasing methane rich hydrocarbon fluids are common here, supporting a wide variety of biological species that hold a symbiotic relationship with the chemosynthetic bacteria. In 1998 a large dead Calyptogena spp. bivalve colony (over 400m2 in size) was discovered off Tokai, Japan. It is unusual for a bivalve colony this size to mostly be dead, raising questions as to what caused their death. In this study we document the radiocarbon 14C age of these bivalve shells to attempt analysing the possible methane seep bahaviour in the past. The measured 14C age ranged in three age groups of 1396±36-1448±34, 1912±31-1938±35 and 5975±34. The 14C age of shells that were alive upon collection and the dissolved inorganic carbon (DIC) in seawater show little difference (˜100 14C age) indicating that shells are not heavily affected by the dead carbon effect from cold seeps that is of biogenic or thermogenic origin, which can make the age to become considerably older than the actual age. Thus the novel calibration model used was based on the seawater DIC collected above the Calyptogena spp. colony site (1133±31), which resulted in the dead shells to be clustered around 1900 Cal AD. This proves to be interesting as the predicted epicenter of the Ansei-Tokai earthquake (M 8.4) in 1854 is extremely close to the bibalve colony site. Using geological data obtained using visual analysis and sub-seafloor structural analysis that show multiple shallow faults and chaotic sediment structure below the colony site, the Calyptogena spp. shells have a strong connection to the coseismic faulting activity and could show potential for radiocarbon dating to be applied on marine samples providing the necessary calibration tools are available.

In situ thermal conductivity of gas-hydrate-bearing sediments of the Mallik 5L-38 well

NASA Astrophysics Data System (ADS)

Henninges, J.; Huenges, E.; Burkhardt, H.

2005-11-01

Detailed knowledge about thermal properties of rocks containing gas hydrate is required in order to quantify processes involving gas hydrate formation and decomposition in nature. In the framework of the Mallik 2002 program, three wells penetrating a continental gas hydrate occurrence under permafrost were successfully equipped with permanent fiber-optic distributed temperature sensing cables. Temperature data were collected over a 21-month period after completing the wells. Thermal conductivity profiles were calculated from the geothermal data as well as from a petrophysical model derived from the available logging data and application of mixing law models. Results indicate that thermal conductivity variations are mainly lithologically controlled with a minor influence from hydrate saturation. Average thermal conductivity values of the hydrate-bearing sediments range between 2.35 and 2.77 W m-1 K-1. Maximum gas hydrate saturations can reach up to about 90% at an average porosity of 0.3.

The effect of hydrate content on seismic attenuation: A case study for Mallik 2L-38 well data, Mackenzie delta, Canada

NASA Astrophysics Data System (ADS)

Chand, Shyam; Minshull, Tim A.

2004-07-01

Observations of velocities in sediments containing gas hydrates show that the strength of sediments increases with hydrate saturation. Hence it is expected that the attenuation of these sediments will decrease with increasing hydrate saturation. However, sonic log measurements in the Mallik 2L-38 well and cross hole tomography measurements in the Mallik field have shown that attenuation increases with hydrate saturation. We studied a range of mechanisms by which increasing hydrate saturation could cause increased attenuation. We found that a difference in permeability between the host sediment and the newly formed hydrate can produce the observed effect. We modelled attenuation in terms of Biot and squirt flow mechanisms in composite media. We have used our model to predict observed attenuations in the Mallik 2L-38 well, Mackenzie Delta, Canada.

Vanishing amplitude of backbone dynamics causes a true protein dynamical transition: H2 NMR studies on perdeuterated C-phycocyanin

NASA Astrophysics Data System (ADS)

Kämpf, Kerstin; Kremmling, Beke; Vogel, Michael

2014-03-01

Using a combination of H2 nuclear magnetic resonance (NMR) methods, we study internal rotational dynamics of the perdeuterated protein C-phycocyanin (CPC) in dry and hydrated states over broad temperature and dynamic ranges with high angular resolution. Separating H2 NMR signals from methyl deuterons, we show that basically all backbone deuterons exhibit highly restricted motion occurring on time scales faster than microseconds. The amplitude of this motion increases when a hydration shell exists, while it decreases upon cooling and vanishes near 175 K. We conclude that the vanishing of the highly restricted motion marks a dynamical transition, which is independent of the time window and of a fundamental importance. This conclusion is supported by results from experimental and computational studies of the proteins myoglobin and elastin. In particular, we argue based on findings in molecular dynamics simulations that the behavior of the highly restricted motion of proteins at the dynamical transition resembles that of a characteristic secondary relaxation of liquids at the glass transition, namely the nearly constant loss. Furthermore, H2 NMR studies on perdeuterated CPC reveal that, in addition to highly restricted motion, small fractions of backbone segments exhibit weakly restricted dynamics when temperature and hydration are sufficiently high.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex

NASA Astrophysics Data System (ADS)

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-01

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Lutetium(iii) aqua ion: On the dynamical structure of the heaviest lanthanoid hydration complex.

PubMed

Sessa, Francesco; Spezia, Riccardo; D'Angelo, Paola

2016-05-28

The structure and dynamics of the lutetium(iii) ion in aqueous solution have been investigated by means of a polarizable force field molecular dynamics (MD). An 8-fold square antiprism (SAP) geometry has been found to be the dominant configuration of the lutetium(iii) aqua ion. Nevertheless, a low percentage of 9-fold complexes arranged in a tricapped trigonal prism (TTP) geometry has been also detected. Dynamic properties have been explored by carrying out six independent MD simulations for each of four different temperatures: 277 K, 298 K, 423 K, 632 K. The mean residence time of water molecules in the first hydration shell at room temperature has been found to increase as compared to the central elements of the lanthanoid series in agreement with previous experimental findings. Water exchange kinetic rate constants at each temperature and activation parameters of the process have been determined from the MD simulations. The obtained structural and dynamical results suggest that the water exchange process for the lutetium(iii) aqua ion proceeds with an associative mechanism, in which the SAP hydration complex undergoes temporary structural changes passing through a 9-fold TTP intermediate. Such results are consistent with the water exchange mechanism proposed for heavy lanthanoid atoms.

Controls on methane expulsion during melting of natural gas hydrate systems. Topic area 2

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

Flemings, Peter

1.1. Project Goal The project goal is to predict, given characteristic climate-induced temperature change scenarios, the conditions under which gas will be expelled from existing accumulations of gas hydrate into the shallow ocean or directly to the atmosphere. When those conditions are met, the fraction of the gas accumulation that escapes and the rate of escape shall be quantified. The predictions shall be applicable in Arctic regions and in gas hydrate systems at the up dip limit of the stability zone on continental margins. The behavior shall be explored in response to two warming scenarios: longer term change due tomore » sea level rise (e.g. 20 thousand years) and shorter term due to atmospheric warming by anthropogenic forcing (decadal time scale). 1.2. Project Objectives During the first budget period, the objectives are to review and categorize the stability state of existing well-studied hydrate reservoirs, develop conceptual and numerical models of the melting process, and to design and conduct laboratory experiments that dissociate methane hydrate in a model sediment column by systematically controlling the temperature profile along the column. The final objective of the first budget period shall be to validate the models against the experiments. In the second budget period, the objectives are to develop a model of gas flow into sediment in which hydrate is thermodynamically stable, and conduct laboratory experiments of this process to validate the model. The developed models shall be used to quantify the rate and volume of gas that escapes from dissociating hydrate accumulations. In addition, specific scaled simulations characteristic of Arctic regions and regions near the stability limit at continental margins shall be performed. 1.3. Project Background and Rationale The central hypothesis proposed is that hydrate melting (dissociation) due to climate change generates free gas that can, under certain conditions, propagate through the gas hydrate stability zone and vent at the seafloor. Gas venting through the regional hydrate stability zone is accomplished by alteration of the regional equilibrium conditions (creation of three phase conditions) by increased salinity and heat due to hydrate formation, due to gas fracturing, or a combination of both. This research will explore the controls on whether methane reaches the seafloor (or atmosphere) as the original hydrate deposit dissociates and what the magnitude of these fluxes are. This hypothesis has significant implications for the forcings and feedbacks associated with climate change. It is described below the observations and models that have led to formulating this hypothesis.« less

Parameterization of Highly Charged Metal Ions Using the 12-6-4 LJ-Type Nonbonded Model in Explicit Water

PubMed Central

2015-01-01

Highly charged metal ions act as catalytic centers and structural elements in a broad range of chemical complexes. The nonbonded model for metal ions is extensively used in molecular simulations due to its simple form, computational speed, and transferability. We have proposed and parametrized a 12-6-4 LJ (Lennard-Jones)-type nonbonded model for divalent metal ions in previous work, which showed a marked improvement over the 12-6 LJ nonbonded model. In the present study, by treating the experimental hydration free energies and ion–oxygen distances of the first solvation shell as targets for our parametrization, we evaluated 12-6 LJ parameters for 18 M(III) and 6 M(IV) metal ions for three widely used water models (TIP3P, SPC/E, and TIP4PEW). As expected, the interaction energy underestimation of the 12-6 LJ nonbonded model increases dramatically for the highly charged metal ions. We then parametrized the 12-6-4 LJ-type nonbonded model for these metal ions with the three water models. The final parameters reproduced the target values with good accuracy, which is consistent with our previous experience using this potential. Finally, tests were performed on a protein system, and the obtained results validate the transferability of these nonbonded model parameters. PMID:25145273

Sedimentological Control on Hydrate Saturation Distribution in Arctic Gas-Hydrate-Bearing Deposits

NASA Astrophysics Data System (ADS)

Behseresht, J.; Peng, Y.; Bryant, S. L.

2010-12-01

Grain size variations along with the relative rates of fluid phases migrating into the zone of hydrate stability, plays an important role in gas-hydrate distribution and its morphologic characteristics. In the Arctic, strata several meters thick containing large saturations of gas hydrate are often separated by layers containing small but nonzero hydrate saturations. Examples are Mt. Elbert, Alaska and Mallik, NW Territories. We argue that this sandwich type hydrate saturation distribution is consistent with having a gas phase saturation within the sediment when the base of gas hydrate stability zone (BGHSZ) was located above the sediment package. The volume change during hydrate formation process derives movement of fluid phases into the GHSZ. We show that this fluid movement -which is mainly governed by characteristic relative permeability curves of the host sediment-, plays a crucial role in the amount of hydrate saturation in the zone of major hydrate saturation. We develop a mechanistic model that enables estimating the final hydrate saturation from an initial gas/water saturation in sediment with known relative permeability curves. The initial gas/water saturation is predicted using variation of capillary entry pressure with depth, which in turn depends on the variation in grain-size distribution. This model provides a mechanistic approach for explaining large hydrate saturations (60%-75%) observed in zones of major hydrate saturation considering the governing characteristic relative permeability curves of the host sediments. We applied the model on data from Mount Elbert well on the Alaskan North Slope. It is shown that, assuming a cocurrent flow of gas and water into the GHSZ, such large hydrate saturations (up to 75%) cannot result from large initial gas saturations (close to 1-Sw,irr) due to limitations on water flux imposed by typical relative permeability curves. They could however result from modest initial gas saturations (ca. 40%) at which we have reasonable phase mobility ratios required for appropriate relative rates of gas and water transporting into GHSZ to form large hydrate saturations. Nevertheless, from the profile of capillary entry pressure vs. depth, we expect large initial gas saturations and thus the final high hydrate saturation suggests another form of water flow: water moves down through accumulated hydrate from the unfrozen water above. For this to happen the water phase must remain connected within the hydrate-bearing sediment. This seems plausible in hydrate bearing sediments because hydrate formation will be stopped before water saturation gets to very low values (lower than Sw,irr) due to salinity build up. The location of small hydrate saturations (10-15%) is consistent with the location of the residual gas phase established during water imbibition into these locations while they serve as a gas source to the layers above.

Estimation of gas hydrate saturation using isotropic and anisotropic models at the location selected after measurement of seismic quality factor

NASA Astrophysics Data System (ADS)

Mundhra, A.; Sain, K.; Shankar, U.

2012-12-01

The Indian National Gas Hydrate Program Expedition (NGHP) 01 discovered gas hydrate in unconsolidated sediments at several drilling sites along the continental margins of Krishna-Godavari Basin, India. Presence of gas hydrate reduces the attenuation of travelling seismic waves which can be measured by estimation of seismic quality factor (Dasgupta and Clark, 1998). Here, we use log spectral ratio method (Sain et al, 2009) to compute quality factor at three locations, among which two have strong and one has no bottom simulating reflector (BSR), along seismic cross-line near one of the drilling site. Interval quality factor for three submarine sedimentary layers bounded by seafloor, BSR, one reflector above and another reflector below the BSR has been measured. To compute quality factor, unprocessed pre-stack seismic data has been used to avoid any influence of processing sequence. We have estimated that interval quality factor lies within 200-220 in the interval having BSR while it varies within 90-100 in other intervals. Thereby, high interval quality factor ascertains that observed BSR is due to presence of gas hydrates. We have performed rock physics modelling by using isotropic and anisotropic models, to quantitatively estimate gas hydrate saturation at one of the location where an interval has high quality factor. Abruptly high measured resistivity and high P-wave velocity in the interval, leads to towering hydrate saturation (Archie,1942 and Helegrud et al, 1999) in comparison to lower gas hydrate saturations estimated by pressure core and chlorinity measurements. Overestimation of saturation is attributed to presence of near vertical fractures that are identified from logging-while-drilling resistivity images. We have carried out anisotropic modeling (Kennedy and Herrick, 2004 and Lee,2009) by incorporating fracture volume and fracture porosity to estimate hydrate saturation and have observed that modeled gas hydrate saturations agree with the lower gas hydrate saturations obtained from pressure core and chlorinity measurements. Therefore, we find that 1) quality factor is significantly higher in the interval bearing gas hydrates and is a useful tool to discover hydrate deposits, 2) anisotropy due to presence of near vertical hydrate filled fractures translates into elevated saturation because of high measured resistivity and velocity and 3) anisotropic model greatly corrects the saturation estimates in fractured medium. References: Archie, G.E., 1942. Petroleum Transactions of AIME, 146, 54-62. Dasgupta, R., Clark, R.A., 1998. Geophysics 63, 2120-2128. Kennedy, W.D., Herrick, D.C., 2004. Petrophysics 45, 38-58. Lee, M.W., 2009. U.S. Geological Survey Scientific Investigations Report 2009-5141, 13. Sain, K., Singh, A.K., Thakur, N.K., Khanna, R.K., 2009.Marine Geophysical Researches 30, 137-145.

The interaction of climate change and methane hydrates

USGS Publications Warehouse

Ruppel, Carolyn D.; Kessler, John D.

2017-01-01

Gas hydrate, a frozen, naturally-occurring, and highly-concentrated form of methane, sequesters significant carbon in the global system and is stable only over a range of low-temperature and moderate-pressure conditions. Gas hydrate is widespread in the sediments of marine continental margins and permafrost areas, locations where ocean and atmospheric warming may perturb the hydrate stability field and lead to release of the sequestered methane into the overlying sediments and soils. Methane and methane-derived carbon that escape from sediments and soils and reach the atmosphere could exacerbate greenhouse warming. The synergy between warming climate and gas hydrate dissociation feeds a popular perception that global warming could drive catastrophic methane releases from the contemporary gas hydrate reservoir. Appropriate evaluation of the two sides of the climate-methane hydrate synergy requires assessing direct and indirect observational data related to gas hydrate dissociation phenomena and numerical models that track the interaction of gas hydrates/methane with the ocean and/or atmosphere. Methane hydrate is likely undergoing dissociation now on global upper continental slopes and on continental shelves that ring the Arctic Ocean. Many factors—the depth of the gas hydrates in sediments, strong sediment and water column sinks, and the inability of bubbles emitted at the seafloor to deliver methane to the sea-air interface in most cases—mitigate the impact of gas hydrate dissociation on atmospheric greenhouse gas concentrations though. There is no conclusive proof that hydrate-derived methane is reaching the atmosphere now, but more observational data and improved numerical models will better characterize the climate-hydrate synergy in the future.

The interaction of climate change and methane hydrates

NASA Astrophysics Data System (ADS)

Ruppel, Carolyn D.; Kessler, John D.

2017-03-01

Gas hydrate, a frozen, naturally-occurring, and highly-concentrated form of methane, sequesters significant carbon in the global system and is stable only over a range of low-temperature and moderate-pressure conditions. Gas hydrate is widespread in the sediments of marine continental margins and permafrost areas, locations where ocean and atmospheric warming may perturb the hydrate stability field and lead to release of the sequestered methane into the overlying sediments and soils. Methane and methane-derived carbon that escape from sediments and soils and reach the atmosphere could exacerbate greenhouse warming. The synergy between warming climate and gas hydrate dissociation feeds a popular perception that global warming could drive catastrophic methane releases from the contemporary gas hydrate reservoir. Appropriate evaluation of the two sides of the climate-methane hydrate synergy requires assessing direct and indirect observational data related to gas hydrate dissociation phenomena and numerical models that track the interaction of gas hydrates/methane with the ocean and/or atmosphere. Methane hydrate is likely undergoing dissociation now on global upper continental slopes and on continental shelves that ring the Arctic Ocean. Many factors—the depth of the gas hydrates in sediments, strong sediment and water column sinks, and the inability of bubbles emitted at the seafloor to deliver methane to the sea-air interface in most cases—mitigate the impact of gas hydrate dissociation on atmospheric greenhouse gas concentrations though. There is no conclusive proof that hydrate-derived methane is reaching the atmosphere now, but more observational data and improved numerical models will better characterize the climate-hydrate synergy in the future.

The interaction of climate change and methane hydrates

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

Ruppel, Carolyn D.; Kessler, John D.

Gas hydrate, a frozen, naturally-occurring, and highly-concentrated form of methane, sequesters significant carbon in the global system and is stable only over a range of low-temperature and moderate-pressure conditions. Gas hydrate is widespread in the sediments of marine continental margins and permafrost areas, locations where ocean and atmospheric warming may perturb the hydrate stability field and lead to release of the sequestered methane into the overlying sediments and soils. Methane and methane-derived carbon that escape from sediments and soils and reach the atmosphere could exacerbate greenhouse warming. The synergy between warming climate and gas hydrate dissociation feeds a popular perceptionmore » that global warming could drive catastrophic methane releases from the contemporary gas hydrate reservoir. Appropriate evaluation of the two sides of the climate-methane hydrate synergy requires assessing direct and indirect observational data related to gas hydrate dissociation phenomena and numerical models that track the interaction of gas hydrates/methane with the ocean and/or atmosphere. Methane hydrate is likely undergoing dissociation now on global upper continental slopes and on continental shelves that ring the Arctic Ocean. Many factors—the depth of the gas hydrates in sediments, strong sediment and water column sinks, and the inability of bubbles emitted at the seafloor to deliver methane to the sea-air interface in most cases—mitigate the impact of gas hydrate dissociation on atmospheric greenhouse gas concentrations though. There is no conclusive proof that hydrate-derived methane is reaching the atmosphere now, but more observational data and improved numerical models will better characterize the climate-hydrate synergy in the future.« less

The interaction of climate change and methane hydrates

DOE PAGES

Ruppel, Carolyn D.; Kessler, John D.

2016-12-14

Gas hydrate, a frozen, naturally-occurring, and highly-concentrated form of methane, sequesters significant carbon in the global system and is stable only over a range of low-temperature and moderate-pressure conditions. Gas hydrate is widespread in the sediments of marine continental margins and permafrost areas, locations where ocean and atmospheric warming may perturb the hydrate stability field and lead to release of the sequestered methane into the overlying sediments and soils. Methane and methane-derived carbon that escape from sediments and soils and reach the atmosphere could exacerbate greenhouse warming. The synergy between warming climate and gas hydrate dissociation feeds a popular perceptionmore » that global warming could drive catastrophic methane releases from the contemporary gas hydrate reservoir. Appropriate evaluation of the two sides of the climate-methane hydrate synergy requires assessing direct and indirect observational data related to gas hydrate dissociation phenomena and numerical models that track the interaction of gas hydrates/methane with the ocean and/or atmosphere. Methane hydrate is likely undergoing dissociation now on global upper continental slopes and on continental shelves that ring the Arctic Ocean. Many factors—the depth of the gas hydrates in sediments, strong sediment and water column sinks, and the inability of bubbles emitted at the seafloor to deliver methane to the sea-air interface in most cases—mitigate the impact of gas hydrate dissociation on atmospheric greenhouse gas concentrations though. There is no conclusive proof that hydrate-derived methane is reaching the atmosphere now, but more observational data and improved numerical models will better characterize the climate-hydrate synergy in the future.« less

Velocities and Attenuations of Gas Hydrate-Bearing Sediments

USGS Publications Warehouse

Lee, Myung W.

2007-01-01

Monopole and dipole logging data at the Mallik 5L-38, Mackenzie Delta, Canada, provide a challenge for sonic velocity and attenuation models used to remotely estimate pore-space gas hydrate content. Velocity and attenuation are linked, with velocity dispersion causing increased attenuation. Sonic waveforms for Mallik 5L-38, however, show no velocity dispersion in gas hydrate-bearing layers, yet are highly attenuated. Attenuation models applied to Mallik 5L-38 data are shown to be inconsistent with the observed velocity measurements, and therefore are suspect in their ability to predict gas hydrate content. A model explicitly linking velocity and attenuation data is presented, accurately predicting gas hydrate content from velocity data alone while demonstrating that the attenuation mechanisms at the Mallik 5L-38 site have not yet been identified.

Clathrate hydrates of oxidants in the ice shell of Europa.

PubMed

Hand, Kevin P; Chyba, Christopher F; Carlson, Robert W; Cooper, John F

2006-06-01

Europa's icy surface is radiolytically modified by high-energy electrons and ions, and photolytically modified by solar ultraviolet photons. Observations from the Galileo Near Infrared Mapping Spectrometer, ground-based telescopes, the International Ultraviolet Explorer, and the Hubble Space Telescope, along with laboratory experiment results, indicate that the production of oxidants, such as H2O2, O2, CO2, and SO2, is a consequence of the surface radiolytic chemistry. Once created, some of the products may be entrained deeper into the ice shell through impact gardening or other resurfacing processes. The temperature and pressure environments of regions within the europan hydrosphere are expected to permit the formation of mixed clathrate compounds. The formation of carbon dioxide and sulfur dioxide clathrates has been examined in some detail. Here we add to this analysis by considering oxidants produced radiolytically on the surface of Europa. Our results indicate that the bulk ice shell could have a approximately 1.7-7.6% by number contamination of oxidants resulting from radiolysis at the surface. Oxidant-hosting clathrates would consequently make up approximately 12-53% of the ice shell by number relative to ice, if oxidants were entrained throughout. We examine, in brief, the consequences of such contamination on bulk ice shell thickness and find that clathrate formation could lead to substantially thinner ice shells on Europa than otherwise expected. Finally, we propose that double occupancy of clathrate cages by O2 molecules could serve as an explanation for the observation of condensed-phase O2 on Europa. Clathrate-sealed, gas-filled bubbles in the near surface ice could also provide an effective trapping mechanism, though they cannot explain the 5771 A (O2)2 absorption.

In situ Low-temperature Pair Distribution Function (PDF) Analysis of CH4 and CO2 Hydrates

NASA Astrophysics Data System (ADS)

Cladek, B.; Everett, M.; McDonnell, M.; Tucker, M.; Keffer, D.; Rawn, C.

2017-12-01

Gas hydrates occur in ocean floor and sub-surface permafrost deposits and are stable at moderate to high pressures and low temperatures. They are a clathrate structure composed of hydrogen bonded water cages that accommodate a wide variety of guest molecules. CO2 and CH4 hydrates both crystallize as the cubic sI hydrate and can form a solid solution. Natural gas hydrates are interesting as a potential methane source and for CO2 sequestration. Long-range diffraction studies on gas hydrates give valuable structural information but do not provide a detailed understanding of the disordered gas molecule interactions with the host lattice. In-situ low temperature total scattering experiments combined with pair distribution function (PDF) analysis are used to investigate the gas molecule motions and guest-cage interactions. CO2 and methane hydrates exhibit different decomposition behavior, and CO2 hydrate has a smaller lattice parameter despite it being a relatively larger molecule. Total scattering studies characterizing both the short- and long-range order simultaneously help to elucidate the structural source of these phenomena. Low temperature neutron total scattering data were collected using the Nanoscale Ordered MAterials Diffractometer (NOMAD) beamline at the Spallation Neutron Source (SNS) on CO2 and CH4 hydrates synthesized with D2O. Guest molecule motion within cages and interactions between gases and cages are investigated through the hydrate stability and decomposition regions. Data were collected from 2-80 K at a pressure of 55 mbar on CO2 and CH4 hydrates, and from 80-270 K at 25 bar on CH4 hydrate. The hydrate systems were modeled with classical molecular dynamic (MD) simulations to provide an analysis of the total energy into guest-guest, guest-host and host-host contributions. Combined Reitveld and Reverse Monte Carlo (RMC) structure refinement were used to fit models of the data. This combined modeling and simulation characterizes the effects of CO2 and CH4 as guest molecules on the structure and decomposition of gas hydrates. Structure and thermodynamic studies will provide a more comprehensive understanding of CO2-CH4 solid solutions, exchange kinetics, and implications on hydrate structure.

Nano-biosilica from marine diatoms: A brand new material for photonic applications

NASA Astrophysics Data System (ADS)

De Stefano, L.; Maddalena, P.; Moretti, L.; Rea, I.; Rendina, I.; De Tommasi, E.; Mocella, V.; De Stefano, M.

2009-07-01

Several biological organisms, from some sea shells to butterflies, exhibit sophisticated optical systems, which have been developed during the evolution of each species. The diatoms are microscopic algae enclosed between two valves of hydrated amorphous silica. These intricate structures, called frustules, show quite symmetric patterns of micrometric and nanometric pores. Their strong similarity with man-made objects suggests to exploit the optical properties of the frustules in light guiding and optical transducing. We have found very interesting results, both from the experimental and numerical points of view.

Germanium Plasmon Enhanced Resonators for Label-Free Terahertz Protein Sensing

NASA Astrophysics Data System (ADS)

Bettenhausen, Maximilian; Römer, Friedhard; Witzigmann, Bernd; Flesch, Julia; Kurre, Rainer; Korneev, Sergej; Piehler, Jacob; You, Changjiang; Kazmierczak, Marcin; Guha, Subhajit; Capellini, Giovanni; Schröder, Thomas

2018-03-01

A Terahertz protein sensing concept based on subwavelength Ge resonators is presented. Ge bowtie resonators, compatible with CMOS fabrication technology, have been designed and characterized with a resonance frequency of 0.5 THz and calculated local intensity enhancement of 10.000. Selective biofunctionalization of Ge resonators on Si wafer was achieved in one step using lipoic acid-HaloTag ligand (LA-HTL) for biofunctionalization and passivation. The results lay the foundation for future investigation of protein tertiary structure and the dynamics of protein hydration shell in response to protein conformation changes.

(YIP-10) Enabling Dynamic Oxidation Mechanisms in Reverse Infiltrated Ultra-High Temperature Ceramic Coated C-C Composites for Application in Hypersonics

DTIC Science & Technology

2013-08-09

of Hf,Zr oxychloride hydrates, triethyl borate , and phenolic resin to form precipitate free sols that turn into stable gels with no catalyst addition...minutes, shows the glass -ceramic coating (that formed a shell upon cooling) was generated from within the UHTC filled C-C composite. Notice, in Figure...generation of the coating during high temperature exposure to oxygen. The formation of a ZrO2-SiO2 glass -ceramic coating on the C-C composite is believed to

Combustion of Methane Hydrate

NASA Astrophysics Data System (ADS)

Roshandell, Melika

A significant methane storehouse is in the form of methane hydrates on the sea floor and in the arctic permafrost. Methane hydrates are ice-like structures composed of water cages housing a guest methane molecule. This caged methane represents a resource of energy and a potential source of strong greenhouse gas. Most research related to methane hydrates has been focused on their formation and dissociation because they can form solid plugs that complicate transport of oil and gas in pipelines. This dissertation explores the direct burning of these methane hydrates where heat from the combustion process dissociates the hydrate into water and methane, and the released methane fuels the methane/air diffusion flame heat source. In contrast to the pipeline applications, very little research has been done on the combustion and burning characteristics of methane hydrates. This is the first dissertation on this subject. In this study, energy release and combustion characteristics of methane hydrates were investigated both theoretically and experimentally. The experimental study involved collaboration with another research group, particularly in the creation of methane hydrate samples. The experiments were difficult because hydrates form at high pressure within a narrow temperature range. The process can be slow and the resulting hydrate can have somewhat variable properties (e.g., extent of clathration, shape, compactness). The experimental study examined broad characteristics of hydrate combustion, including flame appearance, burning time, conditions leading to flame extinguishment, the amount of hydrate water melted versus evaporated, and flame temperature. These properties were observed for samples of different physical size. Hydrate formation is a very slow process with pure water and methane. The addition of small amounts of surfactant increased substantially the hydrate formation rate. The effects of surfactant on burning characteristics were also studied. One finding from the experimental component of the research was that hydrates can burn completely, and that they burn most rapidly just after ignition and then burn steadily when some of the water in the dissociated zone is allowed to drain away. Excessive surfactant in the water creates a foam layer around the hydrate that acts as an insulator. The layer prevents sufficient heat flux from reaching the hydrate surface below the foam to release additional methane and the hydrate flame extinguishes. No self-healing or ice-freezing processes were observed in any of the combustion experiments. There is some variability, but a typical hydrate flame is receiving between one and two moles of water vapor from the liquid dissociated zone of the hydrate for each mole of methane it receives from the dissociating solid region. This limits the flame temperature to approximately 1800 K. In the theoretical portion of the study, a physical model using an energy balance from methane combustion was developed to understand the energy transfer between the three phases of gas, liquid and solid during the hydrate burn. Also this study provides an understanding of the different factors impacting the hydrate's continuous burn, such as the amount of water vapor in the flame. The theoretical study revealed how the water layer thickness on the hydrate surface, and its effect on the temperature gradient through the dissociated zone, plays a significant role in the hydrate dissociation rate and methane release rate. Motivated by the above mentioned observation from the theoretical analysis, a 1-D two-phase numerical simulation based on a moving front model for hydrate dissociation from a thermal source was developed. This model was focused on the dynamic growth of the dissociated zone and its effect on the dissociation rate. The model indicated that the rate of hydrate dissociation with a thermal source is a function of the dissociated zone thickness. It shows that in order for a continuous dissociation and methane release, some of the water from the dissociated zone needs to be drained. The results are consistent with the experimental observations. The understanding derived from the experiments and the numerical model permitted a brief exploration into the potential effects of pressure on the combustion of methane hydrates. The prediction is that combustion should improve under high pressure conditions because the evaporation of water is suppressed allowing more energy into the dissociation. Future experiments are needed to validate these initial findings.

Modeling the formation of methane hydrate-bearing intervals in fine-grained sediments

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

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Sediment grain size exerts a fundamental control on how methane hydrates are distributed within the pore space. Fine-grained muds are the predominant sediments in continental margins, and hydrates in these sediments have often been observed in semi-vertical veins and fractures. In several instances, these hydrate veins/fractures are found in discrete depth intervals a few tens meters thick within the gas hydrate stability zone (GHSZ) surrounded by hydrate-free sediments above and below. As they are not obviously connected with free gas occurring beneath the base of the GHSZ, these isolated hydrate-bearing intervals have been interpreted as formed by microbial methane generatedmore » in situ. To investigate further the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, solute diffusion, and microbial methane generation. The microbial methane generation term depends on the amount of metabolizable organic carbon deposited at the seafloor, which is degraded at a prescribed rate resulting in methane formation beneath the sulfate reduction zone. In the model, methane hydrate precipitates once the dissolved methane concentration is greater than solubility, or hydrate dissolves if concentration goes below solubility. If the deposition of organic carbon at the seafloor is kept constant in time, we found that the predicted amounts of hydrate formed in discrete intervals within the GHSZ are much less than those estimated from observations. We then investigated the effect of temporal variations in the deposition of organic carbon. If greater amounts of organic carbon are deposited during some time interval, methane generation is enhanced during burial in the corresponding sediment interval. With variations in organic carbon deposition that are consistent with observations in continental margin sediments, we were able to reproduce the methane hydrate contents estimated in discrete depth intervals. Our results support the suggestion that in situ microbial methane generation is the source for hydrates within fine-grained sediments.« less

Numerical modeling of the simulated gas hydrate production test at Mallik 2L-38 in the pilot scale pressure reservoir LARS - Applying the "foamy oil" model

NASA Astrophysics Data System (ADS)

Abendroth, Sven; Thaler, Jan; Klump, Jens; Schicks, Judith; Uddin, Mafiz

2014-05-01

In the context of the German joint project SUGAR (Submarine Gas Hydrate Reservoirs: exploration, extraction and transport) we conducted a series of experiments in the LArge Reservoir Simulator (LARS) at the German Research Centre of Geosciences Potsdam. These experiments allow us to investigate the formation and dissociation of hydrates at large scale laboratory conditions. We performed an experiment similar to the field-test conditions of the production test in the Mallik gas hydrate field (Mallik 2L-38) in the Beaufort Mackenzie Delta of the Canadian Arctic. The aim of this experiment was to study the transport behavior of fluids in gas hydrate reservoirs during depressurization (see also Heeschen et al. and Priegnitz et al., this volume). The experimental results from LARS are used to provide details about processes inside the pressure vessel, to validate the models through history matching, and to feed back into the design of future experiments. In experiments in LARS the amount of methane produced from gas hydrates was much lower than expected. Previously published models predict a methane production rate higher than the one observed in experiments and field studies (Uddin et al. 2010; Wright et al. 2011). The authors of the aforementioned studies point out that the current modeling approach overestimates the gas production rate when modeling gas production by depressurization. They suggest that trapping of gas bubbles inside the porous medium is responsible for the reduced gas production rate. They point out that this behavior of multi-phase flow is not well explained by a "residual oil" model, but rather resembles a "foamy oil" model. Our study applies Uddin's (2010) "foamy oil" model and combines it with history matches of our experiments in LARS. Our results indicate a better agreement between experimental and model results when using the "foamy oil" model instead of conventional models of gas flow in water. References Uddin M., Wright J.F. and Coombe D. (2010) - Numerical Study of gas evolution and transport behaviors in natural gas hydrate reservoirs; CSUG/SPE 137439. Wright J.F., Uddin M., Dallimore S.R. and Coombe D. (2011) - Mechanisms of gas evolution and transport in a producing gas hydrate reservoir: an unconventional basis for successful history matching of observed production flow data; International Conference on Gas Hydrates (ICGH 2011).

