WorldWideScience

Sample records for water md simulations

  1. MD SIMULATION FOR NANOCRYSTALS

    Institute of Scientific and Technical Information of China (English)

    马新玲; 杨卫

    2003-01-01

    Molecular dynamic (MD) provided an ab initio simulation for nano-scale mechanical behavior of materials, provided that the inter-atomic potential is accurately prescribed. MD is particularly suitable in simulating the formation, the deformation, and the evolution of nanocrystals under a fast strain rate. To tackle large scale system and nano-seconds time duration, parallel algorithm is desired. The present paper reviews the recent advances in MD simulation for nanocrystals with attention focused on the applications toward nanomechanics. The examined issues are: formation of nanocrystalline metals, nanoindentation on nanocrystals, fast deformation of nanocrystals, orderdisorder transition, and nano-particle impact.

  2. Desorption of water from hydrophilic MCM-41 mesopores: positron annihilation, FTIR and MD simulation studies

    Science.gov (United States)

    Maheshwari, Priya; Dutta, D.; Muthulakshmi, T.; Chakraborty, B.; Raje, N.; Pujari, P. K.

    2017-02-01

    The desorption mechanism of water from the hydrophilic mesopores of MCM-41 was studied using positron annihilation lifetime spectroscopy (PALS) and attenuated total reflection Fourier transform infrared spectroscopy supplemented with molecular dynamics (MD) simulation. PALS results indicated that water molecules do not undergo sequential evaporation in a simple layer-by-layer manner during desorption from MCM-41 mesopores. The results suggested that the water column inside the uniform cylindrical mesopore become stretched during desorption and induces cavitation (as seen in the case of ink-bottle type pores) inside it, keeping a dense water layer at the hydrophilic pore wall, as well as a water plug at both the open ends of the cylindrical pore, until the water was reduced to a certain volume fraction where the pore catastrophically empties. Before being emptied, the water molecules formed clusters inside the mesopores. The formation of molecular clusters below a certain level of hydration was corroborated by the MD simulation study. The results are discussed.

  3. Carbon Nanotubes in Water: MD Simulations of Internal and External Flow, Self Organization

    Science.gov (United States)

    Jaffe, Richard L.; Halicioglu, Timur; Werder, Thomas; Walther, Jens; Koumoutsakos, Petros; Arnold, James (Technical Monitor)

    2001-01-01

    We have developed computational tools, based on particle codes, for molecular dynamics (MD) simulation of carbon nanotubes (CNT) in aqueous environments. The interaction of CNTs with water is envisioned as a prototype for the design of engineering nano-devices, such as artificial sterocillia and molecular biosensors. Large scale simulations involving thousands of water molecules are possible due to our efficient parallel MD code that takes long range electrostatic interactions into account. Since CNTs can be considered as rolled up sheets of graphite, we expect the CNT-water interaction to be similar to the interaction of graphite with water. However, there are fundamental differences between considering graphite and CNTs, since the curvature of CNTs affects their chemical activity and also since capillary effects play an important role for both dynamic and static behaviour of materials inside CNTs. In recent studies Gordillo and Marti described the hydrogen bond structure as well as time dependent properties of water confined in CNTs. We are presenting results from the development of force fields describing the interaction of CNTs and water based on ab-initio quantum mechanical calculations. Furthermore, our results include both water flows external to CNTs and the behaviour of water nanodroplets inside heated CNTs. In the first case (external flows) the hydrophobic behaviour of CNTs is quantified and we analyze structural properties of water in the vicinity of CNTs with diagnostics such as hydrogen bond distribution, water dipole orientation and radial distribution functions. The presence of water leads to attractive forces between CNTs as a result of their hydrophobicity. Through extensive simulations we quantify these attractive forces in terms of the number and separation of the CNT. Results of our simulations involving arrays of CNTs indicate that these exhibit a hydrophobic behaviour that leads to self-organising structures capable of trapping water clusters

  4. Evidence of dynamic crossover phenomena in water and other glass-forming liquids: experiments, MD simulations and theory

    Energy Technology Data Exchange (ETDEWEB)

    Chen, S H; Zhang, Y; Lagi, M [Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Chong, S H [Institute for Molecular Science, Okazaki 444-8585 (Japan); Baglioni, P [Department of Chemistry and CSGI, University of Florence, Sesto Fiorentino, I-50019 Florence (Italy); Mallamace, F, E-mail: sowhsin@mit.ed [Dipartimento di Fisica, Universita di Messina and IRCCS Neurolesi ' Bonino-Pulejo' , I-98166 Messina (Italy)

    2009-12-16

    In a recent quasi-elastic neutron scattering experiment on water confined in a Portland cement paste, we find that this 3D confined water shows a dynamic crossover phenomenon at T{sub L} = 227 +- 5 K. The DSC heat-flow scan upon cooling and an independent measurement of specific heat at constant pressure of confined water in silica gel show a prominent peak at the same temperature. We show in this paper that this type of behavior is common to many other glassy liquids, which also show the crossover temperature in coincidence with the temperature of a small specific heat peak. We also demonstrate with MD simulations that the dynamic crossover phenomenon in confined water is an intrinsic property of bulk water, and is not due to the confinement effect. Recently, an extended version of the mode coupling theory (MCT) including the hopping effect was developed. This theory shows that, instead of a structural arrest transition at T{sub C} predicted by the idealized MCT, a fragile-to-strong dynamic crossover phenomenon takes place instead at T{sub C}, confirming both the experimental and the numerical results. The coherent and incoherent alpha relaxation times can be scaled with the calculated viscosity, showing the same crossover phenomenon. We thus demonstrated with experiments, simulations and theory that a genuine change of dynamical behavior of both water and many glassy liquids happens at the crossover temperature T{sub L}, which is 10-30% higher than the calorimetric glass transition temperature T{sub g}.

  5. Monovalent Ions and Water Dipoles in Contact with Dipolar Zwitterionic Lipid Headgroups-Theory and MD Simulations

    Directory of Open Access Journals (Sweden)

    Aljaž Velikonja

    2013-01-01

    Full Text Available The lipid bilayer is a basic building block of biological membranes and can be pictured as a barrier separating two compartments filled with electrolyte solution. Artificial planar lipid bilayers are therefore commonly used as model systems to study the physical and electrical properties of the cell membranes in contact with electrolyte solution. Among them the glycerol-based polar phospholipids which have dipolar, but electrically neutral head groups, are most frequently used in formation of artificial lipid bilayers. In this work the electrical properties of the lipid layer composed of zwitterionic lipids with non-zero dipole moments are studied theoretically. In the model, the zwitterionic lipid bilayer is assumed to be in contact with aqueous solution of monovalent salt ions. The orientational ordering of water, resulting in spatial variation of permittivity, is explicitly taken into account. It is shown that due to saturation effect in orientational ordering of water dipoles the relative permittivity in the zwitterionic headgroup region is decreased, while the corresponding electric potential becomes strongly negative. Some of the predictions of the presented mean-field theoretical consideration are critically evaluated using the results of molecular dynamics (MD simulation.

  6. Harvesting graphics power for MD simulations

    NARCIS (Netherlands)

    van Meel, J.A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.

    2008-01-01

    We discuss an implementation of molecular dynamics (MD) simulations on a graphic processing unit (GPU) in the NVIDIA CUDA language. We tested our code on a modern GPU, the NVIDIA GeForce 8800 GTX. Results for two MD algorithms suitable for short-ranged and long-ranged interactions, and a congruentia

  7. Non-monotonic dynamics of water in its binary mixture with 1,2-dimethoxy ethane: A combined THz spectroscopic and MD simulation study

    Science.gov (United States)

    Das Mahanta, Debasish; Patra, Animesh; Samanta, Nirnay; Luong, Trung Quan; Mukherjee, Biswaroop; Mitra, Rajib Kumar

    2016-10-01

    A combined experimental (mid- and far-infrared FTIR spectroscopy and THz time domain spectroscopy (TTDS) (0.3-1.6 THz)) and molecular dynamics (MD) simulation technique are used to understand the evolution of the structure and dynamics of water in its binary mixture with 1,2-dimethoxy ethane (DME) over the entire concentration range. The cooperative hydrogen bond dynamics of water obtained from Debye relaxation of TTDS data reveals a non-monotonous behaviour in which the collective dynamics is much faster in the low Xw region (where Xw is the mole fraction of water in the mixture), whereas in Xw ˜ 0.8 region, the dynamics gets slower than that of pure water. The concentration dependence of the reorientation times of water, calculated from the MD simulations, also captures this non-monotonous character. The MD simulation trajectories reveal presence of large amplitude angular jumps, which dominate the orientational relaxation. We rationalize the non-monotonous, concentration dependent orientational dynamics by identifying two different physical mechanisms which operate at high and low water concentration regimes.

  8. Direct NOE simulation from long MD trajectories

    Science.gov (United States)

    Chalmers, G.; Glushka, J. N.; Foley, B. L.; Woods, R. J.; Prestegard, J. H.

    2016-04-01

    A software package, MD2NOE, is presented which calculates Nuclear Overhauser Effect (NOE) build-up curves directly from molecular dynamics (MD) trajectories. It differs from traditional approaches in that it calculates correlation functions directly from the trajectory instead of extracting inverse sixth power distance terms as an intermediate step in calculating NOEs. This is particularly important for molecules that sample conformational states on a timescale similar to molecular reorientation. The package is tested on sucrose and results are shown to differ in small but significant ways from those calculated using an inverse sixth power assumption. Results are also compared to experiment and found to be in reasonable agreement despite an expected underestimation of water viscosity by the water model selected.

  9. Structure and water exchange dynamics of hydrated oxo halo ions in aqueous solution using QMCF MD simulation, large angle X-ray scattering and EXAFS

    Science.gov (United States)

    Eklund, Lars; Hofer, Tomas S.

    2014-01-01

    Theoretical ab initio quantum mechanical charge field molecular dynamics (QMCF MD) has been applied in conjunction with experimental large angle X-ray scattering (LAXS) and EXAFS measurements to study structure and dynamics of the hydrated oxo chloro anions chlorite, ClO2−, chlorate, ClO3−, and perchlorate, ClO4−. In addition, the structures of the hydrated hypochlorite, ClO−, bromate, BrO3−, iodate, IO3− and metaperiodate, IO4−, ions have been determined in aqueous solution by means of LAXS. The structures of the bromate, metaperiodate, and orthoperiodate, H2IO63−, ions have been determined by EXAFS as solid sodium salts and in aqueous solution as well. The results show clearly that the only form of periodate present in aqueous solution is metaperiodate. The Cl-O bond distances in the hydrated oxo chloro anions as determined by LAXS and obtained in the QMCF MD simulations are in excellent agreement, being 0.01–0.02 Å longer than in solid anhydrous salts due to hydration through hydrogen bonding to water molecules. The oxo halo anions, all with unit negative charge, have low charge density making them typical structure breakers, thus the hydrogen bonds formed to the hydrating water molecules are weaker and more short-lived than those between water molecules in pure water. The water exchange mechanism of the oxo chloro anions resembles those of the oxo sulfur anions with a direct exchange at the oxygen atoms for perchlorate and sulfate. The water exchange rate for the perchlorate ion is significantly faster, τ0.5=1.4 ps, compared to the hydrated sulfate ion and pure water, τ0.5=2.6 and 1.7 ps, respectively. The angular radial distribution functions show that the chlorate and sulfite ions have a more complex water exchange mechanism. As the chlorite and chlorate ions are more weakly hydrated than the sulfite ion the spatial occupancy is less well-defined and it is not possible to follow any well-defined migration pattern as it is difficult to

  10. Molecular Dynamics Simulations and XAFS (MD-XAFS)

    Energy Technology Data Exchange (ETDEWEB)

    Schenter, Gregory K.; Fulton, John L.

    2017-01-20

    MD-XAFS (Molecular Dynamics X-ray Adsorption Fine Structure) makes the connection between simulation techniques that generate an ensemble of molecular configurations and the direct signal observed from X-ray measurement.

  11. Realistic interatomic potential for MD simulations

    CERN Document Server

    Eremeichenkova, Y V; Morozov, A F; Eremeichenkova, Yu.V.

    2002-01-01

    The coefficients of interatomic potential of simple form Exp-6 for neon are obtained. Repulsive part is calculated ab-initio in the Hartree-Fock approximation using the basis of atomic orbitals orthogonalized exactly on different lattice sites. Attractive part is determined empirically using single fitting parameter. The potential obtained describes well the equation of state and elastic moduli of neon crystal in wide range of interatomic distances and it is appropriate for molecular dynamic simulations of high temperature properties and phenomena in crystals and liquids.

  12. Biomolecular recognition mechanisms studied by NMR spectroscopy and MD simulations

    NARCIS (Netherlands)

    Hsu, Shang-Te Danny

    2004-01-01

    This thesis describes the use of solution Nuclear Magnetic Resonance (NMR) spectroscopy and Molecular Dynamics (MD) simulations to study the mechanism of biomolecular recognition with two model systems: i) lipid II-binding lantibiotics (lanthionine-containing antibiotics) and ii) the human immunodef

  13. MD SIMULATION OF SUBTILISIN BPN' IN A CRYSTAL ENVIRONMENT

    NARCIS (Netherlands)

    HEINER, AP; BERENDSEN, HJC; VANGUNSTEREN, WF

    1992-01-01

    In this paper we present a molecular dynamics (MD) simulation of subtilisin BPN' in a crystalline environment containing four protein molecules and solvent. Conformational and dynamic properties of the molecules are compared with each other and with respect to the X-ray structure to test the validit

  14. Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design.

    Science.gov (United States)

    Hernández-Rodríguez, Maricarmen; Rosales-Hernández, Martha C; Mendieta-Wejebe, Jessica E; Martínez-Archundia, Marlet; Basurto, José Correa

    2016-01-01

    Molecular Dynamics (MD) simulations is a computational method that employs Newton's laws to evaluate the motions of water, ions, small molecules, and macromolecules or more complex systems, for example, whole viruses, to reproduce the behavior of the biological environment, including water molecules and lipid membranes. Specifically, structural motions, such as those that are dependent of the temperature and solute/ solvent are very important to study the recognition pattern of ligandprotein or protein-protein complexes, in that sense, MD simulations are very useful because these motions can be modeled using this methodology. Furthermore, MD simulations for drug design provide insights into the structural cavities required to design novel structures with higher affinity to the target. Also, the employment of MD simulations to drug design can help to refine the three-dimensional (3D) structure of targets in order to obtain a better sampling of the binding poses and more reliable affinity values with better structural advantages, because they incorporate some biological conditions that include structural motions compared to traditional docking procedures. This work analyzes the concepts and applicability of MD simulations for drug design because molecular structural motions are considered, and these help to identify hot spots, decipher structural details in the reported protein sites, as well as to eliminate sites that could be structural artifacts which could be originated from the structural characterization conditions from MD. Moreover, better free energy values for protein ligand recognition can also be obtained, and these can be validated under experimental procedures due to the robustness of the MD simulation methods.

  15. Application of MD simulations to predict membrane properties of MOFs

    OpenAIRE

    Elda Adatoz; Seda Keskin

    2015-01-01

    Research Article Application of MD Simulations to Predict Membrane Properties of MOFs Elda Adatoz and Seda Keskin Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, 34450 Istanbul, Turkey Correspondence should be addressed to Seda Keskin; Received 22 May 2015; Accepted 13 July 2015 Academic Editor: Yanlin Song Copyright © 2015 E. Adatoz and S. Keskin. This is an open access article distributed under the Creative Commons A...

  16. StandsSIM-MD: a Management Driven forest SIMulator

    Energy Technology Data Exchange (ETDEWEB)

    Barreiro, S.; Rua, J.; Tomé, M.

    2016-07-01

    Aim of the study. The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based) for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines); whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt). Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: Forest Management Driven simulations approach. Multiple Prescriptions-Per-Stand functionality. StandsSIM-MD can be used to support landowners decisions on stand forest management. StandsSIM-MD simulations at regional level can be combined with optimization routines. (Author)

  17. StandsSIM-MD: a Management Driven forest SIMulator

    Directory of Open Access Journals (Sweden)

    Susana Barreiro

    2016-07-01

    Full Text Available Aim of the study: The existing stand level forest simulators available in Portugal were not developed with the aim of including up-to-date model versions and were limited in terms of accounting for forest management. The simulators’ platform, sIMfLOR was recently created to implement different growth models with a common philosophy. The objective was developing one easily-updatable, user-friendly, forest management and climate change sensitive simulator capable of projecting growth for the main tree species in Portugal. Area of the study: Portugal. Material and methods: The new simulator was programmed in a modular form consisting of several modules. The growth module integrates different forest growth and yield models (empirical and process-based for the main wood production tree species in Portugal (eucalypt, umbrella and maritime pines; whereas the management module drives the growth projections along the planning horizon according to a range of forest management approaches and climate (at present only available for eucalypt. Main results: The main result is the StandsSIM-MD Management Driven simulator that overcomes the limitations of the existing stand level simulators. It is a step forward when compared to the models currently available in the sIMfLOR platform covering more tree species, stand structures and stand compositions. It is focused on end-users and it is based on similar concepts regarding the generation of required inputs and generated outputs. Research highlights: -          Forest Management Driven simulations approach -          Multiple Prescriptions-Per-Stand functionality -          StandsSIM-MD can be used to support landowners decisions on stand forest management -          StandsSIM-MD simulations at regional level can be combined with optimization routines Keywords: Forest simulator, Forest Management Approaches; StandsSIM-MD; forest management.

  18. Methanol adsorption studies of electrified ACF by MD simulations

    Institute of Scientific and Technical Information of China (English)

    LIANG Shiqiang; XU Jingzhong

    2004-01-01

    In order to clarify whether static electricity can impose a control on physical adsorption of polar adsorbates, MD simulations were carried out to study the adsorption/desorption behavior of methanol in the nanopores of electrified activated carbon fiber (ACF). Some special phenomena were observed from the MD simulations for methanol adsorption in a mesopore of electrified ACF. For example it takes a shorter time for the adsorbates to reach the adsorption sites on the mesopore wall, the liquid-like methanol is highly condensed, the methanol molecules have a unique distribution of space orientation, and the total energy of equilibrium state dropped a lot. These phenomena indicate the static electricity reinforced the interaction between the polar methanol and the electrified ACF, so that the intensity, stability and regularity of adsorption were increased, and thus we predict that the adsorption capacity will be increased and the adsorption process will be accelerated. When adsorption equilibrium was reached at room temperature, eliminated the electric charges and heated the system, the desorption tendency was evidently observed from our simulations at 60℃ or so.

  19. Kinetics of CH4 and CO2 hydrate dissociation and gas bubble evolution via MD simulation.

    Science.gov (United States)

    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

  20. Electroporation of archaeal lipid membranes using MD simulations.

    Science.gov (United States)

    Polak, Andraž; Tarek, Mounir; Tomšič, Matija; Valant, Janez; Ulrih, Nataša Poklar; Jamnik, Andrej; Kramar, Peter; Miklavčič, Damijan

    2014-12-01

    Molecular dynamics (MD) simulations were used to investigate the electroporation of archaeal lipid bilayers when subjected to high transmembrane voltages induced by a charge imbalance, mimicking therefore millisecond electric pulse experiments. The structural characteristics of the bilayer, a 9:91 mol% 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) were compared to small angle X-ray scattering data. A rather good agreement of the electron density profiles at temperatures of 298 and 343 K was found assessing therefore the validity of the protocols and force fields used in simulations. Compared to dipalmitoyl-phosphatidylcholine (DPPC), the electroporation threshold for the bilayer was found to increase from ~2 V to 4.3 V at 323 K, and to 5.2 V at 298 K. Comparing the electroporation thresholds of the archaeal lipids to those of simple diphytanoyl-phosphatidylcholine (DPhPC) bilayers (2.5 V at 323 K) allowed one to trace back the stability of the membranes to the structure of their lipid head groups. Addition of DPPC in amounts of 50 mol% to the archaeal lipid bilayers decreases their stability and lowers the electroporation thresholds to 3.8 V and 4.1 V at respectively 323 and 298 K. The present study therefore shows how membrane compositions can be selected to cover a wide range of responses to electric stimuli. This provides new routes for the design of liposomes that can be efficiently used as drug delivery carriers, as the selection of their composition allows one to tune in their electroporation threshold for subsequent release of their load.

  1. QM/MM-MD simulations of conjugated polyelectrolytes

    DEFF Research Database (Denmark)

    Sjöqvist, Jonas; Linares, Mathieu; Mikkelsen, Kurt Valentin

    2014-01-01

    description of the solvent in its electronic ground state as well as the chromophore in its electronic ground and excited states, (ii) a conformational sampling by means of classical molecular dynamics (MD) in the respective electronic states, and (iii) spectral response calculations by means of the quantum...

  2. Dynamics of biopolymers on nanomaterials studied by quasielastic neutron scattering and MD simulations

    Science.gov (United States)

    Dhindsa, Gurpreet K.

    Neutron scattering has been proved to be a powerful tool to study the dynamics of biological systems under various conditions. This thesis intends to utilize neutron scattering techniques, combining with MD simulations, to develop fundamental understanding of several biologically interesting systems. Our systems include a drug delivery system containing Nanodiamonds with nucleic acid (RNA), and two specific model proteins, beta-Casein and Inorganic Pyrophosphatase (IPPase). RNA and nanodiamond (ND) both are suitable for drug-delivery applications in nano-biotechnology. The architecturally flexible RNA with catalytic functionality forms nanocomposites that can treat life-threatening diseases. The non-toxic ND has excellent mechanical and optical properties and functionalizable high surface area, and thus actively considered for biomedical applications. In this thesis, we utilized two tools, quasielastic neutron scattering (QENS) and Molecular Dynamics Simulations to probe the effect of ND on RNA dynamics. Our work provides fundamental understanding of how hydrated RNA motions are affected in the RNA-ND nanocomposites. From the experimental and Molecular Dynamics Simulation (MD), we found that hydrated RNA motion is faster on ND surface than a freestanding one. MD Simulation results showed that the failure of Stokes Einstein relation results the presence of dynamic heterogeneities in the biomacromolecules. Radial pair distribution function from MD Simulation confirmed that the hydrophilic nature of ND attracts more water than RNA results the de-confinement of RNA on ND. Therefore, RNA exhibits faster motion in the presence of ND than freestanding RNA. In the second project, we studied the dynamics of a natively disordered protein beta-Casein which lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of beta-Casein are explored by Quasielastic Neutron Scattering (QENS). We investigated the mean square displacement (MSD) of

  3. EMC/FDTD/MD simulation of carrier transport and electrodynamics in two-dimensional electron systems

    OpenAIRE

    Sule, N.; Willis, K. J.; Hagness, S. C.; Knezevic, I.

    2014-01-01

    We present the implementation and application of a multiphysics simulation technique to carrier dynamics under electromagnetic excitation in supported two-dimensional electronic systems. The technique combines ensemble Monte Carlo (EMC) for carrier transport with finite-difference time-domain (FDTD) for electrodynamics and molecular dynamics (MD) for short-range Coulomb interactions among particles. We demonstrate the use of this EMC/FDTD/MD technique by calculating the room-temperature dc an...

  4. Sustainable water recovery from oily wastewater via forward osmosis-membrane distillation (FO-MD).

    Science.gov (United States)

    Zhang, Sui; Wang, Peng; Fu, Xiuzhu; Chung, Tai-Shung

    2014-04-01

    This study proposed and investigated a hybrid forward osmosis - membrane distillation (FO-MD) system for sustainable water recovery from oily wastewater by employing lab-fabricated FO and MD hollow fiber membranes. Stable oil-in-water emulsions of different concentrations with small droplet sizes (<1 μm) were firstly prepared and applied as the feed solution in the FO process. Fouling was immediately observed in the FO mode and was low on the cellulose triacetate (CTA) - based thin film composite (TFC) membranes. Moreover, slight increment of fouling was observed in the first few hours and the water flux was then stabilized over 24 h. The characterizations of water flux and solute rejection in separate FO and MD processes revealed that a high water flux, good NaCl rejection, impressively high retention of oil droplets and partial permeation of acetic acid could be achieved. Finally, an integrated FO-MD system was developed to treat the oily wastewater containing petroleum, surfactant, NaCl and acetic acid at 60 °C in the batch mode. The water flux in FO undergoes three-stage decline due to fouling and reduction in osmotic driving force, but is quite stable in MD regardless of salt concentration. Oily wastewater with relatively high salinity could be effectively recovered by the FO-MD hybrid system while maintaining large water flux, at least 90% feed water recovery could be readily attained with only trace amounts of oil and salts, and the draw solution was re-generated for the next rounds of FO-MD run. Interestingly, significant amount of acetic acid was also retained in the permeate for further reuse as a chemical additive during the production of crude oil. The work has demonstrated that not only water but also organic additives in the wastewater could be effectively recovered by FO-MD systems for reuse or other utilizations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. QM/MM MD simulations of La(III)-phosphopeptide complexes.