Prediction of induction time for methane hydrate formation in the presence or absence of THF in flow loop system by Natarajan model

NASA Astrophysics Data System (ADS)

Talaghat, Mohammad Reza; Jokar, Seyyed Mohammad

2018-03-01

The induction time is a time interval to detect the initial hydrate formation, which is counted from the moment when the stirrer is turned on until the first detection of hydrate formation. The main objective of the present work is to predict and measure the induction time of methane hydrate formation in the presence or absence of tetrahydrofuran (THF) as promoter in the flow loop system. A laboratory flow mini-loop apparatus was set up to measure the induction time of methane hydrate formation. The induction time is predicted using developed Kashchiev and Firoozabadi model and modified model of Natarajan for a flow loop system. Furthermore, the effects of volumetric flow rate of the fluid on the induction time were investigated. The results of the models were compared with experimental data. They show that the induction time of hydrate formation in the presence of THF is very short at high pressure and high volumetric flow rate of the fluid. It decreases with increasing pressure and liquid volumetric flow rate. It is also shown that the modified Natarajan model is more accurate than the Kashchiev and Firoozabadi ones in prediction of the induction time.

A molecular dynamics study of model SI clathrate hydrates: the effect of guest size and guest-water interaction on decomposition kinetics.

PubMed

Das, Subhadip; Baghel, Vikesh Singh; Roy, Sudip; Kumar, Rajnish

2015-04-14

One of the options suggested for methane recovery from natural gas hydrates is molecular replacement of methane by suitable guests like CO2 and N2. This approach has been found to be feasible through many experimental and molecular dynamics simulation studies. However, the long term stability of the resultant hydrate needs to be evaluated; the decomposition rate of these hydrates is expected to depend on the interaction between these guest and water molecules. In this work, molecular dynamics simulation has been performed to illustrate the effect of guest molecules with different sizes and interaction strengths with water on structure I (SI) hydrate decomposition and hence the stability. The van der Waals interaction between water of hydrate cages and guest molecules is defined by Lennard Jones potential parameters. A wide range of parameter spaces has been scanned by changing the guest molecules in the SI hydrate, which acts as a model gas for occupying the small and large cages of the SI hydrate. All atomistic simulation results show that the stability of the hydrate is sensitive to the size and interaction of the guest molecules with hydrate water. The increase in the interaction of guest molecules with water stabilizes the hydrate, which in turn shows a slower rate of hydrate decomposition. Similarly guest molecules with a reasonably small (similar to Helium) or large size increase the decomposition rate. The results were also analyzed by calculating the structural order parameter to understand the dynamics of crystal structure and correlated with the release rate of guest molecules from the solid hydrate phase. The results have been explained based on the calculation of potential energies felt by guest molecules in amorphous water, hydrate bulk and hydrate-water interface regions.

Transient Electromagnetic Modelling and Imaging of Thin Resistive Structures: Applications for Gas Hydrate Assessment

NASA Astrophysics Data System (ADS)

Swidinsky, Andrei

Gas hydrates are a solid, ice-like mixture of water and low molecular weight hydrocarbons. They are found under the permafrost and to a far greater extent under the ocean, usually at water depths greater than 300m. Hydrates are a potential energy resource, a possible factor in climate change, and a geohazard. For these reasons, it is critical that gas hydrate deposits are quantitatively assessed so that their concentrations, locations and distributions may be established. Due to their ice-like nature, hydrates are electrically insulating. Consequently, a method which remotely detects changes in seafloor electrical conductivity, such as marine controlled source electromagnetics (CSEM), is a useful geophysical tool for marine gas hydrate exploration. Hydrates are geometrically complex structures. Advanced electromagnetic modelling and imaging techniques are crucial for proper survey design and data interpretation. I develop a method to model thin resistive structures in conductive host media which may be useful in building approximate geological models of gas hydrate deposits using arrangements of multiple, bent sheets. I also investigate the possibility of interpreting diffusive electromagnetic data using seismic imaging techniques. To be processed in this way, such data must first be transformed into its non-diffusive, seismic-like counterpart. I examine such a transform from both an analytical and a numerical point of view, focusing on methods to overcome inherent numerical instabilities. This is the first step to applying seismic processing techniques to CSEM data to rapidly and efficiently image resistive gas hydrate structures. The University of Toronto marine electromagnetics group has deployed a permanent marine CSEM array offshore Vancouver Island, in the framework of the NEPTUNE Canada cabled observatory, for the purposes of monitoring gas hydrate deposits. In this thesis I also propose and examine a new CSEM survey technique for gas hydrate which would make use of the stationary seafloor transmitter already on the seafloor, along with a cabled receiver array, towed from a ship. I furthermore develop a modelling algorithm to examine the electromagnetic effects of conductive borehole casings which have been proposed to be placed in the vicinity of this permanent marine CSEM array, and make preliminary recommendations about their locations.

Emergence of a Stern Layer from the Incorporation of Hydration Interactions into the Gouy-Chapman Model of the Electrical Double Layer.

PubMed

Brown, Matthew A; Bossa, Guilherme Volpe; May, Sylvio

2015-10-27

In one of the most commonly used phenomenological descriptions of the electrical double layer, a charged solid surface and a diffuse region of mobile ions are separated from each other by a thin charge-depleted Stern layer. The Stern layer acts as a capacitor that improves the classical Gouy-Chapman model by increasing the magnitude of the surface potential and limiting the maximal counterion concentration. We show that very similar Stern-like properties of the diffuse double layer emerge naturally from adding a nonelectrostatic hydration repulsion to the electrostatic Coulomb potential. The interplay of electrostatic attraction and hydration repulsion of the counterions and the surface leads to the formation of a diffuse counterion layer that remains well separated from the surface. In addition, hydration repulsions between the ions limit and control the maximal ion concentration and widen the width of the diffuse double layer. Our mean-field model, which we express in terms of electrostatic and hydration potentials, is physically consistent and conceptually similar to the classical Gouy-Chapman model. It allows the incorporation of ion specificity, accounts for hydration properties of charged surfaces, and predicts Stern layer properties, which we analyze in terms of the effective size of the hydrated counterions.

Analysis of the interplay among charge, hydration and shape of proteins through the modeling of their CZE mobility data.

PubMed

Piaggio, Maria V; Peirotti, Marta B; Deiber, Julio A

2009-07-01

Electrophoretic mobility data of four proteins are analyzed and interpreted through a physicochemical CZE model, which provides estimates of quantities like equivalent hydrodynamic radius (size), effective charge number, shape orientation factor, hydration, actual pK values of ionizing groups, and pH near molecule, among others. Protein friction coefficients are simulated through the creeping flow theory of prolate spheroidal particles. The modeling of the effective electrophoretic mobility of proteins requires consideration of hydrodynamic size and shape coupled to hydration and effective charge. The model proposed predicts native protein hydration within the range of values obtained experimentally from other techniques. Therefore, this model provides consistently other physicochemical properties such as average friction and diffusion coefficients and packing fractal dimension. As the pH varies from native conditions to those that are denaturing the protein, hydration and packing fractal dimension change substantially. Needs for further research are also discussed and proposed.

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

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

Prasad, Saurav, E-mail: saurav7188@gmail.com, E-mail: cyz118212@chemistry.iitd.ac.in; Chakravarty, Charusita

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl–H{sub 2}O and bulk SPC/E water spanning the concentration range 0.025–0.300 molefraction of LiCl at 1more » atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl–H{sub 2}O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H{sub 2}O and LiCl–H{sub 2}O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O–O–O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.« less

Tuning the tetrahedrality of the hydrogen-bonded network of water: Comparison of the effects of pressure and added salts

NASA Astrophysics Data System (ADS)

Prasad, Saurav; Chakravarty, Charusita

2016-06-01

Experiments and simulations demonstrate some intriguing equivalences in the effect of pressure and electrolytes on the hydrogen-bonded network of water. Here, we examine the extent and nature of equivalence effects between pressure and salt concentration using relationships between structure, entropy, and transport properties based on two key ideas: first, the approximation of the excess entropy of the fluid by the contribution due to the atom-atom pair correlation functions and second, Rosenfeld-type excess entropy scaling relations for transport properties. We perform molecular dynamics simulations of LiCl-H2O and bulk SPC/E water spanning the concentration range 0.025-0.300 molefraction of LiCl at 1 atm and pressure range from 0 to 7 GPa, respectively. The temperature range considered was from 225 to 350 K for both the systems. To establish that the time-temperature-transformation behaviour of electrolyte solutions and water is equivalent, we use the additional observation based on our simulations that the pair entropy behaves as a near-linear function of pressure in bulk water and of composition in LiCl-H2O. This allows for the alignment of pair entropy isotherms and allows for a simple mapping of pressure onto composition. Rosenfeld-scaling implies that pair entropy is semiquantitatively related to the transport properties. At a given temperature, equivalent state points in bulk H2O and LiCl-H2O (at 1 atm) are defined as those for which the pair entropy, diffusivity, and viscosity are nearly identical. The microscopic basis for this equivalence lies in the ability of both pressure and ions to convert the liquid phase into a pair-dominated fluid, as demonstrated by the O-O-O angular distribution within the first coordination shell of a water molecule. There are, however, sharp differences in local order and mechanisms for the breakdown of tetrahedral order by pressure and electrolytes. Increasing pressure increases orientational disorder within the first neighbour shell while addition of ions shifts local orientational order from tetrahedral to close-packed as water molecules get incorporated in ionic hydration shells. The variations in local order within the first hydration shell may underlie ion-specific effects, such as the Hofmeister series.

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A.; Daigle, H.

2016-12-01

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction, solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.

Gas hydrate saturation and distribution in the Kumano Forearc Basin of the Nankai Trough

NASA Astrophysics Data System (ADS)

Jia, Jihui; Tsuji, Takeshi; Matsuoka, Toshifumi

2017-02-01

The Kumano Forearc Basin is located to the south-east of the Kii Peninsula, Japan, overlying the accretionary prism in the Nankai Trough. The presence of gas hydrate in submarine sediments of the forearc basin has resulted in the widespread occurrence of bottom simulating reflectors (BSRs) on seismic profiles, and has caused distinct anomalies in logging data in the region. We estimated the in situ gas hydrate saturation from logging data by using three methods: effective rock physics models, Archie's equation, and empirical relationships between acoustic impedance (AI) and water-filled porosity. The results derived from rock physics models demonstrate that gas hydrates are attached to the grain surfaces of the rock matrix and are not floating in pore space. By applying the empirical relationships to the AI distribution derived from model-based AI inversion of the three-dimensional (3D) seismic data, we mapped the spatial distribution of hydrate saturation within the Kumano Basin and characterised locally concentrated gas hydrates. Based on the results, we propose two different mechanisms of free gas supply to explain the process of gas hydrate formation in the basin: (1) migration along inclined strata that dip landwards, and (2) migration through the faults or cracks generated by intensive tectonic movements of the accretionary prism. The dipping strata with relatively low AI in the forearc basin could indicate the presence of hydrate formation due to gas migration along the dipping strata. However, high hydrate concentration is observed at fault zones with high pore pressures, thus the second mechanism likely plays an important role in the genesis of gas hydrates in the Kumano Basin. Therefore, the tectonic activities in the accretionary wedge significantly influence the hydrate saturation and distribution in the Kumano Forearc Basin.

Modeling the Formation of Hydrate-Filled Veins in Fine-Grained Sediments from in Situ Microbial Methane

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

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Continental margin sediments are dominantly fine-grained silt and clay, and methane hydrates in these sediments are often found in semi-vertical veins and fractures. In several instances, these hydrate veins occupy discrete depth intervals that are a few tens of meters thick and are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the gas hydrate stability zone (GHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. To investigate the formation of these hydrate deposits, we applied a time-dependent advection-diffusion-reaction model that includes the effects of sedimentation, compaction,more » solute diffusion, and microbial methane generation. Microbial methane generation depends on the amount of metabolizable organic carbon deposited at the seafloor, whose progressive degradation produces methane beneath the sulfate reduction zone. If the amount of organic carbon entering the methanogenic zone is kept constant in time, we found that the computed amounts of hydrate formed in discrete intervals within the GHSZ are well below those estimated from observations. On the other hand, if the deposition of organic carbon is higher in a given time interval, methane generation during burial is more intense in the corresponding sediment interval, resulting in enhanced hydrate formation. With variations in organic carbon deposition comparable to those generally observed in continental margins, our model was able to reproduce the methane hydrate contents that were estimated from drilling. These results support the suggestion that in situ microbial generation associated with transient organic carbon deposition is the source of methane that forms isolated intervals of hydrate-filled veins in fine-grained sediments.« less

THCM Coupled Model for Hydrate-Bearing Sediments: Data Analysis and Design of New Field Experiments (Marine and Permafrost Settings)

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

Sanchez, Marcelo J.; Santamarina, J. Carlos

Gas hydrates are solid compounds made of water molecules clustered around low molecular weight gas molecules such as methane, hydrogen, and carbon dioxide. Methane hydrates form under pressure (P) and temperature (T) conditions that are common in sub-permafrost layers and in deep marine sediments. Stability conditions constrain the occurrence of gas hydrates to submarine sediments and permafrost regions. The amount of technically recoverable methane trapped in gas hydrate may exceed 104tcf. Gas hydrates are a potential energy resource, can contribute to climate change, and can cause large-scale seafloor instabilities. In addition, hydrate formation can be used for CO2 sequestration (alsomore » through CO2-CH4 replacement), and efficient geological storage seals. The experimental study of hydrate bearing sediments has been hindered by the very low solubility of methane in water (lab testing), and inherent sampling difficulties associated with depressurization and thermal changes during core extraction. This situation has prompted more decisive developments in numerical modeling in order to advance the current understanding of hydrate bearing sediments, and to investigate/optimize production strategies and implications. The goals of this research has been to addresses the complex thermo-hydro-chemo-mechanical THCM coupled phenomena in hydrate-bearing sediments, using a truly coupled numerical model that incorporates sound and proven constitutive relations, satisfies fundamental conservation principles. Analytical solutions aimed at verifying the proposed code have been proposed as well. These tools will allow to better analyze available data and to further enhance the current understanding of hydrate bearing sediments in view of future field experiments and the development of production technology.« less

Non-equilibrium simulation of CH4 production through the depressurization method from gas hydrate reservoirs

NASA Astrophysics Data System (ADS)

Qorbani, Khadijeh; Kvamme, Bjørn

2016-04-01

Natural gas hydrates (NGHs) in nature are formed from various hydrate formers (i.e. aqueous, gas, and adsorbed phases). As a result, due to Gibbs phase rule and the combined first and second laws of thermodynamics CH4-hydrate cannot reach thermodynamic equilibrium in real reservoir conditions. CH4 is the dominant component in NGH reservoirs. It is formed as a result of biogenic degradation of biological material in the upper few hundred meters of subsurface. It has been estimated that the amount of fuel-gas reserve in NGHs exceed the total amount of fossil fuel explored until today. Thus, these reservoirs have the potential to satisfy the energy requirements of the future. However, released CH4 from dissociated NGHs could find its way to the atmosphere and it is a far more aggressive greenhouse gas than CO2, even though its life-time is shorter. Lack of reliable field data makes it difficult to predict the production potential, as well as safety of CH4 production from NGHs. Computer simulations can be used as a tool to investigate CH4 production through different scenarios. Most hydrate simulators within academia and industry treat hydrate phase transitions as an equilibrium process and those which employ the kinetic approach utilize simple laboratory data in their models. Furthermore, it is typical to utilize a limited thermodynamic description where only temperature and pressure projections are considered. Another widely used simplification is to assume only a single route for the hydrate phase transitions. The non-equilibrium nature of hydrate indicates a need for proper kinetic models to describe hydrate dissociation and reformation in the reservoir with respect to thermodynamics variables, CH4 mole-fraction, pressure and temperature. The RetrasoCodeBright (RCB) hydrate simulator has previously been extended to model CH4-hydrate dissociation towards CH4 gas and water. CH4-hydrate is added to the RCB data-base as a pseudo mineral. Phase transitions are treated as non-equilibrium processes under local constraint of mass and heat fluxes. In this work, we have extended RCB by adding another route for dissociation or reformation of CH4-hydrate towards CH4 into the aqueous phase and water. CH4-hydrate formation and dissociation is resolved by looking at supersaturation and undersaturation with respect to thermodynamics variables. Hydrate instability due to undersaturation of CH4 in the contacting water phase is also considered. A complete non-equilibrium thermodynamic package, developed in-house, was combined with RCB to account for competing phase transitions by considering the minimization of Gibb's free energy. The energy differences were calculated from variations in chemical potentials of hydrate and hydrate formers. Mass transport, heat transport and non-equilibrium thermodynamic effects were implemented through classical nucleation theory to model the kinetic rate of hydrate phase transitions. To illustrate our implementations we ran simulations covering time-spans in the order of hundred years. CH4 production was modelled using the depressurization method, where we employed the Messoyakha field data. We discuss our implementations, as well as results obtained from simulations utilizing our modifications.

Liquid-liquid phase separation in aerosol particles: Imaging at the Nanometer Scale

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

O'Brien, Rachel; Wang, Bingbing; Kelly, Stephen T.

2015-04-21

Atmospheric aerosols can undergo phase transitions including liquid-liquid phase separation (LLPS) while responding to changes in the ambient relative humidity (RH). Here, we report results of chemical imaging experiments using environmental scanning electron microscopy (ESEM) and scanning transmission x-ray microscopy (STXM) to investigate the LLPS of micron sized particles undergoing a full hydration-dehydration cycle. Internally mixed particles composed of ammonium sulfate (AS) and either: limonene secondary organic carbon (LSOC), a, 4-dihydroxy-3-methoxybenzeneaceticacid (HMMA), or polyethylene glycol (PEG-400) were studied. Events of LLPS with apparent core-shell particle morphology were observed for all samples with both techniques. Chemical imaging with STXM showed thatmore » both LSOC/AS and HMMA/AS particles were never homogeneously mixed for all measured RH’s above the deliquescence point and that the majority of the organic component was located in the shell. The shell composition was estimated as 65:35 organic: inorganic in LSOC/AS and as 50:50 organic: inorganic for HMMA/AS. PEG-400/AS particles showed fully homogeneous mixtures at high RH and phase separated below 89-92% RH with an estimated 50:50% organic to inorganic mix in the shell. These two chemical imaging techniques are well suited for in-situ analysis of the hygroscopic behavior, phase separation, and surface composition of collected ambient aerosol particles.« less

Influence of Hydration on Proton Transfer in the Guanine-Cytosine Radical Cation (G•+-C) Base Pair: A Density Functional Theory Study

PubMed Central

Kumar, Anil; Sevilla, Michael D.

2009-01-01

On one-electron oxidation all molecules including DNA bases become more acidic in nature. For the GC base pair experiments suggest that a facile proton transfer takes place in the G•+-C base pair from N1 of G•+ to N3 of cytosine. This intra-base pair proton transfer reaction has been extensively considered using theoretical methods for the gas phase and it is predicted that the proton transfer is slightly unfavorable in disagreement with experiment. In the present study, we consider the effect of the first hydration layer on the proton transfer reaction in G•+-C by the use of density functional theory (DFT), B3LYP/6-31+G** calculations of the G•+-C base pair in the presence of 6 and 11 water molecules. Under the influence of hydration of 11 waters, a facile proton transfer from N1 of G•+ to N3 of C is predicted. The zero point energy (ZPE) corrected forward and backward energy barriers, for the proton transfer from N1 of G•+ to N3 of C, was found to be 1.4 and 2.6 kcal/mol, respectively. The proton transferred G•-(H+)C + 11H2O was found to be 1.2 kcal/mol more stable than G•+-C + 11H2O in agreement with experiment. The present calculation demonstrates that the inclusion of the first hydration shell around G•+-C base pair has an important effect on the internal proton transfer energetics. PMID:19485319

Infrared light-induced protein crystallization. Structuring of protein interfacial water and periodic self-assembly

NASA Astrophysics Data System (ADS)

Kowacz, Magdalena; Marchel, Mateusz; Juknaité, Lina; Esperança, José M. S. S.; Romão, Maria João; Carvalho, Ana Luísa; Rebelo, Luís Paulo N.

2017-01-01

We show that a physical trigger, a non-ionizing infrared (IR) radiation at wavelengths strongly absorbed by liquid water, can be used to induce and kinetically control protein (periodic) self-assembly in solution. This phenomenon is explained by considering the effect of IR light on the structuring of protein interfacial water. Our results indicate that the IR radiation can promote enhanced mutual correlations of water molecules in the protein hydration shell. We report on the radiation-induced increase in both the strength and cooperativeness of H-bonds. The presence of a structured dipolar hydration layer can lead to attractive interactions between like-charged biomacromolecules in solution (and crystal nucleation events). Furthermore, our study suggests that enveloping the protein within a layer of structured solvent (an effect enhanced by IR light) can prevent the protein non-specific aggregation favoring periodic self-assembly. Recognizing the ability to affect protein-water interactions by means of IR radiation may have important implications for biological and bio-inspired systems.

An experimental challenge: Unraveling the dependencies of ultrasonic and electrical properties of sandy sediments with pore-filling gas hydrates

NASA Astrophysics Data System (ADS)

Heeschen, Katja; Spangenberg, Erik; Seyberth, Karl; Priegnitz, Mike; Schicks, Judith M.

2016-04-01

The accuracy of gas hydrate quantification using seismic or electric measurements fundamentally depends on the knowledge of any factor describing the dependencies of physical properties on gas hydrate saturation. Commonly, these correlations are the result of laboratory measurements on artificially produced gas hydrates of exact saturation. Thus, the production of gas hydrates and accurate determination of gas hydrate concentrations or those of a substitute are a major concern. Here we present data of both, seismic and electric measurements on accurately quantified pore-filling ice as a substitute for natural gas hydrates. The method was validated using selected gas hydrate saturations in the same experimental set-up as well as literature data from glass bead samples [Spangenberg and Kulenkampff, 2006]. The environmental parameters were chosen to fit those of a possible gas hydrate reservoir in the Danube Delta, which is in the focus of models for joint inversions of seismic and electromagnetic data in the SUGAR III project. The small effective pressures present at this site proved to be yet another challenge for the experiments. Using a more powerful pulse generator and a 4 electrode electric measurement, respectively, models for a wide range of gas hydrate saturations between 20 - 90 % vol. could be established. Spangenberg, E. and Kulenkampff, J., Influence of methane hydrate content on electrical sediment properties. Geophysical Research Letters 2006, 33, (24).

Hydrophilic Solvation Dominates the Terahertz Fingerprint of Amino Acids in Water.

PubMed

Esser, Alexander; Forbert, Harald; Sebastiani, Federico; Schwaab, Gerhard; Havenith, Martina; Marx, Dominik

2018-02-01

Spectroscopy in the terahertz frequency regime is a sensitive tool to probe solvation-induced effects in aqueous solutions. Yet, a systematic understanding of spectral lineshapes as a result of distinct solvation contributions remains terra incognita. We demonstrate that modularization of amino acids in terms of functional groups allows us to compute their distinct contributions to the total terahertz response. Introducing the molecular cross-correlation analysis method provides unique access to these site-specific contributions. Equivalent groups in different amino acids lead to look-alike spectral contributions, whereas side chains cause characteristic but additive complexities. Specifically, hydrophilic solvation of the zwitterionic groups in valine and glycine leads to similar terahertz responses which are fully decoupled from the side chain. The terahertz response due to H-bonding within the large hydrophobic solvation shell of valine turns out to be nearly indistinguishable from that in bulk water in direct comparison to the changes imposed by the charged functional groups that form strong H-bonds with their hydration shells. Thus, the hydrophilic groups and their solvation shells dominate the terahertz absorption difference, while on the same intensity scale, the influence of hydrophobic water can be neglected.

Interaction of Simple Ions with Water: Theoretical Models for the Study of Ion Hydration

ERIC Educational Resources Information Center

Gancheff, Jorge S.; Kremer, Carlos; Ventura, Oscar N.

2009-01-01

A computational experiment aimed to create and systematically analyze models of simple cation hydrates is presented. The changes in the structure (bond distances and angles) and the electronic density distribution of the solvent and the thermodynamic parameters of the hydration process are calculated and compared with the experimental data. The…

Geologic implications of gas hydrates in the offshore of India: results of the National Gas Hydrate Program Expedition 01

USGS Publications Warehouse

Collett, Timothy S.; Boswell, Ray; Cochran, J.R.; Kumar, Pushpendra; Lall, Malcolm; Mazumdar, Aninda; Ramana, Mangipudi Venkata; Ramprasad, Tammisetti; Riedel, Michael; Sain, Kalachand; Sathe, Arun Vasant; Vishwanath, Krishna

2014-01-01

One of the specific objectives of this expedition was to test gas hydrate formation models and constrain model parameters, especially those that account for the formation of concentrated gas hydrate accumulations. The necessary data for characterizing the occurrence of in situ gas hydrate, such as interstitial water chlorinities, core-derived gas chemistry, physical and sedimentological properties, thermal images of the recovered cores, and downhole measured logging data (LWD and/or conventional wireline log data), were obtained from most of the drill sites established during NGHP-01. Almost all of the drill sites yielded evidence for the occurrence of gas hydrate; however, the inferred in situ concentration of gas hydrate varied substantially from site to site. For the most part, the interpretation of downhole logging data, core thermal images, interstitial water analyses, and pressure core images from the sites drilled during NGHP-01 indicate that the occurrence of concentrated gas hydrate is mostly associated with the presence of fractures in the sediments, and in some limited cases, by coarser grained (mostly sand-rich) sediments.

Numerical studies of depressurization-induced gas production from an interbedded marine turbidite gas hydrate reservoir model

USGS Publications Warehouse

Myshakin, Evgeniy; Lin, Jeen-Shang; Uchida, Shun; Seol, Yongkoo; Collett, Timothy S.; Boswell, Ray

2017-01-01

The numerical simulation of thin hydrate-bearing sand layers interbedded with mud layers is investigated. In this model, the lowest hydrate layer occurs at the base of gas hydrate stability and overlies a thinly-interbedded saline aquifer. The predicted gas rates reach 6.25 MMscf/day (1.77 x 105 m3 /day) after 90 days of continuous depressurization with manageable water production. Development of horizontal dissociating interfaces between hydrate-bearing sand and mud layers is a primary determinant of reservoir performance. A set of simulations has been executed to assess uncertainty in in situ permeability and to determine the impact of the saline aquifer on productivity.

Gas hydrate drilling transect across northern Cascadia margin - IODP Expedition 311

USGS Publications Warehouse

Riedel, M.; Collett, T.; Malone, M.J.; Collett, T.S.; Mitchell, M.; Guerin, G.; Akiba, F.; Blanc-Valleron, M.; Ellis, M.; Hashimoto, Y.; Heuer, V.; Higashi, Y.; Holland, M.; Jackson, P.D.; Kaneko, M.; Kastner, M.; Kim, J.-H.; Kitajima, H.; Long, P.E.; Malinverno, A.; Myers, Gwen E.; Palekar, L.D.; Pohlman, J.; Schultheiss, P.; Teichert, B.; Torres, M.E.; Trehu, A.M.; Wang, Jingyuan; Worthmann, U.G.; Yoshioka, H.

2009-01-01

A transect of four sites (U1325, U1326, U1327 and U1329) across the northern Cascadia margin was established during Integrated Ocean Drilling Program Expedition 311 to study the occurrence and formation of gas hydrate in accretionary complexes. In addition to the transect sites, a fifth site (U1328) was established at a cold vent with active fluid flow. The four transect sites represent different typical geological environments of gas hydrate occurrence across the northern Cascadia margin from the earliest occurrence on the westernmost first accreted ridge (Site U1326) to the eastward limit of the gas hydrate occurrence in shallower water (Site U1329). Expedition 311 complements previous gas hydrate studies along the Cascadia accretionary complex, especially ODP Leg 146 and Leg 204 by extending the aperture of the transect sampled and introducing new tools to systematically quantify the gas hydrate content of the sediments. Among the most significant findings of the expedition was the occurrence of up to 20 m thick sand-rich turbidite intervals with gas hydrate concentrations locally exceeding 50% of the pore space at Sites U1326 and U1327. Moreover, these anomalous gas hydrate intervals occur at unexpectedly shallow depths of 50-120 metres below seafloor, which is the opposite of what was expected from previous models of gas hydrate formation in accretionary complexes, where gas hydrate was predicted to be more concentrated near the base of the gas hydrate stability zone just above the bottom-simulating reflector. Gas hydrate appears to be mainly concentrated in turbidite sand layers. During Expedition 311, the visual correlation of gas hydrate with sand layers was clearly and repeatedly documented, strongly supporting the importance of grain size in controlling gas hydrate occurrence. The results from the transect sites provide evidence for a structurally complex, lithology-controlled gas hydrate environment on the northern Cascadia margin. Local shallow occurrences of high gas hydrate concentrations contradict the previous model of gas hydrate formation at an accretionary prism. However, long-lived fluid flow (part of the old model) is still required to explain the shallow high gas hydrate concentrations, although it is most likely not pervasive throughout the entire accretionary prism, but rather localized and focused by the tectonic processes. Differences in the fluid flow regime across all of the transect drill sites indicate site-specific and probably disconnected (compartmented) deeper fluid sources in the various parts of the accretionary prism. The data and future analyses will yield a better understanding of the geologic controls, evolution and ultimate fate of gas hydrate in an accretionary prism as an important contribution to the role of gas hydrate methane gas in slope stability and possibly in climate change. ?? The Geological Society of London 2009.

Estimating pore-space gas hydrate saturations from well log acoustic data

NASA Astrophysics Data System (ADS)

Lee, Myung W.; Waite, William F.

2008-07-01

Relating pore-space gas hydrate saturation to sonic velocity data is important for remotely estimating gas hydrate concentration in sediment. In the present study, sonic velocities of gas hydrate-bearing sands are modeled using a three-phase Biot-type theory in which sand, gas hydrate, and pore fluid form three homogeneous, interwoven frameworks. This theory is developed using well log compressional and shear wave velocity data from the Mallik 5L-38 permafrost gas hydrate research well in Canada and applied to well log data from hydrate-bearing sands in the Alaskan permafrost, Gulf of Mexico, and northern Cascadia margin. Velocity-based gas hydrate saturation estimates are in good agreement with Nuclear Magneto Resonance and resistivity log estimates over the complete range of observed gas hydrate saturations.

Effects of Curing Temperature and Pressure on the Chemical, Physical, and Mechanical Properties of Portland Cement

NASA Astrophysics Data System (ADS)

Pang, Xueyu

This dissertation mainly focuses on studying the fundamental hydration kinetics and mechanisms of Portland cement as well as the effects of curing temperature and pressure on its various properties. An innovative test apparatus has been developed in this study to cure and test cement paste specimens under in-situ conditions, such as down-hole in oil wells with high temperature and high pressure. Two series of tests were performed using cement pastes prepared with four different classes of oilwell cement (namely Class A, C, G, and H cements). Specimens in groups of four were cured at temperatures ranging from ambient to 60 °C and pressures ranging from 0.69 to 51.7 MPa for a period of 48 or 72 hours. The density and w/c ratio of the specimens at the time of casting as well as at the end of the curing period were recorded. Total chemical shrinkage of the cement paste was measured continuously during the entire hydration period while tensile strength was obtained at the end of the curing period using both water pressure and splitting tension test methods. Due to capacity limitations of the test equipment, in-situ tensile strength was obtained for only one test series with a highest curing pressure of 13.1 MPa. Specimens from the other test series were depressurized before the tensile strength tests. Chemical shrinkage test is an important method of measuring cement hydration kinetics in that the normalized total chemical shrinkage is approximately equal to the degree of cement hydration. By studying the correlations between the chemical shrinkage and the non-evaporable water content of cement during hydration, a multi-linear model is first proposed to estimate the normalization factors for different types of cement under different curing conditions. Based on the hydration kinetics data obtained from chemical shrinkage test results, a new approach of modeling the effect of curing temperature and pressure on cement hydration kinetics is proposed. It is found that when a hydration kinetics curve is represented by an unknown function, the effect of curing condition on the curve can be modeled by incorporating a simple scale factor in this function. The relationship between this scale factor and curing condition is described by chemical kinetics laws. While the proposed new approach of modeling cement hydration kinetics has the advantage of being widely applicable to different types of cement, it only explains one influence factor of cement hydration (i.e. the curing condition). In order to take into account other influence factors and to further understand the fundamental mechanisms of cement hydration, a more complex particle-based numerical hydration model is developed by combining the two well-known cement hydration mechanisms, namely the nucleation and growth controlled mechanism and the diffusion controlled mechanism. The model is applied to experimental data of both C3S hydration in dilute suspensions and Class H cement paste hydration. Excellent agreement is observed between experimental and modeled results. Three rate-controlling parameters with clear physical meanings can be identified from the proposed model. Fitted model parameters are found to be in reasonable agreement with experimental observation. The dependencies of these parameters on particle size, cement composition, w/c ratio, and curing condition are also investigated. Finally, the importance of cement hydration kinetics is illustrated by showing their close correlations with the physical and mechanical properties. The various influence factors, including the curing temperature and pressure, of physical and mechanical property test results (particularly density and tensile strength) are evaluated. Potential damage mechanisms of cement paste specimens during depressurization are studied by analyzing the deformation behavior of the entire system consisting of the cement paste and pressurizing water.

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

PubMed Central

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn; Crémière, Antoine; Panieri, Giuliana; Yao, Haoyi; Serov, Pavel

2017-01-01

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ∼380 m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. Results of temperature modelling suggest limited impact of short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site. PMID:28589962

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

DOE PAGES

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn; ...

2017-06-07

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ~380m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. The results of temperature modelling suggest limited impact ofmore » short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.« less

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming.

PubMed

Hong, Wei-Li; Torres, Marta E; Carroll, JoLynn; Crémière, Antoine; Panieri, Giuliana; Yao, Haoyi; Serov, Pavel

2017-06-07

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ∼380 m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. Results of temperature modelling suggest limited impact of short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.