    Science.gov (United States)

    Messner, Christoph B; Bonn, Günther K; Hofer, Thomas S

    2015-01-01

    Several bioanalytical enrichment techniques are based on the interactions of phosphopeptides with Ln(III) ions. In order to gain an improved understanding of these complexes and the respective ion-peptide interactions, hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations of La(III) coordinating to the phosphopeptide VPQLEIVPNSpAEER were conducted. Simulations of di- as well as monoanionic phosphate groups were carried out. The La(III) ion and its first hydration layer, including the sidechain of the phosphoserine residue were treated quantum mechanically at RI-MP2/triple zeta level, whereas the remaining part of the system was treated with classical potentials. The simulation of the dianionic phosphopeptide revealed a 9-fold coordinated La(III) ion, with the phosphopeptide binding bi- as well as monodentate. The mean residence times (τ) of the first shell water molecules were 82 ps and 37 ps for the bi- and monodentate complexes, respectively, which is much higher compared to free La(III) in aqueous solution (τ=17 ps). The simulation of the monoanionic La(III)-phosphopeptide complex revealed a bidentate coordination throughout the 80 ps sampling period. An intramolecular hydrogen bond between the hydrogen of the phosphate group and the backbone was observed and a τ value of 14 ps was obtained, which is much lower as for the dianionic complex.

  6. Application of MD Simulations to Predict Membrane Properties of MOFs

    Directory of Open Access Journals (Sweden)

    Elda Adatoz

    2015-01-01

    Full Text Available Metal organic frameworks (MOFs are a new group of nanomaterials that have been widely examined for various chemical applications. Gas separation using MOF membranes has become an increasingly important research field in the last years. Several experimental studies have shown that thin-film MOF membranes can outperform well known polymer and zeolite membranes due to their higher gas permeances and selectivities. Given the very large number of available MOF materials, it is impractical to fabricate and test the performance of every single MOF membrane using purely experimental techniques. In this study, we used molecular simulations, Monte Carlo and Molecular Dynamics, to estimate both single-gas and mixture permeances of MOF membranes. Predictions of molecular simulations were compared with the experimental gas permeance data of MOF membranes in order to validate the accuracy of our computational approach. Results show that computational methodology that we described in this work can be used to accurately estimate membrane properties of MOFs prior to extensive experimental efforts.

  7. Methanol adsorption studies of electrified ACF by MD simulations

    Institute of Scientific and Technical Information of China (English)

    2004-01-01

    [1]Wang, R. Z., Jia, J. P., Teng, Y. et al., A potential solid adsorption refrigeration pair-active carbon fiber- methanol, Acta Energ. Solar. Sinica (in Chinese), 1997, 18(2): 222-227.[2]Wang, R. Z., Wu, J. Y., Xu, Y. X. et al., Experiment on a continuous heat regenerative adsorption refrigerator using spiral plate heat exchanger as adsorbers, Applied Thermal Eng., 1998, 18(1-2): 13-23.[3]Vagner, C., Finqueneisel, G., Zimny, T. et al., Isotherms and kinetics of methanol vapor adsorption on carbon fibers and activated carbons, New Carbon Materials, 2003, 18(2): 133-136.[4]Wang, D. R., Development and application of activated carbon nanofiber, Carbon (in Chinese), 2003, 1: 35-41.[5]Su, J. C., Qiu, J. Sh., Preparation of activated carbon fiber-based composite adsorbent and its gas separation performance, Carbon Techniques (in Chinese), 2001, 3: 1-4.[6]Gasteiger, J., Marsili, M., Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges, Tetrahedron, 1980, 36: 3219-3288.[7]Cornell, W. D., Cieplak, P., Bayly, C. I. et al., A second generation force field for the simulation of peoteins, nucleic acids, and organic molecules, J. Am. Chem. Soc., 1995, 117: 5179-5197.[8]Ewald, P. P., Die Berechnung optischer und elektrostatischer gitterpotentiale, Ann. Phys., 1921, 64: 253-287.[9]Allen, M. P., Tildesley, D. J., Computer Simulation of Liquids, Oxford: Oxford University Press, 1987, 157-162.[10]Leach, A. R., Molecular Modelling: Principles and Applications, London: Addison Wesley Longman Limited, 1996, 294-298.

  8. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications.

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-07-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package.

  9. Vienna-PTM web server: a toolkit for MD simulations of protein post-translational modifications

    Science.gov (United States)

    Margreitter, Christian; Petrov, Drazen; Zagrovic, Bojan

    2013-01-01

    Post-translational modifications (PTMs) play a key role in numerous cellular processes by directly affecting structure, dynamics and interaction networks of target proteins. Despite their importance, our understanding of protein PTMs at the atomistic level is still largely incomplete. Molecular dynamics (MD) simulations, which provide high-resolution insight into biomolecular function and underlying mechanisms, are in principle ideally suited to tackle this problem. However, because of the challenges associated with the development of novel MD parameters and a general lack of suitable computational tools for incorporating PTMs in target protein structures, MD simulations of post-translationally modified proteins have historically lagged significantly behind the studies of unmodified proteins. Here, we present Vienna-PTM web server (http://vienna-ptm.univie.ac.at), a platform for automated introduction of PTMs of choice to protein 3D structures (PDB files) in a user-friendly visual environment. With 256 different enzymatic and non-enzymatic PTMs available, the server performs geometrically realistic introduction of modifications at sites of interests, as well as subsequent energy minimization. Finally, the server makes available force field parameters and input files needed to run MD simulations of modified proteins within the framework of the widely used GROMOS 54A7 and 45A3 force fields and GROMACS simulation package. PMID:23703210

  10. MD-simulations of Beta-Amyloid Protein Insertion Efficiency and Kinetics into Neuronal Membrane Mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

    2011-03-01

    Early interaction events of beta-amyloid (A β) peptides with the neuronal membranes play a key role in the pathogenesis of Alzheimer's disease. We have used all-atom MD simulations to study the protein insertion efficiency and kinetics of monomeric A β40 and A β42 into phosphatidylcholine lipid bilayers (PC) with and without 40 mole% cholesterol (CHOL) that mimic the cholesterol-enriched and depleted lipid nanodomains of the neuronal plasma membranes. Independent replicates of 200-ns simulations of each protein pre-inserted in the upper lipid layer were generated. In PC bilayers, only 25% of A β40 and 50% of A β42 in the replicates showed complete insertion into the lower lipid layer, whereas the percentages increased to 50% and 100%, respectively, in PC/CHOL bilayers, providing evidence that cholesterol improves the protein insertion efficiency into the bilayers. The rate of protein insertion was proportional to the hydrophobic, transmembrane helix length of the inserted peptide and depended on the cholesterol content. We propose that the lysine snorkeling and C-terminus anchoring of A β to the PC headgroups at the upper and lower lipid/water interfaces represent the dual-transmembrane stabilization mechanisms of A β in the neuronal membrane domains.

  11. Investigation of spreading characteristics of nano-droplet on solid substrate using MD simulations

    Science.gov (United States)

    Sedighi, Nahid

    Surface wettability and spreading of liquid droplets on solid surfaces are of significant fundamental and practical importance in various fields of science and technology, ranging from classical coating and spray systems to the modern micro and nanofluidic devices, and biotechnology. Due to the complexity of solid/liquid/vapor interfaces, there are still difficulties in accurately predicting the behavior of liquid droplets on solid surfaces. Droplet spreading on a surface represents a multi-scale phenomenon with scales ranging from continuum to molecular. In this thesis, molecular dynamics (MD) simulations have been employed to investigate wetting and spreading characteristics of a nanodroplet on solid surfaces. The work focuses on the development of correlations and scaling laws to examine the effect of droplet size on the spreading characters. The dynamic spreading of an initially spherical liquid droplet in contact with a solid surface and surrounded by ambient gas has been studied under forced and spontaneous spreading. An efficient algorithm has been developed to track the liquid-phase interface and the dynamic contact angle. The algorithm was demonstrated to reproduce the entire wetting regime by varying the solid-liquid interaction energy parameters. Extensive simulations have been performed to investigate the effects of surface and liquid droplet characteristics on the wetting phenomena and contact angle. In the first set of the simulations, liquid droplet, solid surface and ambient gas were modeled using argon atoms. The next set of simulations was performed using more realistic potential functions to simulate water SVS-B molecules for liquid, silicon crystal for solid surface, and nitrogen molecules for the ambient gas. Results for the argon droplet indicate a highly complex relationship between the contact angle and surface and liquid parameters. The spreading behavior was analyzed in terms of the temporal evolution of the dynamic contact angle and

  12. Multiscale MD Simulations of Folding Dynamics and Mobility of Beta-Amyloid Peptide on Lipid Bilayer Surfaces

    Science.gov (United States)

    van Tilburg, Scott; Cheng, Kelvin

    2013-03-01

    Early interaction events of beta-amyloid peptides with the neuronal membranes play a key role in the pathogenesis of Alzheimer's disease. We have used multiscale Molecular Dynamics (MD) simulations to study the protein folding dynamics and lateral mobility of beta-amyloid protein on the cholesterol-enriched and -depleted lipid nano-domains. Several independent simulation replicates of all-atom and coarse-grained MD simulations of beta-amyloid on different lipid bilayer nano-domains have been generated. Using Define Secondary Structure of Proteins (DSSP) algorithm and mean-square-distance (MSD) analysis, the protein conformation and the lateral diffusion coefficients of protein, as well as the lipid and water, were calculated as a function of simulation time up to 200 nanoseconds for atomistic and 2 microseconds for coarse-grained simulations per replicate in different bilayer systems. Subtle differences in the conformation and mobility of the protein were observed in lipid bilayers with and without cholesterol. The structural dynamics information obtained from this work will provide useful insights into understanding the role of protein/lipid interactions in the membrane-associated aggregation of protein on neuronal membranes. HHMI-Trinity University and NIH RC1-GM090897-02

  13. Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

    Science.gov (United States)

    Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

    2014-12-18

    The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

  14. "Structure-making" ability of Na+ in dilute aqueous solution: an ONIOM-XS MD simulation study.

    Science.gov (United States)

    Sripa, Pattrawan; Tongraar, Anan; Kerdcharoen, Teerakiat

    2013-02-28

    An ONIOM-XS MD simulation has been performed to characterize the "structure-making" ability of Na(+) in dilute aqueous solution. The region of most interest, i.e., a sphere that includes Na(+) and its surrounding water molecules, was treated at the HF level of accuracy using LANL2DZ and DZP basis sets for the ion and waters, respectively, whereas the rest of the system was described by classical pair potentials. Detailed analyzes of the ONIOM-XS MD trajectories clearly show that Na(+) is able to order the structure of waters in its surroundings, forming two prevalent Na(+)(H(2)O)(5) and Na(+)(H(2)O)(6) species. Interestingly, it is observed that these 5-fold and 6-fold coordinated complexes can convert back and forth with some degrees of flexibility, leading to frequent rearrangements of the Na(+) hydrates as well as numerous attempts of inner-shell water molecules to interchange with waters in the outer region. Such a phenomenon clearly demonstrates the weak "structure-making" ability of Na(+) in aqueous solution.

  15. Structure and Dynamics in Amphiphilic Bilayers: NMR and MD simulation Studies

    OpenAIRE

    2013-01-01

    Solid-state nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations were employed to study molecular structure and dynamics in amphiphilic bilayers. This thesis reports on method development and practical applications to two types of bilayer systems: simple cell membrane models composed of phosphatidylcholine lipids and cholesterol; and liquid crystals composed of ethyleneoxide-based surfactants often used in technological applications and in fundamental studies ...

  16. Molecular dynamics simulation of proton transport with quantum mechanically derived proton hopping rates (Q-HOP MD)

    Science.gov (United States)

    Lill, Markus A.; Helms, Volkhard

    2001-11-01

    A very efficient scheme is presented to simulate proton transport by classical molecular dynamics simulation coupled with quantum mechanically derived proton hopping. Simulated proton transfer rates and proton diffusion constants for an excess proton in a box of water molecules are in good agreement with experimental data and with previous simulations that employed empirical valence bond (EVB) theory. For the first time, the proton occupancy of an aspartic acid residue in water was computed directly by MD simulations. Locally enhanced sampling or multi copy techniques were used to facilitate proton release in simulations of an imidazole ring in a solvent box. Summarizing, a quasiclassical description of proton transfer dynamics has been able to capture important kinetic and thermodynamic features of these systems at less than 50% computational overhead compared to standard molecular dynamics simulations. The method can be easily generalized to simulate the protonation equilibria of a large number of titratable sites. This should make it an attractive method to study proton transport in large biological systems.

  17. Analytical model and MD simulation of nonlinear Richtmyer-Meshkov instability

    Science.gov (United States)

    Nishihara, Katsunobu; Abe, Motomi; Fukuda, Yuko; Zhakhovskii, Vasilii; Matsuoka, Chihiro

    2001-10-01

    We present two topics, an analytical model and moelrcular dynamic (MD) simulations of the Richtmyer-Meshokov instability (RMI). We have developled a selfconsistent analytical model that describes a nonlinear evolution of a vortex sheet in the two-dimensional RMI. The model consists of two kinematic boundary conditions, a modified Birkhoff-Rott equation and an equation for time evolution of circulation at the interface with a finite Atwood number. It is shown that the created vortcity on the interface has strong inhomogeneity, that causes locally streching and compression of the sheet. We discuss the dependence of the Atwood number on the nonlinear dynamics of the sheet. MD approache has been applied for converging shocks and RMI in a dense Lennard-Jones fluid in cylindrical geometry. MD method has fundamental advantages over hydrodymanic simulations such as no limitation of resolution in turbulent state. The appearance of Mach stems in the rippled shocks and turbulent mixing in RMI have been observed when the reflected shock passes through the unstable surface again. We discuss the mode number and Mach number dependence on the mixing.

  18. Direct MD simulation of liquid-solid phase equilibria for three-component plasma

    CERN Document Server

    Hughto, J; Schneider, A S; Medin, Zach; Cumming, Andrew; Berry, D K

    2012-01-01

    The neutron rich isotope 22Ne may be a significant impurity in carbon and oxygen white dwarfs and could impact how the stars freeze. We perform molecular dynamics simulations to determine the influence of 22Ne in carbon-oxygen-neon systems on liquid-solid phase equilibria. Both liquid and solid phases are present simultaneously in our simulation volumes. We identify liquid, solid, and interface regions in our simulations using a bond angle metric. In general we find good agreement for the composition of liquid and solid phases between our MD simulations and the semi analytic model of Medin and Cumming. The trace presence of a third component, neon, does not appear to strongly impact the chemical separation found previously for two component carbon and oxygen systems. This suggests that small amounts of 22Ne may not qualitatively change how the material in white dwarf stars freezes. However, we do find systematically lower melting temperatures (higher Gamma) in our MD simulations compared to the semi analytic ...

  19. Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein.

    Science.gov (United States)

    Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

    2015-10-23

    Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation.

  20. Constant-pH MD Simulations of an Oleic Acid Bilayer.

    Science.gov (United States)

    Vila-Viçosa, Diogo; Teixeira, Vitor H; Baptista, António M; Machuqueiro, Miguel

    2015-05-12

    Oleic acid is a simple molecule with an aliphatic chain and a carboxylic group whose ionization and, consequently, intermolecular interactions are strongly dependent on the solution pH. The titration curve of these molecules was already obtained using different experimental methods, which have shown the lipid bilayer assemblies to be stable between pH 7.0 and 9.0. In this work, we take advantage of our recent implementations of periodic boundary conditions in Poisson-Boltzmann calculations and ionic strength treatment in simulations of charged lipid bilayers, and we studied the ionization dependent behavior of an oleic acid bilayer using a new extension of the stochastic titration constant-pH MD method. With this new approach, we obtained titration curves that are in good agreement with the experimental data. Also, we were able to estimate the slope of the titration curve from charge fluctuations, which is an important test of thermodynamic consistency for the sampling in a constant-pH MD method. The simulations were performed for ionizations up to 50%, because an experimentally observed macroscopic transition to micelles occurs above this value. As previously seen for a binary mixture of a zwitterionic and an anionic lipid, we were able to reproduce experimental results with simulation boxes usually far from neutrality. This observation further supports the idea that a charged membrane strongly influences the ion distribution in its vicinity and that neutrality is achieved significantly far from the bilayer surface. The good results obtained with this extension of the stochastic titration constant-pH MD method strongly supports its usefulness to sample the coupling between configuration and protonation in these types of biophysical systems. This method stands now as a powerful tool to study more realistic lipid bilayers where pH can influence both the lipids and the solutes interacting with them.

  1. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation.

    Science.gov (United States)

    Hou, Yue; Wang, Linbing; Wang, Dawei; Guo, Meng; Liu, Pengfei; Yu, Jianxin

    2017-02-21

    Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM) experiments, Phase Dynamics Theory and Molecular Dynamics (MD) Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

  2. Characterization of Bitumen Micro-Mechanical Behaviors Using AFM, Phase Dynamics Theory and MD Simulation

    Directory of Open Access Journals (Sweden)

    Yue Hou

    2017-02-01

    Full Text Available Fundamental understanding of micro-mechanical behaviors in bitumen, including phase separation, micro-friction, micro-abrasion, etc., can help the pavement engineers better understand the bitumen mechanical performances at macroscale. Recent researches show that the microstructure evolution in bitumen will directly affect its surface structure and micro-mechanical performance. In this study, the bitumen microstructure and micro-mechanical behaviors are studied using Atomic Force Microscopy (AFM experiments, Phase Dynamics Theory and Molecular Dynamics (MD Simulation. The AFM experiment results show that different phase-structure will occur at the surface of the bitumen samples under certain thermodynamic conditions at microscale. The phenomenon can be explained using the phase dynamics theory, where the effects of stability parameter and temperature on bitumen microstructure and micro-mechanical behavior are studied combined with MD Simulation. Simulation results show that the saturates phase, in contrast to the naphthene aromatics phase, plays a major role in bitumen micro-mechanical behavior. A high stress zone occurs at the interface between the saturates phase and the naphthene aromatics phase, which may form discontinuities that further affect the bitumen frictional performance.

  3. AstroMD. A multi-dimensional data analysis tool for astrophysical simulations

    CERN Document Server

    Becciani, U; Gheller, C; Calori, L; Buonomo, F; Imboden, S

    2000-01-01

    Over the past few years, the role of visualization for scientific purpose has grown up enormously. Astronomy makes an extended use of visualization techniques to analyze data, and scientific visualization has became a fundamental part of modern researches in Astronomy. With the evolution of high performance computers, numerical simulations have assumed a great role in the scientific investigation, allowing the user to run simulation with higher and higher resolution. Data produced in these simulations are often multi-dimensional arrays with several physical quantities. These data are very hard to manage and to analyze efficiently. Consequently the data analysis and visualization tools must follow the new requirements of the research. AstroMD is a tool for data analysis and visualization of astrophysical data and can manage different physical quantities and multi-dimensional data sets. The tool uses virtual reality techniques by which the user has the impression of travelling through a computer-based multi-dim...

  4. Mimicking titration experiments with MD simulations: A protocol for the investigation of pH-dependent effects on proteins

    Science.gov (United States)

    Socher, Eileen; Sticht, Heinrich

    2016-03-01

    Protein structure and function are highly dependent on the environmental pH. However, the temporal or spatial resolution of experimental approaches hampers direct observation of pH-induced conformational changes at the atomic level. Molecular dynamics (MD) simulation strategies (e.g. constant pH MD) have been developed to bridge this gap. However, one frequent problem is the sampling of unrealistic conformations, which may also lead to poor pKa predictions. To address this problem, we have developed and benchmarked the pH-titration MD (pHtMD) approach, which is inspired by wet-lab titration experiments. We give several examples how the pHtMD protocol can be applied for pKa calculation including peptide systems, Staphylococcus nuclease (SNase), and the chaperone HdeA. For HdeA, pHtMD is also capable of monitoring pH-dependent dimer dissociation in accordance with experiments. We conclude that pHtMD represents a versatile tool for pKa value calculation and simulation of pH-dependent effects in proteins.

  5. Hybrid Pressure Retarded Osmosis−Membrane Distillation (PRO−MD) Process for Osmotic Power and Clean Water Generation

    KAUST Repository

    Han, Gang

    2015-05-20

    A novel pressure retarded osmosis−membrane distillation (PRO−MD) hybrid process has been experimentally conceived for sustainable production of renewable osmotic power and clean water from various waters. The proposed PRO−MD system may possess unique advantages of high water recovery rate, huge osmotic power generation, well controlled membrane fouling, and minimal environmental impacts. Experimental results show that the PRO−MD hybrid process is promising that not only can harvest osmotic energy from freshwater but also from wastewater. When employing a 2 M NaCl MD concentrate as the draw solution, ultrahigh power densities of 31.0 W/m2 and 9.3 W/m2 have been demonstrated by the PRO subsystem using deionized water and real wastewater brine as the feeds, respectively. Simultaneously, high purity potable water with a flux of 32.5−63.1 L/(m2.h) can be produced by the MD subsystem at 40−60 °C without any detrimental effects of fouling. The energy consumption in the MD subsystem might be further reduced by applying a heat exchanger in the hybrid system and using low-grade heat or solar energy to heat up the feed solution. The newly developed PRO−MD hybrid process would provide insightful guidelines for the exploration of alternative green technologies for renewable osmotic energy and clean water production.

  6. Direct MD simulation of liquid-solid phase equilibria for two-component plasmas

    CERN Document Server

    Schneider, A S; Horowitz, C J; Berry, D K

    2011-01-01

    We determine the liquid-solid phase diagram for carbon-oxygen plasma mixtures using two-phase MD simulations. We identified liquid, solid, and interface regions using a bond angle metric. To study finite size effects, we perform 55296 ion simulations and compare to earlier 27648 ion results. To help monitor non-equilibrium effects, we calculate diffusion constants $D_i$. We find that $D_O$ for oxygen ions in the solid is much smaller than $D_C$ for carbon ions and that both diffusion constants are 80 or more times smaller than diffusion constants in the liquid phase. There is excellent agreement between our phase diagram and that predicted by Medin and Cumming. This suggests that errors from finite size and non-equilibrium effects are small and that the carbon-oxygen phase diagram is now accurately known.

  7. Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

    Science.gov (United States)

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2012-07-15

    The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems.

  8. A study of QM/Langevin-MD simulation for oxygen-evolving center of photosystem II

    Energy Technology Data Exchange (ETDEWEB)

    Uchida, Waka; Kimura, Yoshiro; Wakabayashi, Masamitsu [Department of Biomolecular Engineering, Tokyo Institute of Technology, Nagatsuta, Midori-ku, Yokohama 226-8503 (Japan); Hatakeyama, Makoto; Ogata, Koji; Nakamura, Shinichiro [RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan); Yokojima, Satoshi [Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan and RIKEN Research Cluster for Innovation, Nakamura Laboratory, 2-1 Hirosawa, Wako, Saitama 351-0198 (Japan)

    2013-12-10

    We have performed three QM/Langevin-MD simulations for oxygen-evolving complex (OEC) and surrounding residues, which are different configurations of the oxidation numbers on Mn atoms in the Mn{sub 4}O{sub 5}Ca cluster. By analyzing these trajectories, we have observed sensitivity of the change to the configuration of Mn oxidation state on O atoms of carboxyl on three amino acids, Glu354, Ala344, and Glu333. The distances from Mn to O atoms in residues contacting with the Mn{sub 4}O{sub 5}Ca cluster were analyzed for the three trajectories. We found the good correlation of the distances among the simulations. However, the distances with Glu354, Ala344, and Glu333 have not shown the correlation. These residues can be sensitive index of the changes of Mn oxidation numbers.

  9. Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone.

    Science.gov (United States)

    Küçük, Sami Emre; Biktagirov, Timur; Sezer, Deniz

    2015-10-14

    A computational analysis of the Overhauser effect is reported for the proton, methyl carbon, and carbonyl carbon nuclei of liquid acetone doped with the nitroxide radical TEMPOL. A practical methodology for calculating the dynamic nuclear polarization (DNP) coupling factors by accounting for both dipole-dipole and Fermi-contact interactions is presented. The contribution to the dipolar spectral density function of nuclear spins that are not too far from TEMPOL is computed through classical molecular dynamics (MD) simulations, whereas the contribution of distant spins is included analytically. Fermi contacts are obtained by subjecting a few molecules from every MD snapshot to ab initio quantum mechanical calculations. Scalar interaction is found to be an essential part of the (13)C Overhauser DNP. While mostly detrimental to the carbonyl carbon of acetone it is predicted to result in large enhancements of the methyl carbon signal at magnetic fields of 9 T and beyond. In contrast, scalar coupling is shown to be negligible for the protons of acetone. The additional influence of proton polarization on the carbon DNP (three-spin effect) is also analyzed computationally. Its effect, however, is concluded to be practically insignificant for liquid acetone.