Seepage from an arctic shallow marine gas hydrate reservoir is insensitive to momentary ocean warming

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

Hong, Wei-Li; Torres, Marta E.; Carroll, JoLynn

Arctic gas hydrate reservoirs located in shallow water and proximal to the sediment-water interface are thought to be sensitive to bottom water warming that may trigger gas hydrate dissociation and the release of methane. Here, we evaluate bottom water temperature as a potential driver for hydrate dissociation and methane release from a recently discovered, gas-hydrate-bearing system south of Spitsbergen (Storfjordrenna, ~380m water depth). Modelling of the non-steady-state porewater profiles and observations of distinct layers of methane-derived authigenic carbonate nodules in the sediments indicate centurial to millennial methane emissions in the region. The results of temperature modelling suggest limited impact ofmore » short-term warming on gas hydrates deeper than a few metres in the sediments. We conclude that the ongoing and past methane emission episodes at the investigated sites are likely due to the episodic ventilation of deep reservoirs rather than warming-induced gas hydrate dissociation in this shallow water seep site.« less

X-ray absorption spectroscopy and imaging of heterogeneous hydrothermal mixtures using a diamond microreactor cell

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

Fulton, John L.; Darab, John G.; Hoffmann, Markus M.

2001-04-01

Hydrothermal synthesis is an important route to novel materials. Hydrothermal chemistry is also an important aspect of geochemistry and a variety of waste remediation technologies. There is a significant lack of information about the speciation of inorganic compounds under hydrothermal conditions. For these reasons we describe a high-temperature, high-pressure cell that allows one to acquire both x-ray absorption fine structure (XAFS) spectra and x-ray transmission and absorption images of heterogeneous hydrothermal mixtures. We demonstrate the utility of the method by measuring the Cu(I) speciation in a solution containing both solid and dissolved Cu phases at temperatures up to 325{sup o}C.more » X-ray imaging of the various hydrothermal phases allows micro-XAFS to be collected from different phases within the heterogeneous mixture. The complete structural characterization of a soluble bichloro-cuprous species was determined. In situ XAFS measurements were used to define the oxidation state and the first-shell coordination structure. The Cu--Cl distance was determined to be 2.12 Aa for the CuCl{sub 2}{sup -} species and the complete loss of tightly bound waters of hydration in the first shell was observed. The microreactor cell described here can be used to test thermodynamic models of solubility and redox chemistry of a variety of different hydrothermal mixtures.« less

Kinetics of formation and dissociation of gas hydrates

NASA Astrophysics Data System (ADS)

Manakov, A. Yu; Penkov, N. V.; Rodionova, T. V.; Nesterov, A. N.; Fesenko, E. E., Jr.

2017-09-01

The review covers a wide range of issues related to the nucleation, growth and dissociation of gas hydrates. The attention is focused on publications of the last 10-15 years. Along with the mathematical models used to describe these processes, the results of relevant experimental studies are surveyed. Particular sections are devoted to the gas hydrate self-preservation effect, the water memory effect in the hydrate formation, development of catalysts for hydrate formation and the effect of substances dissolved in the aqueous phase on the formation of hydrates. The main experimental techniques used to study gas hydrates are briefly considered. The bibliography includes 230 references.

Do Pleistocene Glacial-Interglacial Cycles Control Methane Hydrate Formation? An Example from Green Canyon, Gulf of Mexico

NASA Astrophysics Data System (ADS)

Oryan, B.; Malinverno, A.; Goldberg, D.; Fortin, W.

2017-12-01

Well GC955-H was drilled in the Green Canyon region under the Gulf of Mexico Gas Hydrates Joint Industry Project in 2009. Logging-while-drilling resistivity logs obtained at the well indicate that the saturation of gas hydrate varies between high and low values in an alternating fashion. This trend is observed from 180 to 360mbsf, depths that correspond to the Late Pleistocene. Similar gas hydrate saturation patterns have been observed in other Gulf of Mexico locations (Walker Ridge sites WR313-G and 313-H) in Late Pleistocene sediments. Our hypothesis is that these variations in saturation can be explained by sea level changes through time during glacial-interglacial cycles. A higher amount of organic matter is deposited and buried in the sediment column during glacial intervals when sea level is low. Microbes in the sediment column degrade organic matter and produce methane gas as a byproduct. Higher availability of organic matter in the sediment column can increase the concentration of methane in the sediment pore water and in turn lead to the formation of gas hydrate. We use a time-dependent numerical model of the formation of gas hydrate to test this hypothesis. The model predicts the volume and distribution of gas hydrates using mass balance equations. Model inputs include in situ porosity determined from bulk density logs; local thermal gradient estimated from the depth of the bottom of the gas hydrate stability zone in proximity to the well; and sedimentation rate determined using the biostratigraphy of an industry well in the vicinity of GC955-H. Initial results show a good match between gas hydrate saturation predicted by the model and resistivity logs obtained in the well. We anticipate that this correlation will establish whether a causal link exists between the saturation of gas hydrate in this reservoir and glacioeustatic sea level changes in the Late Pleistocene.

Thermodynamics of Small Alkali Metal Halide Cluster Ions: Comparison of Classical Molecular Simulations with Experiment and Quantum Chemistry

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

Vlcek, Lukas; Uhlik, Filip; Moucka, Filip

We evaluate the ability of selected classical molecular models to describe the thermodynamic and structural aspects of gas-phase hydration of alkali halide ions and the formation of small water clusters. To understand the effect of many-body interactions (polarization) and charge penetration effects on the accuracy of a force field, we perform Monte Carlo simulations with three rigid water models using different functional forms to account for these effects: (i) point charge non-polarizable SPC/E, (ii) Drude point charge polarizable SWM4- DP, and (iii) Drude Gaussian charge polarizable BK3. Model predictions are compared with experimental Gibbs free energies and enthalpies of ionmore » hydration, and with microscopic structural properties obtained from quantum DFT calculations. We find that all three models provide comparable predictions for pure water clusters and cation hydration, but differ significantly in their description of anion hydration. None of the investigated classical force fields can consistently and quantitatively reproduce the experimental gas phase hydration thermodynamics. The outcome of this study highlights the relation between the functional form that describes the effective intermolecular interactions and the accuracy of the resulting ion hydration properties.« less

Simultaneous measurement for thermal conductivity, diffusivity, and specific heat of methane hydrate bearing sediments recovered from Nankai-Trough wells

NASA Astrophysics Data System (ADS)

Muraoka, M.; Ohtake, M.; Susuki, N.; Yamamoto, Y.; Suzuki, K.; Tsuji, T.

2014-12-01

This study presents the results of the measurements of the thermal constants of natural methane-hydrate-bearing sediments samples recovered from the Tokai-oki test wells (Nankai-Trough, Japan) in 2004. The thermal conductivity, thermal diffusivity, and specific heat of the samples were simultaneously determined using the hot-disk transient method. The thermal conductivity of natural hydrate-bearing sediments decreases slightly with increasing porosity. In addition, the thermal diffusivity of hydrate-bearing sediment decrease as porosity increases. We also used simple models to calculate the thermal conductivity and thermal diffusivity. The results of the distribution model (geometric-mean model) are relatively consistent with the measurement results. In addition, the measurement results are consistent with the thermal diffusivity, which is estimated by dividing the thermal conductivity obtained from the distribution model by the specific heat obtained from the arithmetic mean. In addition, we discuss the relation between the thermal conductivity and mineral composition of core samples in conference. Acknowledgments. This work was financially supported by MH21 Research Consortium for Methane Hydrate Resources in Japan on the National Methane Hydrate Exploitation Program planned by the Ministry of Economy, Trade and Industry.

A predictive numerical model for potential mapping of the gas hydrate stability zone in the Gulf of Cadiz

NASA Astrophysics Data System (ADS)

Leon, R.; Somoza, L.

2009-04-01

This comunication presents a computational model for mapping the regional 3D distribution in which seafloor gas hydrates would be stable, that is carried out in a Geographical Information System (GIS) environment. The construction of the model is comprised of three primary steps, namely (1) the construction of surfaces for the various variables based on available 3D data (seafloor temperature, geothermal gradient and depth-pressure); (2) the calculation of the gas function equilibrium functions for the various hydrocarbon compositions reported from hydrate and sediment samples; and (3) the calculation of the thickness of the hydrate stability zone. The solution is based on a transcendental function, which is solved iteratively in a GIS environment. The model has been applied in the northernmost continental slope of the Gulf of Cadiz, an area where an abundant supply for hydrate formation, such as extensive hydrocarbon seeps, diapirs and fault structures, is combined with deep undercurrents and a complex seafloor morphology. In the Gulf of Cadiz, model depicts the distribution of the base of the gas hydrate stability zone for both biogenic and thermogenic gas compositions, and explains the geometry and distribution of geological structures derived from gas venting in the Tasyo Field (Gulf of Cadiz) and the generation of BSR levels on the upper continental slope.

Effective-Medium Models for Marine Gas Hydrates, Mallik Revisited

NASA Astrophysics Data System (ADS)

Terry, D. A.; Knapp, C. C.; Knapp, J. H.

2011-12-01

Hertz-Mindlin type effective-medium dry-rock elastic models have been commonly used for more than three decades in rock physics analysis, and recently have been applied to assessment of marine gas hydrate resources. Comparisons of several effective-medium models with derivative well-log data from the Mackenzie River Valley, Northwest Territories, Canada (i.e. Mallik 2L-38 and 5L-38) were made several years ago as part of a marine gas hydrate joint industry project in the Gulf of Mexico. The matrix/grain supporting model (one of the five models compared) was clearly a better representation of the Mallik data than the other four models (2 cemented sand models; a pore-filling model; and an inclusion model). Even though the matrix/grain supporting model was clearly better, reservations were noted that the compressional velocity of the model was higher than the compressional velocity measured via the sonic logs, and that the shear velocities showed an even greater discrepancy. Over more than thirty years, variations of Hertz-Mindlin type effective medium models have evolved for unconsolidated sediments and here, we briefly review their development. In the past few years, the perfectly smooth grain version of the Hertz-Mindlin type effective-medium model has been favored over the infinitely rough grain version compared in the Gulf of Mexico study. We revisit the data from the Mallik wells to review assertions that effective-medium models with perfectly smooth grains are a better predictor than models with infinitely rough grains. We briefly review three Hertz-Mindlin type effective-medium models, and standardize nomenclature and notation. To calibrate the extended effective-medium model in gas hydrates, we use a well accepted framework for unconsolidated sediments through Hashin-Shtrikman bounds. We implement the previously discussed effective-medium models for saturated sediments with gas hydrates and compute theoretical curves of seismic velocities versus gas hydrate saturation to compare with well log data available from the Canadian gas hydrates research site. By directly comparing the infinitely rough and perfectly smooth grain versions of the Hertz-Mindlin type effective-medium model, we provide additional insight to the discrepancies noted in the Gulf of Mexico study.

Dielectric method of high-resolution gas hydrate estimation

NASA Astrophysics Data System (ADS)

Sun, Y. F.; Goldberg, D.

2005-02-01

In-situ dielectric properties of natural gas hydrate are measured for the first time in the Mallik 5L-38 Well in the Mackenzie Delta, Canada. The average dielectric constant of the hydrate zones is 9, ranging from 5 to 20. The average resistivity is >5 ohm.m in the hydrate zones, ranging from 2 to 10 ohm.m at a 1.1 GHz dielectric tool frequency. The dielectric logs show similar trends with sonic and induction resistivity logs, but exhibits inherently higher vertical resolution (<5 cm). The average in-situ hydrate saturation in the well is about 70%, ranging from 20% to 95%. The dielectric estimates are overall in agreement with induction estimates but the induction log tends to overestimate hydrate content up to 15%. Dielectric estimates could be used as a better proxy of in-situ hydrate saturation in modeling hydrate dynamics. The fine-scale structure in hydrate zones could help reveal hydrate formation history.

Hydrate morphology: Physical properties of sands with patchy hydrate saturation

USGS Publications Warehouse

Dai, S.; Santamarina, J.C.; Waite, William F.; Kneafsey, T.J.

2012-01-01

The physical properties of gas hydrate-bearing sediments depend on the volume fraction and spatial distribution of the hydrate phase. The host sediment grain size and the state of effective stress determine the hydrate morphology in sediments; this information can be used to significantly constrain estimates of the physical properties of hydrate-bearing sediments, including the coarse-grained sands subjected to high effective stress that are of interest as potential energy resources. Reported data and physical analyses suggest hydrate-bearing sands contain a heterogeneous, patchy hydrate distribution, whereby zones with 100% pore-space hydrate saturation are embedded in hydrate-free sand. Accounting for patchy rather than homogeneous hydrate distribution yields more tightly constrained estimates of physical properties in hydrate-bearing sands and captures observed physical-property dependencies on hydrate saturation. For example, numerical modeling results of sands with patchy saturation agree with experimental observation, showing a transition in stiffness starting near the series bound at low hydrate saturations but moving toward the parallel bound at high hydrate saturations. The hydrate-patch size itself impacts the physical properties of hydrate-bearing sediments; for example, at constant hydrate saturation, we find that conductivity (electrical, hydraulic and thermal) increases as the number of hydrate-saturated patches increases. This increase reflects the larger number of conductive flow paths that exist in specimens with many small hydrate-saturated patches in comparison to specimens in which a few large hydrate saturated patches can block flow over a significant cross-section of the specimen.

Thermodynamic calculations in the system CH4-H2O and methane hydrate phase equilibria

USGS Publications Warehouse

Circone, S.; Kirby, S.H.; Stern, L.A.

2006-01-01

Using the Gibbs function of reaction, equilibrium pressure, temperature conditions for the formation of methane clathrate hydrate have been calculated from the thermodynamic properties of phases in the system CH4-H 2O. The thermodynamic model accurately reproduces the published phase-equilibria data to within ??2 K of the observed equilibrium boundaries in the range 0.08-117 MPa and 190-307 K. The model also provides an estimate of the third-law entropy of methane hydrate at 273.15 K, 0.1 MPa of 56.2 J mol-1 K-1 for 1/n CH4??H 2O, where n is the hydrate number. Agreement between the calculated and published phase-equilibria data is optimized when the hydrate composition is fixed and independent of the pressure and temperature for the conditions modeled. ?? 2006 American Chemical Society.

Selective Encaging of N2O in N2O-N2 Binary Gas Hydrates via Hydrate-Based Gas Separation.

PubMed

Yang, Youjeong; Shin, Donghoon; Choi, Seunghyun; Woo, Yesol; Lee, Jong-Won; Kim, Dongseon; Shin, Hee-Young; Cha, Minjun; Yoon, Ji-Ho

2017-03-21

The crystal structure and guest inclusion behaviors of nitrous oxide-nitrogen (N 2 O-N 2 ) binary gas hydrates formed from N 2 O/N 2 gas mixtures are determined through spectroscopic analysis. Powder X-ray diffraction results indicate that the crystal structure of all the N 2 O-N 2 binary gas hydrates is identified as the structure I (sI) hydrate. Raman spectra for the N 2 O-N 2 binary gas hydrate formed from N 2 O/N 2 (80/20, 60/40, 40/60 mol %) gas mixtures reveal that N 2 O molecules occupy both large and small cages of the sI hydrate. In contrast, there is a single Raman band of N 2 O molecules for the N 2 O-N 2 binary gas hydrate formed from the N 2 O/N 2 (20/80 mol %) gas mixture, indicating that N 2 O molecules are trapped in only large cages of the sI hydrate. From temperature-dependent Raman spectra and the Predictive Soave-Redlich-Kwong (PSRK) model calculation, we confirm the self-preservation of N 2 O-N 2 binary gas hydrates in the temperature range of 210-270 K. Both the experimental measurements and the PSRK model calculations demonstrate the preferential occupation of N 2 O molecules rather than N 2 molecules in the hydrate cages, leading to a possible process for separating N 2 O from gas mixtures via hydrate formation. The phase equilibrium conditions, pseudo-pressure-composition (P-x) diagram, and gas storage capacity of N 2 O-N 2 binary gas hydrates are discussed in detail.

Pre- and post-drill comparison of the Mount Elbert gas hydrate prospect, Alaska North Slope

USGS Publications Warehouse

Lee, M.W.; Agena, W.F.; Collett, T.S.; Inks, T.L.

2011-01-01

In 2006, the United States Geological Survey (USGS) completed a detailed analysis and interpretation of available 2-D and 3-D seismic data, along with seismic modeling and correlation with specially processed downhole well log data for identifying potential gas hydrate accumulations on the North Slope of Alaska. A methodology was developed for identifying sub-permafrost gas hydrate prospects within the gas hydrate stability zone in the Milne Point area. The study revealed a total of 14 gas hydrate prospects in this area.In order to validate the gas hydrate prospecting protocol of the USGS and to acquire critical reservoir data needed to develop a longer-term production testing program, a stratigraphic test well was drilled at the Mount Elbert prospect in the Milne Point area in early 2007. The drilling confirmed the presence of two prominent gas-hydrate-bearing units in the Mount Elbert prospect, and high quality well logs and core data were acquired. The post-drill results indicate pre-drill predictions of the reservoir thickness and the gas-hydrate saturations based on seismic and existing well data were 90% accurate for the upper unit (hydrate unit D) and 70% accurate for the lower unit (hydrate unit C), confirming the validity of the USGS approach to gas hydrate prospecting. The Mount Elbert prospect is the first gas hydrate accumulation on the North Slope of Alaska identified primarily on the basis of seismic attribute analysis and specially processed downhole log data. Post-drill well log data enabled a better constraint of the elastic model and the development of an improved approach to the gas hydrate prospecting using seismic attributes. ?? 2009.

Molecular simulation of a model of dissolved organic matter.

PubMed

Sutton, Rebecca; Sposito, Garrison; Diallo, Mamadou S; Schulten, Hans-Rolf

2005-08-01

A series of atomistic simulations was performed to assess the ability of the Schulten dissolved organic matter (DOM) molecule, a well-established model humic molecule, to reproduce the physical and chemical behavior of natural humic substances. The unhydrated DOM molecule had a bulk density value appropriate to humic matter, but its Hildebrand solubility parameter was lower than the range of current experimental estimates. Under hydrated conditions, the DOM molecule went through conformational adjustments that resulted in disruption of intramolecular hydrogen bonds (H-bonds), although few water molecules penetrated the organic interior. The radius of gyration of the hydrated DOM molecule was similar to those measured for aquatic humic substances. To simulate humic materials under aqueous conditions with varying pH levels, carboxyl groups were deprotonated, and hydrated Na+ or Ca2+ were added to balance the resulting negative charge. Because of intrusion of the cation hydrates, the model metal-humic structures were more porous, had greater solvent-accessible surface areas, and formed more H-bonds with water than the protonated, hydrated DOM molecule. Relative to Na+, Ca2+ was both more strongly bound to carboxylate groups and more fully hydrated. This difference was attributed to the higher charge of the divalent cation. The Ca-DOM hydrate, however, featured fewer H-bonds than the Na-DOM hydrate, perhaps because of the reduced orientational freedom of organic moieties and water molecules imposed by Ca2+. The present work is, to our knowledge, the first rigorous computational exploration regarding the behavior of a model humic molecule under a range of physical conditions typical of soil and water systems.

Cross Directorate Proposal: Nanostructured Materials for Munitions and Propellants-Production, Modeling, and Characterization

DTIC Science & Technology

2016-07-15

towards hydration and decomposition along with probing their hydration mechanisms, we are now exploring processing and deposition effects for this...oxidizer films and tested for their reactivity. Hydration Mechanism for HI3O8 → HIO3 Previous efforts by our group investigating the hydration ...mechanism of I2O5 → HI3O8 reflected that the hydration mechanism proceeded through a nucleation and growth process followed by a diffusion limited

Adsorption isotherms of water on mica: redistribution and film growth.

PubMed

Malani, Ateeque; Ayappa, K G

2009-01-29

Adsorption isotherms of water on muscovite mica are obtained using grand canonical Monte Carlo simulations over a wide range of relative vapor pressures, p/p(0) at 298 K. Three distinct stages are observed in the adsorption isotherm. A sharp rise in the water coverage occurs for 0 < p/p(0) < 0.1. This is followed by a relatively slow increase in the coverage for 0.1 < or = p/p(0) < or = 0.7. Above p/p(0) = 0.7, a second increase in the coverage occurs due to the adsorption of water with bulklike features. The derived film thickness and isotherm shape for the simple point charge (SPC) water model is in excellent agreement with recent experiments of Balmer et al. [ Langmuir 2008 , 24 , 1566 ]. A novel observation is the significant redistribution of water between adsorbed layers as the water film develops. This redistribution is most pronounced for 0.1 < or = p/p(0) < or = 0.7, where water is depleted from the inner layers and film growth is initiated on the outer layer. During this stage, potassium hydration is found to play a dominant role in the rearrangement of water near the mica surface. The analysis of structural features reveals a strongly bound first layer of water molecules occupying the ditrigonal cavities between the potassium ions. In-plane structure of oxygen in the second layer, which forms part of the first hydration shell of potassium, reveals a liquidlike structure with the oxygen-oxygen pair correlation function displaying features similar to bulk water. Isosteric heats of adsorption were found to be in good agreement with the differential microcalorimetric data of Rakhmatkariev ( Clays Clay Miner. 2006 , 54 , 402 ), over the entire range of pressures investigated. Both SPC and extended simple point charge (SPC/E) water models were found to yield qualitatively similar adsorption and structural characteristics, with the SPC/E model predicting lower coverages than the SPC model for p/p(0) > 0.7.

Dynamics of Permafrost Associated Methane Hydrate in Response to Climate Change

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.

2014-12-01

The formation and melting of methane hydrate and ice are intertwined in permafrost regions. A shortage of methane supply leads to formation of hydrate only at depth, below the base of permafrost. We consider a system with the ground surface initially at 0 oC with neither ice nor hydrate present. We abruptly decrease the temperature from 0 to -10 oC to simulate the effect of marine regression/ global cooling. A low methane supply rate of 0.005 kg m-2 yr-1 from depth leads to distinct ice and hydrate layers: a 100 m continuous hydrate layer is present beneath 850 m at 80 k.y.. However, a high methane supply rate of 0.1 kg m-2 yr-1 leads to 50 m ice-bonded methane hydrate at the base of permafrost, and the hydrate layer distributes between the depth of 350 and 700 m at 80 k.y.. We apply our model to illuminate future melting of hydrate at Mallik, a known Arctic hydrate accumulation. We assume a 600 m thick ice saturated (average 90%) layer extending downward from the ground surface. We increase the surface temperature linearly from -6 to 0 oC for 300 yr and then keep the surface temperature at 0 oC to reflect future climate warming caused by doubling of CO2. Hydrate melting is initiated at the base of the hydrate layer after 15 k.y.. Methane gas starts to vent to the atmosphere at 38 k.y. with an average flux of ~ 0.35 g m-2 yr-1. If the 600 m thick average ice saturation is decreased to half (45%) (or to zero), methane gas starts to vent to the atmosphere at 29 k.y. (or at 20 k.y.) with the same average flux. These results are found by a newly-developed fully-coupled multiphase multicomponent fluid flow and heat transport model. Our thermodynamic equilibrium-based model emphasizes the role of salinity in both ice and hydrate dynamics.

Regional long-term production modeling from a single well test, Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Anderson, B.J.; Kurihara, M.; White, M.D.; Moridis, G.J.; Wilson, S.J.; Pooladi-Darvish, M.; Gaddipati, M.; Masuda, Y.; Collett, T.S.; Hunter, R.B.; Narita, H.; Rose, K.; Boswell, R.

2011-01-01

Following the results from the open-hole formation pressure response test in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well (Mount Elbert well) using Schlumberger's Modular Dynamics Formation Tester (MDT) wireline tool, the International Methane Hydrate Reservoir Simulator Code Comparison project performed long-term reservoir simulations on three different model reservoirs. These descriptions were based on 1) the Mount Elbert gas hydrate accumulation as delineated by an extensive history-matching exercise, 2) an estimation of the hydrate accumulation near the Prudhoe Bay L-pad, and 3) a reservoir that would be down-dip of the Prudhoe Bay L-pad and therefore warmer and deeper. All of these simulations were based, in part, on the results of the MDT results from the Mount Elbert Well. The comparison group's consensus value for the initial permeability of the hydrate-filled reservoir (k = 0.12 mD) and the permeability model based on the MDT history match were used as the basis for subsequent simulations on the three regional scenarios. The simulation results of the five different simulation codes, CMG STARS, HydrateResSim, MH-21 HYDRES, STOMP-HYD, and TOUGH+HYDRATE exhibit good qualitative agreement and the variability of potential methane production rates from gas hydrate reservoirs is illustrated. As expected, the predicted methane production rate increased with increasing in situ reservoir temperature; however, a significant delay in the onset of rapid hydrate dissociation is observed for a cold, homogeneous reservoir and it is found to be repeatable. The inclusion of reservoir heterogeneity in the description of this cold reservoir is shown to eliminate this delayed production. Overall, simulations utilized detailed information collected across the Mount Elbert reservoir either obtained or determined from geophysical well logs, including thickness (37 ft), porosity (35%), hydrate saturation (65%), intrinsic permeability (1000 mD), pore water salinity (5 ppt), and formation temperature (3.3-3.9 ??C). This paper presents the approach and results of extrapolating regional forward production modeling from history-matching efforts on the results from a single well test. ?? 2010 Elsevier Ltd.

Regional long-term production modeling from a single well test, Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

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

Anderson, Brian J.; Kurihara, Masanori; White, Mark D.

2011-02-01

Following the results from the open-hole formation pressure response test in the BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well (Mount Elbert well) using Schlumberger's Modular Dynamics Formation Tester (MDT) wireline tool, the International Methane Hydrate Reservoir Simulator Code Comparison project performed long-term reservoir simulations on three different model reservoirs. These descriptions were based on 1) the Mount Elbert gas hydrate accumulation as delineated by an extensive history-matching exercise, 2) an estimation of the hydrate accumulation near the Prudhoe Bay L-pad, and 3) a reservoir that would be down-dip of the Prudhoe Bay L-pad and therefore warmer and deeper. Allmore » of these simulations were based, in part, on the results of the MDT results from the Mount Elbert Well. The comparison group's consensus value for the initial permeability of the hydrate-filled reservoir (k = 0.12 mD) and the permeability model based on the MDT history match were used as the basis for subsequent simulations on the three regional scenarios. The simulation results of the five different simulation codes, CMG STARS, HydrateResSim, MH-21 HYDRES, STOMP-HYD, and TOUGH+HYDRATE exhibit good qualitative agreement and the variability of potential methane production rates from gas hydrate reservoirs is illustrated. As expected, the predicted methane production rate increased with increasing in situ reservoir temperature; however, a significant delay in the onset of rapid hydrate dissociation is observed for a cold, homogeneous reservoir and it is found to be repeatable. The inclusion of reservoir heterogeneity in the description of this cold reservoir is shown to eliminate this delayed production. Overall, simulations utilized detailed information collected across the Mount Elbert reservoir either obtained or determined from geophysical well logs, including thickness (37 ft), porosity (35%), hydrate saturation (65%), intrinsic permeability (1000 mD), pore water salinity (5 ppt), and formation temperature (3.3–3.9 °C). Finally, this paper presents the approach and results of extrapolating regional forward production modeling from history-matching efforts on the results from a single well test.« less

Seismic Modeling Of Reservoir Heterogeneity Scales: An Application To Gas Hydrate Reservoirs

NASA Astrophysics Data System (ADS)

Huang, J.; Bellefleur, G.; Milkereit, B.

2008-12-01

Natural gas hydrates, a type of inclusion compound or clathrate, are composed of gas molecules trapped within a cage of water molecules. The occurrence of gas hydrates in permafrost regions has been confirmed by core samples recovered from the Mallik gas hydrate research wells located within Mackenzie Delta in Northwest Territories of Canada. Strong vertical variations of compressional and shear sonic velocities and weak surface seismic expressions of gas hydrates indicate that lithological heterogeneities control the distribution of hydrates. Seismic scattering studies predict that typical scales and strong physical contrasts due to gas hydrate concentration will generate strong forward scattering, leaving only weak energy captured by surface receivers. In order to understand the distribution of hydrates and the seismic scattering effects, an algorithm was developed to construct heterogeneous petrophysical reservoir models. The algorithm was based on well logs showing power law features and Gaussian or Non-Gaussian probability density distribution, and was designed to honor the whole statistical features of well logs such as the characteristic scales and the correlation among rock parameters. Multi-dimensional and multi-variable heterogeneous models representing the same statistical properties were constructed and applied to the heterogeneity analysis of gas hydrate reservoirs. The petrophysical models provide the platform to estimate rock physics properties as well as to study the impact of seismic scattering, wave mode conversion, and their integration on wave behavior in heterogeneous reservoirs. Using the Biot-Gassmann theory, the statistical parameters obtained from Mallik 5L-38, and the correlation length estimated from acoustic impedance inversion, gas hydrate volume fraction in Mallik area was estimated to be 1.8%, approximately 2x108 m3 natural gas stored in a hydrate bearing interval within 0.25 km2 lateral extension and between 889 m and 1115 m depth. With parallel 3-D viscoelastic Finite Difference (FD) software, we conducted a 3D numerical experiment of near offset Vertical Seismic Profile. The synthetic results implied that the strong attenuation observed in the field data might be caused by the scattering.

Microwave absorption in substances that form hydration layers with water

NASA Astrophysics Data System (ADS)

Garner, H. R.; Ohkawa, T.; Tuason, O.; Lee, R. L.

1990-12-01

The microwave absorption of certain water soluble polymers (polyethylene glycol, polyvinyl pyrrolidone, proteins, and DNA) in solution is composed of three parts: absorption in the free water, absorption in the substance, and absorption in the hydration layer. Ethanol, sucrose, glycerol, and sodium acetate, which form weak hydrogen bonds or have an ionic nature in aqueous solutions, also have microwave absorption signatures similar to polymers that form hydration layers. The frequency-dependent absorption of the free water and of the hydration layer water is described by a simple Debye relaxation model. The absorption per unit sample volume attributable to the hydration layer is solute concentration dependent, and a simple model is used to describe the dependence. The hydration-layer relaxation time was found to vary from substance to substance and with solute concentration. The relaxation time was also found to be independent of solute length.

Numerical simulations of depressurization-induced gas production from gas hydrate reservoirs at the Walker Ridge 312 site, northern Gulf of Mexico

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

Myshakin, Evgeniy M.; Gaddipati, Manohar; Rose, Kelly

2012-06-01

In 2009, the Gulf of Mexico (GOM) Gas Hydrates Joint-Industry-Project (JIP) Leg II drilling program confirmed that gas hydrate occurs at high saturations within reservoir-quality sands in the GOM. A comprehensive logging-while-drilling dataset was collected from seven wells at three sites, including two wells at the Walker Ridge 313 site. By constraining the saturations and thicknesses of hydrate-bearing sands using logging-while-drilling data, two-dimensional (2D), cylindrical, r-z and three-dimensional (3D) reservoir models were simulated. The gas hydrate occurrences inferred from seismic analysis are used to delineate the areal extent of the 3D reservoir models. Numerical simulations of gas production from themore » Walker Ridge reservoirs were conducted using the depressurization method at a constant bottomhole pressure. Results of these simulations indicate that these hydrate deposits are readily produced, owing to high intrinsic reservoir-quality and their proximity to the base of hydrate stability. The elevated in situ reservoir temperatures contribute to high (5–40 MMscf/day) predicted production rates. The production rates obtained from the 2D and 3D models are in close agreement. To evaluate the effect of spatial dimensions, the 2D reservoir domains were simulated at two outer radii. The results showed increased potential for formation of secondary hydrate and appearance of lag time for production rates as reservoir size increases. Similar phenomena were observed in the 3D reservoir models. The results also suggest that interbedded gas hydrate accumulations might be preferable targets for gas production in comparison with massive deposits. Hydrate in such accumulations can be readily dissociated due to heat supply from surrounding hydrate-free zones. Special cases were considered to evaluate the effect of overburden and underburden permeability on production. The obtained data show that production can be significantly degraded in comparison with a case using impermeable boundaries. The main reason for the reduced productivity is water influx from the surrounding strata; a secondary cause is gas escape into the overburden. The results dictate that in order to reliably estimate production potential, permeability of the surroundings has to be included in a model.« less

Subduction-zone magnetic anomalies and implications for hydrated forearc mantle

USGS Publications Warehouse

Blakely, R.J.; Brocher, T.M.; Wells, R.E.

2005-01-01

Continental mantle in subduction zones is hydrated by release of water from the underlying oceanic plate. Magnetite is a significant byproduct of mantle hydration, and forearc mantle, cooled by subduction, should contribute to long-wavelength magnetic anomalies above subduction zones. We test this hypothesis with a quantitative model of the Cascadia convergent margin, based on gravity and aeromagnetic anomalies and constrained by seismic velocities, and find that hydrated mantle explains an important disparity in potential-field anomalies of Cascadia. A comparison with aeromagnetic data, thermal models, and earthquakes of Cascadia, Japan, and southern Alaska suggests that magnetic mantle may be common in forearc settings and thus magnetic anomalies may be useful in mapping hydrated mantle in convergent margins worldwide. ?? 2005 Geological Society of America.

Predicting the Impact of Multiwalled Carbon Nanotubes on the Cement Hydration Products and Durability of Cementitious Matrix Using Artificial Neural Network Modeling Technique

PubMed Central

Fakhim, Babak; Hassani, Abolfazl; Rashidi, Alimorad; Ghodousi, Parviz

2013-01-01

In this study the feasibility of using the artificial neural networks modeling in predicting the effect of MWCNT on amount of cement hydration products and improving the quality of cement hydration products microstructures of cement paste was investigated. To determine the amount of cement hydration products thermogravimetric analysis was used. Two critical parameters of TGA test are PHPloss and CHloss. In order to model the TGA test results, the ANN modeling was performed on these parameters separately. In this study, 60% of data are used for model calibration and the remaining 40% are used for model verification. Based on the highest efficiency coefficient and the lowest root mean square error, the best ANN model was chosen. The results of TGA test implied that the cement hydration is enhanced in the presence of the optimum percentage (0.3 wt%) of MWCNT. Moreover, since the efficiency coefficient of the modeling results of CH and PHP loss in both the calibration and verification stages was more than 0.96, it was concluded that the ANN could be used as an accurate tool for modeling the TGA results. Another finding of this study was that the ANN prediction in higher ages was more precise. PMID:24489487

Dehydration of multilamellar fatty acid membranes: Towards a computational model of the stratum corneum

NASA Astrophysics Data System (ADS)

MacDermaid, Christopher M.; DeVane, Russell H.; Klein, Michael L.; Fiorin, Giacomo

2014-12-01

The level of hydration controls the cohesion between apposed lamellae of saturated free fatty acids found in the lipid matrix of stratum corneum, the outermost layer of mammalian skin. This multilamellar lipid matrix is highly impermeable to water and ions, so that the local hydration shell of its fatty acids may not always be in equilibrium with the acidity and relative humidity, which significantly change over a course of days during skin growth. The homeostasis of the stratum corneum at each moment of its growth likely requires a balance between two factors, which affect in opposite ways the diffusion of hydrophilic species through the stratum corneum: (i) an increase in water order as the lipid lamellae come in closer contact, and (ii) a decrease in water order as the fraction of charged fatty acids is lowered by pH. Herein molecular dynamics simulations are employed to estimate the impact of both effects on water molecules confined between lamellae of fatty acids. Under conditions where membrane undulations are energetically favorable, the charged fatty acids are able to sequester cations around points of contact between lamellae that are fully dehydrated, while essentially maintaining a multilamellar structure for the entire system. This observation suggests that the undulations of the fatty acid lamellae control the diffusion of hydrophilic species through the water phase by altering the positional and rotational order of water molecules in the embedded/occluded "droplets."

Molecular simulation study on Hofmeister cations and the aqueous solubility of benzene.

PubMed

Ganguly, Pritam; Hajari, Timir; van der Vegt, Nico F A

2014-05-22

We study the ion-specific salting-out process of benzene in aqueous alkali chloride solutions using Kirkwood-Buff (KB) theory of solutions and molecular dynamics simulations with different empirical force field models for the ions and benzene. Despite inaccuracies in the force fields, the simulations indicate that the decrease of the Setchenow salting-out coefficient for the series NaCl > KCl > RbCl > CsCl is determined by direct benzene-cation correlations, with the larger cations showing weak interactions with benzene. Although ion-specific aqueous solubilities of benzene may be affected by indirect ion-ion, ion-water, and water-water correlations, too, these correlations are found to be unimportant, with little to no effect on the Setchenow salting-out coefficients of the various salts. We further considered LiCl, which is experimentally known to be a weaker salting-out agent than NaCl and KCl and, therefore, ranks at an unusual position within the Hofmeister cation series. The simulations indicate that hydrated Li(+) ions can take part of the benzene hydration shell while the other cations are repelled by it. This causes weaker Li(+) exclusion around the solute and a resulting, weaker salting-out propensity of LiCl compared to that of the other salts. Removing benzene-water and benzene-salt electrostatic interactions in the simulations does not affect this mechanism, which may therefore also explain the smaller effect of LiCl, as compared to that of NaCl or KCl, on aqueous solvation and hydrophobic interaction of nonpolar molecules.

A new estimate of the volume and distribution of gas hydrate in the northern Gulf of Mexico

NASA Astrophysics Data System (ADS)

Majumdar, U.; Cook, A.

2016-12-01

In spite of the wealth of information gained over the last several decades about gas hydrate in the northern Gulf of Mexico, there is still considerable uncertainty about the distribution and volume of gas hydrate. In our assessment we build a dataset of basin-wide gas hydrate distribution and thickness, as appraised from publicly available petroleum industry well logs within the gas hydrate stability zone (HSZ), and subsequently develop a Monte Carlo to determine the volumetric estimate of gas hydrate using the dataset. We evaluate the presence of gas hydrate from electrical resistivity well logs, and categorized possible reservoir type (either sand or clay) based on the gamma ray response and resistivity curve characteristics. Out of the 798 wells with resistivity well log data within the HSZ we analyzed, we found evidence of gas hydrate in 124 wells. In this research we present a new stochastic estimate of the gas hydrate volume in the northern Gulf of Mexico guided by our well log dataset. For our Monte Carlo simulation, we divided our assessment area of 200,000 km2 into 1 km2 grid cells. Our volume assessment model incorporates variables unique to our well log dataset such as the likelihood of gas hydrate occurrence, fraction of the HSZ occupied by gas hydrate, reservoir type, and gas hydrate saturation depending on the reservoir, in each grid cell, in addition to other basic variables such as HSZ thickness and porosity. Preliminary results from our model suggests that the total volume of gas at standard temperature and pressure in gas hydrate in the northern Gulf of Mexico is in the range of 430 trillion cubic feet (TCF) to 730 TCF, with a mean volume of 585 TCF. While the reservoir distribution from our well log dataset found gas hydrate in sand reservoirs in 30 wells out of the 124 wells with evidence of gas hydrate ( 24%), we find sand reservoirs contain over half of the total volume of gas hydrate in the Gulf of Mexico, as a result of the relatively high gas hydrate saturation in sand.

Relationship of gas hydrate concentration to porosity and reflection amplitude in a research well, Mackenzie Delta, Canada

USGS Publications Warehouse

Jin, Y.K.; Lee, M.W.; Collett, T.S.

2002-01-01

Well logs acquired at the Mallik 2L-38 gas hydrate research well. Mackenzie Delta, Canada, reveal a distinct trend showing that the resistivity of gas-hydrate-bearing sediments increases with increases in density porosities. This trend, opposite to the general trend of decrease in resistivity with porosity, implies that gas hydrates are more concentrated in the higher porosity. Using the Mallik 2L-38 well data, a proportional gas hydrate concentration (PGHC) model, which states that the gas hydrate concentration in the sediment's pore space is linearly proportional to porosity, is proposed for the general habitat of gas hydrate in sediments. Anomalous data (less than 6% of the total data) outside the dominant observed trend can be explained by local geological characteristics. The anomalous data analysis indicates that highly concentrated gas-hydrate-bearing layers would be expected where sediments have high proportions of gravel and coarse sand. Using the parameters in the PGHC model determined from resistivity-porosity logs, it is possible to qualitatively predict the degree of reflection amplitude variations in seismic profiles. Moderate-to-strong reflections are expected for the Mallik 2L-38 well. ?? 2002 Elsevier Science Ltd. All rights reserved.

Formation of natural gas hydrates in marine sediments 1. Conceptual model of gas hydrate growth conditioned by host sediment properties

USGS Publications Warehouse

Clennell, M.B.; Hovland, M.; Booth, J.S.; Henry, P.; Winters, W.J.

1999-01-01

The stability of submarine gas hydrates is largely dictated by pressure and temperature, gas composition, and pore water salinity. However, the physical properties and surface chemistry of deep marine sediments may also affect the thermodynamic state, growth kinetics, spatial distributions, and growth forms of clathrates. Our conceptual model presumes that gas hydrate behaves in a way analogous to ice in a freezing soil. Hydrate growth is inhibited within fine-grained sediments by a combination of reduced pore water activity in the vicinity of hydrophilic mineral surfaces, and the excess internal energy of small crystals confined in pores. The excess energy can be thought of as a "capillary pressure" in the hydrate crystal, related to the pore size distribution and the state of stress in the sediment framework. The base of gas hydrate stability in a sequence of fine sediments is predicted by our model to occur at a lower temperature (nearer to the seabed) than would be calculated from bulk thermodynamic equilibrium. Capillary effects or a build up of salt in the system can expand the phase boundary between hydrate and free gas into a divariant field extending over a finite depth range dictated by total methane content and pore-size distribution. Hysteresis between the temperatures of crystallization and dissociation of the clathrate is also predicted. Growth forms commonly observed in hydrate samples recovered from marine sediments (nodules, and lenses in muds; cements in sands) can largely be explained by capillary effects, but kinetics of nucleation and growth are also important. The formation of concentrated gas hydrates in a partially closed system with respect to material transport, or where gas can flush through the system, may lead to water depletion in the host sediment. This "freeze-drying" may be detectable through physical changes to the sediment (low water content and overconsolidation) and/or chemical anomalies in the pore waters and metastable presence of free gas within the normal zone of hydrate stability. 

Site selection for DOE/JIP gas hydrate drilling in the northern Gulf of Mexico

USGS Publications Warehouse

Hutchinson, Deborah; Shelander, Dianna; Dai, J.; McConnell, D.; Shedd, William; Frye, Matthew; Ruppel, Carolyn D.; Boswell, R.; Jones, Emrys; Collett, Timothy S.; Rose, Kelly K.; Dugan, Brandon; Wood, Warren T.

2008-01-01

n the late spring of 2008, the Chevron-led Gulf of Mexico Gas Hydrate Joint Industry Project (JIP) expects to conduct an exploratory drilling and logging campaign to better understand gas hydrate-bearing sands in the deepwater Gulf of Mexico. The JIP Site Selection team selected three areas to test alternative geological models and geophysical interpretations supporting the existence of potential high gas hydrate saturations in reservoir-quality sands. The three sites are near existing drill holes which provide geological and geophysical constraints in Alaminos Canyon (AC) lease block 818, Green Canyon (GC) 955, and Walker Ridge (WR) 313. At the AC818 site, gas hydrate is interpreted to occur within the Oligocene Frio volcaniclastic sand at the crest of a fold that is shallow enough to be in the hydrate stability zone. Drilling at GC955 will sample a faulted, buried Pleistocene channel-levee system in an area characterized by seafloor fluid expulsion features, structural closure associated with uplifted salt, and abundant seismic evidence for upward migration of fluids and gas into the sand-rich parts of the sedimentary section. Drilling at WR313 targets ponded sheet sands and associated channel/levee deposits within a minibasin, making this a non-structural play. The potential for gas hydrate occurrence at WR313 is supported by shingled phase reversals consistent with the transition from gas-charged sand to overlying gas-hydrate saturated sand. Drilling locations have been selected at each site to 1) test geological methods and models used to infer the occurrence of gas hydrate in sand reservoirs in different settings in the northern Gulf of Mexico; 2) calibrate geophysical models used to detect gas hydrate sands, map reservoir thicknesses, and estimate the degree of gas hydrate saturation; and 3) delineate potential locations for subsequent JIP drilling and coring operations that will collect samples for comprehensive physical property, geochemical and other analyses

Sensitivity of the global submarine hydrate inventory to scenarios of future climate change

NASA Astrophysics Data System (ADS)

Hunter, S. J.; Goldobin, D. S.; Haywood, A. M.; Ridgwell, A.; Rees, J. G.

2013-04-01

The global submarine inventory of methane hydrate is thought to be considerable. The stability of marine hydrates is sensitive to changes in temperature and pressure and once destabilised, hydrates release methane into sediments and ocean and potentially into the atmosphere, creating a positive feedback with climate change. Here we present results from a multi-model study investigating how the methane hydrate inventory dynamically responds to different scenarios of future climate and sea level change. The results indicate that a warming-induced reduction is dominant even when assuming rather extreme rates of sea level rise (up to 20 mm yr-1) under moderate warming scenarios (RCP 4.5). Over the next century modelled hydrate dissociation is focussed in the top ˜100m of Arctic and Subarctic sediments beneath <500m water depth. Predicted dissociation rates are particularly sensitive to the modelled vertical hydrate distribution within sediments. Under the worst case business-as-usual scenario (RCP 8.5), upper estimates of resulting global sea-floor methane fluxes could exceed estimates of natural global fluxes by 2100 (>30-50TgCH4yr-1), although subsequent oxidation in the water column could reduce peak atmospheric release rates to 0.75-1.4 Tg CH4 yr-1.

Numerical simulation of injection process of warm carbon dioxide into layer saturated with methane and its hydrate

NASA Astrophysics Data System (ADS)

Khasanov, M. K.; Stolpovsky, M. V.; Gimaltdinov, I. K.

2018-05-01

In this article, in a flat-one-dimensional approximation, a mathematical model is presented for injecting warm carbon dioxide into a methane hydrate formation of finite length. It is established that the model of formation of hydrate of carbon dioxide in the absence of an area saturated with methane and water, under certain parameters, leads to thermodynamic contradiction. The mathematical model of carbon dioxide injection with formation of the region saturated with methane and water is constructed.

Estimating pore-space gas hydrate saturations from well log acoustic data

USGS Publications Warehouse

Lee, Myung W.; Waite, William F.

2008-01-01

Relating pore-space gas hydrate saturation to sonic velocity data is important for remotely estimating gas hydrate concentration in sediment. In the present study, sonic velocities of gas hydrate–bearing sands are modeled using a three-phase Biot-type theory in which sand, gas hydrate, and pore fluid form three homogeneous, interwoven frameworks. This theory is developed using well log compressional and shear wave velocity data from the Mallik 5L-38 permafrost gas hydrate research well in Canada and applied to well log data from hydrate-bearing sands in the Alaskan permafrost, Gulf of Mexico, and northern Cascadia margin. Velocity-based gas hydrate saturation estimates are in good agreement with Nuclear Magneto Resonance and resistivity log estimates over the complete range of observed gas hydrate saturations.

Probe conformational dynamics of proteins in aqueous solutions by terahertz spectroscopy

NASA Astrophysics Data System (ADS)

Vinh, Nguyen Q.

2016-10-01

Proteins solvated in their biologically milieu are expected to exhibit strong absorption in the terahertz frequencies, that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamic correlations among solvent water and proteins. The dynamics play an important role in enzymatic activities of proteins, but obtaining an accurate and quantitative pictures of these activities, however, is challenging due to the strong absorption of water. In response, we have developed the world's highest precision, highest sensitivity terahertz-frequency domain spectrometer and a standard terahertz-time domain system to probe the collective dynamics of proteins in aqueous solutions. Operating over the frequency range from 5 GHz up to 3 THz, our spectrometers provide an unparalleled ability to probe directly such questions as the hydration level, the dynamics of water and hydrated proteins over the 100 fs to 1 ns timescale. Employing an effective medium approximation to describe the complex dielectric response of the solvated proteins in solution we find that proteins are surrounded by a loosely and tightly held layers of water molecules that behave as if they are an integral part of the protein. The number of water molecules in the protein hydration shells varies with proteins, which can tell us the average surface structure of proteins. These measurements shed light on the macromolecular motions of proteins in their biologically relevant environment.

Dissolution rates of pure methane hydrate and carbon-dioxide hydrate in undersaturated seawater at 1000-m depth

USGS Publications Warehouse

Rehder, G.; Kirby, S.H.; Durham, W.B.; Stern, L.A.; Peltzer, E.T.; Pinkston, J.; Brewer, P.G.

2004-01-01

To help constrain models involving the chemical stability and lifetime of gas clathrate hydrates exposed at the seafloor, dissolution rates of pure methane and carbon-dioxide hydrates were measured directly on the seafloor within the nominal pressure-temperature (P/T) range of the gas hydrate stability zone. Other natural boundary conditions included variable flow velocity and undersaturation of seawater with respect to the hydrate-forming species. Four cylindrical test specimens of pure, polycrystalline CH4 and CO2 hydrate were grown and fully compacted in the laboratory, then transferred by pressure vessel to the seafloor (1028 m depth), exposed to the deep ocean environment, and monitored for 27 hours using time-lapse and HDTV cameras. Video analysis showed diameter reductions at rates between 0.94 and 1.20 ??m/s and between 9.0 and 10.6 ?? 10-2 ??m/s for the CO2 and CH4 hydrates, respectively, corresponding to dissolution rates of 4.15 ?? 0.5 mmol CO2/m2s and 0.37 ?? 0.03 mmol CH4/m2s. The ratio of the dissolution rates fits a diffusive boundary layer model that incorporates relative gas solubilities appropriate to the field site, which implies that the kinetics of the dissolution of both hydrates is diffusion-controlled. The observed dissolution of several mm (CH4) or tens of mm (CO2) of hydrate from the sample surfaces per day has major implications for estimating the longevity of natural gas hydrate outcrops as well as for the possible roles of CO2 hydrates in marine carbon sequestration strategies. ?? 2003 Elsevier Ltd.

The Dependence of Water Permeability in Quartz Sand on Gas Hydrate Saturation in the Pore Space

NASA Astrophysics Data System (ADS)

Kossel, E.; Deusner, C.; Bigalke, N.; Haeckel, M.

2018-02-01

Transport of fluids in gas hydrate bearing sediments is largely defined by the reduction of the permeability due to gas hydrate crystals in the pore space. Although the exact knowledge of the permeability behavior as a function of gas hydrate saturation is of crucial importance, state-of-the-art simulation codes for gas production scenarios use theoretically derived permeability equations that are hardly backed by experimental data. The reason for the insufficient validation of the model equations is the difficulty to create gas hydrate bearing sediments that have undergone formation mechanisms equivalent to the natural process and that have well-defined gas hydrate saturations. We formed methane hydrates in quartz sand from a methane-saturated aqueous solution and used magnetic resonance imaging to obtain time-resolved, three-dimensional maps of the gas hydrate saturation distribution. These maps were fed into 3-D finite element method simulations of the water flow. In our simulations, we tested the five most well-known permeability equations. All of the suitable permeability equations include the term (1-SH)n, where SH is the gas hydrate saturation and n is a parameter that needs to be constrained. The most basic equation describing the permeability behavior of water flow through gas hydrate bearing sand is k = k0 (1-SH)n. In our experiments, n was determined to be 11.4 (±0.3). Results from this study can be directly applied to bulk flow analysis under the assumption of homogeneous gas hydrate saturation and can be further used to derive effective permeability models for heterogeneous gas hydrate distributions at different scales.

Complex between triple helix of collagen and double helix of DNA in aqueous solution.

PubMed

Mrevlishvili, George M; Svintradze, David V

2005-06-01

We demonstrate in this paper that one example of a biologically important and molecular self-assembling complex system is a collagen-DNA ordered aggregate which spontaneously forms in aqueous solutions. Interaction between the collagen and the DNA leads to destruction of the hydration shell of the triple helix and stabilization of the double helix structure. From a molecular biology point of view this nano-scale self-assembling superstructure could increase the stability of DNA against the nucleases during collagen diseases and the growth of collagen fibrills in the presence of DNA.

Effect of the conditions of REM microalloying of steel on the corrosion activity of nonmetallic inclusions

NASA Astrophysics Data System (ADS)

Movenko, D. A.; Kotel'nikov, G. I.; Pavlov, A. V.; Bytsenko, O. A.

2015-11-01

Experimental heats of low-alloy steel are performed under various conditions of rare-earth metal microalloying and aluminum and calcium deoxidation. Electron-probe microanalysis of nonmetallic inclusions and a metallographic investigation of a metal are used to show that, when interacting with water, nonmetallic cerium oxide inclusions do not form hydrates and, correspondingly, are not aggressive. When aluminum, calcium, and cerium additions are sequentially introduced into a melt, a continuous cerium oxide shell forms on calcium aluminates, protects corrosive nonmetallic inclusions against interaction with water, and weakens local metal corrosion.

Dynamic morphology of gas hydrate on a methane bubble in water: Observations and new insights for hydrate film models

NASA Astrophysics Data System (ADS)

Warzinski, Robert P.; Lynn, Ronald; Haljasmaa, Igor; Leifer, Ira; Shaffer, Frank; Anderson, Brian J.; Levine, Jonathan S.

2014-10-01

Predicting the fate of subsea hydrocarbon gases escaping into seawater is complicated by potential formation of hydrate on rising bubbles that can enhance their survival in the water column, allowing gas to reach shallower depths and the atmosphere. The precise nature and influence of hydrate coatings on bubble hydrodynamics and dissolution is largely unknown. Here we present high-definition, experimental observations of complex surficial mechanisms governing methane bubble hydrate formation and dissociation during transit of a simulated oceanic water column that reveal a temporal progression of deep-sea controlling mechanisms. Synergistic feedbacks between bubble hydrodynamics, hydrate morphology, and coverage characteristics were discovered. Morphological changes on the bubble surface appear analogous to macroscale, sea ice processes, presenting new mechanistic insights. An inverse linear relationship between hydrate coverage and bubble dissolution rate is indicated. Understanding and incorporating these phenomena into bubble and bubble plume models will be necessary to accurately predict global greenhouse gas budgets for warming ocean scenarios and hydrocarbon transport from anthropogenic or natural deep-sea eruptions.

Electrical properties of methane hydrate + sediment mixtures: The σ of CH 4 Hydrate + Sediment

DOE PAGES

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven; ...

2015-07-30

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. We built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EMmore » field surveys. We report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. Finally, these results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.« less

Reflective terahertz (THz) imaging: system calibration using hydration phantoms

NASA Astrophysics Data System (ADS)

Bajwa, Neha; Garritano, James; Lee, Yoon Kyung; Tewari, Priyamvada; Sung, Shijun; Maccabi, Ashkan; Nowroozi, Bryan; Babakhanian, Meghedi; Sanghvi, Sajan; Singh, Rahul; Grundfest, Warren; Taylor, Zachary

2013-02-01

Terahertz (THz) hydration sensing continues to gain traction in the medical imaging community due to its unparalleled sensitivity to tissue water content. Rapid and accurate detection of fluid shifts following induction of thermal skin burns as well as remote corneal hydration sensing have been previously demonstrated in vivo using reflective, pulsed THz imaging. The hydration contrast sensing capabilities of this technology were recently confirmed in a parallel 7 Tesla Magnetic Resonance (MR) imaging study, in which burn areas are associated with increases in local mobile water content. Successful clinical translation of THz sensing, however, still requires quantitative assessments of system performance measurements, specifically hydration concentration sensitivity, with tissue substitutes. This research aims to calibrate the sensitivity of a novel, reflective THz system to tissue water content through the use of hydration phantoms for quantitative comparisons of THz hydration imagery.Gelatin phantoms were identified as an appropriate tissue-mimicking model for reflective THz applications, and gel composition, comprising mixtures of water and protein, was varied between 83% to 95% hydration, a physiologically relevant range. A comparison of four series of gelatin phantom studies demonstrated a positive linear relationship between THz reflectivity and water concentration, with statistically significant hydration sensitivities (p < .01) ranging between 0.0209 - 0.038% (reflectivity: %hydration). The THz-phantom interaction is simulated with a three-layer model using the Transfer Matrix Method with agreement in hydration trends. Having demonstrated the ability to accurately and noninvasively measure water content in tissue equivalent targets with high sensitivity, reflective THz imaging is explored as a potential tool for early detection and intervention of corneal pathologies.

Electrical properties of methane hydrate + sediment mixtures: The σ of CH 4 Hydrate + Sediment

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

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. We built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EMmore » field surveys. We report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. Finally, these results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.« less

Detection and Production of Methane Hydrate

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

George Hirasaki; Walter Chapman; Gerald Dickens

This project seeks to understand regional differences in gas hydrate systems from the perspective of as an energy resource, geohazard, and long-term climate influence. Specifically, the effort will: (1) collect data and conceptual models that targets causes of gas hydrate variance, (2) construct numerical models that explain and predict regional-scale gas hydrate differences in 2-dimensions with minimal 'free parameters', (3) simulate hydrocarbon production from various gas hydrate systems to establish promising resource characteristics, (4) perturb different gas hydrate systems to assess potential impacts of hot fluids on seafloor stability and well stability, and (5) develop geophysical approaches that enable remotemore » quantification of gas hydrate heterogeneities so that they can be characterized with minimal costly drilling. Our integrated program takes advantage of the fact that we have a close working team comprised of experts in distinct disciplines. The expected outcomes of this project are improved exploration and production technology for production of natural gas from methane hydrates and improved safety through understanding of seafloor and well bore stability in the presence of hydrates. The scope of this project was to more fully characterize, understand, and appreciate fundamental differences in the amount and distribution of gas hydrate and how this would affect the production potential of a hydrate accumulation in the marine environment. The effort combines existing information from locations in the ocean that are dominated by low permeability sediments with small amounts of high permeability sediments, one permafrost location where extensive hydrates exist in reservoir quality rocks and other locations deemed by mutual agreement of DOE and Rice to be appropriate. The initial ocean locations were Blake Ridge, Hydrate Ridge, Peru Margin and GOM. The permafrost location was Mallik. Although the ultimate goal of the project was to understand processes that control production potential of hydrates in marine settings, Mallik was included because of the extensive data collected in a producible hydrate accumulation. To date, such a location had not been studied in the oceanic environment. The project worked closely with ongoing projects (e.g. GOM JIP and offshore India) that are actively investigating potentially economic hydrate accumulations in marine settings. The overall approach was fivefold: (1) collect key data concerning hydrocarbon fluxes which is currently missing at all locations to be included in the study, (2) use this and existing data to build numerical models that can explain gas hydrate variance at all four locations, (3) simulate how natural gas could be produced from each location with different production strategies, (4) collect new sediment property data at these locations that are required for constraining fluxes, production simulations and assessing sediment stability, and (5) develop a method for remotely quantifying heterogeneities in gas hydrate and free gas distributions. While we generally restricted our efforts to the locations where key parameters can be measured or constrained, our ultimate aim was to make our efforts universally applicable to any hydrate accumulation.« less

Successful gas hydrate prospecting using 3D seismic - A case study for the Mt. Elbert prospect, Milne Point, North Slope Alaska

USGS Publications Warehouse

Inks, T.L.; Agena, W.F.

2008-01-01

In February 2007, the Mt. Elbert Prospect stratigraphic test well, Milne Point, North Slope Alaska encountered thick methane gas hydrate intervals, as predicted by 3D seismic interpretation and modeling. Methane gas hydrate-saturated sediment was found in two intervals, totaling more than 100 ft., identified and mapped based on seismic character and wavelet modeling.

Hydration forces between aligned DNA helices undergoing B to A conformational change: In-situ X-ray fiber diffraction studies in a humidity and temperature controlled environment.

PubMed

Case, Ryan; Schollmeyer, Hauke; Kohl, Phillip; Sirota, Eric B; Pynn, Roger; Ewert, Kai E; Safinya, Cyrus R; Li, Youli

2017-12-01

Hydration forces between DNA molecules in the A- and B-Form were studied using a newly developed technique enabling simultaneous in situ control of temperature and relative humidity. X-ray diffraction data were collected from oriented calf-thymus DNA fibers in the relative humidity range of 98%-70%, during which DNA undergoes the B- to A-form transition. Coexistence of both forms was observed over a finite humidity range at the transition. The change in DNA separation in response to variation in humidity, i.e. change of chemical potential, led to the derivation of a force-distance curve with a characteristic exponential decay constant of∼2Å for both A- and B-DNA. While previous osmotic stress measurements had yielded similar force-decay constants, they were limited to B-DNA with a surface separation (wall-to-wall distance) typically>5Å. The current investigation confirms that the hydration force remains dominant even in the dry A-DNA state and at surface separation down to∼1.5Å, within the first hydration shell. It is shown that the observed chemical potential difference between the A and B states could be attributed to the water layer inside the major and minor grooves of the A-DNA double helices, which can partially interpenetrate each other in the tightly packed A phase. The humidity-controlled X-ray diffraction method described here can be employed to perform direct force measurements on a broad range of biological structures such as membranes and filamentous protein networks. Copyright © 2017 Elsevier Inc. All rights reserved.

The catalytic effect of H2O on the hydrolysis of CO32- in hydrated clusters and its implication in the humidity driven CO2 air capture.

PubMed

Xiao, Hang; Shi, Xiaoyang; Zhang, Yayun; Liao, Xiangbiao; Hao, Feng; Lackner, Klaus S; Chen, Xi

2017-10-18

The hydration of ions in nanoscale hydrated clusters is ubiquitous and essential in many physical and chemical processes. Here we show that the hydrolysis reaction is strongly affected by relative humidity. The hydrolysis of CO 3 2- with n = 1-8 water molecules is investigated using an ab initio method. For n = 1-5 water molecules, all the reactants follow a stepwise pathway to the transition state. For n = 6-8 water molecules, all the reactants undergo a direct proton transfer to the transition state with overall lower activation free energy. The activation free energy of the reaction is dramatically reduced from 10.4 to 2.4 kcal mol -1 as the number of water molecules increases from 1 to 6. Meanwhile, the degree of hydrolysis of CO 3 2- is significantly increased compared to the bulk water solution scenario. Incomplete hydration shells facilitate the hydrolysis of CO 3 2- with few water molecules to be not only thermodynamically favorable but also kinetically favorable. We showed that the chemical kinetics is not likely to constrain the speed of CO 2 air capture driven by the humidity-swing. Instead, the pore-diffusion of ions is expected to be the time-limiting step in the humidity driven CO 2 air capture. The effect of humidity on the speed of CO 2 air capture was studied by conducting a CO 2 absorption experiment using IER with a high ratio of CO 3 2- to H 2 O molecules. Our result is able to provide valuable insights into designing efficient CO 2 air-capture sorbents.

Ultrafast phosphate hydration dynamics in bulk H{sub 2}O

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

Costard, Rene, E-mail: costard@mbi-berlin.de; Tyborski, Tobias; Fingerhut, Benjamin P., E-mail: fingerhut@mbi-berlin.de

2015-06-07

Phosphate vibrations serve as local probes of hydrogen bonding and structural fluctuations of hydration shells around ions. Interactions of H{sub 2}PO{sub 4}{sup −} ions and their aqueous environment are studied combining femtosecond 2D infrared spectroscopy, ab-initio calculations, and hybrid quantum-classical molecular dynamics (MD) simulations. Two-dimensional infrared spectra of the symmetric (ν{sub S}(PO{sub 2}{sup −})) and asymmetric (ν{sub AS}(PO{sub 2}{sup −})) PO{sub 2}{sup −} stretching vibrations display nearly homogeneous lineshapes and pronounced anharmonic couplings between the two modes and with the δ(P-(OH){sub 2}) bending modes. The frequency-time correlation function derived from the 2D spectra consists of a predominant 50 fs decaymore » and a weak constant component accounting for a residual inhomogeneous broadening. MD simulations show that the fluctuating electric field of the aqueous environment induces strong fluctuations of the ν{sub S}(PO{sub 2}{sup −}) and ν{sub AS}(PO{sub 2}{sup −}) transition frequencies with larger frequency excursions for ν{sub AS}(PO{sub 2}{sup −}). The calculated frequency-time correlation function is in good agreement with the experiment. The ν(PO{sub 2}{sup −}) frequencies are mainly determined by polarization contributions induced by electrostatic phosphate-water interactions. H{sub 2}PO{sub 4}{sup −}/H{sub 2}O cluster calculations reveal substantial frequency shifts and mode mixing with increasing hydration. Predicted phosphate-water hydrogen bond (HB) lifetimes have values on the order of 10 ps, substantially longer than water-water HB lifetimes. The ultrafast phosphate-water interactions observed here are in marked contrast to hydration dynamics of phospholipids where a quasi-static inhomogeneous broadening of phosphate vibrations suggests minor structural fluctuations of interfacial water.« less

Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

PubMed

Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

2010-12-15

We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

Strength Estimation for Hydrate-Bearing Sediments From Direct Shear Tests of Hydrate-Bearing Sand and Silt

NASA Astrophysics Data System (ADS)

Liu, Zhichao; Dai, Sheng; Ning, Fulong; Peng, Li; Wei, Houzhen; Wei, Changfu

2018-01-01

Safe and economic methane gas production, as well as the replacement of methane while sequestering carbon in natural hydrate deposits, requires enhanced geomechanical understanding of the strength and volume responses of hydrate-bearing sediments during shear. This study employs a custom-made apparatus to investigate the mechanical and volumetric behaviors of carbon dioxide hydrate-bearing sediments subjected to direct shear. The results show that both peak and residual strengths increase with increased hydrate saturation and vertical stress. Hydrate contributes mainly the cohesion and dilatancy constraint to the peak strength of hydrate-bearing sediments. The postpeak strength reduction is more evident and brittle in specimens with higher hydrate saturation and under lower stress. Significant strength reduction after shear failure is expected in silty sediments with high hydrate saturation Sh ≥ 0.65. Hydrate contribution to the residual strength is mainly by increasing cohesion at low hydrate saturation and friction at high hydrate saturation. Stress state and hydrate saturation are dominating both the stiffness and the strength of hydrate-bearing sediments; thus, a wave velocity-based peak strength prediction model is proposed and validated, which allows for precise estimation of the shear strength of hydrate-bearing sediments through acoustic logging data. This method is advantageous to geomechanical simulators, particularly when the experimental strength data of natural samples are not available.

Calibration and validation of a numerical model against experimental data of methane hydrate formation and dissociation in a sandy porous medium

NASA Astrophysics Data System (ADS)

Yin, Z.; Moridis, G. J.; Chong, Z. R.; Linga, P.

2017-12-01

Methane hydrates (MH) are known to trap enormous amounts of CH4 in oceanic and permafrost-associated deposits, and are being considered as a potential future energy source. Several powerful numerical simulators were developed to describe the behavior of natural hydrate-bearing sediments (HBS). The complexity and strong nonlinearities in HBS do not allow analytical solutions for code validation. The only reliable method to develop confidence in these models is through comparisons to laboratory and/or field experiments. The objective of this study is to reproduce numerically the results from earlier experiments of MH formation and depressurization (and the corresponding fluid production) in 1.0L reactor involving unconsolidated sand, thus validating and calibrating the TOUGH+Hydrate v1.5 simulator. We faithfully describe the reactor geometry and the experimental process that involves both hydrate formation and dissociation. We demonstrate that the laboratory experiments can only be captured by a kinetic hydration model. There is an excellent agreement between observations and predictions (a) of the cumulative gas depletion (during formation) and production (during dissociation) and (b) of pressure over time. The temperature agreement is less satisfactory, and the deviations are attributed to the fixed locations of the limited number of sensors that cannot fully capture the hydrate heterogeneity. We also predict the spatial distributions over time of the various phase (gas, aqueous and hydrate) saturations. Thus, hydrates form preferentially along the outer boundary of the sand core, and the hydrate front moves inward leaving a significant portion of the sand at the center hydrate-free. During depressurization, dissociation advances again inward from the reactor boundary to the center of the reactor. As expected, methane gas accumulates initially at the locations of most intense dissociation, and then gradually migrates to the upper section of the reactor because of buoyancy and of the pressure gradient caused by the pressure outlet. Sensitivity analysis indicates that the composite thermal conductivity of the HBS and the kinetic parameters of the hydration reaction are the dominant factors. The absolute permeability of the sand does not play a significant role in this small reactor.

Failure Mechanism of Cemented Hydrate-bearing Sand at Microscales

NASA Astrophysics Data System (ADS)

Yoneda, J.; Jin, Y.; Katagiri, J.; Tenma, N.

2016-12-01

On the basis of hypothetical particle-level mechanisms, several constitutive models of hydrate-bearing sediments have been proposed previously for gas production. However, to the best of our knowledge, the microstructural large-strain behaviors of hydrate-bearing sediments has not been reported to date because of the experimental challenges posed by the high-pressure and low-temperature testing conditions. Herein, as a part of a Japanese National hydrate research program (MH21, funded by METI), a novel microtriaxial testing apparatus was developed, and the mechanical large strain behavior of hydrate-bearing sediments with various hydrate saturation values (Sh = 0%, 39%, and 62%) were analyzed using microfocus X-ray computed tomography. Patchy hydrates were observed in the sediments at Sh = 39%. The obtained stress-strain relationships indicated strengthening with increasing hydrate saturation and a brittle failure mode of the hydrate-bearing sand. Localized deformations were quantified via image processing at the submillimeter and micrometer scale. Shear planes and particle deformation and/or rotation were detected, and the shear band thickness decreased with increasing hydrate saturation.