  10. Collision-induced light scattering spectra of krypton layer confined between graphite slabs - MD simulation

    Science.gov (United States)

    Dawid, A.; Wojcieszyk, D.; Gburski, Z.

    2016-12-01

    We have used the molecular dynamics (MD) simulation method to obtain the collision-induced light scattering spectra of the thin krypton layer confined between two parallel graphite slabs. The simulations have been made under constant density, pressure and temperature condition. We have investigated four thin krypton layers of the thickness ranging from 13 to 24 Å. The 2-, 3- and 4-body correlation functions of collision-induced polarizability anisotropy were calculated. The spectra of colliding krypton atoms were simulated as cosine Fourier transform of the total polarizability anisotropy correlation function. The calculated correlation functions and their spectra show substantial dependence on the distance between graphite slabs. The collision-induced light scattering spectrum of krypton bulk sample was also simulated and compared with the krypton layer between graphite walls. The striking differences between these two systems are observed. We have further extended our analysis of krypton movement between graphite slabs by calculating the mean square displacement functions and diffusion coefficients. The decrease of the diffusion of krypton atoms with the increasing distance between graphite walls has been found. The structure of krypton layer has been also investigated by calculating the density profile and pressure tension across the rift. The distance between graphite slabs, for which the highest mobility of krypton's atoms occurred, has been found.

  11. Equilibrium Molecular Dynamics (MD Simulation Study of Thermal Conductivity of Graphene Nanoribbon: A Comparative Study on MD Potentials

    Directory of Open Access Journals (Sweden)

    Asir Intisar Khan

    2015-12-01

    Full Text Available The thermal conductivity of graphene nanoribbons (GNRs has been investigated using equilibrium molecular dynamics (EMD simulation based on Green-Kubo (GK method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order (REBO. Our comparative study includes the estimation of thermal conductivity as a function of temperature, length and width of GNR for both the potentials. The thermal conductivity of graphene nanoribbon decreases with the increase of temperature. Quantum correction has been introduced for thermal conductivity as a function of temperature to include quantum effect below Debye temperature. Our results show that for temperatures up to Debye temperature, thermal conductivity increases, attains its peak and then falls off monotonically. Thermal conductivity is found to decrease with the increasing length for optimized Tersoff potential. However, thermal conductivity has been reported to increase with length using 2nd generation REBO potential for the GNRs of same size. Thermal conductivity, for the specified range of width, demonstrates an increasing trend with the increase of width for both the concerned potentials. In comparison with 2nd generation REBO potential, optimized Tersoff potential demonstrates a better modeling of thermal conductivity as well as provides a more appropriate description of phonon thermal transport in graphene nanoribbon. Such comparative study would provide a good insight for the optimization of the thermal conductivity of graphene nanoribbons under diverse conditions.

  12. A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

    Science.gov (United States)

    Oganesyan, Vasily S.; Chami, Fatima; White, Gaye F.; Thomson, Andrew J.

    2017-01-01

    EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions.

  13. Particle Size Effect on Wetting Kinetics of a Nanosuspension Drop: MD Simulations

    Science.gov (United States)

    Shi, Baiou; Webb, Edmund

    The behavior of nano-fluids, or fluid suspensions containing nanoparticles, has garnered tremendous attention recently for applications in advanced manufacturing. In our previous results from MD simulations, for a wetting system with different advancing contact angles, cases where self-pinning was observed were compared to cases where it was not and relevant forces on particles at the contact line were computed. To advance this work, the roles of particle size and particle loading are examined. Results presented illustrate how particle size affects spreading kinetics and how this connects to dynamic droplet morphology and relevant forces that exist nearby the contact line region. Furthermore, increased particle size in simulations permits a more detailed investigation of particle/substrate interfacial contributions to behavior observed at the advancing contact line. Based on changes in spreading kinetics with particle size, forces between the particle and liquid front are predicted and compared to those computed from simulations. At high loading, particle/particle interactions become relevant and forces computed between particles entrained to an advancing contact line will be presented.

  14. Water Quality Analysis Simulation

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Water Quality analysis simulation Program, an enhancement of the original WASP. This model helps users interpret and predict water quality responses to natural...

  15. Water Quality Analysis Simulation

    Science.gov (United States)

    The Water Quality analysis simulation Program, an enhancement of the original WASP. This model helps users interpret and predict water quality responses to natural phenomena and man-made pollution for variious pollution management decisions.

  16. Estimation of Hydrogen-Exchange Protection Factors from MD Simulation Based on Amide Hydrogen Bonding Analysis

    Science.gov (United States)

    Park, In-Hee; Venable, John D.; Steckler, Caitlin; Cellitti, Susan E.; Lesley, Scott A.; Spraggon, Glen; Brock, Ansgar

    2015-01-01

    Hydrogen exchange (HX) studies have provided critical insight into our understanding of protein folding, structure and dynamics. More recently, Hydrogen Exchange Mass Spectrometry (HX-MS) has become a widely applicable tool for HX studies. The interpretation of the wealth of data generated by HX-MS experiments as well as other HX methods would greatly benefit from the availability of exchange predictions derived from structures or models for comparison with experiment. Most reported computational HX modeling studies have employed solvent-accessible-surface-area based metrics in attempts to interpret HX data on the basis of structures or models. In this study, a computational HX-MS prediction method based on classification of the amide hydrogen bonding modes mimicking the local unfolding model is demonstrated. Analysis of the NH bonding configurations from Molecular Dynamics (MD) simulation snapshots is used to determine partitioning over bonded and non-bonded NH states and is directly mapped into a protection factor (PF) using a logistics growth function. Predicted PFs are then used for calculating deuteration values of peptides and compared with experimental data. Hydrogen exchange MS data for Fatty acid synthase thioesterase (FAS-TE) collected for a range of pHs and temperatures was used for detailed evaluation of the approach. High correlation between prediction and experiment for observable fragment peptides is observed in the FAS-TE and additional benchmarking systems that included various apo/holo proteins for which literature data were available. In addition, it is shown that HX modeling can improve experimental resolution through decomposition of in-exchange curves into rate classes, which correlate with prediction from MD. Successful rate class decompositions provide further evidence that the presented approach captures the underlying physical processes correctly at the single residue level. This assessment is further strengthened in a comparison of

  17. MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery

    Directory of Open Access Journals (Sweden)

    Rongzhong Li

    2015-07-01

    Full Text Available While tRNA and aminoacyl-tRNA synthetases are classes of biomolecules that have been extensively studied for decades, the finer details of how they carry out their fundamental biological functions in protein synthesis remain a challenge. Recent molecular dynamics (MD simulations are verifying experimental observations and providing new insight that cannot be addressed from experiments alone. Throughout the review, we briefly discuss important historical events to provide a context for how far the field has progressed over the past few decades. We then review the background of tRNA molecules, aminoacyl-tRNA synthetases, and current state of the art MD simulation techniques for those who may be unfamiliar with any of those fields. Recent MD simulations of tRNA dynamics and folding and of aminoacyl-tRNA synthetase dynamics and mechanistic characterizations are discussed. We highlight the recent successes and discuss how important questions can be addressed using current MD simulations techniques. We also outline several natural next steps for computational studies of AARS:tRNA complexes.

  18. Atomic level insights into realistic molecular models of dendrimer-drug complexes through MD simulations

    Science.gov (United States)

    Jain, Vaibhav; Maiti, Prabal K.; Bharatam, Prasad V.

    2016-09-01

    Computational studies performed on dendrimer-drug complexes usually consider 1:1 stoichiometry, which is far from reality, since in experiments more number of drug molecules get encapsulated inside a dendrimer. In the present study, molecular dynamic (MD) simulations were implemented to characterize the more realistic molecular models of dendrimer-drug complexes (1:n stoichiometry) in order to understand the effect of high drug loading on the structural properties and also to unveil the atomistic level details. For this purpose, possible inclusion complexes of model drug Nateglinide (Ntg) (antidiabetic, belongs to Biopharmaceutics Classification System class II) with amine- and acetyl-terminated G4 poly(amidoamine) (G4 PAMAM(NH2) and G4 PAMAM(Ac)) dendrimers at neutral and low pH conditions are explored in this work. MD simulation analysis on dendrimer-drug complexes revealed that the drug encapsulation efficiency of G4 PAMAM(NH2) and G4 PAMAM(Ac) dendrimers at neutral pH was 6 and 5, respectively, while at low pH it was 12 and 13, respectively. Center-of-mass distance analysis showed that most of the drug molecules are located in the interior hydrophobic pockets of G4 PAMAM(NH2) at both the pH; while in the case of G4 PAMAM(Ac), most of them are distributed near to the surface at neutral pH and in the interior hydrophobic pockets at low pH. Structural properties such as radius of gyration, shape, radial density distribution, and solvent accessible surface area of dendrimer-drug complexes were also assessed and compared with that of the drug unloaded dendrimers. Further, binding energy calculations using molecular mechanics Poisson-Boltzmann surface area approach revealed that the location of drug molecules in the dendrimer is not the decisive factor for the higher and lower binding affinity of the complex, but the charged state of dendrimer and drug, intermolecular interactions, pH-induced conformational changes, and surface groups of dendrimer do play an

  19. Atomistic MD simulations reveal the protective role of cholesterol in dimeric beta-amyloid induced disruptions in neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Cheng, Sara; Chou, George; Vaughn, Mark; Cheng, K.

    2011-10-01

    Interactions of oligomeric beta-amyloid peptides with neuronal membranes have been linked to the pathogenesis of Alzheimer's disease (AD). The molecular details of the interactions of different lipid components, particularly cholesterol (CHOL), of the membranes with the peptides are not clear. Using an atomistic MD simulations approach, the water permeability barrier, structural geometry and order parameters of binary phosphatidylcholine (PC) and PC/CHOL lipid bilayers were examined from various 200 ns-simulation replicates. Our results suggest that the longer length dimer (2 x 42 residues) perturbs the membrane more than the shorter one (2 x 40 residues). In addition, we discovered a significant protective role of cholesterol in protein-induced disruptions of the membranes. The use of a new Monte-Carlo method in characterizing the structures of the conformal annular lipids in close proximity with the proteins will be introduced. We propose that the neurotoxicity of beta-amyloid peptide may be associated with the nanodomain or raft-like structures of the neuronal membranes in-vivo in the development of AD.

  20. Influence of mold and substrate material combinations on nanoimprint lithography process: MD simulation approach

    Science.gov (United States)

    Yang, Seunghwa; Yu, Suyoung; Cho, Maenghyo

    2014-05-01

    A molecular dynamics (MD) study was performed to examine the effect of mold-substrate material composition on the pattern transferring and defects of the resist polymer in a thermal Nano Imprint Lithography (NIL) process. As candidate materials, single crystalline nickel (Ni), silicon (Si) and silica (SiO2, α-quartz) for the rigid mold substrate, and amorphous poly-(methylmethacrylate) (PMMA) thin film for the resist were considered for common applications in NIL processes. Three different material compositions of Si mold-Ni substrate, Ni mold-Si substrate, and quartz mold-Ni substrate were considered. In accordance with a real NIL process, a sequence of indentation-relaxation-release processes was quasi-statically simulated using isothermal ensemble simulation on tri-layer molecular structures consisting of a mold, resist, and substrate. To correlate the deformed shape and delamination of PMMA resist from the substrate in indentation and release processes, non-bond interaction energy between a rigid mold and resist was calculated for each combination of mold and substrate materials. The Si mold-Ni substrate combination shows successful pattern transfer to the resist polymer even without an anti-sticking layer as a result of the desirable balance of surface free energy for mold and substrate materials. However, Ni mold-Si substrate combination shows a critical delamination of the resist in the release process due to strong van der Waals adhesion between the resist and Ni mold. Similarly, the quartz mold-Ni substrate combination shows the same delamination in pattern transfer, but the adhesion of the resist to the quartz mold is attributed to electrostatic interaction. In order to provide guidelines for material selection in imprint-like processes where surface adsorption and wetting characteristics are critical design parameters, a simple PMMA-rigid plate model is proposed, with which consistent surface interaction characteristics in the full model NIL process

  1. PUPIL: A Software Integration System for Multi-Scale QM/MM-MD Simulations and Its Application to Biomolecular Systems.

    Science.gov (United States)

    Torras, Juan; Roberts, Benjamin P; Seabra, Gustavo M; Trickey, Samuel B

    2015-01-01

    PUPIL (Program for User Package Interfacing and Linking) implements a distinctive multi-scale approach to hybrid quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations. Originally developed to interface different external programs for multi-scale simulation with applications in the materials sciences, PUPIL is finding increasing use in the study of complex biological systems. Advanced MD techniques from the external packages can be applied readily to a hybrid QM/MM treatment in which the forces and energy for the QM region can be computed by any of the QM methods available in any of the other external packages. Here, we give a survey of PUPIL design philosophy, main features, and key implementation decisions, with an orientation to biomolecular simulation. We discuss recently implemented features which enable highly realistic simulations of complex biological systems which have more than one active site that must be treated concurrently. Examples are given.

  2. Distribution of Drug Molecules in Lipid Membranes: Neutron Diffraction and MD Simulations.

    Science.gov (United States)

    Boggara, Mohan; Mihailescu, Ella; Krishnamoorti, Ramanan

    2009-03-01

    Non-steroidal anti-inflammatory drugs (NSAIDs) e.g. Aspirin and Ibuprofen, with chronic usage cause gastro intestinal (GI) toxicity. It has been shown experimentally that NSAIDs pre-associated with phospholipids reduce the GI toxicity and also increase the therapeutic activity of these drugs compared to the unmodified ones. In this study, using neutron diffraction, the DOPC lipid bilayer structure (with and without drug) as well as the distribution of a model NSAID (Ibuprofen) as a function of its position along the membrane normal was obtained at sub-nanometer resolution. It was found that the bilayer thickness reduces as the drug is added. Further, the results are successfully compared with atomistic Molecular Dynamics simulations. Based on this successful comparison and motivated by atomic details from MD, quasi-molecular modeling of the lipid membrane is being carried out and will be presented. The above study is expected to provide an effective methodology to design drug delivery nanoparticles based on a variety of soft condensed matter such as lipids or polymers.

  3. Kinetic Cooperativity, Loop Dynamics, and Allostery from NMR and MD simulations

    Science.gov (United States)

    Bruschweiler, Rafael

    The hallmark of glucokinase (GCK), which catalyzes the phosphorylation of glucose during glycolysis, is its kinetic cooperativity whose understanding at atomic detail has remained open since its discovery over 40 years ago. I will discuss how the origin of kinetic cooperativity is rooted in intramolecular protein dynamics using NMR relaxation data of 17 isoleucines distributed over all parts of GCK. Residues of glucose-free GCK located in the small domain display a distinct exchange behavior involving multiple conformers that are substantially populated, whereas in the glucose-bound form these dynamic processes are quenched. The conformational exchange process directly competes with the enzymatic turnover at physiological glucose concentrations, thereby generating the sigmoidal rate dependence that defines kinetic cooperativity. The flexible nature of protein loops and the timescales of their dynamics are critical for many biologically important events at the molecular level, such as protein interaction and recognition processes. Based on a library of proteins, rules about loop dynamics in terms of amplitude and timescales can be derived using molecular dynamics (MD) simulations and NMR data. These rules have been implemented in the new web server ToeLoop (for Timescales Of Every Loop) that permits the prediction of loop dynamics based on an average 3D protein structure (http://spin.ccic.ohio-state.edu/index.php/loop/index).

  4. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. I. Sensitivity to physical parameters of the pore.

    Science.gov (United States)

    Rizzi, F; Jones, R E; Debusschere, B J; Knio, O M

    2013-05-21

    In this article, uncertainty quantification is applied to molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. We consider a silica pore model connecting two reservoirs containing a solution of sodium (Na(+)) and chloride (Cl(-)) ions in water. An ad hoc concentration control algorithm is developed to simulate a concentration driven counter flow of ions through the pore, with the ionic flux being the main observable extracted from the MD system. We explore the sensitivity of the system to two physical parameters of the pore, namely, the pore diameter and the gating charge. First we conduct a quantitative analysis of the impact of the pore diameter on the ionic flux, and interpret the results in terms of the interplay between size effects and ion mobility. Second, we analyze the effect of gating charge by treating the charge density over the pore surface as an uncertain parameter in a forward propagation study. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of intrinsic noise and quantify the impact of parametric uncertainty on the MD predictions. We highlight the challenges arising from the heterogeneous nature of the system, given the several components involved, and from the substantial effect of the intrinsic thermal noise.

  5. Multiscale simulation of water flow past a C540 fullerene

    Science.gov (United States)

    Walther, Jens H.; Praprotnik, Matej; Kotsalis, Evangelos M.; Koumoutsakos, Petros

    2012-04-01

    We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice-Boltzmann (LB) description for the Navier-Stokes equations. The proposed method links the MD and LB domains using a fully three-dimensional interface and coupling of velocity gradients. The present overlapping domain method implicitly preserves the flux of mass and momentum and bridges flux-based and Schwarz domain decomposition algorithms. We use this method to determine the slip length and hydrodynamic radius for water flow past a buckyball.

  6. Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations

    Directory of Open Access Journals (Sweden)

    Qin Haina

    2012-01-01

    Full Text Available Abstract Background The role of dynamics in protein functions including signal transduction is just starting to be deciphered. Eph receptors with 16 members divided into A- and B- subclasses are respectively activated by 9 A- and B-ephrin ligands. EphA4 is the only receptor capable of binding to all 9 ephrins and small molecules with overlapped interfaces. Results We first determined the structures of the EphA4 ligand binding domain (LBD in two crystals of P1 space group. Noticeably, 8 EphA4 molecules were found in one asymmetric unit and consequently from two crystals we obtained 16 structures, which show significant conformational variations over the functionally critical A-C, D-E, G-H and J-K loops. The 16 new structures, together with previous 9 ones, can be categorized into two groups: closed and open forms which resemble the uncomplexed and complexed structures of the EphA4 LBD respectively. To assess whether the conformational diversity over the loops primarily results from the intrinsic dynamics, we initiated 30-ns molecular dynamics (MD simulations for both closed and open forms. The results indicate that the loops do have much higher intrinsic dynamics, which is further unravelled by NMR H/D exchange experiments. During simulations, the open form has the RMS deviations slightly larger than those of the closed one, suggesting the open form may be less stable in the absence of external contacts. Furthermore, no obvious exchange between two forms is observed within 30 ns, implying that they are dynamically separated. Conclusions Our study provides the first experimental and computational result revealing that the intrinsic dynamics are most likely underlying the conformational diversity observed for the EphA4 LBD loops mediating the binding affinity and specificity. Interestingly, the open conformation of the EphA4 LBD is slightly unstable in the absence of it natural ligand ephrins, implying that the conformational transition from the

  7. Uncertainty quantification in MD simulations of concentration driven ionic flow through a silica nanopore. II. Uncertain potential parameters.

    Science.gov (United States)

    Rizzi, F; Jones, R E; Debusschere, B J; Knio, O M

    2013-05-21

    This article extends the uncertainty quantification analysis introduced in Paper I for molecular dynamics (MD) simulations of concentration driven ionic flow through a silica nanopore. Attention is now focused on characterizing, for a fixed pore diameter of D = 21 Å, the sensitivity of the system to the Lennard-Jones energy parameters, ɛ(Na(+)) and ɛ(Cl(-)), defining the depth of the potential well for the two ions Na(+) and Cl(-), respectively. A forward propagation analysis is applied to map the uncertainty in these parameters to the MD predictions of the ionic fluxes. Polynomial chaos expansions and Bayesian inference are exploited to isolate the effect of the intrinsic noise, stemming from thermal fluctuations of the atoms, and properly quantify the impact of parametric uncertainty on the target MD predictions. A Bayes factor analysis is then used to determine the most suitable regression model to represent the MD noisy data. The study shows that the response surface of the Na(+) conductance can be effectively inferred despite the substantial noise level, whereas the noise partially hides the underlying trend in the Cl(-) conductance data over the studied range. Finally, the dependence of the conductances on the uncertain potential parameters is analyzed in terms of correlations with key bulk transport coefficients, namely, viscosity and collective diffusivities, computed using Green-Kubo time correlations.

  8. Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations.

    Science.gov (United States)

    Oliveira, A Sofia F; Campos, Sara R R; Baptista, António M; Soares, Cláudio M

    2016-06-01

    Cytochrome c oxidases (CcOs) are the terminal enzymes of the respiratory chain in mitochondria and most bacteria. These enzymes reduce dioxygen (O(2)) to water and, simultaneously, generate a transmembrane electrochemical proton gradient. Despite their importance in the aerobic metabolism and the large amount of structural and biochemical data available for the A1-type CcO family, there is still no consensually accepted description of the molecular mechanisms operating in this protein. A substantial number of questions about the CcO's working mechanism remain to be answered, including how the protonation behavior of some key residues is modulated during a reduction cycle and how is the conformation of the protein affected by protonation. The main objective of this work was to study the protonation-conformation coupling in CcOs and identify the molecular factors that control the protonation state of some key residues. In order to directly capture the interplay between protonation and conformational effects, we have performed constant-pH MD simulations of an A1-type CcO inserted into a lipid bilayer in two redox states (oxidized and reduced) at physiological pH. From the simulations, we were able to identify several groups with unusual titration behavior that are highly dependent on the protein redox state, including the A-propionate from heme a and the D-propionate from heme a3, two key groups possibly involved in proton pumping. The protonation state of these two groups is heavily influenced by subtle conformational changes in the protein (notably of R481(I) and R482(I)) and by small changes in the hydrogen bond network.

  9. Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations.

    Science.gov (United States)

    Raczyński, Przemysław; Raczyńska, Violetta; Górny, Krzysztof; Gburski, Zygmunt

    2015-08-15

    Computer simulation technique was used to study the dynamics of cholesterol and POPC phospholipid molecules forming a thin layer on the surface of the carbon and silicon-carbide nanotubes. Each nanotube was surrounded by an ultra-thin film formed by n lipid molecules, where n varies from 15 to 50. All studies were done for five temperatures, including physiological one (T=260, 285, 310, 335 and 360K). The influence of a nanotube on the dynamics of cholesterol or phospholipid molecules in a layer is presented and discussed. The water is ubiquitous in all biological milieus, where the cholesterol or lipids occur. Thus, simulations were performed in a water environment. Moreover, to show different behavior of lipids in systems with water the results were compared with the samples without it. The dynamical and structural observables, such as the mean square displacement, diffusion coefficient, radial distribution function, and activation energy were calculated to qualitatively investigate the behavior of cholesterol and phospholipid molecules in the layers. We observed remarkable differences between the cholesterol dynamics depending whether the ultrathin film surrounds carbon or silicon-carbide nanotube and whether the water environment appeared. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Water Energy Simulation Toolset

    Energy Technology Data Exchange (ETDEWEB)

    2017-05-17

    The Water-Energy Simulation Toolset (WEST) is an interactive simulation model that helps visualize impacts of different stakeholders on water quantity and quality of a watershed. The case study is applied for the Snake River Basin with the fictional name Cutthroat River Basin. There are four groups of stakeholders of interest: hydropower, agriculture, flood control, and environmental protection. Currently, the quality component depicts nitrogen-nitrate contaminant. Users can easily interact with the model by changing certain inputs (climate change, fertilizer inputs, etc.) to observe the change over the entire system. Users can also change certain parameters to test their management policy.

  11. Solvation structure and dynamics of Na+ in liquid ammonia studied by ONIOM-XS MD simulations

    Science.gov (United States)

    Sripradite, Jarukorn; Tongraar, Anan; Kerdcharoen, Teerakiat

    2015-12-01

    The molecular dynamics (MD) technique based on the ONIOM-XS method, known as the ONIOM-XS MD, has been applied to investigate the solvation structure and dynamics of Na+ in liquid ammonia. Regarding the ONIOM-XS MD results, it is observed that Na+ is able to order the surrounding ammonia molecules to form its specific first and second solvation shells with the average coordination numbers of 5.1 and 11.2, respectively. The first solvation shell of Na+ is rather well-defined, forming a preferred 5-fold coordinated complex with a distorted square pyramidal geometry. In this respect, the most preferential Na+(NH3)5 species could convert back and forth to the lower probability Na+(NH3)6 and Na+(NH3)4 configurations. The second solvation shell of Na+ is detectable, in which a number of ammonia molecules, ranging from 7 to 14, are involved in this layer and they are arranged according to recognizable influence of the ion.