Physical Properties of Gas Hydrates: A Review

DOE PAGES

Gabitto, Jorge F.; Tsouris, Costas

2010-01-01

Memore » thane gas hydrates in sediments have been studied by several investigators as a possible future energy resource. Recent hydrate reserves have been estimated at approximately 10 16   m 3 of methane gas worldwide at standard temperature and pressure conditions. In situ dissociation of natural gas hydrate is necessary in order to commercially exploit the resource from the natural-gas-hydrate-bearing sediment. The presence of gas hydrates in sediments dramatically alters some of the normal physical properties of the sediment. These changes can be detected by field measurements and by down-hole logs. An understanding of the physical properties of hydrate-bearing sediments is necessary for interpretation of geophysical data collected in field settings, borehole, and slope stability analyses; reservoir simulation; and production models. This work reviews information available in literature related to the physical properties of sediments containing gas hydrates. A brief review of the physical properties of bulk gas hydrates is included. Detection methods, morphology, and relevant physical properties of gas-hydrate-bearing sediments are also discussed.« less

Prestack Waveform Inversion and Well Log Examination at GC955 and WR313 in the Gulf of Mexico for Estimation of Methane Hydrate Concentrations

NASA Astrophysics Data System (ADS)

Fortin, W.; Goldberg, D.; Kucuk, H. M.

2017-12-01

Gas hydrates are naturally occurring compounds, which, at a molecular scale, are lattice structures of ice embedded with various gas molecules in the lattice voids. Volumetric estimates of associated hydrocarbons vary greatly due to the difficulty in remotely estimating hydrate concentrations in marine sediments but embedded hydrocarbon stores are thought to represent a significant portion of global deposits. Inherent hydrate instabilities obscure our understanding of and complicates processes related to resource extraction and hydrate response to disturbances in the local environment. Understanding the spatial extent and variability of hydrate deposits have important implications for potential economic production, climate change, and assessing natural hazards risks. Seismic reflection techniques are capable of determining the extent of gas hydrate deposits, often through the observation of bottom simulating reflectors (BSRs). However, BSRs are not present everywhere gas hydrates exist. Using high resolution prestack time migrated seismic data and prestack waveform inversion (PWI) we produce highly resolved velocity models and compare them to co-located well logs. Coupling our PWI results with velocity-porosity relationships and nearby well control, we map hydrate properties at GC955 and WR313. Integrating small scale heterogeneities and variations along the velocity model with in-situ measurements, we develop a workflow aimed to quantify hydrate concentrations observed in seismic data over large areas in great detail regardless of the existence of a BSR.

Role of ion hydration for the differential capacitance of an electric double layer.

PubMed

Caetano, Daniel L Z; Bossa, Guilherme V; de Oliveira, Vinicius M; Brown, Matthew A; de Carvalho, Sidney J; May, Sylvio

2016-10-12

The influence of soft, hydration-mediated ion-ion and ion-surface interactions on the differential capacitance of an electric double layer is investigated using Monte Carlo simulations and compared to various mean-field models. We focus on a planar electrode surface at physiological concentration of monovalent ions in a uniform dielectric background. Hydration-mediated interactions are modeled on the basis of Yukawa potentials that add to the Coulomb and excluded volume interactions between ions. We present a mean-field model that includes hydration-mediated anion-anion, anion-cation, and cation-cation interactions of arbitrary strengths. In addition, finite ion sizes are accounted for through excluded volume interactions, described either on the basis of the Carnahan-Starling equation of state or using a lattice gas model. Both our Monte Carlo simulations and mean-field approaches predict a characteristic double-peak (the so-called camel shape) of the differential capacitance; its decrease reflects the packing of the counterions near the electrode surface. The presence of hydration-mediated ion-surface repulsion causes a thin charge-depleted region close to the surface, which is reminiscent of a Stern layer. We analyze the interplay between excluded volume and hydration-mediated interactions on the differential capacitance and demonstrate that for small surface charge density our mean-field model based on the Carnahan-Starling equation is able to capture the Monte Carlo simulation results. In contrast, for large surface charge density the mean-field approach based on the lattice gas model is preferable.

Mathematical modelling of liquid transport in swelling pharmaceutical immediate release tablets.

PubMed

Markl, Daniel; Yassin, Samy; Wilson, D Ian; Goodwin, Daniel J; Anderson, Andrew; Zeitler, J Axel

2017-06-30

Oral dosage forms are an integral part of modern health care and account for the majority of drug delivery systems. Traditionally the analysis of the dissolution behaviour of a dosage form is used as the key parameter to assess the performance of a drug product. However, understanding the mechanisms of disintegration is of critical importance to improve the quality of drug delivery systems. The disintegration performance is primarily impacted by the hydration and subsequent swelling of the powder compact. Here we compare liquid ingress and swelling data obtained using terahertz pulsed imaging (TPI) to a set of mathematical models. The interlink between hydration kinetics and swelling is described by a model based on Darcy's law and a modified swelling model based on that of Schott. Our new model includes the evolution of porosity, pore size and permeability as a function of hydration time. Results obtained from two sets of samples prepared from pure micro-crystalline cellulose (MCC) indicate a clear difference in hydration and swelling for samples of different porosities and particle sizes, which are captured by the model. Coupling a novel imaging technique, such as TPI, and mathematical models allows better understanding of hydration and swelling and eventually tablet disintegration. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

Coupled numerical modeling of gas hydrates bearing sediments from laboratory to field-scale conditions

NASA Astrophysics Data System (ADS)

Sanchez, M. J.; Santamarina, C.; Gai, X., Sr.; Teymouri, M., Sr.

2017-12-01

Stability and behavior of Hydrate Bearing Sediments (HBS) are characterized by the metastable character of the gas hydrate structure which strongly depends on thermo-hydro-chemo-mechanical (THCM) actions. Hydrate formation, dissociation and methane production from hydrate bearing sediments are coupled THCM processes that involve, amongst other, exothermic formation and endothermic dissociation of hydrate and ice phases, mixed fluid flow and large changes in fluid pressure. The analysis of available data from past field and laboratory experiments, and the optimization of future field production studies require a formal and robust numerical framework able to capture the very complex behavior of this type of soil. A comprehensive fully coupled THCM formulation has been developed and implemented into a finite element code to tackle problems involving gas hydrates sediments. Special attention is paid to the geomechanical behavior of HBS, and particularly to their response upon hydrate dissociation under loading. The numerical framework has been validated against recent experiments conducted under controlled conditions in the laboratory that challenge the proposed approach and highlight the complex interaction among THCM processes in HBS. The performance of the models in these case studies is highly satisfactory. Finally, the numerical code is applied to analyze the behavior of gas hydrate soils under field-scale conditions exploring different features of material behavior under possible reservoir conditions.

A mathematical model for predicting the life of polymer electrolyte fuel cell membranes subjected to hydration cycling

NASA Astrophysics Data System (ADS)

Burlatsky, S. F.; Gummalla, M.; O'Neill, J.; Atrazhev, V. V.; Varyukhin, A. N.; Dmitriev, D. V.; Erikhman, N. S.

2012-10-01

Under typical Polymer Electrolyte Membrane Fuel Cell (PEMFC) fuel cell operating conditions, part of the membrane electrode assembly is subjected to humidity cycling due to variation of inlet gas RH and/or flow rate. Cyclic membrane hydration/dehydration would cause cyclic swelling/shrinking of the unconstrained membrane. In a constrained membrane, it causes cyclic stress resulting in mechanical failure in the area adjacent to the gas inlet. A mathematical modeling framework for prediction of the lifetime of a PEMFC membrane subjected to hydration cycling is developed in this paper. The model predicts membrane lifetime as a function of RH cycling amplitude and membrane mechanical properties. The modeling framework consists of three model components: a fuel cell RH distribution model, a hydration/dehydration induced stress model that predicts stress distribution in the membrane, and a damage accrual model that predicts membrane lifetime. Short descriptions of the model components along with overall framework are presented in the paper. The model was used for lifetime prediction of a GORE-SELECT membrane.

Rethinking the global carbon cycle with a large, dynamic and microbially mediated gas hydrate capacitor

NASA Astrophysics Data System (ADS)

Dickens, Gerald R.

2003-08-01

Prominent negative δ13C excursions characterize several past intervals of abrupt (<100 kyr) environmental change. These anomalies, best exemplified by the >2.5‰ drop across the Paleocene/Eocene thermal maximum (PETM) ca. 55.5 Ma, command our attention because they lack explanation with conventional models for global carbon cycling. Increasingly, Earth scientists have argued that they signify massive release of CH4 from marine gas hydrates, although typically without considering the underlying process or the ensuing ramifications of such an interpretation. At the most basic level, a large, dynamic 'gas hydrate capacitor' stores and releases 13C-depleted carbon at rates linked to external conditions such as deep ocean temperature. The capacitor contains three internal reservoirs: dissolved gas, gas hydrate, and free gas. Carbon enters and leaves these reservoirs through microbial decomposition of organic matter, anaerobic oxidation of CH4 in shallow sediment, and seafloor gas venting; carbon cycles between these reservoirs through several processes, including fluid flow, precipitation and dissolution of gas hydrate, and burial. Numerical simulations show that simple gas hydrate capacitors driven by inferred changes in bottom water warming during the PETM can generate a global δ13C excursion that mimics observations. The same modeling extended over longer time demonstrates that variable CH4 fluxes to and from gas hydrates can partly explain other δ13C excursions, rapid and slow, large and small, negative and positive. Although such modeling is rudimentary (because processes and variables in modern and ancient gas hydrate systems remain poorly constrained), acceptance of a vast, externally regulated gas hydrate capacitor forces us to rethink δ13C records and the operation of the global carbon cycle throughout time.

Pore Scale Mechanistic Study of the Preferential Mode of Hydrate Formation in Sediments: Fluid Flow Aspects

NASA Astrophysics Data System (ADS)

Behseresht, J.; Prodanović, M.; Bryant, S. L.

2007-12-01

A spectrum of behavior is encountered in ocean sediments bearing methane hydrates, ranging from essentially static accumulations where hydrate and brine co-exist, to active cold seeps where hydrate and a methane gas phase co-exist in the hydrate stability zone (HSZ). In this and a companion paper (Jain and Juanes) we describe methods to test the following hypothesis: the coupling between drainage and fracturing, both induced by pore pressure, determines whether methane gas entering the HSZ is converted completely to hydrate. Here we describe a novel implementation of the level set method (LSM) to determine the capillarity-controlled displacement of brine by gas from sediment and from fractures within the sediment. Predictions of fluid configurations in infinite-acting model sediments indicate that the brine in drained sediment (after invasion by methane gas) is better connected than previously believed. This increases the availability of water and the rate of counter-diffusion of salinity ions, thus relaxing the limit on hydrate build-up within gas- invaded grain matrix. Simulated drainage of a fracture in sediment shows that points of contact between fracture faces are crucial. They allow residual water saturation to remain within an otherwise gas-filled fracture. Simulations of imbibition, which can occur for example after drainage into surrounding sediment reduces gas phase pressure in the fracture, indicate that the gas/water interfaces at contact points significantly shifts the threshold pressures for withdrawal of gas. During both drainage and imbibition, the contact points greatly increase water availability for hydrate formation within the fracture. We discuss coupling this capillarity-controlled displacement model with a discrete element model for grain-scale mechanics. The coupled model provides a basis for evaluating the macroscopic conditions (thickness of gas accumulation below the hydrate stability zone; average sediment grain size; principal earth stresses) favoring co- existence of methane gas and hydrate in the HSZ. Explaining the range of behavior is useful in assessing resource volumes and evaluating pore-to-core scale flow paths in production strategies.

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

PubMed Central

Ashbaugh, H S; Kaler, E W; Paulaitis, M E

1998-01-01

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution. PMID:9675177

Hydration of Portland cement with additions of calcium sulfoaluminates

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

Le Saout, Gwenn, E-mail: gwenn.le-saout@mines-ales.fr; Lothenbach, Barbara; Hori, Akihiro

2013-01-15

The effect of mineral additions based on calcium aluminates on the hydration mechanism of ordinary Portland cement (OPC) was investigated using isothermal calorimetry, thermal analysis, X-ray diffraction, scanning electron microscopy, solid state nuclear magnetic resonance and pore solution analysis. Results show that the addition of a calcium sulfoaluminate cement (CSA) to the OPC does not affect the hydration mechanism of alite but controls the aluminate dissolution. In the second blend investigated, a rapid setting cement, the amorphous calcium aluminate reacts very fast to ettringite. The release of aluminum ions strongly retards the hydration of alite but the C-S-H has amore » similar composition as in OPC with no additional Al to Si substitution. As in CSA-OPC, the aluminate hydration is controlled by the availability of sulfates. The coupling of thermodynamic modeling with the kinetic equations predicts the amount of hydrates and pore solution compositions as a function of time and validates the model in these systems.« less

Physical Chemical Controls of Methane and other Hydrocarbon gases in Outer Solar System Water-Ice Systems

NASA Astrophysics Data System (ADS)

Osegovic, J. P.; Max, M. D.

2012-12-01

Saturn's moon Enceladus appear to have liquid water under its thin icy surface that has venting water and complex hydrocarbons. Jupiter's moon Europa is locked under a very thick layer of surface ice. Because Saturn's moon Titan contains abundant hydrocarbon gasses and liquids and both Saturn and Jupiter contain abundant hydrocarbon gases, it is likely that Europa also may have significant quantities of hydrocarbon gases in their water-ice systems. Both of these moons have the potential for life. We have begun to explore the impact that gas hydrate, which is a crystalline material composed of water and gas molecules, has on the availability of liquid water on a planet's surface: what conditions need to be present to initiate hydrate formation from a primordial selection of gases, salts, and water, how isolated hydrate systems evolve under the condition of mass transfer from ex-hydrate stability conditions to pro-hydrate stability conditions, the timespan of conditions that hydrate formation can host liquid solutions in an otherwise cooling regime; and the impact that additional chemistry, such as primitive chemosynthesis, may have on the sequestered hydrocarbon gases in hydrate. The analog for gas hydrate on these moons is the Permafrost hydrate system of Earth. Gas hydrate and water ice are stable in a compound cryosphere with ice extending downward from cold surface conditions to about the 273 K isotherm. Hydrate, depending on the mixture of gases in it, is stable from some depth below the surface to some isotherm that could be considerably in excess of 273 K. Salinity may strongly affect stability conditions. In order to estimate the thickness of the gas hydrate stability zone and its effect on 'planetary' heat flow, we model heat production as a function of mass flow. Variables are gravity, ice thickness, temperature of the surrounding medium (space, ice, and water), the thickness of the "ocean", the and the thermophysical properties of the gas being transferred. The model is constrained by the molecular diffusion rate of gas approaching the hydrate phase boundary. The heat produced or consumed by the hydrate system will affect the ice system and phase boundary. Fick's law can be used to model steady state diffusion. Flux is related to the diffusivity of the component and as a function of concentration and the distance over which the reactions take place. Initial model calculations indicate that in some cases, methane (ΔH = -56 kJ/mol for small molecules (CH4, N2, CO2, H2S) may affect the water-ice energy balance sufficiently to contribute to the maintenance of a deep ocean below ice. The effect of the presence of higher density hydrocarbons (ΔH = -72 kJ/mol for ethane and -126 kJ/mol for propane) accentuate the thermal transfer effect but may diffuse too slowly to be a thermal forcing agent in the hydrate system.

Thermodynamic properties of hydrate phases immersed in ice phase

NASA Astrophysics Data System (ADS)

Belosludov, V. R.; Subbotin, O. S.; Krupskii, D. S.; Ikeshoji, T.; Belosludov, R. V.; Kawazoe, Y.; Kudoh, J.

2006-01-01

Thermodynamic properties and the pressure of hydrate phases immersed in the ice phase with the aim to understand the nature of self-preservation effect of methane hydrate in the framework of macroscopic and microscopic molecular models was studied. It was show that increasing of pressure is happen inside methane hydrate phases immersed in the ice phase under increasing temperature and if the ice structure does not destroy, the methane hydrate will have larger pressure than ice phase. This is because of the thermal expansion of methane hydrate in a few times larger than ice one. The thermal expansion of the hydrate is constrained by the thermal expansion of ice because it can remain in a region of stability within the methane hydrate phase diagram. The utter lack of preservation behavior in CS-II methane- ethane hydrate can be explain that the thermal expansion of ethane-methane hydrate coincide with than ice one it do not pent up by thermal expansion of ice. The pressure and density during the crossing of interface between ice and hydrate was found and dynamical and thermodynamic stability of this system are studied in accordance with relation between ice phase and hydrate phase.

Computation on free gas seepage and associated seabed pockmark formation

NASA Astrophysics Data System (ADS)

Su, Z.; Cathles, Lawrence M.; Chen, D. F.; Wu, N. Y.

2010-03-01

Seabed pockmarks formed by seepage of subsurface fluids are very commonly located in areas where gas is present in near-surface sediments. Especially, they are widely observed on the seafloor at hydrate regions around the world. In this paper we consider that capillary sealing is the crucial mechanism for gas entrapment, gas escape, and pockmark formation. In the hydrate system, free gas is trapped beneath the hydrate layer. The gas overpressure increases as the gas accumulates beneath the hydrate. the hydrate layer is a capillary seal. Capillary seals have the property that they fail completely when the gas pressure reaches the point that they are invaded by gas. The release of gas is thus episodic and sudden. We imagine in our model that when it occurs the venting gas will push the overlying water upward at increasingly higher velocities as the gas pipe approaches the seafloor. As the water velocity increases, the near surface sediments will become quick at a depth that is a function of the thickness of free gas column under the hydrate seal and the depth of hydrate seal, leaving a pockmark on the seafloor. The model shows that at least a 22-m-thick free gas layer beneath the hydrate at Blake Ridge is needed to form the 4-m-deep pockmark at the seabed.

Testing short-range migration of microbial methane as a hydrate formation mechanism: Results from Andaman Sea and Kumano Basin drill sites and global implications

NASA Astrophysics Data System (ADS)

Malinverno, Alberto; Goldberg, David S.

2015-07-01

Methane gas hydrates in marine sediments often concentrate in coarse-grained layers surrounded by fine-grained marine muds that are hydrate-free. Methane in these hydrate deposits is typically microbial, and must have migrated from its source as the coarse-grained sediments contain little or no organic matter. In "long-range" migration, fluid flow through permeable layers transports methane from deeper sources into the gas hydrate stability zone (GHSZ). In "short-range" migration, microbial methane is generated within the GHSZ in fine-grained sediments, where small pore sizes inhibit hydrate formation. Dissolved methane can then diffuse into adjacent sand layers, where pore size does not restrict hydrate formation and hydrates can accumulate. Short-range migration has been used to explain hydrate accumulations in sand layers observed in drill sites on the northern Cascadia margin and in the Gulf of Mexico. Here we test the feasibility of short-range migration in two additional locations, where gas hydrates have been found in coarse-grained volcanic ash layers (Site NGHP-01-17, Andaman Sea, Indian Ocean) and turbidite sand beds (Site IODP-C0002, Kumano forearc basin, Nankai Trough, western Pacific). We apply reaction-transport modeling to calculate dissolved methane concentration and gas hydrate amounts resulting from microbial methane generated within the GHSZ. Model results show that short-range migration of microbial methane can explain the overall amounts of methane hydrate observed at the two sites. Short-range migration has been shown to be feasible in diverse margin environments and is likely to be a widespread methane transport mechanism in gas hydrate systems. It only requires a small amount of organic carbon and sediment sequences consisting of thin coarse-grained layers that can concentrate microbial methane generated within thick fine-grained sediment beds; these conditions are common along continental margins around the globe.

Estimates of future warming-induced methane emissions from hydrate offshore west Svalbard for a range of climate models

NASA Astrophysics Data System (ADS)

Marín-Moreno, Héctor; Minshull, Timothy A.; Westbrook, Graham K.; Sinha, Bablu

2015-05-01

Methane hydrate close to the hydrate stability limit in seafloor sediment could represent an important source of methane to the oceans and atmosphere as the oceans warm. We investigate the extent to which patterns of past and future ocean-temperature fluctuations influence hydrate stability in a region offshore West Svalbard where active gas venting has been observed. We model the transient behavior of the gas hydrate stability zone at 400-500 m water depth (mwd) in response to past temperature changes inferred from historical measurements and proxy data and we model future changes predicted by seven climate models and two climate-forcing scenarios (Representative Concentration Pathways RCPs 2.6 and 8.5). We show that over the past 2000 year, a combination of annual and decadal temperature fluctuations could have triggered multiple hydrate-sourced methane emissions from seabed shallower than 400 mwd during episodes when the multidecadal average temperature was similar to that over the last century (˜2.6°C). These temperature fluctuations can explain current methane emissions at 400 mwd, but decades to centuries of ocean warming are required to generate emissions in water deeper than 420 m. In the venting area, future methane emissions are relatively insensitive to the choice of climate model and RCP scenario until 2050 year, but are more sensitive to the RCP scenario after 2050 year. By 2100 CE, we estimate an ocean uptake of 97-1050 TgC from marine Arctic hydrate-sourced methane emissions, which is 0.06-0.67% of the ocean uptake from anthropogenic CO2 emissions for the period 1750-2011.

A petroleum system model for gas hydrate deposits in northern Alaska

USGS Publications Warehouse

Lorenson, T.D.; Collett, Timothy S.; Wong, Florence L.

2011-01-01

Gas hydrate deposits are common on the North Slope of Alaska around Prudhoe Bay, however the extent of these deposits is unknown outside of this area. As part of a United States Geological Survey (USGS) and the Bureau of Land Management (BLM) gas hydrate research collaboration, well cutting and mud gas samples have been collected and analyzed from mainly industry-drilled wells on the Alaska North Slope for the purpose of prospecting for gas hydrate deposits. On the Alaska North Slope, gas hydrates are now recognized as an element within a petroleum systems approach or TPS (Total Petroleum System). Since 1979, 35 wells have been samples from as far west as Wainwright to Prudhoe Bay in the east. Geochemical studies of known gas hydrate occurrences on the North Slope have shown a link between gas hydrate and more deeply buried conventional oil and gas deposits. Hydrocarbon gases migrate from depth and charge the reservoir rock within the gas hydrate stability zone. It is likely gases migrated into conventional traps as free gas, and were later converted to gas hydrate in response to climate cooling concurrent with permafrost formation. Gas hydrate is known to occur in one of the sampled wells, likely present in 22 others based gas geochemistry and inferred by equivocal gas geochemistry in 11 wells, and absent in one well. Gas migration routes are common in the North Slope and include faults and widespread, continuous, shallowly dipping permeable sand sections that are potentially in communication with deeper oil and gas sources. The application of this model with the geochemical evidence suggests that gas hydrate deposits may be widespread across the North Slope of Alaska.

Seismic character of gas hydrates on the Southeastern U.S. continental margin

USGS Publications Warehouse

Lee, M.W.; Hutchinson, D.R.; Agena, W.F.; Dillon, William P.; Miller, J.J.; Swift, B.A.

1994-01-01

Gas hydrates are stable at relatively low temperature and high pressure conditions; thus large amounts of hydrates can exist in sediments within the upper several hundred meters below the sea floor. The existence of gas hydrates has been recognized and mapped mostly on the basis of high amplitude Bottom Simulating Reflections (BSRs) which indicate only that an acoustic contrast exists at the lower boundary of the region of gas hydrate stability. Other factors such as amplitude blanking and change in reflection characteristics in sediments where a BSR would be expected, which have not been investigated in detail, are also associated with hydrated sediments and potentially disclose more information about the nature of hydratecemented sediments and the amount of hydrate present. Our research effort has focused on a detailed analysis of multichannel seismic profiles in terms of reflection character, inferred distribution of free gas underneath the BSR, estimation of elastic parameters, and spatial variation of blanking. This study indicates that continuous-looking BSRs in seismic profiles are highly segmented in detail and that the free gas underneath the hydrated sediment probably occurs as patches of gas-filled sediment having variable thickness. We also present an elastic model for various types of sediments based on seismic inversion results. The BSR from sediments of high ratio of shear to compressional velocity, estimated as about 0.52, encased in sediments whose ratios are less than 0.35 is consistent with the interpretation of gasfilled sediments underneath hydrated sediments. This model contrasts with recent results in which the BSR is explained by increased concentrations of hydrate near the base of the hydrate stability field and no underlying free gas is required. 

Characterization of Gas-Hydrate Sediment: In Situ Evaluation of Hydrate Saturation in Pores of Pressured Sedimental Samples

NASA Astrophysics Data System (ADS)

Jin, Y.; Konno, Y.; Kida, M.; Nagao, J.

2014-12-01

Hydrate saturation of gas-hydrate bearing sediment is a key of gas production from natural gas-hydrate reservoir. Developable natural gas-hydrates by conventional gas/oil production apparatus almost exist in unconsolidated sedimental layer. Generally, hydrate saturations of sedimental samples are directly estimated by volume of gas generated from dissociation of gas hydrates in pore spaces, porosity data and volume of the sediments. Furthermore, hydrate saturation can be also assessed using velocity of P-wave through sedimental samples. Nevertheless, hydrate saturation would be changed by morphological variations (grain-coating, cementing and pore-filling model) of gas hydrates in pore spaces. Jin et al.[1,2] recently observed the O-H stretching bands of H2O molecules of methane hydrate in porous media using an attenuated total reflection IR (ATR-IR) spectra. They observed in situ hydrate formation/dissociation process in sandy samples (Tohoku Keisya number 8, grain size of ca. 110 μm). In this presentation, we present IR spectroscopy approach to in situ evaluation of hydrate saturation of pressured gas-hydrate sediments. This work was supported by funding from the Research Consortium for Methane Hydrate Resources in Japan (MH21 Research Consortium) planned by the Ministry of Economy, Trade and Industry (METI), Japan. [1] Jin, Y.; Konno, Y.; Nagao, J. Energy Fules, 2012, 26, 2242-2247. [2] Jin, Y.; Oyama, H.; Nagao, J. Jpn. J. Appl. Phys. 2009, 48, No. 108001.

Hydrophobic amino acids as a new class of kinetic inhibitors for gas hydrate formation

PubMed Central

Sa, Jeong-Hoon; Kwak, Gye-Hoon; Lee, Bo Ram; Park, Da-Hye; Han, Kunwoo; Lee, Kun-Hong

2013-01-01

As the foundation of energy industry moves towards gas, flow assurance technology preventing pipelines from hydrate blockages becomes increasingly significant. However, the principle of hydrate inhibition is still poorly understood. Here, we examined natural hydrophobic amino acids as novel kinetic hydrate inhibitors (KHIs), and investigated hydrate inhibition phenomena by using them as a model system. Amino acids with lower hydrophobicity were found to be better KHIs to delay nucleation and retard growth, working by disrupting the water hydrogen bond network, while those with higher hydrophobicity strengthened the local water structure. It was found that perturbation of the water structure around KHIs plays a critical role in hydrate inhibition. This suggestion of a new class of KHIs will aid development of KHIs with enhanced biodegradability, and the present findings will accelerate the improved control of hydrate formation for natural gas exploitation and the utilization of hydrates as next-generation gas capture media. PMID:23938301

Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 1 of 2

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

Bryant, Steven; Juanes, Ruben

In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understandingmore » large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate saturations. Large volumes (of order one pore volume) of gaseous and aqueous phases must be transported into the gas hydrate stability zone. The driver for this transport is the pressure sink induced by a reduction in occupied pore volume that accompanies the formation of hydrate from gas and water. Pore-scale imbibition models and bed-scale multiphase flow models indicate that the rate-limiting step in converting gas to hydrate is the supply of water to the hydrate stability zone. Moreover, the water supply rate is controlled by capillarity-driven flux for conditions typical of the Alaska North Slope. A meter-scale laboratory experiment confirms that significant volumes of fluid phases move into the hydrate stability zone and that capillarity is essential for the water flux. The model shows that without capillarity-driven flux, large saturations of hydrate cannot form. The observations of thick zones of large saturation at Mallik and Mt Elbert thus suggest that the primary control on these systems is the rate of transport of gaseous and aqueous phases, driven by the pressure sink at the base of the gas hydrate stability zone. A key finding of our project is the elucidation of ?capillary fracturing? as a dominant gas transport mechanism in low-permeability media. We initially investigate this phenomenon by means of grain-scale simulations in which we extended a discrete element mechanics code (PFC, by Itasca) to incorporate the dynamics of first single-phase and then multiphase flow. A reductionist model on a square lattice allows us to determine some of the fundamental dependencies of the mode of gas invasion (capillary fingering, viscous fingering, and fracturing) on the parameters of the system. We then show that the morphology of the gas-invaded region exerts a fundamental control on the fabric of methane hydrate formation, and on the overpressures caused by methane hydrate dissociation. We demonstrate the existence of the different invasion regimes by means of controlled laboratory experiments in a radial cell. We collapse the behavior in the form of a phase diagram fully characterized by two dimensionless groups: a modified capillary number and a ?fracturing number? that reflects the balance between the pressure forces that act to open conduits in the granular pack, and frictional forces that resist it. We use all this small-scale knowledge to propose simple mechanistic models of gas migration and hydrate formation at the geologic bed scale. We propose that methane transport in lake and oceanic sediments is controlled by dynamic conduits, which dilate and release gas as the falling hydrostatic pressure reduces the effective stress below the tensile strength of the sediments. We test our model against a four-month record of hydrostatic load and methane flux in Upper Mystic Lake, Mass., USA, and show that it captures the complex episodicity of methane ebullition. Our quantitative conceptualization opens the door to integrated modeling of methane transport to constrain global methane release from lakes and other methane-rich sediment systems, and to assess its climate feedbacks.« less

Mechanisms Leading to Co-Existence of Gas Hydrate in Ocean Sediments [Part 2 of 2

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

Bryant, Steven; Juanes, Ruben

In this project we have sought to explain the co-existence of gas and hydrate phases in sediments within the gas hydrate stability zone. We have focused on the gas/brine interface at the scale of individual grains in the sediment. The capillary forces associated with a gas/brine interface play a dominant role in many processes that occur in the pores of sediments and sedimentary rocks. The mechanical forces associated with the same interface can lead to fracture initiation and propagation in hydrate-bearing sediments. Thus the unifying theme of the research reported here is that pore scale phenomena are key to understandingmore » large scale phenomena in hydrate-bearing sediments whenever a free gas phase is present. Our analysis of pore-scale phenomena in this project has delineated three regimes that govern processes in which the gas phase pressure is increasing: fracturing, capillary fingering and viscous fingering. These regimes are characterized by different morphology of the region invaded by the gas. On the other hand when the gas phase pressure is decreasing, the corresponding regimes are capillary fingering and compaction. In this project, we studied all these regimes except compaction. Many processes of interest in hydrate-bearing sediments can be better understood when placed in the context of the appropriate regime. For example, hydrate formation in sub-permafrost sediments falls in the capillary fingering regime, whereas gas invasion into ocean sediments is likely to fall into the fracturing regime. Our research provides insight into the mechanisms by which gas reservoirs are converted to hydrate as the base of the gas hydrate stability zone descends through the reservoir. If the reservoir was no longer being charged, then variation in grain size distribution within the reservoir explain hydrate saturation profiles such as that at Mt. Elbert, where sand-rich intervals containing little hydrate are interspersed between intervals containing large hydrate saturations. Large volumes (of order one pore volume) of gaseous and aqueous phases must be transported into the gas hydrate stability zone. The driver for this transport is the pressure sink induced by a reduction in occupied pore volume that accompanies the formation of hydrate from gas and water. Pore-scale imbibition models and bed-scale multiphase flow models indicate that the rate-limiting step in converting gas to hydrate is the supply of water to the hydrate stability zone. Moreover, the water supply rate is controlled by capillarity-driven flux for conditions typical of the Alaska North Slope. A meter-scale laboratory experiment confirms that significant volumes of fluid phases move into the hydrate stability zone and that capillarity is essential for the water flux. The model shows that without capillarity-driven flux, large saturations of hydrate cannot form. The observations of thick zones of large saturation at Mallik and Mt Elbert thus suggest that the primary control on these systems is the rate of transport of gaseous and aqueous phases, driven by the pressure sink at the base of the gas hydrate stability zone. A key finding of our project is the elucidation of ?capillary fracturing? as a dominant gas transport mechanism in low-permeability media. We initially investigate this phenomenon by means of grain-scale simulations in which we extended a discrete element mechanics code (PFC, by Itasca) to incorporate the dynamics of first singlephase and then multiphase flow. A reductionist model on a square lattice allows us to determine some of the fundamental dependencies of the mode of gas invasion (capillary fingering, viscous fingering, and fracturing) on the parameters of the system. We then show that the morphology of the gas-invaded region exerts a fundamental control on the fabric of methane hydrate formation, and on the overpressures caused by methane hydrate dissociation. We demonstrate the existence of the different invasion regimes by means of controlled laboratory experiments in a radial cell. We collapse the behavior in the form of a phase diagram fully characterized by two dimensionless groups: a modified capillary number and a ?fracturing number? that reflects the balance between the pressure forces that act to open conduits in the granular pack, and frictional forces that resist it. We use all this small-scale knowledge to propose simple mechanistic models of gas migration and hydrate formation at the geologic bed scale. We propose that methane transport in lake and oceanic sediments is controlled by dynamic conduits, which dilate and release gas as the falling hydrostatic pressure reduces the effective stress below the tensile strength of the sediments. We test our model against a four-month record of hydrostatic load and methane flux in Upper Mystic Lake, Mass., USA, and show that it captures the complex episodicity of methane ebullition. Our quantitative conceptualization opens the door to integrated modeling of methane transport to constrain global methane release from lakes and other methane-rich sediment systems, and to assess its climate feedbacks.« less

Testing a thermo-chemo-hydro-geomechanical model for gas hydrate-bearing sediments using triaxial compression laboratory experiments

NASA Astrophysics Data System (ADS)

Gupta, S.; Deusner, C.; Haeckel, M.; Helmig, R.; Wohlmuth, B.