  12. Insights into proton translocation in cbb3 oxidase from MD simulations.

    Science.gov (United States)

    Carvalheda, Catarina A; Pisliakov, Andrei V

    2017-05-01

    Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb3) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations. At the moment, the functioning mechanism of C-type oxidases, in particular the proton transfer/pumping mechanism presumably via a single proton channel, is still poorly understood. In this work we used all-atom molecular dynamics simulations and continuum electrostatics calculations to obtain atomic-level insights into the hydration and dynamics of a cbb3 oxidase. We provide the details of the water dynamics and proton transfer pathways for both the "chemical" and "pumped" protons, and show that formation of protonic connections is strongly affected by the protonation state of key residues, namely H243, E323 and H337. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Roles of Ⅴ/Ⅲ ratio and mixture degree in GaN growth: CFD and MD simulation study

    Institute of Scientific and Technical Information of China (English)

    Zhou An; Xiu Xiang-Qian; Zhang Rong; Xie Zi-Li; Hua Xue-Mei; Liu Bin; Han Ping

    2013-01-01

    To understand the mechanism of Gallium nitride (GaN) film growth is of great importance for their potential applications.In this paper,we investigate the growth behavior of the GaN film by combining computational fluid dynamics (CFD) and molecular dynamics (MD) simulations.Both of the simulations show that Ⅴ/Ⅲ mixture degree can have important impacts on the deposition behavior,and it is found that the more uniform the mixture is,the better the growth is.Besides,by using MD simulations,we illustrate the whole process of the GaN growth.Furthermore,we also find that the Ⅴ/Ⅲ ratio can affect the final roughness of the GaN film.When the Ⅴ/Ⅲ ratio is high,the surface of final GaN film is smooth.The present study provides insights into GaN growth from the macroscopic and microscopic views,which may provide some suggestions on better experimental GaN preparation.

  14. Structure determination of a flexible cyclic peptide based on NMR and MD simulation 3J-coupling.

    Science.gov (United States)

    Gattin, Zrinka; Zaugg, Judith; van Gunsteren, Wilfred F

    2010-03-15

    Molecular dynamics (MD) simulations, in which experimental values such as nuclear Overhauser effects (NOEs), dipolar couplings, (3)J-coupling constants or crystallographic structure factors are used to bias the values of specific molecular properties towards experimental ones, are often carried out to study the structure refinement of peptides and proteins. However, (3)J-coupling constants are usually not employed because of the multiplicity of torsional angle values (phi) corresponding to each (3)J-coupling constant value. Here, we apply the method of adaptively enforced restraining using a local-elevation (LE) biasing potential energy function in which a memory function penalizes conformations in case both the average and the current (3)J-values deviate from the experimental target value. Then, the molecule is forced to sample other parts of the conformational space, thereby being able to cross high energy barriers and to bring the simulated average close to the measured value. Herein, we show the applicability of this method in structure refinement of a cyclo-beta-tetrapeptide by enforcing the (3)J-value restraining with LE on twelve backbone torsional angles. The resulting structural ensemble satisfies the experimental (3)J-coupling data better than the NMR model structure derived using conventional single-structure refinement based on these data. Thus, application of local-elevation search MD simulation in combination with biasing towards (3)J-coupling makes it possible to use (3)J-couplings quantitatively in structure determination of peptides.

  15. Coupling all-atom molecular dynamics simulations of ions in water with Brownian dynamics

    CERN Document Server

    Erban, Radek

    2015-01-01

    Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and parameterized using MD simulations. It is given as a system of coupled stochastic and ordinary differential equations, describing the ion position, velocity and acceleration. The stochastic coarse-grained model provides an intermediate description between all-atom MD simulations and Brownian dynamics (BD) models. It is used to develop a multiscale method which uses all-atom MD simulations in parts of the computational domain and (less detailed) BD simulations in the remainder of the domain.

  16. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands.

    Science.gov (United States)

    Khandelwal, Akash; Lukacova, Viera; Comez, Dogan; Kroll, Daniel M; Raha, Soumyendu; Balaz, Stefan

    2005-08-25

    To alleviate the problems in the receptor-based design of metalloprotein ligands due to inadequacies in the force-field description of coordination bonds, a four-tier approach was devised. Representative ligand-metalloprotein interaction energies are obtained by subsequent application of (1) docking with metal-binding-guided selection of modes, (2) optimization of the ligand-metalloprotein complex geometry by combined quantum mechanics and molecular mechanics (QM/MM) methods, (3) conformational sampling of the complex with constrained metal bonds by force-field-based molecular dynamics (MD), and (4) a single point QM/MM energy calculation for the time-averaged structures. The QM/MM interaction energies are, in a linear combination with the desolvation-characterizing changes in the solvent-accessible surface areas, correlated with experimental data. The approach was applied to structural correlation of published binding free energies of a diverse set of 28 hydroxamate inhibitors to zinc-dependent matrix metalloproteinase 9 (MMP-9). Inclusion of steps 3 and 4 significantly improved both correlation and prediction. The two descriptors explained 90% of variance in inhibition constants of all 28 inhibitors, ranging from 0.08 to 349 nM, with the average unassigned error of 0.318 log units. The structural and energetic information obtained from the time-averaged MD simulation results helped understand the differences in binding modes of related compounds.

  17. QM/MD simulation of SWNT nucleation on transition-metal carbide nanoparticles.

    Science.gov (United States)

    Page, Alister J; Yamane, Honami; Ohta, Yasuhito; Irle, Stephan; Morokuma, Keiji

    2010-11-10

    The mechanism and kinetics of single-walled carbon nanotube (SWNT) nucleation from Fe- and Ni-carbide nanoparticle precursors have been investigated using quantum chemical molecular dynamics (QM/MD) methods. The dependence of the nucleation mechanism and its kinetics on environmental factors, including temperature and metal-carbide carbon concentration, has also been elucidated. It was observed that SWNT nucleation occurred via three distinct stages, viz. the precipitation of the carbon from the metal-carbide, the formation of a "surface/subsurface" carbide intermediate species, and finally the formation of a nascent sp(2)-hybidrized carbon structure supported by the metal catalyst. The SWNT cap nucleation mechanism itself was unaffected by carbon concentration and/or temperature. However, the kinetics of SWNT nucleation exhibited distinct dependences on these same factors. In particular, SWNT nucleation from Ni(x)C(y) nanoparticles proceeded more favorably compared to nucleation from Fe(x)C(y) nanoparticles. Although SWNT nucleation from Fe(x)C(y) and Ni(x)C(y) nanoparticle precursors occurred via an identical route, the ultimate outcomes of these processes also differed substantially. Explicitly, the Ni(x)-supported sp(2)-hybridized carbon structures tended to encapsulate the catalyst particle itself, whereas the Fe(x)-supported structures tended to form isolated SWNT cap structures on the catalyst surface. These differences in SWNT nucleation kinetics were attributed directly to the relative strengths of the metal-carbon interaction, which also dictates the precipitation of carbon from the nanoparticle bulk and the longevity of the resultant surface/subsurface carbide species. The stability of the surface/subsurface carbide was also influenced by the phase of the nanoparticle itself. The observations agree well with experimentally available data for SWNT growth on iron and nickel catalyst particles.

  18. Effects of Fatty Acids on Low-Sulfur Diesel Lubricity:Experimental Investigation, DFT Calculation and MD Simulation

    Institute of Scientific and Technical Information of China (English)

    Luo Hui; Fan Weiyu; Li Yang; Zhao Pinhui; Nan Guozhi

    2013-01-01

    The continuous reduction in sulfur content of fuels would lead to diesel fuel with poor lubricity which could re-sult in engine pump failure. In the present work, fatty acids were adopted as lubricity additives to low-sulfur diesel fuel. It was attempted to correlate the molecular structures of fatty acids, such as carbon chain length, degree of saturation and hy-droxylation, to their lubricity enhancement, which was evaluated by the High-Frequency Reciprocating Rig (HFRR) meth-od. The efifciency order was supported by the density functional theory (DFT) calculations and the molecular dynamics (MD) simulations. The lubricity enhancing properties of fatty acids are mainly determined by the cohesive energy of adsorbed iflms formed on iron surface. The greater the cohesive energy, the more efifciently the fatty acid would enhance the lubricity of low-sulfur diesel fuel.

  19. Continuum simulations of water flow in carbon nanotube membranes

    DEFF Research Database (Denmark)

    Popadić, A.; Walther, Jens Honore; Koumoutsakos, P-

    2014-01-01

    We propose the use of the Navier–Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier–Stokes equations are combined with slip lengths extracted from molecular dynamics (MD) simulati......We propose the use of the Navier–Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretizations of the Navier–Stokes equations are combined with slip lengths extracted from molecular dynamics (MD...... that flows at nanoscale channels can be described by continuum solvers with proper boundary conditions that reflect the molecular interactions of the liquid with the walls of the nanochannel....

  20. Accelerating all-atom MD simulations of lipids using a modified virtual-sites technique

    DEFF Research Database (Denmark)

    Loubet, Bastien; Kopec, Wojciech; Khandelia, Himanshu

    2014-01-01

    We present two new implementations of the virtual sites technique which completely suppresses the degrees of freedom of the hydrogen atoms in a lipid bilayer allowing for an increased time step of 5 fs in all-atom simulations of the CHARMM36 force field. One of our approaches uses the derivation ...

  1. X-ray structure, thermodynamics, elastic properties and MD simulations of cardiolipin/dimyristoylphosphatidylcholine mixed membranes

    DEFF Research Database (Denmark)

    Boscia, Alexander L.; Treece, Bradley W.; Mohammadyani, Dariush

    2014-01-01

    to cholesterol in that it thickens and stiffens DMPC membranes, orders chains, and is positioned under the umbrella of the PC headgroup. CL may be necessary for hydrophobic matching to inner mitochondrial membrane proteins. Differential scanning calorimetry, S Xray and CGMD simulations all suggest that TMCL does...

  2. Exploring Beta-Amyloid Protein Transmembrane Insertion Behavior and Residue-Specific Lipid Interactions in Lipid Bilayers Using Multiscale MD Simulations

    Science.gov (United States)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2013-03-01

    Beta-amyloid (Abeta) interactions with neurons are linked to Alzheimer's. Using a multiscale MD simulation strategy that combines the high efficiency of phase space sampling of coarse-grained MD (CGD) and the high spatial resolution of Atomistic MD (AMD) simulations, we studied the Abeta insertion dynamics in cholesterol-enriched and -depleted lipid bilayers that mimic the neuronal membranes domains. Forward (AMD-CGD) and reverse (CGD-AMD) mappings were used. At the atomistic level, cholesterol promoted insertion of Abeta with high (folded) or low (unfolded) helical contents of the lipid insertion domain (Lys28-Ala42), and the insertions were stabilized by the Lys28 snorkeling and Ala42-anchoring to the polar lipid groups of the bilayer up to 200ns. After the forward mapping, the folded inserted state switched to a new extended inserted state with the Lys28 descended to the middle of the bilayer while the unfolded inserted state migrated to the membrane surface up to 4000ns. The two new states remained stable for 200ns at the atomistic scale after the reverse mapping. Our results suggested that different Abeta membrane-orientation states separated by free energy barriers can be explored by the multiscale MD more effectively than by Atomistic MD simulations alone. NIH RC1-GM090897-02

  3. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations.

    Science.gov (United States)

    Vener, M V; Odinokov, A V; Wehmeyer, C; Sebastiani, D

    2015-06-01

    Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic

  4. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

    Energy Technology Data Exchange (ETDEWEB)

    Vener, M. V., E-mail: mikhail.vener@gmail.com [Mendeleev University of Chemical Technology, Moscow (Russian Federation); Odinokov, A. V. [Photochemistry Center of the Russian Academy of Sciences, Moscow (Russian Federation); Wehmeyer, C. [Free University, Berlin (Germany); Sebastiani, D. [Martin-Luther-Universität Halle-Wittenberg, Halle (Germany)

    2015-06-07

    Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)–glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898–915 (2011)]. These structures are stabilized by the short {sup +}N–H⋯O{sup −} bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm{sup −1}. It is caused by the asymmetric stretching vibrations of the {sup +}N–H⋯O{sup −} fragment. Result of the present paper suggests that infrared spectroscopy in the 2000–2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is

  5. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations

    Science.gov (United States)

    Vener, M. V.; Odinokov, A. V.; Wehmeyer, C.; Sebastiani, D.

    2015-06-01

    Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short +N-H⋯O- bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm-1. It is caused by the asymmetric stretching vibrations of the +N-H⋯O- fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic

  6. MD Simulation for Head-on Collision of Liquid Nanodroplets Obeying Modified L-J Potential

    CERN Document Server

    Bell, Alexander J

    2015-01-01

    This project models and studies the `head-on' collision of liquid helium nanodroplets within a vacuum, using molecular dynamics simulation techniques. Programs written in MATLAB and C are utilized in tandem to facilitate computer experimentation that achieves this goal. The most expensive computation, that of collision simulation, is handled by a HPC cluster `ALICE' at the University of Leicester. Colliding droplets are modelled as roughly spherical collections of points, cut from a simple cubic lattice, obeying a modified Lennard-Jones potential, with average velocities initialized to ensure a `head-on' collision. These point-sets are then allowed to collide within a cuboid region, designed to take advantage of the observed angular distribution of post-collision fragmentation (favoring a plane orthogonal to `collision axis'). To implement the developed theoretical model, an existing C script by D. C. Rapaport, for modelling a homogeneous liquid state, is edited by the author to fit the given, highly heteroge...

  7. MD simulation of atomic displacement cascades near chromium-rich clusters in FeCr alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.ru [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Svetukhin, V. [Ulyanovsk State University, Research Institute of Technology, 42 Leo Tolstoy St., 432970 Ulyanovsk (Russian Federation); Gaganidze, E. [Karlsruhe Institute of Technology, Institute for Applied Materials, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Karlsruhe (Germany)

    2013-11-15

    The paper reports simulation of cascades in Fe–9 at.%Cr binary alloy containing chromium-rich clusters. The simulation is performed by the molecular dynamics method at the initial temperature of 300 K and primary knock-on atom energy of 15 and 20 keV. Spherical clusters containing 95 at.% of Cr with diameter of 1–5 nm have been considered. The properties of cascade evolution in the presence of chromium-rich cluster are studied. It is shown that these clusters tend to dissolve in collision cascades. However, clusters with diameter of ⩾3 nm exhibit only slight modifications and can be considered stable. Parameters of small (1–2 nm) clusters can change significantly and, in some cases, a 1 nm cluster can be totally dissolved.

  8. Alkali halide nanocrystal growth and etching studied by AFM and modeled by MD simulations.

    Science.gov (United States)

    Garcia-Manyes, Sergi; Verdaguer, Albert; Gorostiza, Pau; Sanz, Fausto

    2004-02-08

    NaCl hillocks have been grown on the NaCl(100) monocrystalline surface by simply making the tip of an atomic force microscope cantilever interact with the surface. A quantitative discussion about the hillock dissolution process as well as physical stability of these ionic surfaces has been made. Molecular dynamics simulations helped us to interpret the experimental data. An explanation for the hillock formation and dissolution phenomena is also discussed.

  9. MD simulation of the effect of contact area and tip radius on nanoindentation

    Institute of Scientific and Technical Information of China (English)

    CHEN; Shangda; KE; Fujiu

    2004-01-01

    Molecular dynamics simulations of nanoindentation are performed on monocrystal copper. A new "contact atoms" method is presented for calculating the contact area. Compared with conventional methods, this method can provide the contact area more accurately not only for sink-in but also for pile-up situation. The effect of tip radius on indentation is investigated too. The results indicate that the measured hardness of the material will become higher as the tip radius increases.

  10. Constant-pH MD Simulations of DMPA/DMPC Lipid Bilayers.

    Science.gov (United States)

    Santos, Hugo A F; Vila-Viçosa, Diogo; Teixeira, Vitor H; Baptista, António M; Machuqueiro, Miguel

    2015-12-08

    Current constant-pH molecular dynamics (CpHMD) simulations provide a proper treatment of pH effects on the structure and dynamics of soluble biomolecules like peptides and proteins. However, addressing such effects on lipid membrane assemblies has remained problematic until now, despite the important role played by lipid ionization at physiological pH in a plethora of biological processes. Modeling (de)protonation events in these systems requires a proper consideration of the physicochemical features of the membrane environment, including a sound treatment of solution ions. Here, we apply our recent CpHMD-L method to the study of pH effects on a 25% DMPA/DMPC bilayer membrane model, closely reproducing the correct lipid phases of this system, namely, gel-fluid coexistence at pH 4 and a fluid phase at pH 7. A significant transition is observed for the membrane ionization and mechanical properties at physiological pH, providing a molecular basis for the well-established role of phosphatidic acid (PA) as a key player in the regulation of many cellular events. Also, as reported experimentally, we observed pH-induced PA-PA lipid aggregation at acidic pH. By including the titration of anionic phospholipids, the current methodology makes possible to simulate lipid bilayers with increased realism. To the best of our knowledge, this is the first simulation study dealing with a continuous phospholipid bilayer with pH titration of all constituent lipids.

  11. Osmotically and thermally isolated forward osmosis-membrane distillation (fo-md) integrated module for water treatment applications

    KAUST Repository

    Ghaffour, Noreddine

    2016-09-01

    An integrated forward osmosis-membrane distillation (FO-MD) module and systems and methods incorporating the module is disclosed providing higher efficiencies and using less energy. The FO-MD module is osmotically and thermally isolated. The isolation can prevent mixing of FO draw solution/FO permeate and MD feed, and minimize dilution of FO draw solution and cooling of MD feed. The module provides MD feed solution and FO draw solution streams that flow in the same module but are separated by an isolation barrier. The osmotically and thermally isolated FO-MD integrated module, systems and methods offer higher driving forces of both FO and MD processes, higher recovery, and wider application than previously proposed hybrid FO- MD systems.

  12. Evaluation of GEOS-5 sulfur dioxide simulations during the Frostburg, MD 2010 field campaign

    Directory of Open Access Journals (Sweden)

    V. Buchard

    2013-08-01

    Full Text Available Sulfur dioxide (SO2 is a major atmospheric pollutant with a strong anthropogenic component mostly produced by the combustion of fossil fuel and other industrial activities. As a precursor of sulfate aerosols that affect climate, air quality, and human health, this gas needs to be monitored on a global scale. Global climate and chemistry models including aerosol processes along with their radiative effects are important tools for climate and air quality research. Validation of these models against in-situ and satellite measurements is essential to ascertain the credibility of these models and to guide model improvements. In this study the Goddard Chemistry, Aerosol, Radiation, and Transport (GOCART module running on-line inside the Goddard Earth Observing System version 5 (GEOS-5 model is used to simulate aerosol and SO2 concentrations. Data taken in November 2010 over Frostburg, Maryland during an SO2 field campaign involving ground instrumentation and aircraft are used to evaluate GEOS-5 simulated SO2 concentrations. Preliminary data analysis indicated the model overestimated surface SO2 concentration, which motivated the examination of mixing processes in the model and the specification of SO2 anthropogenic emission rates. As a result of this analysis, a revision of anthropogenic emission inventories in GEOS-5 was implemented, and the vertical placement of SO2 sources was updated. Results show that these revisions improve the model agreement with observations locally and in regions outside the area of this field campaign. In particular, we use the ground-based measurements collected by the United States Environmental Protection Agency (US EPA for the year 2010 to evaluate the revised model simulations over North America.

  13. Evaluation of GEOS-5 Sulfur Dioxide Simulations During the Frostburg, MD 2010 Field Campaign.

    Science.gov (United States)

    Buchard, V.; Da Silva, A. M.; Colarco, P.; Krotkov, N.; Dickerson, R. R.; Stehr, J. W.; Mount, G.; Spenei, E.; Arkinson, H. L.; He, H.

    2013-01-01

    Sulfur dioxide (SO2) is a major atmospheric pollutant with a strong anthropogenic component mostly produced by the combustion of fossil fuel and other industrial activities. As a precursor of sulfate aerosols that affect climate, air quality, and human health, this gas needs to be monitored on a global scale. Global climate and chemistry models including aerosol processes along with their radiative effects are important tools for climate and air quality research. Validation of these models against in-situ and satellite measurements is essential to ascertain the credibility of these models and to guide model improvements. In this study the Goddard Chemistry, Aerosol, Radiation, and Transport (GOCART) module running on-line inside the Goddard Earth Observing System version 5 (GEOS-5) model is used to simulate aerosol and SO2 concentrations. Data taken in November 2010 over Frostburg, Maryland during an SO2 field campaign involving ground instrumentation and aircraft are used to evaluate GEOS-5 simulated SO2 concentrations. Preliminary data analysis indicated the model overestimated surface SO2 concentration, which motivated the examination of mixing processes in the model and the specification of SO2 anthropogenic emission rates. As a result of this analysis, a revision of anthropogenic emission inventories in GEOS-5 was implemented, and the vertical placement of SO2 sources was updated. Results show that these revisions improve the model agreement with observations locally and in regions outside the area of this field campaign. In particular, we use the ground-based measurements collected by the United States Environmental Protection Agency (US EPA) for the year 2010 to evaluate the revised model simulations over North America.

  14. Microsecond-Scale MD Simulations of HIV-1 DIS Kissing-Loop Complexes Predict Bulged-In Conformation of the Bulged Bases and Reveal Interesting Differences between Available Variants of the AMBER RNA Force Fields.

    Science.gov (United States)

    Havrila, Marek; Zgarbová, Marie; Jurečka, Petr; Banáš, Pavel; Krepl, Miroslav; Otyepka, Michal; Šponer, Jiří

    2015-12-10

    We report an extensive set of explicit solvent molecular dynamics (MD) simulations (∼25 μs of accumulated simulation time) of the RNA kissing-loop complex of the HIV-1 virus initiation dimerization site. Despite many structural investigations by X-ray, NMR, and MD techniques, the position of the bulged purines of the kissing complex has not been unambiguously resolved. The X-ray structures consistently show bulged-out positions of the unpaired bases, while several NMR studies show bulged-in conformations. The NMR studies are, however, mutually inconsistent regarding the exact orientations of the bases. The earlier simulation studies predicted the bulged-out conformation; however, this finding could have been biased by the short simulation time scales. Our microsecond-long simulations reveal that all unpaired bases of the kissing-loop complex stay preferably in the interior of the kissing-loop complex. The MD results are discussed in the context of the available experimental data and we suggest that both conformations are biochemically relevant. We also show that MD provides a quite satisfactory description of this RNA system, contrasting recent reports of unsatisfactory performance of the RNA force fields for smaller systems such as tetranucleotides and tetraloops. We explain this by the fact that the kissing complex is primarily stabilized by an extensive network of Watson-Crick interactions which are rather well described by the force fields. We tested several different sets of water/ion parameters but they all lead to consistent results. However, we demonstrate that a recently suggested modification of van der Waals interactions of the Cornell et al. force field deteriorates the description of the kissing complex by the loss of key stacking interactions stabilizing the interhelical junction and excessive hydrogen-bonding interactions.

  15. Role of active site rigidity in activity: MD simulation and fluorescence study on a lipase mutant.

    Directory of Open Access Journals (Sweden)

    Md Zahid Kamal

    Full Text Available Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site.

  16. Carbon nanoscroll from C4H/C4F-type graphene superlattice: MD and MM simulation insights.

    Science.gov (United States)

    Liu, Zilong; Xue, Qingzhong; Tao, Yehan; Li, Xiaofang; Wu, Tiantian; Jin, Yakang; Zhang, Zhongyang

    2015-02-01

    Morphology manipulation opens up a new avenue for controlling and tailoring the functional properties of graphene, enabling the exploration of graphene-based nanomaterials. Through mixing single-side-hydrogenated graphene (C4H) with fluorinated graphene (C4F) on one single sheet, the C4H/C4F-type graphene superlattices can self-scroll at room temperature. We demonstrate using molecular dynamic (MD) simulations that different proportions, sizes, directions of hydrogenation and fluorination, and geometry of graphene have a great influence on the self-scrolling of superlattices into a variety of well-defined carbon nanoscrolls (CNSs), thus providing a controllable approach to tune their structures. Based on molecular mechanics (MM) simulations, the CNSs bear more than eight times the radial pressure than that of their multiwalled carbon nanotube (MWNT) counterparts, and an excellent radial elasticity of CNSs is also shown. Compared with conventional CNSs, these novel CNSs are endowed with more ample and flexible heterogeneous structures due to the on-demand hydrogenation and fluorination. Besides, this work provides a feasible route to achieve the necessary electronic and optical changes to be applied in graphene device applications.

  17. MD simulations of the formation of stable clusters in mixtures of alkaline salts and imidazolium-based ionic liquids.

    Science.gov (United States)

    Méndez-Morales, Trinidad; Carrete, Jesús; Bouzón-Capelo, Silvia; Pérez-Rodríguez, Martín; Cabeza, Óscar; Gallego, Luis J; Varela, Luis M

    2013-03-21

    Structural and dynamical properties of room-temperature ionic liquids containing the cation 1-butyl-3-methylimidazolium ([BMIM](+)) and three different anions (hexafluorophosphate, [PF6](-), tetrafluoroborate, [BF4](-), and bis(trifluoromethylsulfonyl)imide, [NTf2](-)) doped with several molar fractions of lithium salts with a common anion at 298.15 K and 1 atm were investigated by means of molecular dynamics simulations. The effect of the size of the salt cation was also analyzed by comparing these results with those for mixtures of [BMIM][PF6] with NaPF6. Lithium/sodium solvation and ionic mobilities were analyzed via the study of radial distribution functions, coordination numbers, cage autocorrelation functions, mean-square displacements (including the analysis of both ballistic and diffusive regimes), self-diffusion coefficients of all the ionic species, velocity and current autocorrelation functions, and ionic conductivity in all the ionic liquid/salt systems. We found that lithium and sodium cations are strongly coordinated in two different positions with the anion present in the mixture. Moreover, [Li](+) and [Na](+) cations were found to form bonded-like, long-lived aggregates with the anions in their first solvation shell, which act as very stable kinetic entities within which a marked rattling motion of salt ions takes place. With very long MD simulation runs, this phenomenon is proved to be on the basis of the decrease of self-diffusion coefficients and ionic conductivities previously reported in experimental and computational results.

  18. Continuum Simulations of Water Flow in Carbon Nanotube Membranes

    Science.gov (United States)

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

    2014-11-01

    We propose the use of the Navier-Stokes equations subject to partial-slip boundary conditions to simulate water flows in Carbon NanoTube (CNT) membranes. The finite volume discretisations of the Navier-Stokes equations are combined with slip lengths extracted from Molecular Dynamics (MD) simulations to predict the pressure losses at the CNT entrance as well as the enhancement of the flow rate in the CNT. The flow quantities calculated from the present hybrid approach are in excellent agreement with pure MD results while they are obtained at a fraction of the computational cost. The method enables simulations of system sizes and times well beyond the present capabilities of MD simulations. Our simulations provide an asymptotic flow rate enhancement and indicate that the pressure losses at the CNT ends can be reduced by reducing their curvature. More importantly, our results suggest that flows at nanoscale channels can be described by continuum solvers with proper boundary conditions that reflect the molecular interactions of the liquid with the walls of the nanochannel.

  19. New scoring functions for virtual screening from molecular dynamics simulations with a quantum-refined force-field (QRFF-MD). Application to cyclin-dependent kinase 2.

    Science.gov (United States)

    Ferrara, Ph; Curioni, A; Vangrevelinghe, E; Meyer, T; Mordasini, T; Andreoni, W; Acklin, P; Jacoby, E

    2006-01-01

    A recently introduced new methodology based on ultrashort (50-100 ps) molecular dynamics simulations with a quantum-refined force-field (QRFF-MD) is here evaluated in its ability both to predict protein-ligand binding affinities and to discriminate active compounds from inactive ones. Physically based scoring functions are derived from this approach, and their performance is compared to that of several standard knowledge-based scoring functions. About 40 inhibitors of cyclin-dependent kinase 2 (CDK2) representing a broad chemical diversity were considered. The QRFF-MD method achieves a correlation coefficient, R(2), of 0.55, which is significantly better than that obtained by a number of traditional approaches in virtual screening but only slightly better than that obtained by consensus scoring (R(2) = 0.50). Compounds from the Available Chemical Directory, along with the known active compounds, were docked into the ATP binding site of CDK2 using the program Glide, and the 650 ligands from the top scored poses were considered for a QRFF-MD analysis. Combined with structural information extracted from the simulations, the QRFF-MD methodology results in similar enrichment of known actives compared to consensus scoring. Moreover, a new scoring function is introduced that combines a QRFF-MD based scoring function with consensus scoring, which results in substantial improvement on the enrichment profile.

  20. Mixed brush made of 4-arm stars and linear chains: MD simulations

    Science.gov (United States)

    Su, Chan-Fei; Merlitz, Holger; Wu, Chen-Xu; Sommer, Jens-Uwe

    2016-12-01

    We investigate the structural properties of binary polymer brushes, composed of functional 4-armed star polymers and chemically identical linear polymers of different molecular weights. The molecular dynamics simulations confirm recent self-consistent field studies, in which a considerable potential of these systems for the design of switchable surfaces has been claimed. The length of the linear chains serves as a control parameter, which, while passing over a critical value, induces a sharp transition of the molecular conformation. We investigate these transitions at different grafting densities and summarize our findings in a phase diagram. The temperature dependence of the brush structure is investigated in a non-selective solvent, and non-trivial variations of the surface composition are observed. The quantity of these latter effects would be insufficient to build switchable systems, and we argue that a minor quantity of solvent selectivity would suffice to enable the desired feature of an environment-responsive coating.

  1. Influence of alkane chain length on adsorption on an α-alumina surface by MD simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turgut, C. [Department of Science and Analysis of Materials (SAM), CRP-Gabriel Lippmann, L-4422 Belvaux (Luxembourg); Institut Jean Lamour (IJL) CNRS UMR 7198, Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, F-54506 Vandoeuvre-les-Nancy Cedex (France); Pandiyan, S. [Department of Science and Analysis of Materials (SAM), CRP-Gabriel Lippmann, L-4422 Belvaux (Luxembourg); Mether, L. [Department of Physics, University of Helsinki, P.O. Box 43, FI-00014 (Finland); Belmahi, M. [Institut Jean Lamour (IJL) CNRS UMR 7198, Université de Lorraine, Faculté des Sciences et Technologies, BP 70239, F-54506 Vandoeuvre-les-Nancy Cedex (France); Nordlund, K. [Department of Physics, University of Helsinki, P.O. Box 43, FI-00014 (Finland); Philipp, P., E-mail: philipp@lippmann.lu [Department of Science and Analysis of Materials (SAM), CRP-Gabriel Lippmann, L-4422 Belvaux (Luxembourg)

    2015-06-01

    Plasma surface techniques provide both an efficient and ecological tool for the functionalization of surfaces. Hence, a proper understanding of the plasma–surface interactions of precursors and radicals during the deposition process is of great importance. Especially during the initial deposition process, the deposition of molecules and fragments is difficult to investigate by experimental techniques and import insights can be obtained by molecular dynamics simulations. In this work, the reactive force field developed by the group of Kieffer at the University of Michigan was used to study the adsorption of single linear alkane chains on an α-alumina surface. The chain length was changed from 6 backbone carbon atoms to 16 carbon atoms, the deposition energy from 0.01 to 10 eV and the incidence angle from 0° to 60° with respect to the surface normal. Results show that the adsorption depends a lot on the ratio of deposition energy to alkane chain length and the incidence angle. More grazing incidence reduces the adsorption probability and a low ratio of energy to chain length increases it.

  2. Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

    Science.gov (United States)

    Landreh, Michael; Marklund, Erik G.; Uzdavinys, Povilas; Degiacomi, Matteo T.; Coincon, Mathieu; Gault, Joseph; Gupta, Kallol; Liko, Idlir; Benesch, Justin L. P.; Drew, David; Robinson, Carol V.

    2017-01-01

    Na+/H+ antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na+/H+ exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids. By comparing wild-type NapA with engineered variants, we show that the unfolding of the protein in the gas phase involves the disruption of inter-domain contacts. Lipids around the domain interface protect the native fold in the gas phase by mediating contacts between the mobile protein segments. We speculate that elevator-type antiporters such as NapA, and likely NHA2, use a subset of annular lipids as structural support to facilitate large-scale conformational changes within the membrane. PMID:28071645

  3. Integrating mass spectrometry with MD simulations reveals the role of lipids in Na(+)/H(+) antiporters.

    Science.gov (United States)

    Landreh, Michael; Marklund, Erik G; Uzdavinys, Povilas; Degiacomi, Matteo T; Coincon, Mathieu; Gault, Joseph; Gupta, Kallol; Liko, Idlir; Benesch, Justin L P; Drew, David; Robinson, Carol V

    2017-01-10

    Na(+)/H(+) antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na(+)/H(+) exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids. By comparing wild-type NapA with engineered variants, we show that the unfolding of the protein in the gas phase involves the disruption of inter-domain contacts. Lipids around the domain interface protect the native fold in the gas phase by mediating contacts between the mobile protein segments. We speculate that elevator-type antiporters such as NapA, and likely NHA2, use a subset of annular lipids as structural support to facilitate large-scale conformational changes within the membrane.

  4. The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics.

    Directory of Open Access Journals (Sweden)

    Sourav Roy

    Full Text Available Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN based on the surface complementarity (Sm of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process.

  5. Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

    Science.gov (United States)

    Landreh, Michael; Marklund, Erik G.; Uzdavinys, Povilas; Degiacomi, Matteo T.; Coincon, Mathieu; Gault, Joseph; Gupta, Kallol; Liko, Idlir; Benesch, Justin L. P.; Drew, David; Robinson, Carol V.

    2017-01-01

    Na+/H+ antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na+/H+ exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids. By comparing wild-type NapA with engineered variants, we show that the unfolding of the protein in the gas phase involves the disruption of inter-domain contacts. Lipids around the domain interface protect the native fold in the gas phase by mediating contacts between the mobile protein segments. We speculate that elevator-type antiporters such as NapA, and likely NHA2, use a subset of annular lipids as structural support to facilitate large-scale conformational changes within the membrane.

  6. Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-09-01

    Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.

  7. Effect of Aggregation on the Mechanical Properties of Ionomers from MD Simulations

    Science.gov (United States)

    Sampath, Janani; Hall, Lisa M.

    Ionomers are polymers with a small fraction of charged monomers; these bound ions, along with free counterions, tend to aggregate together strongly in the absence of solvent. Ionic aggregates can act like temporary cross-links, giving rise to interesting mechanical properties. We perform coarse-grained molecular dynamics simulations of ionomers with various spacings of charges along the chain, representing experimental precisely spaced, neutralized poly(ethylene-co-acrylic acid) materials. We calculate aggregate morphology, dynamics, and scattering profiles and study the systems during uniaxial tensile strain to understand how aggregate structure changes under deformation and affects mechanical properties. Anisotropic structure factors (parallel and perpendicular to the direction of pull) and visualization shows that the aggregates align, in qualitative agreement with experimental findings. Stress-strain curves at different strain rates are also obtained. A modification of the model to account for unneutralized acid groups by adjusting their Lennard-Jones interaction strengths with each other and with ionic groups will also be discussed. This material is based upon work supported by the National Science Foundation under Grant 1463103.

  8. MD simulation of atomic displacement cascades in Fe-10 at.%Cr binary alloy

    Energy Technology Data Exchange (ETDEWEB)

    Tikhonchev, M., E-mail: tikhonchev@sv.ulsu.r [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Joint Stock Company, ' State Scientific Center Research Institute of Atomic Reactors' , 433510 Dimitrovgrad-10 (Russian Federation); Svetukhin, V.; Kadochkin, A. [Ulyanovsk State University, Leo Tolstoy Str., 42, Ulyanovsk 432970 (Russian Federation); Gaganidze, E. [Forschungszentrum Karlsruhe, IMF II, 3640, D-76021 Karlsruhe (Germany)

    2009-12-15

    Molecular dynamics simulation of atomic displacement cascades up to 20 keV has been performed in Fe-10 at.%Cr binary alloy at a temperature of 600 K. The N-body interatomic potentials of Finnis-Sinclair type were used. According to the obtained results the dependence of 'surviving' defects amount is well approximated by power function that coincides with other researchers' results. Obtained cascade efficiency for damage energy in the range from 10 to 20 keV is approx0.2 NRT that is slightly higher than for pure alpha-Fe. In post-cascade area Cr fraction in interstitials is in range 2-5% that is essentially lower than Cr content in the base alloy. The results on size and amount of vacancy and interstitial clusters generated in displacement cascades are obtained. For energies of 2 keV and higher the defect cluster average size increases and it is well approximated by a linear dependence on cascade energy both for interstitials and vacancies.

  9. Effect of pH on the structure, function, and stability of human calcium/calmodulin-dependent protein kinase IV: combined spectroscopic and MD simulation studies.

    Science.gov (United States)

    Naz, Huma; Shahbaaz, Mohd; Bisetty, Krishna; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-06-01

    Human calcium/calmodulin-dependent protein kinase IV (CAMKIV) is a member of Ser/Thr protein kinase family. It is regulated by the calcium-calmodulin dependent signal through a secondary messenger, Ca(2+), which leads to the activation of its autoinhibited form. The over-expression and mutation in CAMKIV as well as change in Ca(2+) concentration is often associated with numerous neurodegenerative diseases and cancers. We have successfully cloned, expressed, and purified a functionally active kinase domain of human CAMKIV. To observe the effect of different pH conditions on the structural and functional properties of CAMKIV, we have used spectroscopic techniques such as circular diachroism (CD) absorbance and fluorescence. We have observed that within the pH range 5.0-11.5, CAMKIV maintained both its secondary and tertiary structures, along with its function, whereas significant aggregation was observed at acidic pH (2.0-4.5). We have also performed ATPase activity assays under different pH conditions and found a significant correlation between the structure and enzymatic activities of CAMKIV. In-silico validations were further carried out by modeling the 3-dimensional structure of CAMKIV and then subjecting it to molecular dynamics (MD) simulations to understand its conformational behavior in explicit water conditions. A strong correlation between spectroscopic observations and the output of molecular dynamics simulation was observed for CAMKIV.

  10. Understanding self-assembly of charged-neutral block copolymer (BCP) and surfactant complexes using molecular dynamics (MD) simulation

    Science.gov (United States)

    Goswami, Monojoy; Sumpter, Bobby; Kilbey, Michael

    Here we report the formation of phase separated BCP-surfactant complexes resulting from the electrostatic self-assembly of charge-neutral block copolymers with oppositely charged surfactants. Complexation behaviors of oppositely charged polyelectrolytes has gained considerable attention in the field of soft condensed matter physics due to their potential application as functional nanomaterials for batteries, wastewater treatment and drug delivery systems. Numerous experiments have examined the self-assembled structures resulting from complexation of charge-neutral BCP and surfactants, however, there is a lack of comprehensive understanding at the fundamental level. To help bridge this gap, we use, MD simulations to study self-assembly and dynamics of the BCP-surfactant complex at the molecular level. Our results show an overcharging effect in BCPs with hydrophobic neutral blocks and a formation of core-shell colloidal structure. Hydrophilic neutral blocks, on the other hand, show stable, hairy colloidal structures with neutral blocks forming a loosely-bound, fuzzy outer layer. Our results qualitatively agree with previous SANS and SAXS experiments. This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Materials Science and Engineering Division.

  11. Degradation of the Adhesive Properties of MD-944 Diode Tape by Simulated Low Earth Orbit Environmental Factors

    Science.gov (United States)

    Albyn, K.; Finckenor, M.

    2006-01-01

    The International Space Station (ISS) solar arrays utilize MD-944 diode tape with silicone pressure-sensitive adhesive to protect the underlying diodes and also provide a high-emittance surface. On-orbit, the silicone adhesive will be exposed and ultimately convert to a glass-like silicate due to atomic oxygen (AO). The current operational plan is to retract ISS solar array P6 and leave it stored under load for a long duration (6 mo or more). The exposed silicone adhesive must not cause the solar array to stick to itself or cause the solar array to fail during redeployment. The Environmental Effects Branch at Marshall Space Flight Center, under direction from the ISS Program Office Environments Team, performed simulated space environment exposures with 5-eV AO, near ultraviolet radiation and ionizing radiation. The exposed diode tape samples were put under preload and then the resulting blocking force was measured using a tensile test machine. Test results indicate that high-energy AO, ultraviolet radiation, and electron ionizing radiation exposure all reduce the blocking force for a silicone-to-silicone bond. AO exposure produces the most significant reduction in blocking force

  12. Calibrating and Validating a Simulation Model to Identify Drivers of Urban Land Cover Change in the Baltimore, MD Metropolitan Region

    Directory of Open Access Journals (Sweden)

    Claire Jantz

    2014-09-01

    Full Text Available We build upon much of the accumulated knowledge of the widely used SLEUTH urban land change model and offer advances. First, we use SLEUTH’s exclusion/attraction layer to identify and test different urban land cover change drivers; second, we leverage SLEUTH’s self-modification capability to incorporate a demographic model; and third, we develop a validation procedure to quantify the influence of land cover change drivers and assess uncertainty. We found that, contrary to our a priori expectations, new development is not attracted to areas serviced by existing or planned water and sewer infrastructure. However, information about where population and employment growth is likely to occur did improve model performance. These findings point to the dominant role of centrifugal forces in post-industrial cities like Baltimore, MD. We successfully developed a demographic model that allowed us to constrain the SLEUTH model forecasts and address uncertainty related to the dynamic relationship between changes in population and employment and urban land use. Finally, we emphasize the importance of model validation. In this work the validation procedure played a key role in rigorously assessing the impacts of different exclusion/attraction layers and in assessing uncertainty related to population and employment forecasts.

  13. Injection MD

    CERN Document Server

    Bartmann, W; Bracco, C; Drosdal, L; Gianfelice, E; Goddard, B; Kain, V; Papaphilippou, Y; Vanbavinckhove, G

    2012-01-01

    This note summarizes the results obtained at injection during the 2nd MD block and the floating MD block in July. Highlights are presented for injection in the LHC with the Q20 SPS optics, influence of the supercycle and injection with 25 ns bunch spacing. Beams were successfully injected into the LHC using the Q20 optics [1, 3]. Small corrections were needed to steer the beam in the transfer lines. Dispersion measurements were conducted for both beams. The horizontal normalized dispersion in TI2 was a factor 2 smaller for Q20 with respect to Q26, for TI8 on the other hand the opposite was observed. The results for injection loss dependency on super cycle composition show only a small increase in losses for beam 2. The losses observed must therefore mainly come from other sources such as shot-by-shot stability or quality of scraping. For the injection with 25 ns bunch spacing bunches were injected for both beams. For B1 up to the maximum of 288 bunches. For B2 on the other only up to 144 bunches were injected...

  14. Conformational analysis of the Sda determinant-containing tetrasaccharide and two mimics in aqueous solution by using 1H NMR ROESY spectroscopy in combination with MD simulations

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G. [Utrecht University, Department of Bio-Organic Chemistry, Bijvoet Center (Netherlands)

    2000-01-15

    The conformational behaviour of the spacer-linked synthetic Sd{sup a} tetrasaccharide {beta}-d-GalpNAc-(1{sup {yields}}4)-[{alpha}-Neu5Ac-(2{sup {yields}}3)]-{beta}-d-Galp-(1{sup {yields}}4)-{beta}-d-GlcpNAc-(1{sup {yields}}O) (CH{sub 2}){sub 5}NH{sub 2} (1) and the two mimics {beta}-d-Galp-(1{sup {yields}}4)-[{alpha}-Neu5Ac-(2{sup {yields}}3)]-{beta}-d-Galp-(1{sup {yields}}4)-{beta}-d-GlcpNAc-(1{sup {yields}}O)(CH{sub 2}){sub 5}NH{sub 2} (2) and {beta}-d-GlcpNAc-(1{sup {yields}}4)-[{alpha}-Neu5Ac-(2{sup {yields}}3)]-{beta}-d-Galp-(1{sup {yields}}4)-{beta}-d-GlcpNAc-(1{sup {yields}}O) (CH{sub 2}){sub 5}NH{sub 2} (3) were investigated by {sup 1}H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D {sup 1}H ROESY cross-peak intensities (ROEs) of the tetrasaccharides were compared with calculated ROEs derived from MD trajectories using the CROSREL program. Analysis of these data indicated that the oligosaccharidic skeletons of the compounds 1-3 are rather rigid, especially the {beta}-d-Hex(NAc)-(1{sup {yields}}4)-[{alpha}-Neu5Ac-(2{sup {yields}}3)]-{beta}-d-Galp fragments. The {alpha}- Neu5-Ac-(2{sup {yields}}3)-{beta}-d-Galp linkage occurred in two different energy minima in the three-dimensional structure of the compounds 1-3 in aqueous solution. Experimental data and dynamics simulations supported the finding that the higher energy rotamer (CHEAT forcefield) was abundant in compounds 1 and 3 due to the existence of a hydrogen bond between the carboxyl group of the sialic acid and the acetamido group of the terminal monosaccharide (GalNAc or GlcNAc) unit. The conformational similarity between 1 and 3 leads to the suggestion that also their activities will be alike.

  15. Conformational Ensemble of the Poliovirus 3CD Precursor Observed by MD Simulations and Confirmed by SAXS: A Strategy to Expand the Viral Proteome?

    Science.gov (United States)

    Moustafa, Ibrahim M; Gohara, David W; Uchida, Akira; Yennawar, Neela; Cameron, Craig E

    2015-11-23

    The genomes of RNA viruses are relatively small. To overcome the small-size limitation, RNA viruses assign distinct functions to the processed viral proteins and their precursors. This is exemplified by poliovirus 3CD protein. 3C protein is a protease and RNA-binding protein. 3D protein is an RNA-dependent RNA polymerase (RdRp). 3CD exhibits unique protease and RNA-binding activities relative to 3C and is devoid of RdRp activity. The origin of these differences is unclear, since crystal structure of 3CD revealed "beads-on-a-string" structure with no significant structural differences compared to the fully processed proteins. We performed molecular dynamics (MD) simulations on 3CD to investigate its conformational dynamics. A compact conformation of 3CD was observed that was substantially different from that shown crystallographically. This new conformation explained the unique properties of 3CD relative to the individual proteins. Interestingly, simulations of mutant 3CD showed altered interface. Additionally, accelerated MD simulations uncovered a conformational ensemble of 3CD. When we elucidated the 3CD conformations in solution using small-angle X-ray scattering (SAXS) experiments a range of conformations from extended to compact was revealed, validating the MD simulations. The existence of conformational ensemble of 3CD could be viewed as a way to expand the poliovirus proteome, an observation that may extend to other viruses.

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

    Science.gov (United States)

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

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

    CERN Document Server

    Kretov, D A

    2005-01-01

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

  18. Comparative analysis of termoscale effects, isomerization and stability of TM-nanoclusters (Pd,Ni,Fe and Si in dependence on interatomic potentials. MD-simulations

    Directory of Open Access Journals (Sweden)

    Galashev А.Е.

    2011-05-01

    Full Text Available Basing on the MD-simulated data the comparison of physicochemical properties of TM-nanoclusters (Pd,Ni,Fe, and Si-nanoparticles has been carried on in the purpose to understand the specificity of structure changes in depending on nature of interatomic bonds and initial structures (fcc, bcc, icosahedral – Ih. MDsimulation of thermic evolution including melting of TM- and Si- clusters was carried on up to 2000K.

  19. Multiscale simulation of water flow past a C540 fullerene

    DEFF Research Database (Denmark)

    Walther, Jens Honore; Praprotnik, Matej; Kotsalis, Evangelos M.

    2012-01-01

    We present a novel, three-dimensional, multiscale algorithm for simulations of water flow past a fullerene. We employ the Schwarz alternating overlapping domain method to couple molecular dynamics (MD) of liquid water around the C540 buckyball with a Lattice–Boltzmann (LB) description for the Nav...... algorithms. We use this method to determine the slip length and hydrodynamic radius for water flow past a buckyball....

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  1. All-atom Molecular Dynamic Simulations and NMR Spectra Study on Intermolecular Interactions of N,N-dimethylacetamide-Water System

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Zai-you Tan; San-lai Luo

    2008-01-01

    N,N-dimethylacetamide (DMA) has been investigated extensively in studying models of peptide bonds. An all-atom MD simulation and the NMR spectra were performed to investigate the interactions in the DMA- water system. The radial distribution functions (RDFs) and the hydrogen-bonding network were used in MD simulations. There are strong hydrogen bonds and weak C-H…O contacts in the mixtures, as shown by the analysis of the RDFs. The insight structures in the DMA-water mixtures can be classified into different regions by the analysis of the hydrogen-bonding network. Chemical shifts of the hydrogen atom of water molecule with concentration and temperatures are adopted to study the interactions in the mixtures. The results of NMR spectra show good agreement with the statistical results of hydrogen bonds in MD simulations.