2017-09-01

Natural gas hydrates are considered a potential resource for gas production on industrial scales. Gas hydrates contribute to the strength and stiffness of the hydrate-bearing sediments. During gas production, the geomechanical stability of the sediment is compromised. Due to the potential geotechnical risks and process management issues, the mechanical behavior of the gas hydrate-bearing sediments needs to be carefully considered. In this study, we describe a coupling concept that simplifies the mathematical description of the complex interactions occurring during gas production by isolating the effects of sediment deformation and hydrate phase changes. Central to this coupling concept is the assumption that the soil grains form the load-bearing solid skeleton, while the gas hydrate enhances the mechanical properties of this skeleton. We focus on testing this coupling concept in capturing the overall impact of geomechanics on gas production behavior though numerical simulation of a high-pressure isotropic compression experiment combined with methane hydrate formation and dissociation. We consider a linear-elastic stress-strain relationship because it is uniquely defined and easy to calibrate. Since, in reality, the geomechanical response of the hydrate-bearing sediment is typically inelastic and is characterized by a significant shear-volumetric coupling, we control the experiment very carefully in order to keep the sample deformations small and well within the assumptions of poroelasticity. The closely coordinated experimental and numerical procedures enable us to validate the proposed simplified geomechanics-to-flow coupling, and set an important precursor toward enhancing our coupled hydro-geomechanical hydrate reservoir simulator with more suitable elastoplastic constitutive models.

Exploration of the Ca2+ interaction modes of the nifedipine calcium channel antagonist.

PubMed

Liu, Huichun; Zhang, Liang; Li, Ping; Cukier, Robert I; Bu, Yuxiang

2007-02-02

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model.

PubMed

Tomar, Dheeraj S; Weber, Valéry; Pettitt, B Montgomery; Asthagiri, D

2014-04-17

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute-solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance.

Strengthening mechanism of cemented hydrate-bearing sand at microscales

NASA Astrophysics Data System (ADS)

Yoneda, Jun; Jin, Yusuke; Katagiri, Jun; Tenma, Norio

2016-07-01

On the basis of hypothetical particle-level mechanisms, several constitutive models of hydrate-bearing sediments have been proposed previously for gas production. However, to the best of our knowledge, the microstructural large-strain behaviors of hydrate-bearing sediments have not been reported to date because of the experimental challenges posed by the high-pressure and low-temperature testing conditions. Herein, a novel microtriaxial testing apparatus was developed, and the mechanical large-strain behavior of hydrate-bearing sediments with various hydrate saturation values (Sh = 0%, 39%, and 62%) was analyzed using microfocus X-ray computed tomography. Patchy hydrates were observed in the sediments at Sh = 39%. The obtained stress-strain relationships indicated strengthening with increasing hydrate saturation and a brittle failure mode of the hydrate-bearing sand. Localized deformations were quantified via image processing at the submillimeter and micrometer scale. Shear planes and particle deformation and/or rotation were detected, and the shear band thickness decreased with increasing hydrate saturation.

Light scattering evidence of selective protein fouling on biocompatible block copolymer micelles

NASA Astrophysics Data System (ADS)

Giacomelli, Fernando C.; Stepánek, Petr; Schmidt, Vanessa; Jäger, Eliézer; Jäger, Alessandro; Giacomelli, Cristiano

2012-07-01

Selective protein fouling on block copolymer micelles with well-known potential for tumour-targeting drug delivery was evidenced by using dynamic light scattering measurements. The stability and interaction of block copolymer micelles with model proteins (BSA, IgG, lysozyme and CytC) is reported for systems featuring a hydrophobic (poly[2-(diisopropylamino)-ethyl methacrylate]) (PDPA) core and hydrophilic coronas comprising poly(ethylene oxide)/poly(glycerol monomethacrylate) (PEO-b-PG2MA) or poly[2-(methacryloyloxy)ethyl phosphorylcholine] (PMPC). The results revealed that protein size and hydrophilic chain density play important roles in the observed interactions. The PEO113-b-PG2MA30-b-PDPA50 nanoparticles are stable and protein adsorption is prevented at all investigated protein environments. The successful protein-repellent characteristic of these nanoparticles is attributed to a high hydrophilic surface chain density (>0.1 chains per nm2) and to the length of the hydrophilic chains. On the other hand, although PMPC also has protein-repellent characteristics, the low surface chain density of the hydrophilic shell is supposed to enable interactions with small proteins. The PMPC40-b-PDPA70 micelles are stable in BSA and IgG environments due to weak repulsion forces between PMPC and the proteins, to the hydration layer, and particularly to a size-effect where the large BSA (RH = 4.2 nm) and IgG (RH = 7.0 nm) do not easily diffuse within the PMPC shell. Conversely, a clear interaction was observed with the 2.1 nm radius lysozyme. The lysozyme protein can diffuse within the PMPC micellar shell towards the PDPA hydrophobic core in a process favored by its smaller size and the low hydrophilic PMPC surface chain density (~0.049 chains per nm2) as compared to PEO-b-PG2MA (~0.110 chains per nm2). The same behavior was not evidenced with the 2.3 nm radius positively charged CytC, probably due to its higher surface hydrophilicity and the consequent chemical incompatibility with PDPA.Selective protein fouling on block copolymer micelles with well-known potential for tumour-targeting drug delivery was evidenced by using dynamic light scattering measurements. The stability and interaction of block copolymer micelles with model proteins (BSA, IgG, lysozyme and CytC) is reported for systems featuring a hydrophobic (poly[2-(diisopropylamino)-ethyl methacrylate]) (PDPA) core and hydrophilic coronas comprising poly(ethylene oxide)/poly(glycerol monomethacrylate) (PEO-b-PG2MA) or poly[2-(methacryloyloxy)ethyl phosphorylcholine] (PMPC). The results revealed that protein size and hydrophilic chain density play important roles in the observed interactions. The PEO113-b-PG2MA30-b-PDPA50 nanoparticles are stable and protein adsorption is prevented at all investigated protein environments. The successful protein-repellent characteristic of these nanoparticles is attributed to a high hydrophilic surface chain density (>0.1 chains per nm2) and to the length of the hydrophilic chains. On the other hand, although PMPC also has protein-repellent characteristics, the low surface chain density of the hydrophilic shell is supposed to enable interactions with small proteins. The PMPC40-b-PDPA70 micelles are stable in BSA and IgG environments due to weak repulsion forces between PMPC and the proteins, to the hydration layer, and particularly to a size-effect where the large BSA (RH = 4.2 nm) and IgG (RH = 7.0 nm) do not easily diffuse within the PMPC shell. Conversely, a clear interaction was observed with the 2.1 nm radius lysozyme. The lysozyme protein can diffuse within the PMPC micellar shell towards the PDPA hydrophobic core in a process favored by its smaller size and the low hydrophilic PMPC surface chain density (~0.049 chains per nm2) as compared to PEO-b-PG2MA (~0.110 chains per nm2). The same behavior was not evidenced with the 2.3 nm radius positively charged CytC, probably due to its higher surface hydrophilicity and the consequent chemical incompatibility with PDPA. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30623a

Volume properties and spectroscopy: A terahertz Raman investigation of hen egg white lysozyme

NASA Astrophysics Data System (ADS)

Sassi, Paola; Perticaroli, Stefania; Comez, Lucia; Giugliarelli, Alessandra; Paolantoni, Marco; Fioretto, Daniele; Morresi, Assunta

2013-12-01

The low frequency depolarized Raman spectra of 100 mg/ml aqueous solutions of hen egg white lysozyme (HEWL) have been collected in the 25-85 °C range. Short and long exposures to high temperatures have been used to modulate the competition between the thermally induced reversible and irreversible denaturation processes. A peculiar temperature evolution of spectra is evidenced under prolonged exposure of the protein solution at temperatures higher than 65 °C. This result is connected to the self-assembling of polypeptide chains and testifies the sensitivity of the technique to the properties of both protein molecule and its surrounding. Solvent free spectra have been obtained after subtraction of elastic and solvent components and assigned to a genuine vibrational contribution of hydrated HEWL. A straight similarity is observed between the solvent-free THz Raman feature and the vibrational density of states as obtained by molecular dynamics simulations; according to this, we verify the relation between this spectroscopic observable and the effective protein volume, and distinguish the properties of this latter respect to those of the hydration shell in the pre-melting region.

Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water

NASA Astrophysics Data System (ADS)

Ulman, Kanchan; Busch, Sebastian; Hassanali, Ali A.

2018-06-01

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.

Transport of ions through a (6,6) carbon nanotube under electric fields

NASA Astrophysics Data System (ADS)

Shen, Li; Xu, Zhen; Zhou, Zhe-Wei; Hu, Guo-Hui

2014-11-01

The transport of water and ions through carbon nanotubes (CNTs) is crucial in nanotechnology and biotechnology. Previous investigation indicated that the ions can hardly pass through (6,6) CNTs due to their hydrated shells. In the present study, utilizing molecular dynamics simulation, it is shown that the energy barrier mainly originating from the hydrated water molecules could be overcome by applying an electric field large enough in the CNT axis direction. Potential of mean force is calculated to show the reduction of energy barrier when the electric field is present for (Na+, K+, Cl-) ions. Consequently, ionic flux through (6,6) CNTs can be found once the electric field becomes larger than a threshold value. The variation of the coordination numbers of ions at different locations from the bulk to the center of the CNT is also explored to elaborate this dynamic process. The thresholds of the electric field are different for Na+, K+, and Cl- due to their characteristics. This consequence might be potentially applied in ion selectivity in the future.

Formation of natural gas hydrates in marine sediments. Gas hydrate growth and stability conditioned by host sediment properties

USGS Publications Warehouse

Clennell, M.B.; Henry, P.; Hovland, M.; Booth, J.S.; Winters, W.J.; Thomas, M.

2000-01-01

The stability conditions of submarine gas hydrates (methane clathrates) are largely dictated by pressure, temperature, gas composition, and pore water salinity. However, the physical properties and surface chemistry of the host sediments also affect the thermodynamic state, growth kinetics, spatial distributions, and growth forms of clathrates. Our model presumes that gas hydrate behaves in a way analogous to ice in the pores of a freezing soil, where capillary forces influence the energy balance. Hydrate growth is inhibited within fine-grained sediments because of the excess internal phase pressure of small crystals with high surface curvature that coexist with liquid water in small pores. Therefore, the base of gas hydrate stability in a sequence of fine sediments is predicted by our model to occur at a lower temperature, and so nearer to the seabed than would be calculated from bulk thermodynamic equilibrium. The growth forms commonly observed in hydrate samples recovered from marine sediments (nodules, sheets, and lenses in muds; cements in sand and ash layers) can be explained by a requirement to minimize the excess of mechanical and surface energy in the system.

Methane Hydrate Formation from Enhanced Organic Carbon Burial During Glacial Lowstands: Examples from the Gulf of Mexico

NASA Astrophysics Data System (ADS)

Malinverno, A.; Cook, A.; Daigle, H.; Oryan, B.

2017-12-01

Methane hydrates in fine-grained marine sediments are often found within veins and fractures occupying discrete depth intervals that are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the methane hydrate stability zone (MHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. We investigate here the hypothesis that these hydrate deposits form in sediments that were deposited during glacial lowstands and contain higher amounts of labile particulate organic carbon (POC), leading to enhanced microbial methanogenesis. During Pleistocene lowstands, river loads are deposited near the steep top of the continental slope and turbidity currents transport organic-rich, fine-grained sediments to deep waters. Faster sedimentation rates during glacial periods result in better preservation of POC because of decreased exposure times to oxic conditions. The net result is that more labile POC enters the methanogenic zone and more methane is generated in these sediments. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent deposition of labile POC at the seafloor controlled by glacioeustatic sea level variations in the last 250 kyr. The model is run for parameters estimated at three sites drilled by the 2009 Gulf of Mexico Joint Industry Project: Walker Ridge in the Terrebonne Basin (WR313-G and WR313-H) and Green Canyon near the canyon embayment into the Sigsbee Escarpment (GC955-H). In the model, gas hydrate forms in sediments with higher labile POC content deposited during the glacial cycle between 230 and 130 kyr (marine isotope stages 6 and 7). The corresponding depth intervals in the three sites contain hydrates, as shown by high bulk electrical resistivities and resistive subvertical fracture fills. This match supports the hypothesis that enhanced POC burial during glacial lowstands can result in hydrate formation from in situ microbial methanogenesis. Our results have implications for carbon cycling during glacial/interglacial cycles and for hydrate accumulation in the MHSZ. In particular, once hydrate-bearing intervals formed during glacial periods are buried beneath the MHSZ and dissociate, gas bubbles can rise and recycle microbial methane into the MHSZ.

Hydrate Evolution in Response to Ongoing Environmental Shifts

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

Rempel, Alan

Natural gas hydrates have the potential to become a vital domestic clean-burning energy source. However, past changes in environmental conditions have caused hydrates to become unstable and trigger both massive submarine landslides and the development of crater-like pockmarks, thereby releasing methane into the overlying seawater and atmosphere, where it acts as a powerful greenhouse gas. This project was designed to fill critical gaps in our understanding of domestic hydrate resources and improve forecasts for their response to environmental shifts. Project work can be separated into three interrelated components, each involving the development of predictive mathematical models. The first project componentmore » concerns the role of sediment properties on the development and dissociation of concentrated hydrate anomalies. To this end, we developed numerical models to predict equilibrium solubility of methane in twophase equilibrium with hydrate as a function of measureable porous medium characteristics. The second project component concerned the evolution of hydrate distribution in heterogeneous reservoirs. To this end, we developed numerical models to predict the growth and decay of anomalies in representative physical environments. The third project component concerned the stability of hydrate-bearing slopes under changing environmental conditions. To this end, we developed numerical treatments of pore pressure evolution and consolidation, then used "infinite-slope" analysis to approximate the landslide potential in representative physical environments, and developed a "rate-and-state" frictional formulation to assess the stability of finite slip patches that are hypothesized to develop in response to the dissociation of hydrate anomalies. The increased predictive capabilities that result from this work provide a framework for interpreting field observations of hydrate anomalies in terms of the history of environmental forcing that led to their development. Moreover, by taking explicit account of anomaly dissociation, project results are designed to help improve forecasts for changes in slope stability that could pose significant threats to energy infrastructure, disrupt hydrate reserves, and pollute the atmosphere with vast quantities of methane. This report presents the details of our work and outlines some of the highlights from our findings.« less

Modeling complicated rheological behaviors in encapsulating shells of lipid-coated microbubbles accounting for nonlinear changes of both shell viscosity and elasticity

NASA Astrophysics Data System (ADS)

Li, Qian; Matula, Thomas J.; Tu, Juan; Guo, Xiasheng; Zhang, Dong

2013-02-01

It has been accepted that the dynamic responses of ultrasound contrast agent (UCA) microbubbles will be significantly affected by the encapsulating shell properties (e.g., shell elasticity and viscosity). In this work, a new model is proposed to describe the complicated rheological behaviors in an encapsulating shell of UCA microbubbles by applying the nonlinear ‘Cross law’ to the shell viscous term in the Marmottant model. The proposed new model was verified by fitting the dynamic responses of UCAs measured with either a high-speed optical imaging system or a light scattering system. The comparison results between the measured radius-time curves and the numerical simulations demonstrate that the ‘compression-only’ behavior of UCAs can be successfully simulated with the new model. Then, the shell elastic and viscous coefficients of SonoVue microbubbles were evaluated based on the new model simulations, and compared to the results obtained from some existing UCA models. The results confirm the capability of the current model for reducing the dependence of bubble shell parameters on the initial bubble radius, which indicates that the current model might be more comprehensive to describe the complex rheological nature (e.g., ‘shear-thinning’ and ‘strain-softening’) in encapsulating shells of UCA microbubbles by taking into account the nonlinear changes of both shell elasticity and shell viscosity.

Modeling complicated rheological behaviors in encapsulating shells of lipid-coated microbubbles accounting for nonlinear changes of both shell viscosity and elasticity.

PubMed

Li, Qian; Matula, Thomas J; Tu, Juan; Guo, Xiasheng; Zhang, Dong

2013-02-21

It has been accepted that the dynamic responses of ultrasound contrast agent (UCA) microbubbles will be significantly affected by the encapsulating shell properties (e.g., shell elasticity and viscosity). In this work, a new model is proposed to describe the complicated rheological behaviors in an encapsulating shell of UCA microbubbles by applying the nonlinear 'Cross law' to the shell viscous term in the Marmottant model. The proposed new model was verified by fitting the dynamic responses of UCAs measured with either a high-speed optical imaging system or a light scattering system. The comparison results between the measured radius-time curves and the numerical simulations demonstrate that the 'compression-only' behavior of UCAs can be successfully simulated with the new model. Then, the shell elastic and viscous coefficients of SonoVue microbubbles were evaluated based on the new model simulations, and compared to the results obtained from some existing UCA models. The results confirm the capability of the current model for reducing the dependence of bubble shell parameters on the initial bubble radius, which indicates that the current model might be more comprehensive to describe the complex rheological nature (e.g., 'shear-thinning' and 'strain-softening') in encapsulating shells of UCA microbubbles by taking into account the nonlinear changes of both shell elasticity and shell viscosity.

Submarine landslides triggered by destabilization of high-saturation hydrate anomalies

NASA Astrophysics Data System (ADS)

Handwerger, Alexander L.; Rempel, Alan W.; Skarbek, Rob M.

2017-07-01

Submarine landslides occur along continental margins at depths that often intersect the gas hydrate stability zone, prompting suggestions that slope stability may be affected by perturbations that arise from changes in hydrate stability. Here we develop a numerical model to identify the conditions under which the destabilization of hydrates results in slope failure. Specifically, we focus on high-saturation hydrate anomalies at fine-grained to coarse-grained stratigraphic boundaries that can transmit bridging stresses that decrease the effective stress at sediment contacts and disrupt normal sediment consolidation. We evaluate slope stability before and after hydrate destabilization. Hydrate anomalies act to significantly increase the overall slope stability due to large increases in effective cohesion. However, when hydrate anomalies destabilize there is a loss of cohesion and increase in effective stress that causes the sediment grains to rapidly consolidate and generate pore pressures that can either trigger immediate slope failure or weaken the surrounding sediment until the pore pressure diffuses away. In cases where failure does not occur, the sediment can remain weakened for months. In cases where failure does occur, we quantify landslide dynamics using a rate and state frictional model and find that landslides can display either slow or dynamic (i.e., catastrophic) motion depending on the rate-dependent properties, size of the stress perturbation, and the size of the slip patch relative to a critical nucleation length scale. Our results illustrate the fundamental mechanisms through which the destabilization of gas hydrates can pose a significant geohazard.

Electrical properties of methane hydrate + sediment mixtures

USGS Publications Warehouse

Du Frane, Wyatt L.; Stern, Laura A.; Constable, Steven; Weitemeyer, Karen A.; Smith, Megan M; Roberts, Jeffery J.

2015-01-01

Knowledge of the electrical properties of multicomponent systems with gas hydrate, sediments, and pore water is needed to help relate electromagnetic (EM) measurements to specific gas hydrate concentration and distribution patterns in nature. Toward this goal, we built a pressure cell capable of measuring in situ electrical properties of multicomponent systems such that the effects of individual components and mixing relations can be assessed. We first established the temperature-dependent electrical conductivity (σ) of pure, single-phase methane hydrate to be ~5 orders of magnitude lower than seawater, a substantial contrast that can help differentiate hydrate deposits from significantly more conductive water-saturated sediments in EM field surveys. Here we report σ measurements of two-component systems in which methane hydrate is mixed with variable amounts of quartz sand or glass beads. Sand by itself has low σ but is found to increase the overall σ of mixtures with well-connected methane hydrate. Alternatively, the overall σ decreases when sand concentrations are high enough to cause gas hydrate to be poorly connected, indicating that hydrate grains provide the primary conduction path. Our measurements suggest that impurities from sand induce chemical interactions and/or doping effects that result in higher electrical conductivity with lower temperature dependence. These results can be used in the modeling of massive or two-phase gas-hydrate-bearing systems devoid of conductive pore water. Further experiments that include a free water phase are the necessary next steps toward developing complex models relevant to most natural systems.

Distributional prediction of Pleistocene forearc minibasin turbidites in the NE Nankai Trough area (off central Japan)

NASA Astrophysics Data System (ADS)

Egawa, K.; Furukawa, T.; Saeki, T.; Suzuki, K.; Narita, H.

2011-12-01

Natural gas hydrate-related sequences commonly provide unclear seismic images due to bottom simulating reflector, a seismic indicator of the theoretical base of gas hydrate stability zone, which usually causes problems for fully analyzing the detailed sedimentary structures and seismic facies. Here we propose an alternative technique to predict the distributional pattern of gas hydrate-related deep-sea turbidites with special reference to a Pleistocene forearc minibasin in the northeastern Nankai Trough area, off central Japan, from the integrated 3D structural and sedimentologic modeling. Structural unfolding and stratigraphic backstripping successively modeled a simple horseshoe-shaped paleobathymetry of the targeted turbidite sequence. Based on best-fit matching of net-to-gross ratio (or sand fraction) between the model and wells, subsequent turbidity current modeling on the restored paleobathymetric surface during a single flow event demonstrated excellent prediction results showing the morphologically controlled turbidity current evolution and selective turbidite sand distribution within the modeled minibasin. Also, multiple turbidity current modeling indicated the stacking sheet turbidites with regression and proximal/distal onlaps in the minibasin due to reflections off an opposing slope, whose sedimentary features are coincident with the seismic interpretation. Such modeling works can help us better understand the depositional pattern of gas hydrate-related, unconsolidated turbidites and also can improve gas hydrate reservoir characterization. This study was financially supported by MH21 Research Consortium.

X-Ray Micro-CT Observations of Hydrate Pore Habit and Lattice Boltzmann Simulations on Permeability Evolution in Hydrate Bearing Sediments (HBS)

NASA Astrophysics Data System (ADS)

Chen, X.; Espinoza, N.; Verma, R.; Prodanovic, M.

2017-12-01

We use X-ray micro-computed tomography (μCT) to observe xenon hydrate growth. During xenon hydrate formation in a single pore and a sandpack, we observe heterogeneous (patchy) hydrate distribution at both pore (10 μm) and core scales (10 cm). These results present similarities with earlier observations on naturally occurring and synthetic hydrate-bearing sediment (HBS). Based on image analyses of xenon hydrate in the single pore, we find that, under the quasi-isothermal condition, the xenon volumetric growth rate versus overpressurization curve fits an Arrhenius type equation. Using the μCT images of HBS, we are able to calculate the permeability of HBS using a lattice Boltzmann method. We find the reduced permeability versus hydrate saturation curve fits a simple Corey-type model as suggested by earlier studies. However, patchy distribution of hydrate does not permit a straightforward interpretation of the saturation exponent. This work provides fundamental observations of hydrate growth and pore habit in sediments and how hydrate habit affects the hydraulic conductivity of HBS. Further implications can be extended to the strength, seismic velocities and electrical properties of HBS.

Multibody dynamic analysis using a rotation-free shell element with corotational frame

NASA Astrophysics Data System (ADS)

Shi, Jiabei; Liu, Zhuyong; Hong, Jiazhen

2018-03-01

Rotation-free shell formulation is a simple and effective method to model a shell with large deformation. Moreover, it can be compatible with the existing theories of finite element method. However, a rotation-free shell is seldom employed in multibody systems. Using a derivative of rigid body motion, an efficient nonlinear shell model is proposed based on the rotation-free shell element and corotational frame. The bending and membrane strains of the shell have been simplified by isolating deformational displacements from the detailed description of rigid body motion. The consistent stiffness matrix can be obtained easily in this form of shell model. To model the multibody system consisting of the presented shells, joint kinematic constraints including translational and rotational constraints are deduced in the context of geometric nonlinear rotation-free element. A simple node-to-surface contact discretization and penalty method are adopted for contacts between shells. A series of analyses for multibody system dynamics are presented to validate the proposed formulation. Furthermore, the deployment of a large scaled solar array is presented to verify the comprehensive performance of the nonlinear shell model.

Dual-energy X-ray absorptiometry: analysis of pediatric fat estimate errors due to tissue hydration effects.

PubMed

Testolin, C G; Gore, R; Rivkin, T; Horlick, M; Arbo, J; Wang, Z; Chiumello, G; Heymsfield, S B

2000-12-01

Dual-energy X-ray absorptiometry (DXA) percent (%) fat estimates may be inaccurate in young children, who typically have high tissue hydration levels. This study was designed to provide a comprehensive analysis of pediatric tissue hydration effects on DXA %fat estimates. Phase 1 was experimental and included three in vitro studies to establish the physical basis of DXA %fat-estimation models. Phase 2 extended phase 1 models and consisted of theoretical calculations to estimate the %fat errors emanating from previously reported pediatric hydration effects. Phase 1 experiments supported the two-compartment DXA soft tissue model and established that pixel ratio of low to high energy (R values) are a predictable function of tissue elemental content. In phase 2, modeling of reference body composition values from birth to age 120 mo revealed that %fat errors will arise if a "constant" adult lean soft tissue R value is applied to the pediatric population; the maximum %fat error, approximately 0.8%, would be present at birth. High tissue hydration, as observed in infants and young children, leads to errors in DXA %fat estimates. The magnitude of these errors based on theoretical calculations is small and may not be of clinical or research significance.

Mathematical modeling of the gas extraction from the gas hydrate deposit taking into account the replacement technology

NASA Astrophysics Data System (ADS)

Musakaev, N. G.; Khasanov, M. K.; Borodin, S. L.

2018-03-01

In the work on the basis of methods and equations of mechanics of multiphase systems the mathematical model of the process of carbon dioxide burial in the reservoir saturated with methane hydrate is proposed. Estimates are obtained that allow for this problem to neglect diffusion mixing of carbon dioxide and methane. The features of the process of methane displacement from CH4 hydrate by filling them with carbon dioxide are studied.

Gas hydrate hunting in China seas

NASA Astrophysics Data System (ADS)

Yang, J.; Zhang, X.; Chen, J.; Xiang, Q.; Ye, Y.; Gong, J.

2003-04-01

Gas hydrate research is a hotspot now in geosciences. Many countries have carried on gas hydrate survey and research for many years. China, as a country with large sea areas unfolded gas hydrate research work in its marine areas in 1999 and tries to keep pace with the advanced countries on gas hydrate study. Substantial funds were launched by various governmental and non-governmental funding agencies to support gas hydrate research. Many institutions on marine geosciences are involved in. China Geological Survey (CGS) has launched several research projects in the sea. So far, some fieldwork such as seismic survey, sampling, profiling, underwater video imaging have been done in South China Sea and East China Sea areas. Some preliminary results have been achieved. BSRs are found in many seismic profiles. Some potential gas hydrate bearing areas are marked and potential amount of gas hydrate resources is calculated. At the same time, gas hydrate laboratory was founded and successful experiments have been carried out to model the gas hydrate synthesis in accordance with the geological condition of the China seas. Now, gas hydrate detecting techniques such as sampling equipment (PCS), seismic data processing, interpretation and the formation mechanism study as well as environmental effect research are undergoing. Though China's gas hydrate research work is still at its initial stage, China is willing to be an active member in the international society of gas hydrate study and hopes to contribute its effort.

Skin hydration analysis by experiment and computer simulations and its implications for diapered skin.

PubMed

Saadatmand, M; Stone, K J; Vega, V N; Felter, S; Ventura, S; Kasting, G; Jaworska, J

2017-11-01

Experimental work on skin hydration is technologically challenging, and mostly limited to observations where environmental conditions are constant. In some cases, like diapered baby skin, such work is practically unfeasible, yet it is important to understand potential effects of diapering on skin condition. To overcome this challenge, in part, we developed a computer simulation model of reversible transient skin hydration effects. Skin hydration model by Li et al. (Chem Eng Sci, 138, 2015, 164) was further developed to simulate transient exposure conditions where relative humidity (RH), wind velocity, air, and skin temperature can be any function of time. Computer simulations of evaporative water loss (EWL) decay after different occlusion times were compared with experimental data to calibrate the model. Next, we used the model to investigate EWL and SC thickness in different diapering scenarios. Key results from the experimental work were: (1) For occlusions by RH=100% and free water longer than 30 minutes the absorbed amount of water is almost the same; (2) Longer occlusion times result in higher water absorption by the SC. The EWL decay and skin water content predictions were in agreement with experimental data. Simulations also revealed that skin under occlusion hydrates mainly because the outflux is blocked, not because it absorbs water from the environment. Further, simulations demonstrated that hydration level is sensitive to time, RH and/or free water on skin. In simulated diapering scenarios, skin maintained hydration content very close to the baseline conditions without a diaper for the entire duration of a 24 hours period. Different diapers/diaper technologies are known to have different profiles in terms of their ability to provide wetness protection, which can result in consumer-noticeable differences in wetness. Simulation results based on published literature using data from a number of different diapers suggest that diapered skin hydrates within ranges considered reversible. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Dissolution of methane bubbles with hydrate armoring in deep ocean conditions

NASA Astrophysics Data System (ADS)

Kovalchuk, Margarita; Socolofsky, Scott

2017-11-01

The deep ocean is a storehouse of natural gas. Methane bubble moving upwards from marine sediments may become trapped in gas hydrates. It is uncertain precisely how hydrate armoring affects dissolution, or mass transfer from the bubble to the surrounding water column. The Texas A&M Oilspill Calculator was used to simulate a series of gas bubble dissolution experiments conducted in the United States Department of Energy National Energy Technology Laboratory High Pressure Water Tunnel. Several variations of the mass transfer coefficient were calculated based on gas or hydrate phase solubility and clean or dirty bubble correlations. Results suggest the mass transfer coefficient may be most closely modeled with gas phase solubility and dirty bubble correlation equations. Further investigation of hydrate bubble dissolution behavior will refine current numeric models which aid in understanding gas flux to the atmosphere and plumes such as oil spills. Research funded in part by the Texas A&M University 2017 Undergraduate Summer Research Grant and a Grant from the Methane Gas Hydrates Program of the US DOE National Energy Technology Laboratory.

Analysis of experimental heats of dilution of aqueous solutions of NaBPh 4 by use of the mean spherical approximation and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

M'halla, Jalel; M'halla, Sondes; Wipff, Georges

2003-03-01

Calorimetric measurements of heats of dilution: QDC→0 =- nsφL,sexp, of aqueous solutions of NaBPh 4 are determined at 25 °C in the concentration range: 0

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Submarine slope failures in the Beaufort Sea; Influence of gas hydrate decomposition

NASA Astrophysics Data System (ADS)

Grozic, J. L.; Dallimore, S.

2012-12-01

The continental shelf of the Beaufort Sea is composed of complex of marine and non-marine sequences of clay, silt, and sand. In many areas of the shelf these sediments contain occurrences of ice-bonded permafrost and associated pressure and temperature conditions that are conducive to the occurrence of methane gas hydrates. This complex environment is undergoing dramatic warming, where changes in sea level, ocean bottom temperatures, and geothermal regimes are inducing permafrost thawing and gas hydrate decomposition. Decomposition is inferred to be occurring at the base and top of the gas hydrate stability zone, which will cause sediment weakening and the generation of excess water and free gas. In such settings, the overlying permafrost cap may act as a permeability barrier, which could result in significant excess pore pressures and reduction in sediment stability. The shelf to slope transition is thought to be an area of extensive regional instability with acoustic records indicating there is upwards of 500 km of slumps and glides extending over the entire Beaufort margin. Some of these slide regions are coincident with up-dip limit of the permafrost gas hydrate stability zone. In this paper, a two dimensional model of the Beaufort shelf was constructed to examine the influence of gas hydrate decomposition on slope stability. The model relies on available data on the Beaufort sediments generated from offshore hydrocarbon exploration in the 1980s and 90s, as well as knowledge available from multidisciplinary marine research programs conducted in the outer shelf area. The slope stability model investigates the influence of marine transgression and ocean bottom warming by coupling soil deformation with hydrate dissociation during undrained conditions. By combining mechanical and thermal loading of the sediment, a more accurate indication of slope stability was obtained. The stability analysis results indicate a relatively low factor of safety for the Beaufort sediments without the presence of permafrost and gas hydrate, owing to the relative slope steepness compared to other submarine failures. Including the effects of the permafrost and gas hydrate in the sediments can result in an increase of the factor of safety under static conditions. However, modeling of the temporal effects of transgression of the Beaufort Shelf (considering change in pressure and temperature), indicates that, for a reasonable assumption of between 5-35% hydrate content, the factor of safety reduces to below unity and failure occurs.

Effect of gas hydrates melting on seafloor slope stability

NASA Astrophysics Data System (ADS)

Sultan, N.; Cochonat, P.; Foucher, J. P.; Mienert, J.; Haflidason, H.; Sejrup, H. P.

2003-04-01

Quantitative studies of kinetics of gas hydrate formation and dissociation is of a particular concern to the petroleum industry for an evaluation of environmental hazards in deep offshore areas. Gas hydrate dissociation can generate excess pore pressure that considerably decreases the strength of the soil. In this paper, we present a theoretical study of the thermodynamic chemical equilibrium of gas hydrate in soil, which is based on models previously reported by Handa (1989), Sloan (1998) and Henry (1999). Our study takes into account the influence of temperature, pressure, pore water chemistry, and the pore size distribution of the sediment. This model fully accounts for the latent heat effects, as done by Chaouch and Briaud (1997) and Delisle et al. (1998). It uses a new formulation based on the enthalpy form of the law of conservation of energy. The model allows for the evaluation of the excess pore pressure generated during gas hydrate dissociation using the Soave’s (1972) equation of state. Fluid flow in response to the excess pore pressure is simulated using the finite element method. In the second part of the paper, we present and discuss an application of the model through a back-analysis of the case of the giant Storegga slide on the Norwegian margin. Two of the most important changes during and since the last deglaciation (hydrostatic pressure due to the change of the sea level and the increase of the sea water temperature) were considered in the calculation. Simulation results are presented and discussed. Chaouch, A., &Briaud, J.-L., 1997. Post melting behavior of gas hydrates in soft ocean sediments, OTC-8298, in 29th offshore technology conference proceedings, v. 1, Geology, earth sciences and environmental factors: Society of Petroleum Engineers, p. 217-224. Delisle, G.; Beiersdorf, H.; Neben, S.; Steinmann, D., 1998. The geothermal field of the North Sulawesi accretionary wedge and a model on BSR migration in unstable depositional environments. in Henriet, J.-P.; Mienert, J. (Ed.): Gas hydrates: relevance to world margin stability and climate change. Geological Society Special Publication, 137. The Geological Society: London, UK, p. 267-274. Handa,Y.P., 1989. Effect of Hydrostatic Pressure and Salinity on the Stability of Gas Hydrates. J.Phys.Chem., Vol.94, p.2652-2657. Henry, P., Thomas, M.; Clennell, M.B., 1999. Formation of Natural Gas Hydrates in Marine Sediments 2. Thermodynamic Calculations of Stability Conditions in Porous Sediments,” J. Geophys. Res., 104, p. 23005. Sloan, E.D. Jr., 1998. Clathrate hydrates of natural gases. Marcel Dekker Inc., 2nd edition, New York, pp. 705. Soave G, 1972. Equilibrium

X-ray diffraction microscopy on frozen hydrated specimens

NASA Astrophysics Data System (ADS)

Nelson, Johanna

X-rays are excellent for imaging thick samples at high resolution because of their large penetration depth compared to electrons and their short wavelength relative to visible light. To image biological material, the absorption contrast of soft X-rays, especially between the carbon and oxygen K-shell absorption edges, can be utilized to give high contrast, high resolution images without the need for stains or labels. Because of radiation damage and the desire for high resolution tomography, live cell imaging is not feasible. However, cells can be frozen in vitrified ice, which reduces the effect of radiation damage while maintaining their natural hydrated state. X-ray diffraction microscopy (XDM) is an imaging technique which eliminates the limitations imposed by current focusing optics simply by removing them entirely. Far-field coherent diffraction intensity patterns are collected on a pixelated detector allowing every scattered photon to be collected within the limits of the detector's efficiency and physical size. An iterative computer algorithm is then used to invert the diffraction intensity into a real space image with both absorption and phase information. This technique transfers the emphasis away from fabrication and alignment of optics, and towards data processing. We have used this method to image a pair of freeze-dried, immuno-labeled yeast cells to the highest resolution (13 nm) yet obtained for a whole eukaryotic cell. We discuss successes and challenges in working with frozen hydrated specimens and efforts aimed at high resolution imaging of vitrified eukaryotic cells in 3D.

Dynamic analysis of rotor flex-structure based on nonlinear anisotropic shell models

NASA Astrophysics Data System (ADS)

Bauchau, Olivier A.; Chiang, Wuying

1991-05-01

In this paper an anisotropic shallow shell model is developed that accommodates transverse shearing deformations and arbitrarily large displacements and rotations, but strains are assumed to remain small. Two kinematic models are developed, the first using two DOF to locate the direction of the normal to the shell's midplane, the second using three. The latter model allows for an automatic compatibility of the shell model with beam models. The shell model is validated by comparing its predictions with several benchmark problems. In actual helicopter rotor blade problems, the shell model of the flex structure is shown to give very different results shown compared to beam models. The lead-lag and torsion modes in particular are strongly affected, whereas flapping modes seem to be less affected.

Polymersome Carriers: from Self-Assembly to siRNA and Protein Therapeutics

PubMed Central

Christian, David A.; Cai, Shenshen; Bowen, Diana M.; Kim, Younghoon; Pajerowski, J. David; Discher, Dennis E.

2009-01-01

Polymersomes are polymer-based vesicular shells that form upon hydration of amphiphilic block copolymers. These high molecular weight amphiphiles impart physicochemical properties that allow polymersomes to stably encapsulate or integrate a broad range of active molecules. This robustness together with recently described mechanisms for controlled breakdown of degradable polymersomes as well as escape from endolysosomes suggests that polymersomes might be usefully viewed as having structure/property/function relationships somewhere between lipid vesicles and viral capsids. Here we summarize the assembly and development of controlled release polymersomes to encapsulate therapeutics ranging from small molecule anti-cancer drugs to siRNA and therapeutic proteins. PMID:18977437

Dielectric constant of ionic solutions: a field-theory approach.

PubMed

Levy, Amir; Andelman, David; Orland, Henri

2012-06-01

We study the variation of the dielectric response of a dielectric liquid (e.g. water) when a salt is added to the solution. Employing field-theoretical methods, we expand the Gibbs free energy to first order in a loop expansion and calculate self-consistently the dielectric constant. We predict analytically the dielectric decrement which depends on the ionic strength in a complex way. Furthermore, a qualitative description of the hydration shell is found and is characterized by a single length scale. Our prediction fits rather well a large range of concentrations for different salts using only one fit parameter related to the size of ions and dipoles.

Gas hydrate concentration estimated from P- and S-wave velocities

NASA Astrophysics Data System (ADS)

Carcione, J. M.; Gei, D.

2003-04-01

We estimate the concentration of gas hydrate at the Mallik 2L-38 research site, Mackenzie Delta, Canada, using P- and S-wave velocities obtained from well logging and vertical seismic profiles (VSP). The theoretical velocities are obtained from a poro-viscoelastic model based on a Biot-type approach. It considers the existence of two solids (grains and gas hydrate) and a fluid mixture and is based on the assumption that hydrate fills the pore space and shows interconnection. The moduli of the matrix formed by gas hydrate are obtained from the percolation model described by Leclaire et al., (1994). An empirical mixing law introduced by Brie et al., (1995) provides the effective bulk modulus of the fluid phase, giving Wood's modulus at low frequency and Voigt's modulus at high frequencies. The dry-rock moduli are estimated from the VSP profile where the rock is assumed to be fully saturated with water, and the quality factors are obtained from the velocity dispersion observed between the sonic and VSP velocities. Attenuation is described by using a constant-Q model for the dry rock moduli. The amount of dissipation is estimated from the difference between the seismic velocities and the sonic-log velocities. We estimate the amount of gas hydrate by fitting the sonic-log and seismic velocities to the theoretical velocities, using the concentration of gas hydrate as fitting parameter. We obtain hydrate concentrations up to 75 %, average values of 43 and 47 % from the VSP P- and S-wave velocities, respectively, and 47 and 42 % from the sonic-log P- and S-wave velocities, respectively. These averages are computed from 897 to 1110 m, excluding the zones where there is no gas hydrate. We found that modeling attenuation is important to obtain reliable results. largeReferences} begin{description} Brie, A., Pampuri, F., Marsala A.F., Meazza O., 1995, Shear Sonic Interpretation in Gas-Bearing Sands, SPE Annual Technical Conference and Exhibition, Dallas, 1995. Carcione, J.M. and Gei, D., Gas hydrate concentration estimated from P- and S-wave velocities at the Mallik 2L-38 research well, Mackenzie Delta, Canada, submitted to Geophysics. Gei, D. and Carcione, J.M., Acoustic properties of sediments saturated with gas hydrate, free gas and water, Geophysical Prospecting, in press. Leclarie, Ph., Cohen-Tenoudji, F., and Aguirre-Puente, J., 1994, Extension of Biot's theory of wave propagation to frozen porous media, J. Acoust. Soc. Am., 96, 6, 3753-3768.

Conditional Solvation Thermodynamics of Isoleucine in Model Peptides and the Limitations of the Group-Transfer Model

PubMed Central

2015-01-01

The hydration thermodynamics of the amino acid X relative to the reference G (glycine) or the hydration thermodynamics of a small-molecule analog of the side chain of X is often used to model the contribution of X to protein stability and solution thermodynamics. We consider the reasons for successes and limitations of this approach by calculating and comparing the conditional excess free energy, enthalpy, and entropy of hydration of the isoleucine side chain in zwitterionic isoleucine, in extended penta-peptides, and in helical deca-peptides. Butane in gauche conformation serves as a small-molecule analog for the isoleucine side chain. Parsing the hydrophobic and hydrophilic contributions to hydration for the side chain shows that both of these aspects of hydration are context-sensitive. Furthermore, analyzing the solute–solvent interaction contribution to the conditional excess enthalpy of the side chain shows that what is nominally considered a property of the side chain includes entirely nonobvious contributions of the background. The context-sensitivity of hydrophobic and hydrophilic hydration and the conflation of background contributions with energetics attributed to the side chain limit the ability of a single scaling factor, such as the fractional solvent exposure of the group in the protein, to map the component energetic contributions of the model-compound data to their value in the protein. But ignoring the origin of cancellations in the underlying components the group-transfer model may appear to provide a reasonable estimate of the free energy for a given error tolerance. PMID:24650057

Probing methane hydrate nucleation through the forward flux sampling method.

PubMed

Bi, Yuanfei; Li, Tianshu

2014-11-26

Understanding the nucleation of hydrate is the key to developing effective strategies for controlling methane hydrate formation. Here we present a computational study of methane hydrate nucleation, by combining the forward flux sampling (FFS) method and the coarse-grained water model mW. To facilitate the application of FFS in studying the formation of methane hydrate, we developed an effective order parameter λ on the basis of the topological analysis of the tetrahedral network. The order parameter capitalizes the signature of hydrate structure, i.e., polyhedral cages, and is capable of efficiently distinguishing hydrate from ice and liquid water while allowing the formation of different hydrate phases, i.e., sI, sII, and amorphous. Integration of the order parameter λ with FFS allows explicitly computing hydrate nucleation rates and obtaining an ensemble of nucleation trajectories under conditions where spontaneous hydrate nucleation becomes too slow to occur in direct simulation. The convergence of the obtained hydrate nucleation rate was found to depend crucially on the convergence of the spatial distribution for the spontaneously formed hydrate seeds obtained from the initial sampling of FFS. The validity of the approach is also verified by the agreement between the calculated nucleation rate and that inferred from the direct simulation. Analyzing the obtained large ensemble of hydrate nucleation trajectories, we show hydrate formation at 220 K and 500 bar is initiated by the nucleation events occurring in the vicinity of water-methane interface, and facilitated by a gradual transition from amorphous to crystalline structure. The latter provides the direct support to the proposed two-step nucleation mechanism of methane hydrate.

Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

PubMed

Uddin, M; Coombe, D

2014-03-20

Molecular dynamics simulations of gas hydrate dissociation comparing the behavior of CH4 and CO2 hydrates are presented. These simulations were based on a structurally correct theoretical gas hydrate crystal, coexisting with water. The MD system was first initialized and stabilized via a thorough energy minimization, constant volume-temperature ensemble and constant volume-energy ensemble simulations before proceeding to constant pressure-temperature simulations for targeted dissociation pressure and temperature responses. Gas bubble evolution mechanisms are demonstrated as well as key investigative properties such as system volume, density, energy, mean square displacements of the guest molecules, radial distribution functions, H2O order parameter, and statistics of hydrogen bonds. These simulations have established the essential similarities between CH4 and CO2 hydrate dissociation. The limiting behaviors at lower temperature (no dissociation) and higher temperature (complete melting and formation of a gas bubble) have been illustrated for both hydrates. Due to the shift in the known hydrate stability curves between guest molecules caused by the choice of water model as noted by other authors, the intermediate behavior (e.g., 260 K) showed distinct differences however. Also, because of the more hydrogen-bonding capability of CO2 in water, as reflected in its molecular parameters, higher solubility of dissociated CO2 in water was observed with a consequence of a smaller size of gas bubble formation. Additionally, a novel method for analyzing hydrate dissociation based on H-bond breakage has been proposed and used to quantify the dissociation behaviors of both CH4 and CO2 hydrates. Activation energies Ea values from our MD studies were obtained and evaluated against several other published laboratory and MD values. Intrinsic rate constants were estimated and upscaled. A kinetic reaction model consistent with macroscale fitted kinetic models has been proposed to indicate the macroscopic consequences of this analysis.

Rib fractures under anterior-posterior dynamic loads: experimental and finite-element study.

PubMed

Li, Zuoping; Kindig, Matthew W; Kerrigan, Jason R; Untaroiu, Costin D; Subit, Damien; Crandall, Jeff R; Kent, Richard W

2010-01-19

The purpose of this study was to investigate whether using a finite-element (FE) mesh composed entirely of hexahedral elements to model cortical and trabecular bone (all-hex model) would provide more accurate simulations than those with variable thickness shell elements for cortical bone and hexahedral elements for trabecular bone (hex-shell model) in the modeling human ribs. First, quasi-static non-injurious and dynamic injurious experiments were performed using the second, fourth, and tenth human thoracic ribs to record the structural behavior and fracture tolerance of individual ribs under anterior-posterior bending loads. Then, all-hex and hex-shell FE models for the three ribs were developed using an octree-based and multi-block hex meshing approach, respectively. Material properties of cortical bone were optimized using dynamic experimental data and the hex-shell model of the fourth rib and trabecular bone properties were taken from the literature. Overall, the reaction force-displacement relationship predicted by both all-hex and hex-shell models with nodes in the offset middle-cortical surfaces compared well with those measured experimentally for all the three ribs. With the exception of fracture locations, the predictions from all-hex and offset hex-shell models of the second and fourth ribs agreed better with experimental data than those from the tenth rib models in terms of reaction force at fracture (difference <15.4%), ultimate failure displacement and time (difference <7.3%), and cortical bone strains. The hex-shell models with shell nodes in outer cortical surfaces increased static reaction forces up to 16.6%, compared to offset hex-shell models. These results indicated that both all-hex and hex-shell modeling strategies were applicable for simulating rib responses and bone fractures for the loading conditions considered, but coarse hex-shell models with constant or variable shell thickness were more computationally efficient and therefore preferred. Copyright 2009 Elsevier Ltd. All rights reserved.

New hydrate formation methods in a liquid-gas medium

NASA Astrophysics Data System (ADS)

Chernov, A. A.; Pil'Nik, A. A.; Elistratov, D. S.; Mezentsev, I. V.; Meleshkin, A. V.; Bartashevich, M. V.; Vlasenko, M. G.

2017-01-01

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated.

New hydrate formation methods in a liquid-gas medium.

PubMed

Chernov, A A; Pil'nik, A A; Elistratov, D S; Mezentsev, I V; Meleshkin, A V; Bartashevich, M V; Vlasenko, M G

2017-01-18

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated.

New hydrate formation methods in a liquid-gas medium

PubMed Central

Chernov, A. A.; Pil’nik, A. A.; Elistratov, D. S.; Mezentsev, I. V.; Meleshkin, A. V.; Bartashevich, M. V.; Vlasenko, M. G.

2017-01-01

Conceptually new methods of hydrate formation are proposed. The first one is based on the shock wave impact on a water-bubble medium. It is shown that the hydrate formation rate in this process is typically very high. A gas hydrate of carbon dioxide was produced. The process was experimentally studied using various initial conditions, as well as different external action magnitudes. The obtained experimental data are in good agreement with the proposed model. Other methods are based on the process of boiling liquefied gas in an enclosed volume of water (explosive boiling of a hydrating agent and the organization of cyclic boiling-condensation process). The key features of the methods are the high hydrate formation rate combined with a comparatively low power consumption leading to a great expected efficiency of the technologies based on them. The set of experiments was carried out. Gas hydrates of refrigerant R134a, carbon dioxide and propane were produced. The investigation of decomposition of a generated gas hydrate sample was made. The criteria of intensification of the hydrate formation process are formulated. PMID:28098194

THREE-DIMENSIONAL MODELING OF THE DYNAMICS OF THERAPEUTIC ULTRASOUND CONTRAST AGENTS

PubMed Central

Hsiao, Chao-Tsung; Lu, Xiaozhen; Chahine, Georges

2010-01-01

A 3-D thick-shell contrast agent dynamics model was developed by coupling a finite volume Navier-Stokes solver and a potential boundary element method flow solver to simulate the dynamics of thick-shelled contrast agents subjected to pressure waves. The 3-D model was validated using a spherical thick-shell model validated by experimental observations. We then used this model to study shell break-up during nonspherical deformations resulting from multiple contrast agent interaction or the presence of a nearby solid wall. Our simulations indicate that the thick viscous shell resists the contrast agent from forming a re-entrant jet, as normally observed for an air bubble oscillating near a solid wall. Instead, the shell thickness varies significantly from location to location during the dynamics, and this could lead to shell break-up caused by local shell thinning and stretching. PMID:20950929

Pore fluid geochemistry from the Mount Elbert Gas Hydrate Stratigraphic Test Well, Alaska North Slope

USGS Publications Warehouse

Torres, M.E.; Collett, T.S.; Rose, K.K.; Sample, J.C.; Agena, W.F.; Rosenbaum, E.J.

2011-01-01

The BPXA-DOE-USGS Mount Elbert Gas Hydrate Stratigraphic Test Well was drilled and cored from 606.5 to 760.1. m on the North Slope of Alaska, to evaluate the occurrence, distribution and formation of gas hydrate in sediments below the base of the ice-bearing permafrost. Both the dissolved chloride and the isotopic composition of the water co-vary in the gas hydrate-bearing zones, consistent with gas hydrate dissociation during core recovery, and they provide independent indicators to constrain the zone of gas hydrate occurrence. Analyses of chloride and water isotope data indicate that an observed increase in salinity towards the top of the cored section reflects the presence of residual fluids from ion exclusion during ice formation at the base of the permafrost layer. These salinity changes are the main factor controlling major and minor ion distributions in the Mount Elbert Well. The resulting background chloride can be simulated with a one-dimensional diffusion model, and the results suggest that the ion exclusion at the top of the cored section reflects deepening of the permafrost layer following the last glaciation (???100 kyr), consistent with published thermal models. Gas hydrate saturation values estimated from dissolved chloride agree with estimates based on logging data when the gas hydrate occupies more than 20% of the pore space; the correlation is less robust at lower saturation values. The highest gas hydrate concentrations at the Mount Elbert Well are clearly associated with coarse-grained sedimentary sections, as expected from theoretical calculations and field observations in marine and other arctic sediment cores. ?? 2009 Elsevier Ltd.

Quantifying Hydrate Formation in Gas-rich Environments Using the Method of Characteristics

NASA Astrophysics Data System (ADS)

You, K.; Flemings, P. B.; DiCarlo, D. A.

2015-12-01

Methane hydrates hold a vast amount of methane globally, and have huge energy potential. Methane hydrates in gas-rich environments are the most promising production targets. We develop a one-dimensional analytical solution based on the method of characteristics to explore hydrate formation in such environments (Figure 1). Our solution shows that hydrate saturation is constant with time and space in a homogeneous system. Hydrate saturation is controlled by the initial thermodynamic condition of the system, and changed by the gas fractional flow. Hydrate saturation increases with the initial distance from the hydrate phase boundary. Different gas fractional flows behind the hydrate solidification front lead to different gas saturations at the hydrate solidification front. The higher the gas saturation at the front, the less the volume available to be filled by hydrate, and hence the lower the hydrate saturation. The gas fractional flow depends on the relative permeability curves, and the forces that drive the flow. Viscous forces (the drive for flow induced from liquid pressure gradient) dominate the flow, and hydrate saturation is independent on the gas supply rates and the flow directions at high gas supply rates. Hydrate saturation can be estimated as one minus the ratio of the initial to equilibrium salinity. Gravity forces (the drive for flow induced from the gravity) dominate the flow, and hydrate saturation depends on the flow rates and the flow directions at low gas supply rates. Hydrate saturation is highest for upward flow, and lowest for downward flow. Hydrate saturation decreases with the flow rate for upward flow, and increases with the flow rate for downward flow. This analytical solution illuminates how hydrate is formed by gas (methane, CO2, ethane, propane) flowing into brine-saturated sediments at both the laboratory and geological scales (Figure 1). It provides an approach to generalize the understanding of hydrate solidification in gas-rich environments, although complicated numerical models have been developed previously. Examples of gas expulsion into hydrate stability zones and the associated hydrate formation in both laboratory and geological scales, and CO2 sequestration into CO2-hydrates near the seafloor and under the permafrost will be presented.

Gas hydrate dissociation off Svalbard induced by isostatic rebound rather than global warming.

PubMed

Wallmann, Klaus; Riedel, M; Hong, W L; Patton, H; Hubbard, A; Pape, T; Hsu, C W; Schmidt, C; Johnson, J E; Torres, M E; Andreassen, K; Berndt, C; Bohrmann, G

2018-01-08

Methane seepage from the upper continental slopes of Western Svalbard has previously been attributed to gas hydrate dissociation induced by anthropogenic warming of ambient bottom waters. Here we show that sediment cores drilled off Prins Karls Foreland contain freshwater from dissociating hydrates. However, our modeling indicates that the observed pore water freshening began around 8 ka BP when the rate of isostatic uplift outpaced eustatic sea-level rise. The resultant local shallowing and lowering of hydrostatic pressure forced gas hydrate dissociation and dissolved chloride depletions consistent with our geochemical analysis. Hence, we propose that hydrate dissociation was triggered by postglacial isostatic rebound rather than anthropogenic warming. Furthermore, we show that methane fluxes from dissociating hydrates were considerably smaller than present methane seepage rates implying that gas hydrates were not a major source of methane to the oceans, but rather acted as a dynamic seal, regulating methane release from deep geological reservoirs.

Fundamentals and applications of gas hydrates.

PubMed

Koh, Carolyn A; Sloan, E Dendy; Sum, Amadeu K; Wu, David T

2011-01-01

Fundamental understanding of gas hydrate formation and decomposition processes is critical in many energy and environmental areas and has special importance in flow assurance for the oil and gas industry. These areas represent the core of gas hydrate applications, which, albeit widely studied, are still developing as growing fields of research. Discovering the molecular pathways and chemical and physical concepts underlying gas hydrate formation potentially can lead us beyond flowline blockage prevention strategies toward advancing new technological solutions for fuel storage and transportation, safely producing a new energy resource from natural deposits of gas hydrates in oceanic and arctic sediments, and potentially facilitating effective desalination of seawater. The state of the art in gas hydrate research is leading us to new understanding of formation and dissociation phenomena that focuses on measurement and modeling of time-dependent properties of gas hydrates on the basis of their well-established thermodynamic properties.

Molecular modeling of the dissociation of methane hydrate in contact with a silica surface.

PubMed

Bagherzadeh, S Alireza; Englezos, Peter; Alavi, Saman; Ripmeester, John A

2012-03-15

We use constant energy, constant volume (NVE) molecular dynamics simulations to study the dissociation of the fully occupied structure I methane hydrate in a confined geometry between two hydroxylated silica surfaces between 36 and 41 Å apart, at initial temperatures of 283, 293, and 303 K. Simulations of the two-phase hydrate/water system are performed in the presence of silica, with and without a 3 Å thick buffering water layer between the hydrate phase and silica surfaces. Faster decomposition is observed in the presence of silica, where the hydrate phase is prone to decomposition from four surfaces, as compared to only two sides in the case of the hydrate/water simulations. The existence of the water layer between the hydrate phase and the silica surface stabilizes the hydrate phase relative to the case where the hydrate is in direct contact with silica. Hydrates bound between the silica surfaces dissociate layer-by-layer in a shrinking core manner with a curved decomposition front which extends over a 5-8 Å thickness. Labeling water molecules shows that there is exchange of water molecules between the surrounding liquid and intact cages in the methane hydrate phase. In all cases, decomposition of the methane hydrate phase led to the formation of methane nanobubbles in the liquid water phase. © 2012 American Chemical Society

Stability of Gas Hydrates on Continental Margins: Implications of Subsurface Fluid Flow

NASA Astrophysics Data System (ADS)

Nunn, J. A.

2008-12-01

Gas hydrates are found at or just below the sediment-ocean interface in continental margins settings throughout the world. They are also found on land in high latitude regions such as the north slope of Alaska. While gas hydrate occurrence is common, gas hydrates are stable under a fairly restricted range of temperatures and pressures. In a purely conductive thermal regime, near surface temperatures depend on basal heat flow, thermal conductivity of sediments, and temperature at the sediment-water or sediment-air interface. Thermal conductivity depends on porosity and sediment composition. Gas hydrates are most stable in areas of low heat flow and high thermal conductivity which produce low temperature gradients. Older margins with thin continental crust and coarse grained sediments would tend to be colder. Another potentially important control on subsurface temperatures is advective heat transport by recharge/discharge of groundwater. Upward fluid flow depresses temperature gradients over a purely conductive regime with the same heat flow which would make gas hydrates more stable. Downward fluid flow would have the opposite effect. However, regional scale fluid flow may substantially increase heat flow in discharge areas which would destabilize gas hydrates. For example, discharge of topographically driven groundwater along the coast in the Central North Slope of Alaska has increased surface heat flow in some areas by more than 50% over a purely conductive thermal regime. Fluid flow also alters the pressure regime which can affect gas hydrate stability. Modeling results suggest a positive feedback between gas hydrate formation/disassociation and fluid flow. Disassociation of gas hydrates or permafrost due to global warming could increase permeability. This could enhance fluid flow and associated heat transport causing a more rapid and/or more spatially extensive gas hydrate disassociation than predicted solely from conductive propagation of temporal changes in surface or water bottom temperature. Model results from both the North Slope of Alaska and the Gulf of Mexico are compared.

Inadequate Hydration, BMI, and Obesity Among US Adults: NHANES 2009-2012.

PubMed

Chang, Tammy; Ravi, Nithin; Plegue, Melissa A; Sonneville, Kendrin R; Davis, Matthew M

2016-07-01

Improving hydration is a strategy commonly used by clinicians to prevent overeating with the goal of promoting a healthy weight among patients. The relationship between weight status and hydration, however, is unclear. Our objective was to assess the relationship between inadequate hydration and BMI and inadequate hydration and obesity among adults in the United States. Our study used a nationally representative sample from the National Health and Nutrition Examination Survey (NHANES) 2009 to 2012, and included adults aged 18 to 64 years. The primary outcome of interest was body mass index (BMI), measured in continuous values and also categorized as obese (BMI ≥30) or not (BMI <30). Individuals with urine osmolality values of 800 mOsm/kg or greater were considered to be inadequately hydrated. Linear and logistic regressions were performed with continuous BMI and obesity status as the outcomes, respectively. Models were adjusted for known confounders including age, race/ethnicity, sex, and income-to-poverty ratio. In this nationally representative sample (n = 9,528; weighted n = 193.7 million), 50.8% were women, 64.5% were non-Hispanic white, and the mean age was 41 years. Mean urine osmolality was 631.4 mOsm/kg (SD = 236.2 mOsm/kg); 32.6% of the sample was inadequately hydrated. In adjusted models, adults who were inadequately hydrated had higher BMIs (1.32 kg/m(2); 95% CI, 0.85-1.79; P <.001) and higher odds of being obese (OR = 1.59; 95% CI, 1.35-1.88; P <.001) compared with hydrated adults. We found a significant association between inadequate hydration and elevated BMI and inadequate hydration and obesity, even after controlling for confounders. This relationship has not previously been shown on a population level and suggests that water, an essential nutrient, may deserve greater focus in weight management research and clinical strategies. © 2016 Annals of Family Medicine, Inc.

Temperature effect on the small-to-large crossover lengthscale of hydrophobic hydration

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

Djikaev, Y. S., E-mail: idjikaev@buffalo.edu; Ruckenstein, E.

2013-11-14

The thermodynamics of hydration is expected to change gradually from entropic for small solutes to enthalpic for large ones. The small-to-large crossover lengthscale of hydrophobic hydration depends on the thermodynamic conditions of the solvent such as temperature, pressure, presence of additives, etc. We attempt to shed some light on the temperature dependence of the crossover lengthscale by using a probabilistic approach to water hydrogen bonding that allows one to obtain an analytic expression for the number of bonds per water molecule as a function of both its distance to a solute and solute radius. Incorporating that approach into the densitymore » functional theory, one can examine the solute size effects on its hydration over the entire small-to-large lengthscale range at a series of different temperatures. Knowing the dependence of the hydration free energy on the temperature and solute size, one can also obtain its enthalpic and entropic contributions as functions of both temperature and solute size. These functions can provide some interesting insight into the temperature dependence of the crossover lengthscale of hydrophobic hydration. The model was applied to the hydration of spherical particles of various radii in water in the temperature range from T = 293.15 K to T = 333.15 K. The model predictions for the temperature dependence of the hydration free energy of small hydrophobes are consistent with the experimental and simulational data on the hydration of simple molecular solutes. Three alternative definitions for the small-to-large crossover length-scale of hydrophobic hydration are proposed, and their temperature dependence is obtained. Depending on the definition and temperature, the small-to-large crossover in the hydration mechanism is predicted to occur for hydrophobes of radii from one to several nanometers. Independent of its definition, the crossover length-scale is predicted to decrease with increasing temperature.« less

Characterization of gas hydrate distribution using conventional 3D seismic data in the Pearl River Mouth Basin, South China Sea

USGS Publications Warehouse

Wang, Xiujuan; Qiang, Jin; Collett, Timothy S.; Shi, Hesheng; Yang, Shengxiong; Yan, Chengzhi; Li, Yuanping; Wang, Zhenzhen; Chen, Duanxin

2016-01-01

A new 3D seismic reflection data volume acquired in 2012 has allowed for the detailed mapping and characterization of gas hydrate distribution in the Pearl River Mouth Basin in the South China Sea. Previous studies of core and logging data showed that gas hydrate occurrence at high concentrations is controlled by the presence of relatively coarse-grained sediment and the upward migration of thermogenic gas from the deeper sediment section into the overlying gas hydrate stability zone (BGHSZ); however, the spatial distribution of the gas hydrate remains poorly defined. We used a constrained sparse spike inversion technique to generate acoustic-impedance images of the hydrate-bearing sedimentary section from the newly acquired 3D seismic data volume. High-amplitude reflections just above the bottom-simulating reflectors (BSRs) were interpreted to be associated with the accumulation of gas hydrate with elevated saturations. Enhanced seismic reflections below the BSRs were interpreted to indicate the presence of free gas. The base of the BGHSZ was established using the occurrence of BSRs. In areas absent of well-developed BSRs, the BGHSZ was calculated from a model using the inverted P-wave velocity and subsurface temperature data. Seismic attributes were also extracted along the BGHSZ that indicate variations reservoir properties and inferred hydrocarbon accumulations at each site. Gas hydrate saturations estimated from the inversion of acoustic impedance of conventional 3D seismic data, along with well-log-derived rock-physics models were also used to estimate gas hydrate saturations. Our analysis determined that the gas hydrate petroleum system varies significantly across the Pearl River Mouth Basin and that variability in sedimentary properties as a product of depositional processes and the upward migration of gas from deeper thermogenic sources control the distribution of gas hydrates in this basin.

Temperature dependence of the hydrated electron's excited-state relaxation. II. Elucidating the relaxation mechanism through ultrafast transient absorption and stimulated emission spectroscopy

NASA Astrophysics Data System (ADS)

Farr, Erik P.; Zho, Chen-Chen; Challa, Jagannadha R.; Schwartz, Benjamin J.

2017-08-01

The structure of the hydrated electron, particularly whether it exists primarily within a cavity or encompasses interior water molecules, has been the subject of much recent debate. In Paper I [C.-C. Zho et al., J. Chem. Phys. 147, 074503 (2017)], we found that mixed quantum/classical simulations with cavity and non-cavity pseudopotentials gave different predictions for the temperature dependence of the rate of the photoexcited hydrated electron's relaxation back to the ground state. In this paper, we measure the ultrafast transient absorption spectroscopy of the photoexcited hydrated electron as a function of temperature to confront the predictions of our simulations. The ultrafast spectroscopy clearly shows faster relaxation dynamics at higher temperatures. In particular, the transient absorption data show a clear excess bleach beyond that of the equilibrium hydrated electron's ground-state absorption that can only be explained by stimulated emission. This stimulated emission component, which is consistent with the experimentally known fluorescence spectrum of the hydrated electron, decreases in both amplitude and lifetime as the temperature is increased. We use a kinetic model to globally fit the temperature-dependent transient absorption data at multiple temperatures ranging from 0 to 45 °C. We find the room-temperature lifetime of the excited-state hydrated electron to be 137 ±40 fs, in close agreement with recent time-resolved photoelectron spectroscopy (TRPES) experiments and in strong support of the "non-adiabatic" picture of the hydrated electron's excited-state relaxation. Moreover, we find that the excited-state lifetime is strongly temperature dependent, changing by slightly more than a factor of two over the 45 °C temperature range explored. This temperature dependence of the lifetime, along with a faster rate of ground-state cooling with increasing bulk temperature, should be directly observable by future TRPES experiments. Our data also suggest that the red side of the hydrated electron's fluorescence spectrum should significantly decrease with increasing temperature. Overall, our results are not consistent with the nearly complete lack of temperature dependence predicted by traditional cavity models of the hydrated electron but instead agree qualitatively and nearly quantitatively with the temperature-dependent structural changes predicted by the non-cavity hydrated electron model.

Methane Hydrate Formation from Enhanced Organic Carbon Burial During Glacial Lowstands: Examples from the Gulf of Mexico

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

Malinverno, Alberto; Cook, Ann; Daigle, Hugh

Methane hydrates in fine-grained marine sediments are often found within veins and fractures occupying discrete depth intervals that are surrounded by hydrate-free sediments. As they are not connected with gas sources beneath the base of the methane hydrate stability zone (MHSZ), these isolated hydrate-bearing intervals have been interpreted as formed by in situ microbial methane. We investigate here the hypothesis that these hydrate deposits form in sediments that were deposited during glacial lowstands and contain higher amounts of labile particulate organic carbon (POC), leading to enhanced microbial methanogenesis. During Pleistocene lowstands, river loads are deposited near the steep top ofmore » the continental slope and turbidity currents transport organic-rich, fine-grained sediments to deep waters. Faster sedimentation rates during glacial periods result in better preservation of POC because of decreased exposure times to oxic conditions. The net result is that more labile POC enters the methanogenic zone and more methane is generated in these sediments. To test this hypothesis, we apply an advection-diffusion-reaction model with a time-dependent deposition of labile POC at the seafloor controlled by glacioeustatic sea level variations in the last 250 kyr. The model is run for parameters estimated at three sites drilled by the 2009 Gulf of Mexico Joint Industry Project: Walker Ridge in the Terrebonne Basin (WR313-G and WR313-H) and Green Canyon near the canyon embayment into the Sigsbee Escarpment (GC955-H). In the model, gas hydrate forms in sediments with higher labile POC content deposited during the glacial cycle between 230 and 130 kyr (marine isotope stages 6 and 7). The corresponding depth intervals in the three sites contain hydrates, as shown by high bulk electrical resistivities and resistive subvertical fracture fills. This match supports the hypothesis that enhanced POC burial during glacial lowstands can result in hydrate formation from in situ microbial methanogenesis. Our results have implications for carbon cycling during glacial/interglacial cycles and for hydrate accumulation in the MHSZ. In particular, once hydrate-bearing intervals formed during glacial periods are buried beneath the MHSZ and dissociate, gas bubbles can rise and recycle microbial methane into the MHSZ.« less

Massive blow-out craters formed by hydrate-controlled methane expulsion from the Arctic seafloor

NASA Astrophysics Data System (ADS)

Andreassen, K.; Hubbard, A.; Winsborrow, M.; Patton, H.; Vadakkepuliyambatta, S.; Plaza-Faverola, A.; Gudlaugsson, E.; Serov, P.; Deryabin, A.; Mattingsdal, R.; Mienert, J.; Bünz, S.