  2. Corrosion protection properties and interfacial adhesion mechanism of an epoxy/polyamide coating applied on the steel surface decorated with cerium oxide nanofilm: Complementary experimental, molecular dynamics (MD) and first principle quantum mechanics (QM) simulation methods

    Science.gov (United States)

    Bahlakeh, Ghasem; Ramezanzadeh, Bahram; Saeb, Mohammad Reza; Terryn, Herman; Ghaffari, Mehdi

    2017-10-01

    The effect of cerium oxide treatment on the corrosion protection properties and interfacial interaction of steel/epoxy was studied by electrochemical impedance spectroscopy, (EIS) classical molecular dynamics (MD) and first principle quantum mechanics (QM) simulation methods X-ray photoelectron spectroscopy (XPS) was used to verify the chemical composition of the Ce film deposited on the steel. To probe the role of the curing agent in epoxy adsorption, computations were compared for an epoxy, aminoamide and aminoamide modified epoxy. Moreover, to study the influence of water on interfacial interactions the MD simulations were executed for poly (aminoamide)-cured epoxy resin in contact with the different crystallographic cerium dioxide (ceria, CeO2) surfaces including (100), (110), and (111) in the presence of water molecules. It was found that aminoamide-cured epoxy material was strongly adhered to all types of CeO2 substrates, so that binding to ceria surfaces followed the decreasing order CeO2 (111) > CeO2 (100) > CeO2 (110) in both dry and wet environments. Calculation of interaction energies noticed an enhanced adhesion to metal surface due to aminoamide curing of epoxy resin; where facets (100) and (111) revealed electrostatic and Lewis acid-base interactions, while an additional hydrogen bonding interaction was identified for CeO2 (110). Overall, MD simulations suggested decrement of adhesion to CeO2 in wet environment compared to dry conditions. Additionally, contact angle, pull-off test, cathodic delamination and salt spray analyses were used to confirm the simulation results. The experimental results in line with modeling results revealed that Ce layer deposited on steel enhanced substrate surface free energy, work of adhesion, and interfacial adhesion strength of the epoxy coating. Furthermore, decrement of adhesion of epoxy to CeO2 in presence of water was affirmed by experimental results. EIS results revealed remarkable enhancement of the corrosion

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

    Institute of Scientific and Technical Information of China (English)

    PAN Haihua; TAO Jinhui; WU Tao; TANG Ruikang

    2007-01-01

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

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

    Science.gov (United States)

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

    2017-04-01

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

  5. Modeling the Self-Assembly and Stability of DHPC Micelles Using Atomic Resolution and Coarse Grained MD Simulations.

    Science.gov (United States)

    Kraft, Johan F; Vestergaard, Mikkel; Schiøtt, Birgit; Thøgersen, Lea

    2012-05-08

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomistic resolution force fields to model the experimentally observed behavior of the lipid 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), which is a widely used lipid for biophysical characterization of membrane proteins. It becomes clear from our results that a satisfactory modeling of DHPC aggregates in solution poses different demands to the force field than do the modeling of bilayers. First, the representation of the short tailed lipid DHPC in the coarse grained force field MARTINI is assessed with the intend of successfully self-assemble micelles with structural characteristics comparable to experimental data. Then, the use of the recently presented polarizable water model in MARTINI is shown to be essential for producing micelles that are structurally in accordance with experiments. For the atomistic representations of DHPC micelles in solution the GROMOS96 force field with lipid parameters by A. Kukol fails to maintain stable micelles, whereas the most recent CHARMM36 lipid parameters and GROMOS96 with the so-called Berger lipid parameters both succeed in this regard.

  6. Ab initio MD simulations of Mg2SiO4 liquid at high pressures and temperatures relevant to the Earth's mantle

    Science.gov (United States)

    Martin, G. B.; Kirtman, B.; Spera, F. J.

    2010-12-01

    Computational studies implementing Density Functional Theory (DFT) methods have become very popular in the Materials Sciences in recent years. DFT codes are now used routinely to simulate properties of geomaterials—mainly silicates and geochemically important metals such as Fe. These materials are ubiquitous in the Earth’s mantle and core and in terrestrial exoplanets. Because of computational limitations, most First Principles Molecular Dynamics (FPMD) calculations are done on systems of only 100 atoms for a few picoseconds. While this approach can be useful for calculating physical quantities related to crystal structure, vibrational frequency, and other lattice-scale properties (especially in crystals), it would be useful to be able to compute larger systems especially for extracting transport properties and coordination statistics. Previous studies have used codes such as VASP where CPU time increases as N2, making calculations on systems of more than 100 atoms computationally very taxing. SIESTA (Soler, et al. 2002) is a an order-N (linear-scaling) DFT code that enables electronic structure and MD computations on larger systems (N 1000) by making approximations such as localized numerical orbitals. Here we test the applicability of SIESTA to simulate geosilicates in the liquid and glass state. We have used SIESTA for MD simulations of liquid Mg2SiO4 at various state points pertinent to the Earth’s mantle and congruous with those calculated in a previous DFT study using the VASP code (DeKoker, et al. 2008). The core electronic wave functions of Mg, Si, and O were approximated using pseudopotentials with a core cutoff radius of 1.38, 1.0, and 0.61 Angstroms respectively. The Ceperly-Alder parameterization of the Local Density Approximation (LDA) was used as the exchange-correlation functional. Known systematic overbinding of LDA was corrected with the addition of a pressure term, P 1.6 GPa, which is the pressure calculated by SIESTA at the experimental

  7. LDRD Final Report (08-ERD-037): Important Modes to Drive Protein MD Simulations to the Next Conformational Level

    Energy Technology Data Exchange (ETDEWEB)

    Sadigh, B

    2011-04-07

    Every action in biology is performed by dynamic proteins that convert between multiple states in order to engage their functions. Often binding to various ligands is essential for the rates of desired transitions to be enhanced. The goal of computational biology is to study these transitions and discover the different states to fully understand the protein's normal and diseased function, design drugs to target/bias specific states, and understand all of the interactions in between. We have developed a new methodology that is capable of calculating the absolute free energy of proteins while taking into account all the interactions with the solvent molecules. The efficiency of the new scheme is an order of magnitude greater than any existing technique. This method is now implemented in the massively parallel popular MD program package NAMD. This now makes it possible to calculate the relative stability of different conformational states of biological macromolecules as well as their binding free energies to various ligands.

  8. Systematic evaluation of bundled SPC water for biomolecular simulations.

    Science.gov (United States)

    Gopal, Srinivasa M; Kuhn, Alexander B; Schäfer, Lars V

    2015-04-07

    In bundled SPC water models, the relative motion of groups of four water molecules is restrained by distance-dependent potentials. Bundled SPC models have been used in hybrid all-atom/coarse-grained (AA/CG) multiscale simulations, since they enable to couple atomistic SPC water with supra-molecular CG water models that effectively represent more than a single water molecule. In the present work, we systematically validated and critically tested bundled SPC water models as solvent for biomolecular simulations. To that aim, we investigated both thermodynamic and structural properties of various biomolecular systems through molecular dynamics (MD) simulations. Potentials of mean force of dimerization of pairs of amino acid side chains as well as hydration free energies of single side chains obtained with bundled SPC and standard (unrestrained) SPC water agree closely with each other and with experimental data. Decomposition of the hydration free energies into enthalpic and entropic contributions reveals that in bundled SPC, this favorable agreement of the free energies is due to a larger degree of error compensation between hydration enthalpy and entropy. The Ramachandran maps of Ala3, Ala5, and Ala7 peptides are similar in bundled and unrestrained SPC, whereas for the (GS)2 peptide, bundled water leads to a slight overpopulation of extended conformations. Analysis of the end-to-end distance autocorrelation times of the Ala5 and (GS)2 peptides shows that sampling in more viscous bundled SPC water is about two times slower. Pronounced differences between the water models were found for the structure of a coiled-coil dimer, which is instable in bundled SPC but not in standard SPC. In addition, the hydration of the active site of the serine protease α-chymotrypsin depends on the water model. Bundled SPC leads to an increased hydration of the active site region, more hydrogen bonds between water and catalytic triad residues, and a significantly slower exchange of water

  9. Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations

    Directory of Open Access Journals (Sweden)

    Yufei Yue

    2015-05-01

    Full Text Available Protein arginine methyltransferases (PRMTs catalyze the transfer of the methyl group from S-adenosyl-l-methionine (AdoMet to arginine residues. There are three types of PRMTs (I, II and III that produce different methylation products, including asymmetric dimethylarginine (ADMA, symmetric dimethylarginine (SDMA and monomethylarginine (MMA. Since these different methylations can lead to different biological consequences, understanding the origin of product specificity of PRMTs is of considerable interest. In this article, the quantum mechanical/molecular mechanical (QM/MM molecular dynamics (MD and free energy simulations are performed to study SDMA catalyzed by the Type II PRMT5 on the basis of experimental observation that the dimethylated product is generated through a distributive fashion. The simulations have identified some important interactions and proton transfers during the catalysis. Similar to the cases involving Type I PRMTs, a conserved Glu residue (Glu435 in PRMT5 is suggested to function as general base catalyst based on the result of the simulations. Moreover, our results show that PRMT5 has an energetic preference for the first methylation on Nη1 followed by the second methylation on a different ω-guanidino nitrogen of arginine (Nη2.The first and second methyl transfers are estimated to have free energy barriers of 19–20 and 18–19 kcal/mol respectively. The computer simulations suggest a distinctive catalytic mechanism of symmetric dimethylation that seems to be different from asymmetric dimethylation.

  10. Cryptanalysis of MD2

    DEFF Research Database (Denmark)

    Knudsen, Lars Ramkilde; Mathiassen, John Erik; Muller, Frédéric

    2010-01-01

    This paper considers the hash function MD2 which was developed by Ron Rivest in 1989. Despite its age, MD2 has withstood cryptanalytic attacks until recently. This paper contains the state-of-the-art cryptanalytic results on MD2, in particular collision and preimage attacks on the full hash...

  11. In silico thermodynamics stability change analysis involved in BH4 responsive mutations in phenylalanine hydroxylase: QM/MM and MD simulations analysis.

    Science.gov (United States)

    Chadha, Nidhi; Tiwari, Anjani K; Kumar, Vikas; Milton, Marilyn D; Mishra, Anil K

    2015-01-01

    The mammalian tetrahydrobiopterin (BH4)-dependent phenylalanine hydroxylases (PAH), involved in important metabolic pathways of phenylalanine, belong to non-heme iron-containing aromatic acid hydroxylases' enzyme (AAH) family. AAHs utilize BH4 as protein co-factor and thus promote hydroxylation reactions of their substrates. Any alterations in BH4 -mediated AAH's pathway or mutations in these enzymes are responsible for various disorders, and thus highlights the importance of mutational analysis to assess the effect on their biosynthetic pathways. Our present studies are aimed at single-site mutations in PAH that lead to thermodynamic stability change upon folding and further validation of designed non-reduced BH2 designed co-factors. We have presented single-site mutational analysis of PAH where single-site mutations have been identified from known literature. Further, in silico studies with the PAH, in silico mutant PAH, and crystallized known mutant A313T forms, involved QM/MM and Molecular Dynamics (MD) simulations analysis. The modified co-factor A showed high affinity with PAH and all mutant PAH with high G-score of -14.851. The best pose high affinity co-factor A subjected to QM/MM optimization which leads to square-pyramidal coordination of non-heme active site. The structural and energetic information obtained from the production phase of 20 ns MD simulation of co-factor-metalloprotein complex results helped to understand the binding mode and involvement of three molecules throughout the reaction pathways' catalysis of PAH. The free energies of binding (dG) of A were found to be -68.181 kcal/mol and -72.249 for 1DMW and 1TDW for A313T mutant. Binding of Co-factor A do not perturb the coordination environment of iron at the active site which resides in 2-Histdine and 1-Glutamate triad, and may enhance the percentage response towards co-factor-mediated therapy.

  12. Molecular dynamics simulations of the ice temperature dependence of water ice photodesorption

    CERN Document Server

    Arasa, C; Cuppen, H M; van Dishoweck, E F; Kroes, G -J; 10.1063/1.3422213

    2010-01-01

    The ultraviolet (UV) photodissociation of amorphous water ice at different ice temperatures is investigated using molecular dynamics (MD) simulations and analytical potentials. Previous MD calculations of UV photodissociation of amorphous and crystalline water ice at 10 K [S. Andersson et al., J. Chem. Phys. 124, 064715 (2006)] revealed -for both types of ice- that H atom, OH, and H2O desorption are the most important processes after photoexcitation in the uppermost layers of the ice. Water desorption takes place either by direct desorption of recombined water, or when, after dissociation, an H atom transfers part of its kinetic energy to one of the surrounding water molecules which is thereby kicked out from the ice. We present results of MD simulations of UV photodissociation of amorphous ice at 10, 20, 30, and 90 K in order to analyze the effect of ice temperature on UV photodissociation processes. Desorption and trapping probabilities are calculated for photoexcitation of H2O in the top four monolayers an...

  13. Water Conservation Education with a Rainfall Simulator.

    Science.gov (United States)

    Kok, Hans; Kessen, Shelly

    1997-01-01

    Describes a program in which a rainfall simulator was used to promote water conservation by showing water infiltration, water runoff, and soil erosion. The demonstrations provided a good background for the discussion of issues such as water conservation, crop rotation, and conservation tillage practices. The program raised awareness of…

  14. Quasielastic neutron scattering measurements and ab initio MD-simulations on single ion motions in molten NaF

    Energy Technology Data Exchange (ETDEWEB)

    Demmel, F. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Mukhopadhyay, S. [ISIS Facility, Rutherford Appleton Laboratory, Didcot OX11 0QX (United Kingdom); Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ (United Kingdom)

    2016-01-07

    The ionic stochastic motions in the molten alkali halide NaF are investigated by quasielastic neutron scattering and first principles molecular dynamics simulation. Quasielastic neutron scattering was employed to extract the diffusion behavior of the sodium ions in the melt. An extensive first principles based simulation on a box of up to 512 particles has been performed to complement the experimental data. From that large box, a smaller 64-particle box has then been simulated over a runtime of 60 ps. A good agreement between calculated and neutron data on the level of spectral shape has been obtained. The obtained sodium diffusion coefficients agree very well. The simulation predicts a fluorine diffusion coefficient similar to the sodium one. Applying the Nernst-Einstein equation, a remarkable large cross correlation between both ions can be deduced. The velocity cross correlations demonstrate a positive correlation between the ions over a period of 0.1 ps. That strong correlation is evidence that the unlike ions do not move completely statistically independent and have a strong association over a short period of time.

  15. Modeling the Self-assembly and Stability of DHPC Micelles using Atomic Resolution and Coarse Grained MD Simulations

    DEFF Research Database (Denmark)

    Kraft, Johan Frederik; Vestergaard, Mikkel; Schiøtt, Birgit

    2012-01-01

    Membrane mimics such as micelles and bicelles are widely used in experiments involving membrane proteins. With the aim of being able to carry out molecular dynamics simulations in environments comparable to experimental conditions, we set out to test the ability of both coarse grained and atomist...

  16. Fusion Simulation Project. Workshop sponsored by the U.S. Department of Energy Rockville, MD, May 16-18, 2007

    Energy Technology Data Exchange (ETDEWEB)

    None

    2007-05-16

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.

  17. Fusion Simulation Project. Workshop Sponsored by the U.S. Department of Energy, Rockville, MD, May 16-18, 2007

    Energy Technology Data Exchange (ETDEWEB)

    Kritz, A.; Keyes, D.

    2007-05-18

    The mission of the Fusion Simulation Project is to develop a predictive capability for the integrated modeling of magnetically confined plasmas. This FSP report adds to the previous activities that defined an approach to integrated modeling in magnetic fusion. These previous activities included a Fusion Energy Sciences Advisory Committee panel that was charged to study integrated simulation in 2002. The report of that panel [Journal of Fusion Energy 20, 135 (2001)] recommended the prompt initiation of a Fusion Simulation Project. In 2003, the Office of Fusion Energy Sciences formed a steering committee that developed a project vision, roadmap, and governance concepts [Journal of Fusion Energy 23, 1 (2004)]. The current FSP planning effort involved forty-six physicists, applied mathematicians and computer scientists, from twenty-one institutions, formed into four panels and a coordinating committee. These panels were constituted to consider: Status of Physics Components, Required Computational and Applied Mathematics Tools, Integration and Management of Code Components, and Project Structure and Management. The ideas, reported here, are the products of these panels, working together over several months and culminating in a three-day workshop in May 2007.

  18. Omega currents in voltage-gated ion channels: what can we learn from uncovering the voltage-sensing mechanism using MD simulations?

    Science.gov (United States)

    Tarek, Mounir; Delemotte, Lucie

    2013-12-17

    Ion channels conduct charged species through otherwise impermeable biological membranes. Their activity supports a number of physiological processes, and genetic mutations can disrupt their function dramatically. Among these channels, voltage gated cation channels (VGCCs) are ubiquitous transmembrane proteins involved in electrical signaling. In addition to their selectivity for ions, their function requires membrane-polarization-dependent gating. Triggered by changes in the transmembrane voltage, the activation and deactivation of VGCCs proceed through a sensing mechanism that prompts motion of conserved positively charged (basic) residues within the S4 helix of a four-helix bundle, the voltage sensor domain (VSD). Decades of experimental investigations, using electrophysiology, molecular biology, pharmacology, and spectroscopy, have revealed details about the function of VGCCs. However, in 2005, the resolution of the crystal structure of the activated state of one member of the mammalian voltage gated potassium (Kv) channels family (the Kv1.2) enabled researchers to make significant progress in understanding the structure-function relationship in these proteins on a molecular level. In this Account, we review the use of a complementary technique, molecular dynamics (MD) simulations, that has offered new insights on this timely issue. Starting from the "open-activated state" crystal structure, we have carried out large-scale all atom MD simulations of the Kv1.2 channel embedded in its lipidic environment and submitted to a hyperpolarizing (negative) transmembrane potential. We then used steered MD simulations to complete the full transition to the resting-closed state. Using these procedures, we have followed the operation of the VSDs and uncovered three intermediate states between their activated and deactivated conformations. Each conformational state is characterized by its network of salt bridges and by the occupation of the gating charge transfer center by a

  19. pH-controlled doxorubicin anticancer loading and release from carbon nanotube noncovalently modified by chitosan: MD simulations.

    Science.gov (United States)

    Rungnim, Chompoonut; Rungrotmongkol, Thanyada; Poo-Arporn, Rungtiva P

    2016-11-01

    In the present study, we describe here the pH condition activating doxorubicin (DOX) anticancer drugs loading and release over single-wall carbon nanotube (SWNT) non-covalently wrapped with chitosan (CS). The possibility of drug displacement on DOX/CS/SWNT nanocarrier was investigated using molecular dynamics simulations. The drug loading and release were monitored via displacement analysis and binding energy calculations. The simulated results clearly showed that the drugs well interacted with the CS/SWNT at physiological pH (pH 7.4), where CS was in the deprotonated form. Contrastingly, in weakly acidic environments (pH 5.0-6.5) which is a pH characteristics of certain cancer environments, the protonated CS became loosen wrapped around the SWNT and triggered drugs release as a result of charge-charge repulsion between CS and drug molecules. The obtained data fulfil the understanding at atomic level of drug loading and release controlled by pH-sensitive polymer, which might be useful for further cancer therapy researches.

  20. NPT Ensemble MD Simulation Investigation on the Mechanical Properties of HMX/F2311 Polymer-bonded Explosive

    Institute of Scientific and Technical Information of China (English)

    XIAO Ji-Jun; ZHANG Hang; HUANG Hui; LI Jing-Shang; ZHU Wei; XIAO He-Ming

    2008-01-01

    Molecular dynamics simulation was applied to investigate the mechanical properties of β-octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine(β-HMX)-based polymer-bonded explosive(PBX)with F2311 fluorine rubber(It is produced by copolymerization of vinylidene difluoride and chlorotrifluoroethylene in the molar ratio 1 over 1).The elastic constants for β-HMX crystal and the HMX-based PBX were computed using a static elastic constant analysis method,and the engineering moduli and Poisson ratios were derived by Reuss average.Based on the value of Cauchy pressure and the ratio of bulk modulus to shear modulus,it is indicated that the ductibility of crystalline HMX can be effectively improved by blending the polymer in a small amount.

  1. Comparative MD Simulations Indicate a Dual Role for Arg1323.50 in Dopamine-Dependent D2R Activation.

    Directory of Open Access Journals (Sweden)

    Ralf C Kling

    Full Text Available Residue Arg3.50 belongs to the highly conserved DRY-motif of class A GPCRs, which is located at the bottom of TM3. On the one hand, Arg3.50 has been reported to help stabilize the inactive state of GPCRs, but on the other hand has also been shown to be crucial for stabilizing active receptor conformations and mediating receptor-G protein coupling. The combined results of these studies suggest that the exact function of Arg3.50 is likely to be receptor-dependent and must be characterized independently for every GPCR. Consequently, we now present comparative molecular-dynamics simulations that use our recently described inactive-state and Gα-bound active-state homology models of the dopamine D2 receptor (D2R, which are either bound to dopamine or ligand-free, performed to identify the function of Arg1323.50 in D2R. Our results are consistent with a dynamic model of D2R activation in which Arg1323.50 adopts a dual role, both by stabilizing the inactive-state receptor conformation and enhancing dopamine-dependent D2R-G protein coupling.

  2. Metal Ion Coordination Essential for Specific Molecular Interactions of Butea monosperma Lectin: ITC and MD Simulation Studies.

    Science.gov (United States)

    Abhilash, J; Haridas, M

    2015-05-01

    Crystal structure of Butea monosperma seed lectin (BML) was analyzed and the metal ion geometry identified. In order to understand the role of metal ions for the structural stability and ligand binding, studies of demetallized protein were carried out. Binding of different ligands like GalNAc, lactose, and galactose onto native and demetallized protein was studied by isothermal titration calorimetry as well as molecular simulation methods. Molecular dynamics was applied to the structure after removing the coordinates of metal ions, to identify the effect of demetallization in silico. Docking studies of different sugar molecules as well as the fungal α-amylase was carried out and compared the interactions in the native and apo states. It was found that metal ions are important for the ligand binding with increased affinity. However, their absence did not make any alteration to the secondary structure. Though the metal ions were not coordinated to the loops contacting the α-amylase, the absence of metal ions reduced the protein-protein binding strength due to long-range changes in irregular structures of the lectin.

  3. Energies and 2'-Hydroxyl Group Orientations of RNA Backbone Conformations. Benchmark CCSD(T)/CBS Database, Electronic Analysis, and Assessment of DFT Methods and MD Simulations.

    Science.gov (United States)

    Mládek, Arnošt; Banáš, Pavel; Jurečka, Petr; Otyepka, Michal; Zgarbová, Marie; Šponer, Jiří

    2014-01-14

    Sugar-phosphate backbone is an electronically complex molecular segment imparting RNA molecules high flexibility and architectonic heterogeneity necessary for their biological functions. The structural variability of RNA molecules is amplified by the presence of the 2'-hydroxyl group, capable of forming multitude of intra- and intermolecular interactions. Bioinformatics studies based on X-ray structure database revealed that RNA backbone samples at least 46 substates known as rotameric families. The present study provides a comprehensive analysis of RNA backbone conformational preferences and 2'-hydroxyl group orientations. First, we create a benchmark database of estimated CCSD(T)/CBS relative energies of all rotameric families and test performance of dispersion-corrected DFT-D3 methods and molecular mechanics in vacuum and in continuum solvent. The performance of the DFT-D3 methods is in general quite satisfactory. The B-LYP-D3 method provides the best trade-off between accuracy and computational demands. B3-LYP-D3 slightly outperforms the new PW6B95-D3 and MPW1B95-D3 and is the second most accurate density functional of the study. The best agreement with CCSD(T)/CBS is provided by DSD-B-LYP-D3 double-hybrid functional, although its large-scale applications may be limited by high computational costs. Molecular mechanics does not reproduce the fine energy differences between the RNA backbone substates. We also demonstrate that the differences in the magnitude of the hyperconjugation effect do not correlate with the energy ranking of the backbone conformations. Further, we investigated the 2'-hydroxyl group orientation preferences. For all families, we conducted a QM and MM hydroxyl group rigid scan in gas phase and solvent. We then carried out set of explicit solvent MD simulations of folded RNAs and analyze 2'-hydroxyl group orientations of different backbone families in MD. The solvent energy profiles determined primarily by the sugar pucker match well with the

  4. Simulated water productivity in Gansu Province, China

    Science.gov (United States)

    Zhan, Jinyan; Sun, Zhongxiao; Wang, Zhan; Chen, Jiancheng; Li, Zhaohua

    Economic value of water and economic analysis of water use management in Gansu Province of China have attracted widespread public attention. With the socioeconomic development, research on water resources has become more important than before. In this study, we define "water productivity" as the changes of economic production outputs of sectoral activities in every cubic meter of water input, which is also the technical coefficient of water resource use in each sector. According to Computable General Equilibrium (CGE) framework, based on the Input-Output Table 2007 and water resources bulletin of Gansu Province, we introduced the water into the ORANI-G (A Generic Single-Country Computable General Equilibrium model) model through the nested constant elasticity of substitution (CES) production function to analyze the changes of economic productions caused by water supply changes. We then examined water productivity in different sectors. Empirical results showed that current water productivity is underestimated. Agricultural water productivity is lower than that of the secondary and tertiary industries, even although agricultural water use is the largest part of water use in Gansu Province, and therefore improving agricultural water productivity can greatly mitigate the water shortage. Simulation results indicate that industrial transformation and development of water-saving industries will also mitigate water scarcity. Moreover, sensitivity analysis shows that the empirical results are robust under different scenarios. The results also show that higher constant elasticity of substitution rate (CES) between water and other production factors will contribute to sustainable development.