2017-06-01

Widespread methane release from thawing Arctic gas hydrates is a major concern, yet the processes, sources, and fluxes involved remain unconstrained. We present geophysical data documenting a cluster of kilometer-wide craters and mounds from the Barents Sea floor associated with large-scale methane expulsion. Combined with ice sheet/gas hydrate modeling, our results indicate that during glaciation, natural gas migrated from underlying hydrocarbon reservoirs and was sequestered extensively as subglacial gas hydrates. Upon ice sheet retreat, methane from this hydrate reservoir concentrated in massive mounds before being abruptly released to form craters. We propose that these processes were likely widespread across past glaciated petroleum provinces and that they also provide an analog for the potential future destabilization of subglacial gas hydrate reservoirs beneath contemporary ice sheets.

Structural and Stratigraphic Controls on Methane Hydrate occurrence and distribution: Gulf of Mexico, Walker Ridge 313 and Green Canyon 955: Final Report

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

Jaiswal, Priyank

The goal of this project was to determine structural and stratigraphic controls on hydrate occurrence and distribution in Green Canyon (GC) 955 and Walker Ridge (WR) 313 blocks using seismic and well data. Gas hydrate was discovered in these blocks in coarse- and fine-grained sediments during the 2009 Joint Industrial project (JIP) Leg 11 drilling expedition. Although the immediate interest of the exploration community is exclusively hydrate which is present in coarse–grained sediments, factors that control hydrate and free gas distribution in the two blocks and whether coarse and fine-grained hydrate-bearing units are related in any manner, formed the coremore » of this research. The project spanned from 10/01/2012 to 07/31/2016. In the project, in both the leased blocks, the interval spanning the gas hydrate stability zone (GHSZ) was characterized using a joint analysis of sparse Ocean Bottom Seismic (OBS) and dense, surface–towed multichannel seismic (MCS) data. The project team had the luxury of calibrating their results with two well logs. Advance processing methods such as depth migration and full-waveform inversion (FWI) were used for seismic data analysis. Hydrate quantification was achieved through interpretation of the FWI velocity field using appropriate rock physics models at both blocks. The seismic modeling/inversion methodology (common to both GC955 and WR313 blocks) was as follows. First, the MCS data were depth migrated using a P-wave velocity (VP) model constructed using inversion of reflection arrival times of a few (four in both cases) key horizons carefully picked in the OBS data to farthest possible offsets. Then, the resolution of the traveltime VP model was improved to wavelength scale by inverting OBS gathers up to the highest frequency possible (21.75 Hz for GC955 and 17.5 for WR313) using FWI. Finally, the hydrate saturation (or the volume fraction) was estimated at the well location assuming one of the other hydrate morphology (filling the primary or the secondary porosity) was extrapolated out from the wells using the FWI VP as a guide. General outcomes were as follows. First and foremost, an imaging methodology using sparse seismic data, which is easily replicable at other sites with similar datasets, has been demonstrated. The end product of this methodology at both the leased blocks is quantitative estimates of hydrate distribution. Second, at both locations there is strong evidence that the base of the GHSZ, which does not appear as a clear Bottom Simulating Reflection (BSR), manifests in the VP perturbations created by FWI, suggesting that FWI is sensitive to subtle compositional changes in shallow sediments and establishes it as a valuable tool for investigations of hydrate-bearing basins. Third, through joint interpretation of the depth migrated image and the FWI VP model, how structure and stratigraphy jointly determine hydrate and free gas distribution in both blocks could be clearly visualized. The joint interpretation also suggests that the coarse and fine grained hydrate-bearing sediments at both leased are connected. Site specific results, in addition to general results, are as follows. At GC955 the overlying fine-grained hydrate-bearing unit could have been sourced from the underlying hydrate coarse-grained channel-levee complex through a chimney feature. The channel-levee system at GC955 is compartmentalized by faults, of which only a few may be impermeable. Although compartmentalized, the channel-levee system in the GC955 as a whole might be in communication except selected zones. At WR313 the overlying fine-grained fracture-filled hydrate unit appears to be sourced from below the GHSZ. The reason that only a particular fine-grained unit has hydrate, despite having lower porosity that the bounding units, could be the presence of secondary porosity (such as those formed from clay dewatering under compaction). In conclusion, the project was a pioneering effort in in joint analysis of OBS and MCS datasets for advancing the knowledge about a hydrate and free–gas system dynamics using advanced processing methods such as FWI and depth migration. Results obtained in this project can greatly advance the tools and techniques used for delineating specific hydrate prospects. Results obtained in this project can also be seamlessly incorporated into other DOE funded project on modeling the potential productivity and commercial viability of hydrate from sand-dominated reservoirs. The OBS and MCS data in this project were acquired in 2012 (after the JIP II drilling) by the USGS and therefore the results are a posteriori. Nonetheless, the seismic inversion workflow established through this project can be used to generate various what-if quantification scenarios even in absence of logs and serve as a valuable tool for guiding drilling operations. Results from this project can augment other DOE sponsored projects on determining the commercial viability of methane production from the Gulf of Mexico.« less

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

NASA Astrophysics Data System (ADS)

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D.

2016-08-01

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better than the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.

Atomistic modeling of structure II gas hydrate mechanics: Compressibility and equations of state

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

Vlasic, Thomas M.; Servio, Phillip; Rey, Alejandro D., E-mail: alejandro.rey@mcgill.ca

2016-08-15

This work uses density functional theory (DFT) to investigate the poorly characterized structure II gas hydrates, for various guests (empty, propane, butane, ethane-methane, propane-methane), at the atomistic scale to determine key structure and mechanical properties such as equilibrium lattice volume and bulk modulus. Several equations of state (EOS) for solids (Murnaghan, Birch-Murnaghan, Vinet, Liu) were fitted to energy-volume curves resulting from structure optimization simulations. These EOS, which can be used to characterize the compressional behaviour of gas hydrates, were evaluated in terms of their robustness. The three-parameter Vinet EOS was found to perform just as well if not better thanmore » the four-parameter Liu EOS, over the pressure range in this study. As expected, the Murnaghan EOS proved to be the least robust. Furthermore, the equilibrium lattice volumes were found to increase with guest size, with double-guest hydrates showing a larger increase than single-guest hydrates, which has significant implications for the widely used van der Waals and Platteeuw thermodynamic model for gas hydrates. Also, hydrogen bonds prove to be the most likely factor contributing to the resistance of gas hydrates to compression; bulk modulus was found to increase linearly with hydrogen bond density, resulting in a relationship that could be used predictively to determine the bulk modulus of various structure II gas hydrates. Taken together, these results fill a long existing gap in the material chemical physics of these important clathrates.« less

Theoretical investigation of local proton conductance in the proton exchange membranes

NASA Astrophysics Data System (ADS)

Singh, Raman K.; Tsuneda, Takao; Miyatake, Kenji; Watanabe, Masahiro

2014-07-01

The hydrated structures of the proton exchange membranes were theoretically investigated using long-range corrected density functional theory to make clear why perfluorinated polymer membrane Nafion is superior to other membranes in the proton conductivity at low humidity. For exploring the possibility of the proton conductance in the vehicle mechanism with low hydration numbers, we examined the relay model of protonated water clusters between the sulfonic acid groups in Nafion and concluded that this relay model may contribute to the high proton conductivity of Nafion with less-hydrated sulfonic acid groups.

Estimating the Aqueous Solubility of Pharmaceutical Hydrates

PubMed Central

Franklin, Stephen J.; Younis, Usir S.; Myrdal, Paul B.

2016-01-01

Estimation of crystalline solute solubility is well documented throughout the literature. However, the anhydrous crystal form is typically considered with these models, which is not always the most stable crystal form in water. In this study an equation which predicts the aqueous solubility of a hydrate is presented. This research attempts to extend the utility of the ideal solubility equation by incorporating desolvation energetics of the hydrated crystal. Similar to the ideal solubility equation, which accounts for the energetics of melting, this model approximates the energy of dehydration to the entropy of vaporization for water. Aqueous solubilities, dehydration and melting temperatures, and log P values were collected experimentally and from the literature. The data set includes different hydrate types and a range of log P values. Three models are evaluated, the most accurate model approximates the entropy of dehydration (ΔSd) by the entropy of vaporization (ΔSvap) for water, and utilizes onset dehydration and melting temperatures in combination with log P. With this model, the average absolute error for the prediction of solubility of 14 compounds was 0.32 log units. PMID:27238488

Identifying the morphologies of gas hydrate distribution using P-wave velocity and density: a test from the GMGS2 expedition in the South China Sea

NASA Astrophysics Data System (ADS)

Liu, Tao; Liu, Xuewei

2018-06-01

Pore-filling and fracture-filling are two basic distribution morphologies of gas hydrates in nature. A clear knowledge of gas hydrate morphology is important for better resource evaluation and exploitation. Improper exploitation may cause seafloor instability and exacerbate the greenhouse effect. To identify the gas hydrate morphologies in sediments, we made a thorough analysis of the characteristics of gas hydrate bearing sediments (GHBS) based on rock physics modeling. With the accumulation of gas hydrate in sediments, both the velocities of two types of GHBS increase, and their densities decrease. Therefore, these two morphologies cannot be differentiated only by velocity or density. After a series of tests, we found the attribute ρ {{V}{{P}}}0.5 as a function of hydrate concentration show opposite trends for these two morphologies due to their different formation mechanisms. The morphology of gas hydrate can thus be identified by comparing the measured ρ {{V}{{P}}}0.5 with its background value, which means the ρ {{V}{{P}}}0.5 of the hydrate-free sediments. In 2013, China’s second gas hydrate expedition was conducted by Guangzhou Marine Geologic Survey to explore gas hydrate resources in the northern South China Sea, and both two hydrate morphologies were recovered. We applied this method to three sites, which include two pore-filling and three fracture-filling hydrate layers. The data points, that agree with the actual situations, account for 72% and 82% of the total for the two pore-filling hydrate layers, respectively, and 86%, 74%, and 69% for the three fracture-filling hydrate layers, respectively.

Analysis of repeated signals during shell fights in the hermit crab Pagurus bernhardus

PubMed Central

Briffa, M.; Elwood, R. W.; Dick, J. T. A.

1998-01-01

Shell exchanges between hermit crabs may occur after a period of shell rapping, when the initiating or attacking crab brings its shell rapidly and repeatedly into contact with the shell of the non-initiator or defender, in a series of bouts. There are two opposing models of hermit crab shell exchange and the function of shell rapping. The negotiation model views shell exchange as a mutualistic activity, in which the initiator supplies information about the quality of its shell via the fundamental frequency of the rapping sound. The aggression model views shell rapping as either detrimental to the defending crab, or as providing it with information about the initiator's ability or motivation to continue, or both. The negotiation model makes no predictions about the temporal pattern of rapping, but under the aggression model it would be expected that crabs that rapped more vigorously would be more likely to effect an exchange. Repeating the signal could be expected under either model. Crabs that achieve an exchange rap more vigorously, rapping is more persistent when a clear gain in shell quality may be achieved, and the vigour is greater when the relative resource-holding potential (or 'fighting ability') is high. These findings support the aggression model rather than the negotiation model. Contrary to the predictions of game theory, crabs that do not effect an exchange appear to signal that they are about to give up. The data suggest that rapping is performed repeatedly because the accumulation of all of the performances acts as a signal of stamina.

A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence

PubMed Central

Luis, Daniel Porfirio; García-González, Alcione; Saint-Martin, Humberto

2016-01-01

Monte Carlo and molecular dynamics simulations were done with three recent water models TIP4P/2005 (Transferable Intermolecular Potential with 4 Points/2005), TIP4P/Ice (Transferable Intermolecular Potential with 4 Points/ Ice) and TIP4Q (Transferable Intermolecular Potential with 4 charges) combined with two models for methane: an all-atom one OPLS-AA (Optimal Parametrization for the Liquid State) and a united-atom one (UA); a correction for the C–O interaction was applied to the latter and used in a third set of simulations. The models were validated by comparison to experimental values of the free energy of hydration at 280, 300, 330 and 370 K, all under a pressure of 1 bar, and to the experimental radial distribution functions at 277, 283 and 291 K, under a pressure of 145 bar. Regardless of the combination rules used for σC,O, good agreement was found, except when the correction to the UA model was applied. Thus, further simulations of the sI hydrate were performed with the united-atom model to compare the thermal expansivity to the experiment. A final set of simulations was done with the UA methane model and the three water models, to study the sI hydrate-liquid water-gas coexistence at 80, 230 and 400 bar. The melting temperatures were compared to the experimental values. The results show the need to perform simulations with various different models to attain a reliable and robust molecular image of the systems of interest. PMID:27240339

Phase and flow behavior of mixed gas hydrate systems during gas injection

NASA Astrophysics Data System (ADS)

Darnell, K.; Flemings, P. B.; DiCarlo, D. A.

2017-12-01

We present one-dimensional, multi-phase flow model results for injections of carbon dioxide and nitrogen mixtures, or flue gas, into methane hydrate bearing reservoirs. Our flow model is coupled to a thermodynamic simulator that predicts phase stabilities as a function of composition, so multiple phases can appear, disappear, or change composition as the injection invades the reservoir. We show that the coupling of multi-phase fluid flow with phase behavior causes preferential phase fractionation in which each component flows through the system at different speeds and in different phases. We further demonstrate that phase and flow behavior within the reservoir are driven by hydrate stability of each individual component in addition to the hydrate stability of the injection composition. For example, if carbon dioxide and nitrogen are both individually hydrate stable at the reservoir P-T conditions, then any injection composition will convert all available water into hydrate and plug the reservoir. In contrast, if only carbon dioxide is hydrate stable at the reservoir P-T conditions, then nitrogen preferentially stays in the gaseous phase, while the carbon dioxide partitions into the hydrate and liquid water phases. For all injections of this type, methane originally held in hydrate is released by dissociation into the nitrogen-rich gaseous phase. The net consequence is that a gas phase composed of nitrogen and methane propagates through the reservoir in a fast-moving front. A slower-moving front lags behind where carbon dioxide and nitrogen form a mixed hydrate, but methane is absent due to dissociation-induced methane stripping from the first, fast-moving front. The entire composition path traces through the phase space as the flow develops with each front moving at different, constant velocities. This behavior is qualitatively similar to the dynamics present in enhanced oil recovery or enhanced coalbed methane recovery. These results explain why the inclusion of nitrogen in mixed gas injection into methane hydrate reservoirs has been far more successful at producing methane than pure carbon dioxide injections. These results also provide a test for the validity of equilibrium thermodynamics in transport-dominated mixed hydrate systems that can be validated by laboratory-scale flow-through experiments.

Cellulose Nanofibers as a Modifier for Rheology, Curing and Mechanical Performance of Oil Well Cement.

PubMed

Sun, Xiuxuan; Wu, Qinglin; Lee, Sunyoung; Qing, Yan; Wu, Yiqiang

2016-08-16

The influence of nanocellulose on oil well cement (OWC) properties is not known in detail, despite recent advances in nanocellulose technology and its related composite materials. The effect of cellulose nanofibers (CNFs) on flow, hydration, morphology, and strength of OWC was investigated using a range of spectroscopic methods coupled with rheological modelling and strength analysis. The Vom-Berg model showed the best fitting result of the rheology data. The addition of CNFs increased the yield stress of OWC slurry and degree of hydration value of hydrated CNF-OWC composites. The flexural strength of hydrated OWC samples was increased by 20.7% at the CNF/OWC ratio of 0.04 wt%. Excessive addition of CNFs into OWC matrix had a detrimental effect on the mechanical properties of hydrated CNF-OWC composites. This phenomenon was attributed to the aggregation of CNFs as observed through coupled morphological and elemental analysis. This study demonstrates a sustainable reinforcing nano-material for use in cement-based formulations.

Cellulose Nanofibers as a Modifier for Rheology, Curing and Mechanical Performance of Oil Well Cement

NASA Astrophysics Data System (ADS)

Sun, Xiuxuan; Wu, Qinglin; Lee, Sunyoung; Qing, Yan; Wu, Yiqiang

2016-08-01

The influence of nanocellulose on oil well cement (OWC) properties is not known in detail, despite recent advances in nanocellulose technology and its related composite materials. The effect of cellulose nanofibers (CNFs) on flow, hydration, morphology, and strength of OWC was investigated using a range of spectroscopic methods coupled with rheological modelling and strength analysis. The Vom-Berg model showed the best fitting result of the rheology data. The addition of CNFs increased the yield stress of OWC slurry and degree of hydration value of hydrated CNF-OWC composites. The flexural strength of hydrated OWC samples was increased by 20.7% at the CNF/OWC ratio of 0.04 wt%. Excessive addition of CNFs into OWC matrix had a detrimental effect on the mechanical properties of hydrated CNF-OWC composites. This phenomenon was attributed to the aggregation of CNFs as observed through coupled morphological and elemental analysis. This study demonstrates a sustainable reinforcing nano-material for use in cement-based formulations.

Cellulose Nanofibers as a Modifier for Rheology, Curing and Mechanical Performance of Oil Well Cement

PubMed Central

Sun, Xiuxuan; Wu, Qinglin; Lee, Sunyoung; Qing, Yan; Wu, Yiqiang

2016-01-01

The influence of nanocellulose on oil well cement (OWC) properties is not known in detail, despite recent advances in nanocellulose technology and its related composite materials. The effect of cellulose nanofibers (CNFs) on flow, hydration, morphology, and strength of OWC was investigated using a range of spectroscopic methods coupled with rheological modelling and strength analysis. The Vom-Berg model showed the best fitting result of the rheology data. The addition of CNFs increased the yield stress of OWC slurry and degree of hydration value of hydrated CNF-OWC composites. The flexural strength of hydrated OWC samples was increased by 20.7% at the CNF/OWC ratio of 0.04 wt%. Excessive addition of CNFs into OWC matrix had a detrimental effect on the mechanical properties of hydrated CNF-OWC composites. This phenomenon was attributed to the aggregation of CNFs as observed through coupled morphological and elemental analysis. This study demonstrates a sustainable reinforcing nano-material for use in cement-based formulations. PMID:27526784

Dissecting the THz spectrum of liquid water from first principles via correlations in time and space.

PubMed

Heyden, Matthias; Sun, Jian; Funkner, Stefan; Mathias, Gerald; Forbert, Harald; Havenith, Martina; Marx, Dominik

2010-07-06

Solvation of molecules in water is at the heart of a myriad of molecular phenomena and of crucial importance to understanding such diverse issues as chemical reactivity or biomolecular function. Complementing well-established approaches, it has been shown that laser spectroscopy in the THz frequency domain offers new insights into hydration from small solutes to proteins. Upon introducing spatially-resolved analyses of the absorption cross section by simulations, the sensitivity of THz spectroscopy is traced back to characteristic distance-dependent modulations of absorption intensities for bulk water. The prominent peak at approximately 200 cm(-1) is dominated by first-shell dynamics, whereas a concerted motion involving the second solvation shell contributes most significantly to the absorption at about 80 cm(-1) approximately 2.4 THz. The latter can be understood in terms of an umbrella-like motion of two hydrogen-bonded tetrahedra along the connecting hydrogen bond axis. Thus, a modification of the hydrogen bond network, e.g., due to the presence of a solute, is expected to affect vibrational motion and THz absorption intensity at least on a length scale that corresponds to two layers of solvating water molecules. This result provides a molecular mechanism explaining the experimentally determined sensitivity of absorption changes in the THz domain in terms of distinct, solute-induced dynamical properties in solvation shells of (bio)molecules--even in the absence of well-defined resonances.

Surface zwitterionicalization of poly(vinylidene fluoride) membranes from the entrapped reactive core-shell silica nanoparticles.

PubMed

Zhu, Li-Jing; Zhu, Li-Ping; Zhang, Pei-Bin; Zhu, Bao-Ku; Xu, You-Yi

2016-04-15

We demonstrate the preparation and properties of poly(vinylidene fluoride) (PVDF) filtration membranes modified via surface zwitterionicalization mediated by reactive core-shell silica nanoparticles (SiO2 NPs). The organic/inorganic hybrid SiO2 NPs grafted with poly(methyl meth acrylate)-block-poly(2-dimethylaminoethyl methacrylate) copolymer (PMMA-b-PDMAEMA) shell were prepared by surface-initiated reversible addition fragmentation chain transfer (SI-RAFT) polymerization and then used as a membrane-making additive of PVDF membranes. The PDMAEMA exposed on membrane surface and pore walls were quaternized into zwitterionic poly(sulfobetaine methacrylate) (PSBMA) using 1,3-propane sultone (1,3-PS) as the quaternization agent. The membrane surface chemistry and morphology were analyzed by attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS) and scanning electron microscopy (SEM), respectively. The hydrophilicity, permeability and antifouling ability of the investigated membranes were evaluated in detail. It was found that the PSBMA chains brought highly-hydrophilic and strong fouling resistant characteristics to PVDF membranes due to the powerful hydration of zwitterionic surface. The SiO2 cores and PMMA chains in the hybrid NPs play a role of anchors for the linking of PSBMA chains to membrane surface. Compared to the traditional strategies for membrane hydrophilic modification, the developed method in this work combined the advantages of both blending and surface reaction. Copyright © 2016 Elsevier Inc. All rights reserved.

Numerical analysis of wellbore instability in gas hydrate formation during deep-water drilling

NASA Astrophysics Data System (ADS)

Zhang, Huaiwen; Cheng, Yuanfang; Li, Qingchao; Yan, Chuanliang; Han, Xiuting

2018-02-01

Gas hydrate formation may be encountered during deep-water drilling because of the large amount and wide distribution of gas hydrates under the shallow seabed of the South China Sea. Hydrates are extremely sensitive to temperature and pressure changes, and drilling through gas hydrate formation may cause dissociation of hydrates, accompanied by changes in wellbore temperatures, pore pressures, and stress states, thereby leading to wellbore plastic yield and wellbore instability. Considering the coupling effect of seepage of drilling fluid into gas hydrate formation, heat conduction between drilling fluid and formation, hydrate dissociation, and transformation of the formation framework, this study established a multi-field coupling mathematical model of the wellbore in the hydrate formation. Furthermore, the influences of drilling fluid temperatures, densities, and soaking time on the instability of hydrate formation were calculated and analyzed. Results show that the greater the temperature difference between the drilling fluid and hydrate formation is, the faster the hydrate dissociates, the wider the plastic dissociation range is, and the greater the failure width becomes. When the temperature difference is greater than 7°C, the maximum rate of plastic deformation around the wellbore is more than 10%, which is along the direction of the minimum horizontal in-situ stress and associated with instability and damage on the surrounding rock. The hydrate dissociation is insensitive to the variation of drilling fluid density, thereby implying that the change of the density of drilling fluids has a minimal effect on the hydrate dissociation. Drilling fluids that are absorbed into the hydrate formation result in fast dissociation at the initial stage. As time elapses, the hydrate dissociation slows down, but the risk of wellbore instability is aggravated due to the prolonged submersion in drilling fluids. For the sake of the stability of the wellbore in deep-water drilling through hydrate formation, the drilling fluid with low temperatures should be given priority. The drilling process should be kept under balanced pressures, and the drilling time should be shortened.

Feasibility Study on a Microwave-Based Sensor for Measuring Hydration Level Using Human Skin Models

PubMed Central

Brendtke, Rico; Wiehl, Michael; Groeber, Florian; Schwarz, Thomas; Walles, Heike; Hansmann, Jan

2016-01-01

Tissue dehydration results in three major types of exsiccosis—hyper-, hypo-, or isonatraemia. All three types entail alterations of salt concentrations leading to impaired biochemical processes, and can finally cause severe morbidity. The aim of our study was to demonstrate the feasibility of a microwave-based sensor technology for the non-invasive measurement of the hydration status. Electromagnetic waves at high frequencies interact with molecules, especially water. Hence, if a sample contains free water molecules, this can be detected in a reflected microwave signal. To develop the sensor system, human three-dimensional skin equivalents were instituted as a standardized test platform mimicking reproducible exsiccosis scenarios. Therefore, skin equivalents with a specific hydration and density of matrix components were generated and microwave measurements were performed. Hydration-specific spectra allowed deriving the hydration state of the skin models. A further advantage of the skin equivalents was the characterization of the impact of distinct skin components on the measured signals to investigate mechanisms of signal generation. The results demonstrate the feasibility of a non-invasive microwave-based hydration sensor technology. The sensor bears potential to be integrated in a wearable medical device for personal health monitoring. PMID:27046226

Feasibility Study on a Microwave-Based Sensor for Measuring Hydration Level Using Human Skin Models.

PubMed

Brendtke, Rico; Wiehl, Michael; Groeber, Florian; Schwarz, Thomas; Walles, Heike; Hansmann, Jan

2016-01-01

Tissue dehydration results in three major types of exsiccosis--hyper-, hypo-, or isonatraemia. All three types entail alterations of salt concentrations leading to impaired biochemical processes, and can finally cause severe morbidity. The aim of our study was to demonstrate the feasibility of a microwave-based sensor technology for the non-invasive measurement of the hydration status. Electromagnetic waves at high frequencies interact with molecules, especially water. Hence, if a sample contains free water molecules, this can be detected in a reflected microwave signal. To develop the sensor system, human three-dimensional skin equivalents were instituted as a standardized test platform mimicking reproducible exsiccosis scenarios. Therefore, skin equivalents with a specific hydration and density of matrix components were generated and microwave measurements were performed. Hydration-specific spectra allowed deriving the hydration state of the skin models. A further advantage of the skin equivalents was the characterization of the impact of distinct skin components on the measured signals to investigate mechanisms of signal generation. The results demonstrate the feasibility of a non-invasive microwave-based hydration sensor technology. The sensor bears potential to be integrated in a wearable medical device for personal health monitoring.

Ecosystem Modelling for Impact Assessment of Possible Methane Leakage during Methane Hydrate Utilization

NASA Astrophysics Data System (ADS)

Yamazaki, T.; Nakano, Y.; Monoe, D.; Oomi, T.; Doi, T.; Nakata, K.; Fukushima, T.

2005-05-01

Natural methane hydrate has been scientifically studied as a carbon reservoir globally. However, in Japan, the potential for energy resource has been industrially highlighted. There is less domestic oil and natural gas resources in Japan, but many potential deposition areas for methane hydrate in ocean around Japan are the reasons. Less CO2 discharge from methane compared with coal, oil and conventional natural gas when the same calorie value we get is considered as the advantage for energy resource. However, because methane hydrate distributes in shallower sediment layer in ocean floor, accidental leakage of methane may occur while we utilize methane hydrate. Methane itself has 21-times impact on the greenhouse effect, if it reaches the atmosphere. Therefore, it is necessary to estimate the behavior in the environment after the leakage, if we want to use methane hydrate as energy resource. The mass balance after leakage of methane on seafloor and in water column is numerically studied through the analyses of methane emissions from natural cold seepages and hydrothermal activities in this research. The outline structure of mass balance ecosystem model creating is introduced and some preliminary examination results from the test calculation are discussed.

Lattice constants and expansivities of gas hydrates from 10 K up to the stability limit

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

Hansen, T. C.; Falenty, A.; Kuhs, W. F.

2016-02-07

The lattice constants of hydrogenated and deuterated CH{sub 4}-, CO{sub 2}-, Xe- (clathrate structure type I) and N{sub 2}-hydrates (clathrate structure type II) from 10 K up to the stability limit were established in neutron- and synchrotron diffraction experiments and were used to derive the related thermal expansivities. The following results emerge from this analysis: (1) The differences of expansivities of structure type I and II hydrates are fairly small. (2) Despite the larger guest-size of CO{sub 2} as compared to methane, CO{sub 2}-hydrate has the smaller lattice constants at low temperatures, which is ascribed to the larger attractive guest-hostmore » interaction of the CO{sub 2}-water system. (3) The expansivity of CO{sub 2}-hydrate is larger than for CH{sub 4}-hydrate which leads to larger lattice constants for the former at temperatures above ∼150 K; this is likely due to the higher motional degrees of freedom of the CO{sub 2} guest molecules. (4) The cage occupancies of Xe- and CO{sub 2}-hydrates affect significantly the lattice constants. (5) Similar to ice Ih, the deuterated compounds have generally slightly larger lattice constants which can be ascribed to the somewhat weaker H-bonding. (6) Compared to ice Ih, the high temperature expansivities are about 50% larger; in contrast to ice Ih and the empty hydrate, there is no negative thermal expansion at low temperature. (7) A comparison of the experimental results with lattice dynamical work, with models based on an Einstein oscillator model, and results from inelastic neutron scattering suggest that the contribution of the guest atoms’ vibrational energy to thermal expansion is important, most prominently for CO{sub 2}- and Xe-hydrates.« less

Volatile inventories in clathrate hydrates formed in the primordial nebula.

PubMed

Mousis, Olivier; Lunine, Jonathan I; Picaud, Sylvain; Cordier, Daniel

2010-01-01

The examination of ambient thermodynamic conditions suggests that clathrate hydrates could exist in the Martian permafrost, on the surface and in the interior of Titan, as well as in other icy satellites. Clathrate hydrates are probably formed in a significant fraction of planetesimals in the solar system. Thus, these crystalline solids may have been accreted in comets, in the forming giant planets and in their surrounding satellite systems. In this work, we use a statistical thermodynamic model to investigate the composition of clathrate hydrates that may have formed in the primordial nebula. In our approach, we consider the formation sequence of the different ices occurring during the cooling of the nebula, a reasonable idealization of the process by which volatiles are trapped in planetesimals. We then determine the fractional occupancies of guests in each clathrate hydrate formed at a given temperature. The major ingredient of our model is the description of the guest-clathrate hydrate interaction by a spherically averaged Kihara potential with a nominal set of parameters, most of which are fitted to experimental equilibrium data. Our model allows us to find that Kr, Ar and N2 can be efficiently encaged in clathrate hydrates formed at temperatures higher than approximately 48.5 K in the primitive nebula, instead of forming pure condensates below 30 K. However, we find at the same time that the determination of the relative abundances of guest species incorporated in these clathrate hydrates strongly depends on the choice of the parameters of the Kihara potential and also on the adopted size of cages. Indeed, by testing different potential parameters, we have noted that even minor dispersions between the different existing sets can lead to non-negligible variations in the determination of the volatiles trapped in clathrate hydrates formed in the primordial nebula. However, these variations are not found to be strong enough to reverse the relative abundances between the different volatiles in the clathrate hydrates themselves. On the other hand, if contraction or expansion of the cages due to temperature variations are imposed in our model, the Ar and Kr mole fractions can be modified up to several orders of magnitude in clathrate hydrates. Moreover, mole fractions of other molecules such as N2 or CO are also subject to strong changes with the variation of the size of the cages. Our results may affect the predictions of the composition of the planetesimals formed in the outer solar system. In particular, the volatile abundances calculated in the giant planets' atmospheres should be altered because these quantities are proportional to the mass of accreted and vaporized icy planetesimals. For similar reasons, the estimates of the volatile budgets accreted by icy satellites and comets may also be altered by our calculations. For instance, under some conditions, our calculations predict that the abundance of argon in the atmosphere of Titan should be higher than the value measured by Huygens. Moreover, the Ar abundance in comets could be higher than the value predicted by models invoking the incorporation of volatiles in the form of clathrate hydrates in these bodies.

Sensitivity of the Arctic Ocean gas hydrate to climate changes in the period of 1948-2015

NASA Astrophysics Data System (ADS)

Malakhova, Valentina V.; Golubeva, Elena N.; Iakshina, Dina F.

2017-11-01

The objective of the present study is to analyze the interactions between a methane hydrates stability zone and the ocean temperature variations and to define the hydrate sensitivity to the contemporary warming in the Arctic Ocean. To obtain the spatial-temporary variability of the ocean bottom temperature we employ the ICMMG regional Arctic-North Atlantic ocean model that has been developed in the Institute of Computational Mathematics and Mathematical Geophysics. With the ice-ocean model the Arctic bottom water temperatures were analyzed. The resulting warming ocean bottom water is spatially inhomogeneous, with a strong impact by the Atlantic inflow on shallow regions of 200-500 m depth. Results of the mathematical modeling of the dynamics of methane hydrate stability zone in the Arctic Ocean sediment are reported. We find that the reduction of the methane hydrate stability zone occurs in the Arctic Ocean between 250 and 400 m water depths within the upper 100 m of sediment in the area influenced by the Atlantic inflow. We have identified the areas of the Arctic Ocean where an increase in methane release is probable to occur at the present time.

Synthesis of core-shell AlOOH hollow nanospheres by reacting Al nanoparticles with water

NASA Astrophysics Data System (ADS)

Lozhkomoev, A. S.; Glazkova, E. A.; Bakina, O. V.; Lerner, M. I.; Gotman, I.; Gutmanas, E. Y.; Kazantsev, S. O.; Psakhie, S. G.

2016-05-01

A novel route for the synthesis of boehmite nanospheres with a hollow core and the shell composed of highly crumpled AlOOH nanosheets by oxidizing Al nanopowder in pure water under mild processing conditions is described. The stepwise events of Al transformation into boehmite are followed by monitoring the pH in the reaction medium. A mechanism of formation of hollow AlOOH nanospheres with a well-defined shape and crystallinity is proposed which includes the hydration of the Al oxide passivation layer, local corrosion of metallic Al accompanied by hydrogen evolution, the rupture of the protective layer, the dissolution of Al from the particle interior and the deposition of AlOOH nanosheets on the outer surface. In contrast to previously reported methods of boehmite nanoparticle synthesis, the proposed method is simple, and environmentally friendly and allows the generation of hydrogen gas as a by-product. Due to their high surface area and high, slit-shaped nanoporosity, the synthesized AlOOH nanostructures hold promise for the development of more effective catalysts, adsorbents, vaccines and drug carriers.

A mild alkali treated jute fibre controlling the hydration behaviour of greener cement paste

PubMed Central

Jo, Byung-Wan; Chakraborty, Sumit

2015-01-01

To reduce the antagonistic effect of jute fibre on the setting and hydration of jute reinforced cement, modified jute fibre reinforcement would be a unique approach. The present investigation deals with the effectiveness of mild alkali treated (0.5%) jute fibre on the setting and hydration behaviour of cement. Setting time measurement, hydration test and analytical characterizations of the hardened samples (viz., FTIR, XRD, DSC, TGA, and free lime estimation) were used to evaluate the effect of alkali treated jute fibre. From the hydration test, the time (t) required to reach maximum temperature for the hydration of control cement sample is estimated to be 860 min, whilst the time (t) is measured to be 1040 min for the hydration of a raw jute reinforced cement sample. However, the time (t) is estimated to be 1020 min for the hydration of an alkali treated jute reinforced cement sample. Additionally, from the analytical characterizations, it is determined that fibre-cement compatibility is increased and hydration delaying effect is minimized by using alkali treated jute fibre as fibre reinforcement. Based on the analyses, a model has been proposed to explain the setting and hydration behaviour of alkali treated jute fibre reinforced cement composite. PMID:25592665