  5. QM/MM MD and free energy simulations of G9a-like protein (GLP and its mutants: understanding the factors that determine the product specificity.

    Directory of Open Access Journals (Sweden)

    Yuzhuo Chu

    Full Text Available Certain lysine residues on histone tails could be methylated by protein lysine methyltransferases (PKMTs using S-adenosyl-L-methionine (AdoMet as the methyl donor. Since the methylation states of the target lysines play a fundamental role in the regulation of chromatin structure and gene expression, it is important to study the property of PKMTs that allows a specific number of methyl groups (one, two or three to be added (termed as product specificity. It has been shown that the product specificity of PKMTs may be controlled in part by the existence of specific residues at the active site. One of the best examples is a Phe/Tyr switch found in many PKMTs. Here quantum mechanical/molecular mechanical (QM/MM molecular dynamics (MD and free energy simulations are performed on wild type G9a-like protein (GLP and its F1209Y and Y1124F mutants for understanding the energetic origin of the product specificity and the reasons for the change of product specificity as a result of single-residue mutations at the Phe/Tyr switch as well as other positions. The free energy barriers of the methyl transfer processes calculated from our simulations are consistent with experimental data, supporting the suggestion that the relative free energy barriers may determine, at least in part, the product specificity of PKMTs. The changes of the free energy barriers as a result of the mutations are also discussed based on the structural information obtained from the simulations. The results suggest that the space and active-site interactions around the ε-amino group of the target lysine available for methyl addition appear to among the key structural factors in controlling the product specificity and activity of PKMTs.

  6. Thermal evolution of nanocrystalline co-sputtered Ni–Zr alloy films: Structural, magnetic and MD simulation studies

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Debarati, E-mail: debarati@barc.gov.in [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Rao, T.V. Chandrasekhar; Bhushan, K.G. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Ali, Kawsar [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Debnath, A. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Singh, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Arya, A. [Material Science Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Bhattacharya, S. [Technical Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Basu, S. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India)

    2015-11-15

    Monophasic and homogeneous Ni{sub 10}Zr{sub 7} nanocrystalline alloy films were successfully grown at room temperature by co-sputtering in an indigenously developed three-gun DC/RF magnetron sputtering unit. The films could be produced with long-range crystallographic and chemical order in the alloy, thus overcoming the widely acknowledged inherent proclivity of the glass forming Ni–Zr couple towards amorphization. Crystallinity of these alloys is a desirable feature with regard to improved efficacy in applications such as hydrogen storage, catalytic activity and nuclear reactor engineering, to name a few. Thermal stability of this crystalline phase, being vital for transition to viable applications, was investigated through systematic annealing of the alloy films at 473 K, 673 K and 923 K for various durations. While the films were stable at 473 K, the effect of annealing at 673 K was to create segregation into nanocrystalline Ni (superparamagnetic) and amorphous Ni + Zr (non-magnetic) phases. Detailed analyses of the physical and magnetic structures before and after annealing were performed through several techniques effectual in analyzing stratified configurations and the findings were all consistent with each other. Polarized neutron and X-ray reflectometry, grazing incidence x-ray diffraction, time-of-flight secondary ion mass spectroscopy and X-ray photoelectron spectroscopy were used to gauge phase separation at nanometer length scales. SQUID based magnetometry was used to investigate macroscopic magnetic properties. Simulated annealing performed on this system using molecular dynamic calculations corroborated well with the experimental results. This study provides a thorough understanding of the creation and thermal evolution of a crystalline Ni–Zr alloy. - Highlights: • Nanocrystalline Ni{sub 10}Zr{sub 7} alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize.

  7. Engagement of CF3 group in N-H···F-C hydrogen bond in the solution state: NMR spectroscopy and MD simulation studies.

    Science.gov (United States)

    Chaudhari, Sachin Rama; Mogurampelly, Santosh; Suryaprakash, N

    2013-01-31

    Unambiguous evidence for the engagement of CF(3) group in N-H···F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional (1)H, (19)F, and natural abundant (15)N NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF(3) groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, (19)F-(19)F NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

  8. Using thermodynamic integration MD simulation to compute relative protein-ligand binding free energy of a GSK3β kinase inhibitor and its analogs.

    Science.gov (United States)

    Lee, Hsing-Chou; Hsu, Wen-Chi; Liu, An-Lun; Hsu, Chia-Jen; Sun, Ying-Chieh

    2014-06-01

    Thermodynamic integration molecular dynamics simulation was used to investigate how TI-MD simulation preforms in reproducing relative protein-ligand binding free energy of a pair of analogous GSK3β kinase inhibitors of available experimental data (see Fig. 1), and to predict the affinity for other analogs. The computation for the pair gave a ΔΔG of 1.0 kcal/mol, which was in reasonably good agreement with the experimental value of -0.1 kcal/mol. The error bar was estimated at 0.5 kcal/mol. Subsequently, we employed the same protocol to proceed with simulations to find analogous inhibitors with a stronger affinity. Four analogs with a substitution at one site inside the binding pocket were the first to be tried, but no significant enhancement in affinity was found. Subsequent simulations for another 7 analogs was focused on substitutions at the benzene ring of another site, which gave two analogs (analogs 9 and 10) with ΔΔG values of -0.6 and -0.8 kcal/mol, respectively. Both analogs had a OH group at the meta position and another OH group at the ortho position at the other side of the benzene ring, as shown in Table 3. To explore further, another 4 analogs with this characteristic were investigated. Three analogs with ΔΔG values of -2.2, -1.7 and -1.2 kcal/mol, respectively, were found. Hydrogen bond analysis suggested that the additional hydrogen bonds of the added OH groups with Gln185 and/or Asn64, which did not appear in the reference inhibitor or as an analog with one substitution only in the examined cases, were the main contributors to an enhanced affinity. A prediction for better inhibitors should interest experimentalists of enzyme and/or cell assays. Analysis of the interactions between GSK3β kinase and the investigated analogs will be useful in the design of GSK3β kinase inhibitors for compounds of this class. Copyright © 2014 Elsevier Inc. All rights reserved.

  9. Muscular Dystrophy (MD)

    Science.gov (United States)

    ... fight respiratory infections. Some individuals may benefit from occupational therapy and assistive technology. Some ... (MD) are a group of more than 30 genetic diseases characterized by progressive weakness and degeneration of the ...

  10. ProtoMD: A prototyping toolkit for multiscale molecular dynamics

    Science.gov (United States)

    Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.

    2016-05-01

    ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters needed in traditional CG-MD methods. The toolkit integrates 'GROMACS wrapper' to initiate MD simulations, and 'MDAnalysis' to analyze and manipulate trajectory files. It facilitates experimentation with a spectrum of coarse-grained variables, prototyping rare events (such as chemical reactions), or simulating nanocharacterization experiments such as terahertz spectroscopy, AFM, nanopore, and time-of-flight mass spectroscopy. ProtoMD is written in python and is freely available under the GNU General Public License from github.com/CTCNano/proto_md.

  11. Adaptive resolution simulation of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Praprotnik, Matej [Max-Planck-Institut fuer Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany); Matysiak, Silvina [Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 77005 (United States); Delle Site, Luigi [Max-Planck-Institut fuer Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany); Kremer, Kurt [Max-Planck-Institut fuer Polymerforschung, Ackermannweg 10, D-55128 Mainz (Germany); Clementi, Cecilia [Department of Chemistry, Rice University, 6100 Main Street, Houston, TX 7700 (United States)

    2007-07-25

    Water plays a central role in biological systems and processes, and is equally relevant in a large range of industrial and technological applications. Being the most important natural solvent, its presence uniquely influences biological function as well as technical processes. Because of their importance, aqueous solutions are among the most experimentally and theoretically studied systems. However, many questions still remain open. Both experiments and theoretical models are usually restricted to specific cases. In particular all-atom simulations of biomolecules and materials in water are computationally very expensive and often not possible, mainly due to the computational effort to obtain water-water interactions in regions not relevant for the problem under consideration. In this paper we present a coarse-grained model that can reproduce the behaviour of liquid water at a standard temperature and pressure remarkably well. The model is then used in a multiscale simulation of liquid water, where a spatially adaptive molecular resolution procedure allows one to change from a coarse-grained to an all-atom representation on-the-fly. We show that this approach leads to the correct description of essential thermodynamic and structural properties of liquid water. Our adaptive multiscale scheme allows for significantly greater extensive simulations than existing approaches by taking explicit water into account only in the regions where the atomistic details are physically relevant. (fast track communication)

  12. Global Cloud Liquid Water Path Simulations(.

    Science.gov (United States)

    Lemus, Lilia; Rikus, Lawrie; Martin, C.; Platt, R.

    1997-01-01

    A new parameterization of cloud liquid water and ice content has been included in the Bureau of Meteorology Global Assimilation and Prediction System. The cloud liquid water content is derived from the mean cloud temperatures in the model using an empirical relationship based on observations. The results from perpetual January and July simulations are presented and show that the total cloud water path steadily decreases toward high latitudes, with two relative maxima at midlatitudes and a peak at low latitudes. To validate the scheme, the simulated fields need to be processed to produce liquid water paths that can be directly compared with the corresponding field derived from Special Sensor Microwave/Imager (SSM/I) data. This requires the identification of cloud ice water content within the parameterization and a prescription to account for the treatment of strongly precipitating subgrid-scale cloud. The resultant cloud liquid water paths agree qualitatively with the SSM/I data but show some systematic errors that are attributed to corresponding errors in the model's simulation of cloud amounts. Given that a more quantitative validation requires substantial improvement in the model's diagnostic cloud scheme, the comparison with the SSM/I data indicates that the cloud water path, derived from the cloud liquid water content parameterization introduced in this paper, is consistent with the observations and can be usefully incorporated in the prediction system.

  13. Simulating water markets with transaction costs

    Science.gov (United States)

    Erfani, Tohid; Binions, Olga; Harou, Julien J.

    2014-06-01

    This paper presents an optimization model to simulate short-term pair-wise spot-market trading of surface water abstraction licenses (water rights). The approach uses a node-arc multicommodity formulation that tracks individual supplier-receiver transactions in a water resource network. This enables accounting for transaction costs between individual buyer-seller pairs and abstractor-specific rules and behaviors using constraints. Trades are driven by economic demand curves that represent each abstractor's time-varying water demand. The purpose of the proposed model is to assess potential hydrologic and economic outcomes of water markets and aid policy makers in designing water market regulations. The model is applied to the Great Ouse River basin in Eastern England. The model assesses the potential weekly water trades and abstractions that could occur in a normal and a dry year. Four sectors (public water supply, energy, agriculture, and industrial) are included in the 94 active licensed water diversions. Each license's unique environmental restrictions are represented and weekly economic water demand curves are estimated. Rules encoded as constraints represent current water management realities and plausible stakeholder-informed water market behaviors. Results show buyers favor sellers who can supply large volumes to minimize transactions. The energy plant cooling and agricultural licenses, often restricted from obtaining water at times when it generates benefits, benefit most from trades. Assumptions and model limitations are discussed. This article was corrected on 13 JUN 2014. See the end of the full text for details.

  14. MD-2 binds cholesterol.

    Science.gov (United States)

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  15. Scenario simulation of water security in China

    Institute of Scientific and Technical Information of China (English)

    OUYANG Zhi-yun; ZHAO Tong-qian; WANG Ru-song; Leif S(O)RLUND; ZHANG Qiao-xian

    2004-01-01

    Limited water resources, increasing demand, low use efficiency, and serious pollution result in severe water resource difficult in China. The evaluation of addressing water problems and the search for effective countermeasures that ensure sustainable water use are key to China's sustainable development. The "compound water security" consists of food security, life security, environmental security, and economic security. By establishing a conceptual model, the water security of China has been simulated in terms of four scenarios called BAU(the business-as-usual scenario), TEC(the technology and economics scenario), IVL(the institution, values, and lifestyles scenario) and TSD(toward sustainable development) in this paper. The results indicated that water crises, especially water shortages, are being experienced now and will continue to do so for a relatively long time in China and that it is possible to reach a basic balance between supply and demand of water and grain under the TSD developing pattern by a series of approaches including technological innovation, policy adjustments, and behaviour inducement.

  16. Ab Initio MD Simulations of the Brønsted Acidity of Glutathione in Aqueous Solutions: Predicting pKa Shifts of the Cysteine Residue.

    Science.gov (United States)

    Tummanapelli, Anil Kumar; Vasudevan, Sukumaran

    2015-12-10

    The tripeptide glutathione (GSH) is one of the most abundant peptides and the major repository for nonprotein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thiol-disulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influence the redox couple, and hence the pKa value of the cysteine residue of GSH is critical to its functioning. Here we report ab initio Car-Parrinello molecular dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. We show that the free-energy landscape for the protonation-deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared with the isolated cysteine amino acid.

  17. Interaction between water molecules and zinc sulfide nanoparticles studied by temperature-programmed desorption and molecular dynamics simulations.

    Science.gov (United States)

    Zhang, Hengzhong; Rustad, James R; Banfield, Jillian F

    2007-06-14

    We have investigated the bonding of water molecules to the surfaces of ZnS nanoparticles (approximately 2-3 nm sphalerite) using temperature-programmed desorption (TPD). The activation energy for water desorption was derived as a function of the surface coverage through kinetic modeling of the experimental TPD curves. The binding energy of water equals the activation energy of desorption if it is assumed that the activation energy for adsorption is nearly zero. Molecular dynamics (MD) simulations of water adsorption on 3 and 5 nm sphalerite nanoparticles provided insights into the adsorption process and water binding at the atomic level. Water binds with the ZnS nanoparticle surface mainly via formation of Zn-O bonds. As compared with bulk ZnS crystals, ZnS nanoparticles can adsorb more water molecules per unit surface area due to the greatly increased curvature, which increases the distance between adjacent adsorbed molecules. Results from both TPD and MD show that the water binding energy increases with decreasing the water surface coverage. We attribute the increase in binding energy with decreasing surface water coverage to the increasing degree of surface under-coordination as removal of water molecules proceeds. MD also suggests that the water binding energy increases with decreasing particle size due to the further distance and hence lower interaction between adsorbed water molecules on highly curved smaller particle surfaces. Results also show that the binding energy, and thus the strength of interaction of water, is highest in isolated nanoparticles, lower in nanoparticle aggregates, and lowest in bulk crystals. Given that water binding is driven by surface energy reduction, we attribute the decreased binding energy for aggregated as compared to isolated particles to the decrease in surface energy that occurs as the result of inter-particle interactions.

  18. Combined phase-field and MD simulations of diffusion drop and ordering at [Ni{sub x}Zr{sub 1-x}]{sub liquid}-Zr{sub crystal} interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Guerdane, M.; Wendler, F.; Nestler, B. [Institute of Materials and Processes, Karlsruhe University of Applied Sciences (Germany)

    2010-07-01

    We combine phase-field (PF) modeling and molecular dynamics (MD) simulations to show that the velocity of the solidification front in a two-phase [Ni{sub x}Zr{sub 1-x}]{sub liquid}-Zr{sub crystal} structure is strongly affected by the drop of the liquid diffusion when approaching the solid-liquid interface. The latter is defined through a suitable order parameter that distinguishes between crystalline and liquid atomic environment. The diffusion drop near the interface is attributed to the pronounced short range order inherent to the Ni{sub x}Zr{sub 1-x} melt. The system transforms into a massive lateral ordering in the vicinity of the Zr crystalline wall. Our combined PF-MD analysis points out the shortcoming of the standard interpolation procedure, usually applied in constructing the phase dependent diffusivity, to describe the confinement effect caused by the crystalline wall at low temperatures.

  19. TES buffer-induced phase separation of aqueous solutions of several water-miscible organic solvents at 298.15 K: phase diagrams and molecular dynamic simulations.

    Science.gov (United States)

    Taha, Mohamed; Lee, Ming-Jer

    2013-06-28

    Water and the organic solvents tetrahydrofuran, 1,3-dioxolane, 1,4-dioxane, 1-propanol, 2-propanol, tert-butanol, acetonitrile, or acetone are completely miscible in all proportions at room temperature. Here, we present new buffering-out phase separation systems that the above mentioned organic aqueous solutions can be induced to form two liquid phases in the presence of a biological buffer 2-[[1,3-dihydroxy-2-(hydroxymethyl)propan-2-yl]amino]ethanesulfonic acid (TES). The lower liquid phase is rich in water and buffer, and the upper phase is organic rich. This observation has both practical and mechanistic interests. The phase diagrams of these systems were constructed by experimental measurements at ambient conditions. Molecular dynamic (MD) simulations were performed for TES + water + THF system to understand the interactions between TES, water, and organic solvent at molecular level. Several composition-sets for this system, beyond and inside the liquid-liquid phase-splitting region, have been simulated. Interestingly, the MD simulation for compositions inside the phase separation region showed that THF molecules are forced out from the water network to start forming a new liquid phase. The hydrogen-bonds, hydrogen-bonds lifetimes, hydrogen-bond energies, radial distribution functions, coordination numbers, the electrostatic interactions, and the van der Waals interactions between the different pairs have been calculated. Additionally, MD simulations for TES + water + tert-butanol∕acetonitrile∕acetone phase separation systems were simulated. The results from MD simulations provide an explanation for the buffering-out phenomena observed in [TES + water + organic solvent] systems by a mechanism controlled by the competitive interactions of the buffer and the organic solvent with water. The molecular mechanism reported here is helpful for designing new benign separation materials.

  20. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

    Science.gov (United States)

    2015-01-01

    The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect

  1. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes.

    Science.gov (United States)

    König, Gerhard; Hudson, Phillip S; Boresch, Stefan; Woodcock, H Lee

    2014-04-08

    THE RELIABILITY OF FREE ENERGY SIMULATIONS (FES) IS LIMITED BY TWO FACTORS: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect

  2. Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

    Science.gov (United States)

    Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

    2016-12-07

    Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

  3. All-atom Molecular Dynamic Simulations Combined with the Chemical Shifts Study on the Weak Interactions of Ethanol-water System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Rong; LUO San-Lai; WU Wen-Juan

    2008-01-01

    All-atom molecular dynamics(MD)simulation combined with chemical shifts was performed to investigate the interactions over the entire concentration range of the ethanol(EtOH)-water system.The results of the simulation were adopted to explain the NMR experiments by hydrogen bonding analysis.The strong hydrogen bonds and weak C-H…O contacts coexist in the mixtures through the analysis of the radial distribution functions.And the liquid structures in the whole concentration of EtOH-water mixtures can be classified into three regions by the statistic analysis of the hydrogen-bonding network in the MD simulations.Moreover,the chemical shifts of the hydrogen atom are in agreement witb the statistical results of the average number hydrogen bonds in the MD simulations.Interestingly,the excess relative extent Eηrel calculated by the MD simulations and chemical shifts in the EtOH aqueous solutions shows the largest deviation at XEtOH≈0.18.The excess properties present good agreement with the excess enthalpy in the concentration dependence.

  4. 33 CFR 110.72 - Blackhole Creek, Md.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Blackhole Creek, Md. 110.72... ANCHORAGE REGULATIONS Special Anchorage Areas § 110.72 Blackhole Creek, Md. The waters on the west side of Blackhole Creek, a tributary of Magothy River, southwest of a line bearing 310°30′ from the most...

  5. Predict the glass transition temperature of glycerol-water binary cryoprotectant by molecular dynamic simulation.

    Science.gov (United States)

    Li, Dai-Xi; Liu, Bao-Lin; Liu, Yi-shu; Chen, Cheng-lung

    2008-04-01

    Vitrification is proposed to be the best way for the cryopreservation of organs. The glass transition temperature (T(g)) of vitrification solutions is a critical parameter of fundamental importance for cryopreservation by vitrification. The instruments that can detect the thermodynamic, mechanical and dielectric changes of a substance may be used to determine the glass transition temperature. T(g) is usually measured by using differential scanning calorimetry (DSC). In this study, the T(g) of the glycerol-aqueous solution (60%, wt/%) was determined by isothermal-isobaric molecular dynamic simulation (NPT-MD). The software package Discover in Material Studio with the Polymer Consortium Force Field (PCFF) was used for the simulation. The state parameters of heat capacity at constant pressure (C(p)), density (rho), amorphous cell volume (V(cell)) and specific volume (V(specific)) and radial distribution function (rdf) were obtained by NPT-MD in the temperature range of 90-270K. These parameters showed a discontinuity at a specific temperature in the plot of state parameter versus temperature. The temperature at the discontinuity is taken as the simulated T(g) value for glycerol-water binary solution. The T(g) values determined by simulation method were compared with the values in the literatures. The simulation values of T(g) (160.06-167.51K) agree well with the DSC results (163.60-167.10K) and the DMA results (159.00K). We drew the conclusion that molecular dynamic simulation (MDS) is a potential method for investigating the glass transition temperature (T(g)) of glycerol-water binary cryoprotectants and may be used for other vitrification solutions.

  6. Resilience Simulation for Water, Power & Road Networks

    Science.gov (United States)

    Clark, S. S.; Seager, T. P.; Chester, M.; Eisenberg, D. A.; Sweet, D.; Linkov, I.

    2014-12-01

    The increasing frequency, scale, and damages associated with recent catastrophic events has called for a shift in focus from evading losses through risk analysis to improving threat preparation, planning, absorption, recovery, and adaptation through resilience. However, neither underlying theory nor analytic tools have kept pace with resilience rhetoric. As a consequence, current approaches to engineering resilience analysis often conflate resilience and robustness or collapse into a deeper commitment to the risk analytic paradigm proven problematic in the first place. This research seeks a generalizable understanding of resilience that is applicable in multiple disciplinary contexts. We adopt a unique investigative perspective by coupling social and technical analysis with human subjects research to discover the adaptive actions, ideas and decisions that contribute to resilience in three socio-technical infrastructure systems: electric power, water, and roadways. Our research integrates physical models representing network objects with examination of the knowledge systems and social interactions revealed by human subjects making decisions in a simulated crisis environment. To ensure a diversity of contexts, we model electric power, water, roadway and knowledge networks for Phoenix AZ and Indianapolis IN. We synthesize this in a new computer-based Resilient Infrastructure Simulation Environment (RISE) to allow individuals, groups (including students) and experts to test different network design configurations and crisis response approaches. By observing simulated failures and best performances, we expect a generalizable understanding of resilience may emerge that yields a measureable understanding of the sensing, anticipating, adapting, and learning processes that are essential to resilient organizations.

  7. Molecular origin of drug release by water boiling inside carbon nanotubes from reactive molecular dynamics simulation and DFT perspectives.

    Science.gov (United States)

    Ganji, M Darvish; Mirzaei, Sh; Dalirandeh, Z

    2017-07-05

    Owing to their nanosized hollow cylindrical structure, CNTs hold the promise to be utilized as desired materials for encapsulating molecules which demonstrate wide inferences in drug delivery. Here we evaluate the possibility of drug release from the CNTs with various types and edge chemistry by reactive MD simulation to explain the scientifically reliable relations for proposed process. It was shown that heating of CNTs (up to 750 K) cannot be used for release of incorporated drug (phenylalanine) into water and even carbonated water solvent with very low boiling temperature. This is due to the strong physisorption (π-stacking interaction) between the aromatic of encapsulated drug and CNT sidewall which causes the drug to bind the nanotube sidewall. We have further investigated the interaction nature and release mechanism of water and drug confined/released within/from the CNTs by DFT calculations and the results confirmed our MD simulation findings. The accuracy of DFT method was also validated against the experimental and theoretical values at MP2/CCSD level. Therefore, we find that boiling of water/carbonated water confined within the CNTs could not be a suitable technique for efficient drug release. Our atomistic simulations provide a well-grounded understanding for the release of drug molecules confined within CNTs.

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

    Science.gov (United States)

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

    2013-04-02

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

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

    KAUST Repository

    Lardhi, Sheikha F.

    2013-05-01

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

  10. Polymer and Water Dynamics in Poly(vinyl alcohol/Poly(methacrylate Networks. A Molecular Dynamics Simulation and Incoherent Neutron Scattering Investigation

    Directory of Open Access Journals (Sweden)

    Ester Chiessi

    2011-10-01

    Full Text Available Chemically cross-linked polymer networks of poly(vinyl alcohol/poly(methacrylate form monolitic hydrogels and microgels suitable for biomedical applications, such as in situ tissue replacement and drug delivery. In this work, molecular dynamics (MD simulation and incoherent neutron scattering methods are used to study the local polymer dynamics and the polymer induced modification of water properties in poly(vinyl alcohol/poly(methacrylate hydrogels. This information is particularly relevant when the diffusion of metabolites and drugs is a requirement for the polymer microgel functionality. MD simulations of an atomic detailed model of the junction domain at the experimental hydration degree were carried out at 283, 293 and 313 K. The polymer-water interaction, the polymer connectivity and the water dynamics were investigated as a function of temperature. Simulation results are compared with findings of elastic and quasi-elastic incoherent neutron scattering measurements, experimental approaches which sample the same space-time window of MD simulations. This combined analysis shows a supercooled water component and an increase of hydrophilicity and mobility with temperature of these amphiphilic polymer networks.

  11. Molecular dynamic simulations of iron (II) hydroxide in high temperature and supercritical water

    Science.gov (United States)

    Meng, Yuanliang

    In this study, the iron (II) hydroxide -- water system has been investigated at high temperatures by using molecular dynamics (MD) simulations. The simulation results reveal that at infinite dilution both Fe2+ cation and OH- anion have 6 water molecules within their first hydration shell and both types of ionic species experience a dramatic increase in their diffusion coefficients at near and supercritical conditions. The process of iron (II) hydroxide cluster formation has been simulated. The nano-clusters of larger sizes formed in supercritical water tend to be in an amorphous state. After having been quenched by an inert gas bath, iron (II) hydroxide nano-clusters with various structures have been produced. The geometries and associated binding energies of these species are given in detail. The vibrational spectra of iron (II) hydroxide clusters are also derived and compared with the spectrum of a bulk solid. The obtained results have a practical value for the analysis of potential corrosion products in supercritical water-cooled reactor (SCWR) which is employed in the new generation nuclear power plant design (GEN IV). This work also illustrates the process of hydrothermal synthesis of oxide nano-particles.

  12. Simulating Water Markets to Help Design Water Rights Regimes

    Science.gov (United States)

    Harou, J. J.; Erfani, T.; Huskova, I.; Binions, O.

    2012-12-01

    In many catchments in England no further licenses are available from the Environmental regulator that provides them. The possibility of trading water between license holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. Although trading licenses has been possible since several years, it very rarely happens (roughly 50 trades in 8 years). Several barriers to trade exist including lack of sufficient and prolonged scarcity, license-holder unwillingness to risk future renewal, likelihood license will be downgraded during a trade, duration of time required for approving a trade, etc. Regulators seek to make policy changes so that their inability to grant new licenses will not harm the local and national economy. What policy changes will most cost-effectively increase trading and allow it to effectively reduce the economic cost of scarcity events? A screening tool that could help evaluate problems and advantages of different regulatory solutions, and that could serve to test, assuming transaction costs can be quantified, their effect on trading under specific conditions would be useful. We propose such a water market simulator that predicts economically efficient pair-wise trade (between willing buyers and sellers) and represents the interaction of trades with natural hydrological flows, engineered infrastructure and a particular regulatory regime. The model emulates license-holders' willingness to engage in short-term trade transactions. In their initial form different 'agents' (license holders) are represented using an economic benefit function of water use which is supplemented by rules to represent behavioral or other characteristics of realistic system behavior. A case study based on the river Ouse basin (UK) is made to test the model. The model simulates the catchment weekly over several years considering reservoirs and pair-wise specific transaction costs. Several regulatory policies are tested

  13. Analysis of Mesoscopic Structured 2-Propanol/Water Mixtures Using Pressure Perturbation Calorimetry and Molecular Dynamic Simulation.

    Science.gov (United States)

    Bye, Jordan W; Freeman, Colin L; Howard, John D; Herz, Gregor; McGregor, James; Falconer, Robert J

    2017-01-01

    In this paper we demonstrate the application of pressure perturbation calorimetry (PPC) to the characterization of 2-propanol/water mixtures. PPC of different 2-propanol/water mixtures provides two useful measurements: (i) the change in heat (ΔQ); and (ii) the [Formula: see text] value. The results demonstrate that the ΔQ values of the mixtures deviate from that expected for a random mixture, with a maximum at ~20-25 mol% 2-propanol. This coincides with the concentration at which molecular dynamics (MD) simulations show a maximum deviation from random distribution, and also the point at which alcohol-alcohol hydrogen bonds become dominant over alcohol-water hydrogen bonds. Furthermore, the [Formula: see text] value showed transitions at 2.5 mol% 2-propanol and at approximately 14 mol% 2-propanol. Below 2.5 mol% 2-propanol the values of [Formula: see text] are negative; this is indicative of the presence of isolated 2-propanol molecules surrounded by water molecules. Above 2.5 mol% 2-propanol [Formula: see text] rises, reaching a maximum at ~14 mol% corresponding to a point where mixed alcohol-water networks are thought to dominate. The values and trends identified by PPC show excellent agreement not only with those obtained from MD simulations but also with results in the literature derived using viscometry, THz spectroscopy, NMR and neutron diffraction.

  14. Arnold Aberman, MD.

    Science.gov (United States)

    Aberman, A

    1995-10-01

    When the United States embarked on its effort to provide universal health insurance, the Canadian Medicare System was cited as a possible model for American health care. Often touted as an example of low-cost, high quality medicine, the Canadian system has mirrored the problems of health care across its southern border. With rocketing health care expenditures and financing having largely been decentralized to the individual provinces, local officials have struggled to cut costs and services. A central focus of these efforts has been a move to decrease the numbers of physicians, most notably a 10% decrease in medical school class size in 1993. While some Western provinces have experimented with the privatization of health care, the Canadian system still remains the epitome of government operated fee-for-service medicine. Given the likelihood of dramatic change in the American Medicare system, Canadian academic centers offer a unique perspective on the impact of capitation, evolving relationships with government payors, and the flip side of market oriented reforms. At the helm of one of Canada's largest schools is Arnold Aberman, MD, dean of the University of Toronto Faculty of Medicine. Born in Montreal, Quebec, Aberman received his MD from McGill University, but then did his residency both in Canada and the US, followed by a pulmonary fellowship at Albert Einstein College of Medicine and the Cardiovascular Research Institute of the University of California, San Francisco. Interviewed at his office in Toronto, Aberman reflected on the trials and tribulations confronting medicine on both sides of the 48th parallel.

  15. Simulations of asteroid impacts on water

    Science.gov (United States)

    Gisler, G. R.; Weaver, R. P.; Gittings, M. L.

    2002-05-01

    We have performed a series of two-dimensional and three-dimensional simulations of asteroid impacts into an ocean using the SAGE code from Los Alamos National Laboratory and Science Applications International Corporation. The SAGE code is a compressible Eulerian hydrodynamics code using continuous adaptive mesh refinement for following discontinuities with a fine grid while treating the bulk of the simulation more coarsely. We have used realistic equations of state for the atmosphere, sea water, the oceanic crust and mantle. In two dimensions, we threw asteroid impactors at 20 km/s vertically through an exponential atmosphere into a 5 km deep ocean. The impactors were composed of mantle material (3.32 g/cc) with diameters of 250m, 500m, and 1000m, chosen to compare with the previous work of Crawford and Mader. We also performed some runs with asteroids composed of iron (7.8 g/cc). Because some of the iron asteroids produced craters that penetrated the basalt crust, we included a layer of mantle material in all simulations. A vertical impact produces a large underwater cavity with nearly vertical walls followed by a collapse starting from the bottom and subsequent vertical jetting. Tsunamis up to a kilometer in initial height were generated and followed out to 100 km from the point of impact. In the three-dimensional run, an impactor of iron was thrown at 20 km/s at an angle of 45 degrees. Differences between this run and the vertical two-dimensional runs will be discussed.

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

    Science.gov (United States)

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

    2013-07-01

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

  17. Integrated Water Resources Simulation Model for Rural Community

    Science.gov (United States)

    Li, Y.-H.; Liao, W.-T.; Tung, C.-P.

    2012-04-01

    The purpose of this study is to develop several water resources simulation models for residence houses, constructed wetlands and farms and then integrate these models for a rural community. Domestic and irrigation water uses are the major water demand in rural community. To build up a model estimating domestic water demand for residence houses, the average water use per person per day should be accounted first, including water uses of kitchen, bathroom, toilet and laundry. On the other hand, rice is the major crop in the study region, and its productive efficiency sometimes depends on the quantity of irrigation water. The water demand can be estimated by crop water use, field leakage and water distribution loss. Irrigation water comes from rainfall, water supply system and reclaimed water which treated by constructed wetland. In recent years, constructed wetlands play an important role in water resources recycle. They can purify domestic wastewater for water recycling and reuse. After treating from constructed wetlands, the reclaimed water can be reused in washing toilets, watering gardens and irrigating farms. Constructed wetland is one of highly economic benefits for treating wastewater through imitating the processing mechanism of natural wetlands. In general, the treatment efficiency of constructed wetlands is determined by evapotranspiration, inflow, and water temperature. This study uses system dynamics modeling to develop models for different water resource components in a rural community. Furthermore, these models are integrated into a whole system. The model not only is utilized to simulate how water moves through different components, including residence houses, constructed wetlands and farms, but also evaluates the efficiency of water use. By analyzing the flow of water, the water resource simulation model can optimizes water resource distribution under different scenarios, and the result can provide suggestions for designing water resource system of a

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

    Science.gov (United States)

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

    2017-09-08

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

  19. ADT fast losses MD

    CERN Document Server

    Priebe, A; Dehning, B; Redaelli, S; Salvachua Ferrando, BM; Sapinski, M; Solfaroli Camillocci, M; Valuch, D

    2013-01-01

    The fast beam losses in the order of 1 ms are expected to be a potential major luminosity limitation for higher beam energies after the LHC long shutdown (LS1). Therefore a Quench Test is planned in the winter 2013 to estimate the quench limit in this timescale and revise the current models. This experiment was devoted to determination the LHC Transverse Damper (ADT) as a system for fast losses induction. A non-standard operation of the ADT was used to develop the beam oscillation instead of suppressing them. The sign flip method had allowed us to create the fast losses within several LHC turns at 450 GeV during the previous test (26th March 2012). Thus, the ADT could be potentially used for the studies of the UFO ("Unidentied Falling Object") impact on the cold magnets. Verification of the system capability and investigations of the disturbed beam properties were the main objectives of this MD. During the experiment, the pilot bunches of proton beam were excited independently in the horizontal and vertical ...

  20. Full molecular dynamics simulations of liquid water and carbon tetrachloride for two-dimensional Raman spectroscopy in the frequency domain

    CERN Document Server

    Jo, Ju-Yeon; Tanimura, Yoshitaka

    2016-01-01

    Frequency-domain two-dimensional Raman signals, which are equivalent to coherent two-dimensional Raman scattering (COTRAS) signals, for liquid water and carbon tetrachloride were calculated using an equilibrium-nonequilibrium hybrid MD simulation algorithm. We elucidate mechanisms governing the 2D signal pro?les involving anharmonic mode-mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal pro?les and intensities can be utilized to analyze recently developed single-beam 2D spectra, whose signals are generated from a coherently controlled pulse, allowing the single-beam measurement to be carried out more efficiently.

  1. Adaptive resolution simulation of an atomistic protein in MARTINI water

    NARCIS (Netherlands)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-01-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coa

  2. Water-mediated conformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, quantum mechanics based calculations, and experimental data.

    Science.gov (United States)

    Cruz, Víctor; Ramos, Javier; Martínez-Salazar, Javier

    2011-04-28

    An exhaustive umbrella sampling simulation of the alanine dipeptide in solution is reported. The presence of stable Y conformations in solution is assessed by both quantum calculations and experimental data from X-ray and NMR protein-solved structures available in the protein coil library. The agreement between experimental and simulation Ramachandran plots of the dipeptide in solution is excellent. A suitable explanation of the stabilization of the Y conformation mediated by water for the alanine dipeptide is discussed on the basis of Car-Parrinello MD calculations of the dipeptide in water.

  3. DSMC simulation of Europa water vapor plumes

    Science.gov (United States)

    Berg, J. J.; Goldstein, D. B.; Varghese, P. L.; Trafton, L. M.

    2016-10-01

    A computational investigation of the physics of water vapor plumes on Europa was performed with a focus on characteristics relevant to observation and spacecraft mission operations. The direct simulation Monte Carlo (DSMC) method was used to model the plume expansion assuming a supersonic vent source. The structure of the plume was determined, including the number density, temperature, and velocity fields. The possibility of ice grain growth above the vent was considered and deemed probable for large (diameter > ∼20 m) vents at certain Mach numbers. Additionally, preexisting grains of three diameters (0.1, 1, 50 μm) were included and their trajectories examined. A preliminary study of photodissociation of H2O into OH and H was performed to demonstrate the behavior of daughter species. A set of vent parameters was evaluated including Mach number (Mach 2, 3, 5), reduced temperature as a proxy for flow energy loss to the region surrounding the vent, and mass flow rate. Plume behavior was relatively insensitive to these factors, with the notable exception of mass flow rate. With an assumed mass flow rate of ∼1000 kg/s, a canopy shock occurred and a maximum integrated line of sight column density of ∼1020 H2O molecules/m2 was calculated, comparing favorably with observation (Roth et al., 2014a).

  4. Data driven, predictive molecular dynamics for nanoscale flow simulations under uncertainty.

    Science.gov (United States)

    Angelikopoulos, Panagiotis; Papadimitriou, Costas; Koumoutsakos, Petros

    2013-11-27

    For over five decades, molecular dynamics (MD) simulations have helped to elucidate critical mechanisms in a broad range of physiological systems and technological innovations. MD simulations are synergetic with experiments, relying on measurements to calibrate their parameters and probing "what if scenarios" for systems that are difficult to investigate experimentally. However, in certain systems, such as nanofluidics, the results of experiments and MD simulations differ by several orders of magnitude. This discrepancy may be attributed to the spatiotemporal scales and structural information accessible by experiments and simulations. Furthermore, MD simulations rely on parameters that are often calibrated semiempirically, while the effects of their computational implementation on their predictive capabilities have only been sporadically probed. In this work, we show that experimental and MD investigations can be consolidated through a rigorous uncertainty quantification framework. We employ a Bayesian probabilistic framework for large scale MD simulations of graphitic nanostructures in aqueous environments. We assess the uncertainties in the MD predictions for quantities of interest regarding wetting behavior and hydrophobicity. We focus on three representative systems: water wetting of graphene, the aggregation of fullerenes in aqueous solution, and the water transport across carbon nanotubes. We demonstrate that the dominant mode of calibrating MD potentials in nanoscale fluid mechanics, through single values of water contact angle on graphene, leads to large uncertainties and fallible quantitative predictions. We demonstrate that the use of additional experimental data reduces uncertainty, improves the predictive accuracy of MD models, and consolidates the results of experiments and simulations.

  5. Mesoscopic Simulation of Aggregates in Surfactant/Oil/Water Systems

    Institute of Scientific and Technical Information of China (English)

    苑世领; 蔡政亭; 徐桂英

    2003-01-01

    The aggregates in sodium dedecylsulphate(SDS)/dimethylbenzene/water systems have been investigated using dissipative particles dynamic(DPD) simulation method.Through analyzing three-dimensional structures of aggregates,three simulated results are found.One is the phase separation,which is clearly observed by water density and the aggregates in the simulated cell;another is the water morphology in reverse micelle,which can be found through the isodensity slice of water including bound water,trapped water and bulky water;the third is about the water/oil interface,i.e.,ionic surfactant molecules,SDS,prefer to exist in the interface between water and oil phase at the low concentraion.

  6. Molecular dynamics simulations of triflic acid and triflate ion/water mixtures: a proton conducting electrolytic component in fuel cells.

    Science.gov (United States)

    Sunda, Anurag Prakash; Venkatnathan, Arun

    2011-11-30

    Triflic acid is a functional group of perflourosulfonated polymer electrolyte membranes where the sulfonate group is responsible for proton conduction. However, even at extremely low hydration, triflic acid exists as a triflate ion. In this work, we have developed a force-field for triflic acid and triflate ion by deriving force-field parameters using ab initio calculations and incorporated these parameters with the Optimized Potentials for Liquid Simulations - All Atom (OPLS-AA) force-field. We have employed classical molecular dynamics (MD) simulations with the developed force field to characterize structural and dynamical properties of triflic acid (270-450 K) and triflate ion/water mixtures (300 K). The radial distribution functions (RDFs) show the hydrophobic nature of CF(3) group and presence of strong hydrogen bonding in triflic acid and temperature has an insignificant effect. Results from our MD simulations show that the diffusion of triflic acid increases with temperature. The RDFs from triflate ion/water mixtures shows that increasing hydration causes water molecules to orient around the SO(3)(-) group of triflate ions, solvate the hydronium ions, and other water molecules. The diffusion of triflate ions, hydronium ion, and water molecules shows an increase with hydration. At λ = 1, the diffusion of triflate ion is 30 times lower than the diffusion of triflic acid due to the formation of stable triflate ion-hydronium ion complex. With increasing hydration, water molecules break the stability of triflate ion-hydronium ion complex leading to enhanced diffusion. The RDFs and diffusion coefficients of triflate ions, hydronium ions and water molecules resemble qualitatively the previous findings using per-fluorosulfonated membranes.

  7. MD5算法研究%MD5 Algorithm

    Institute of Scientific and Technical Information of China (English)

    张裔智; 赵毅; 汤小斌

    2008-01-01

    随着网络技术的迅速发展,信息加密技术已成为保障网络安全的一种重要手段,加密算法已经成为人们的一个研究热点.本文对MD5算法进行了深入研究,介绍MD5算法的产生背景、应用及其算法流程,并提出了MD5算法的一个改进方案.

  8. Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation.

    Science.gov (United States)

    Cen, Min; Fan, Jian Fen; Liu, Dong Yan; Song, Xue Zeng; Liu, Jian; Zhou, Wei Qun; Xiao, He Ming

    2013-02-01

    Molecular dynamic (MD) simulations have been performed to study the behaviors of ten kinds of cyclo-hexa-peptides (CHPs) composed of amino acids with the diverse hydrophilic/hydrophobic side chains at the water/cyclohexane interface. All the CHPs take the "horse-saddle" conformations at the interface and the hydrophilicity/hydrophobicity of the side chains influences the backbones' structural deformations. The orientations and distributions of the CHPs at the interface and the differences of interaction energies (ΔΔE) between the CHPs and the two liquid phases have been determined. RDF analysis shows that the H-bonds were formed between the O(C) atoms of the CHPs' backbones and H(w) atoms of water molecules. N atoms of the CHPs' backbones formed the H-bonds or van der Waals interactions with the water solvent. It was found that there is a parallel relationship between ΔΔE and the lateral diffusion coefficients (D ( xy )) of the CHPs at the interface. The movements of water molecules close to the interface are confined to some extent, indicating that the dynamics of the CHPs and interfacial water molecules are strongly coupled.

  9. Computer simulation of the NASA water vapor electrolysis reactor

    Science.gov (United States)

    Bloom, A. M.

    1974-01-01

    The water vapor electrolysis (WVE) reactor is a spacecraft waste reclamation system for extended-mission manned spacecraft. The WVE reactor's raw material is water, its product oxygen. A computer simulation of the WVE operational processes provided the data required for an optimal design of the WVE unit. The simulation process was implemented with the aid of a FORTRAN IV routine.

  10. Launch Environment Water Flow Simulations Using Smoothed Particle Hydrodynamics

    Science.gov (United States)

    Vu, Bruce T.; Berg, Jared J.; Harris, Michael F.; Crespo, Alejandro C.

    2015-01-01

    This paper describes the use of Smoothed Particle Hydrodynamics (SPH) to simulate the water flow from the rainbird nozzle system used in the sound suppression system during pad abort and nominal launch. The simulations help determine if water from rainbird nozzles will impinge on the rocket nozzles and other sensitive ground support elements.

  11. Unraveling the dynamics and structure of functionalized self-assembled monolayers on gold using 2D IR spectroscopy and MD simulations.

    Science.gov (United States)

    Yan, Chang; Yuan, Rongfeng; Pfalzgraff, William C; Nishida, Jun; Wang, Lu; Markland, Thomas E; Fayer, Michael D

    2016-05-03

    Functionalized self-assembled monolayers (SAMs) are the focus of ongoing investigations because they can be chemically tuned to control their structure and dynamics for a wide variety of applications, including electrochemistry, catalysis, and as models of biological interfaces. Here we combine reflection 2D infrared vibrational echo spectroscopy (R-2D IR) and molecular dynamics simulations to determine the relationship between the structures of functionalized alkanethiol SAMs on gold surfaces and their underlying molecular motions on timescales of tens to hundreds of picoseconds. We find that at higher head group density, the monolayers have more disorder in the alkyl chain packing and faster dynamics. The dynamics of alkanethiol SAMs on gold are much slower than the dynamics of alkylsiloxane SAMs on silica. Using the simulations, we assess how the different molecular motions of the alkyl chain monolayers give rise to the dynamics observed in the experiments.

  12. The molecular mechanism of bisphenol A (BPA as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD simulations.

    Directory of Open Access Journals (Sweden)

    Lanlan Li

    Full Text Available Bisphenol A (BPA can interact with nuclear receptors and affect the normal function of nuclear receptors in very low doses, which causes BPA to be one of the most controversial endocrine disruptors. However, the detailed molecular mechanism about how BPA interferes the normal function of nuclear receptors is still undiscovered. Herein, molecular dynamics simulations were performed to explore the detailed interaction mechanism between BPA with three typical nuclear receptors, including hERα, hERRγ and hPPARγ. The simulation results and calculated binding free energies indicate that BPA can bind to these three nuclear receptors. The binding affinities of BPA were slightly lower than that of E2 to these three receptors. The simulation results proved that the binding process was mainly driven by direct hydrogen bond and hydrophobic interactions. In addition, structural analysis suggested that BPA could interact with these nuclear receptors by mimicking the action of natural hormone and keeping the nuclear receptors in active conformations. The present work provided the structural evidence to recognize BPA as an endocrine disruptor and would be important guidance for seeking safer substitutions of BPA.

  13. Folding Thermodynamics and Mechanism of Five Trp-Cage Variants from Replica-Exchange MD Simulations with RSFF2 Force Field.

    Science.gov (United States)

    Zhou, Chen-Yang; Jiang, Fan; Wu, Yun-Dong

    2015-11-10

    To test whether our recently developed residue-specific force field RSFF2 can reproduce the mutational effect on the thermal stability of Trp-cage mini-protein and decipher its detailed folding mechanism, we carried out long-time replica-exchange molecular dynamics (REMD) simulations on five Trp-cage variants, including TC5b and TC10b. Initiated from their unfolded structures, the simulations not only well-reproduce their experimental structures but also their melting temperatures and folding enthalpies reasonably well. For each Trp-cage variant, the overall folding free energy landscape is apparently two-state, but some intermediate states can be observed when projected on more detailed coordinates. We also found different variants have the same major folding pathway, including the well formed PII-helix in the unfolded state, the formation of W6-P12/P18/P19 contacts and the α-helix before the transition state, the following formation of most native contacts, and the final native loop formation. The folding mechanism derived here is consistent with many previous simulations and experiments.

  14. Molecular Dynamics Simulations of the Nucleation of Water: Determining the Sticking Probability and Formation Energy of a Cluster

    CERN Document Server

    Tanaka, Kyoko K; Tanaka, Hidekazu

    2014-01-01

    We performed molecular dynamics (MD) simulations of the nucleation of water vapor in order to test nucleation theories. Simulations were performed for a wide range of supersaturation ratios (S = 3-25) and water temperatures (Tw=300-390K). We obtained the nucleation rates and the formation free energies of a subcritical cluster from the cluster size distribution. The classical nucleation theory (CNT) and the modified classical nucleation theory (MCNT) overestimate the nucleation rates in all cases. The semi-phenomenological (SP) model, which corrects the MCNT prediction using the second virial coefficient of a vapor, reproduces the formation free energy of a cluster with the size < 20 to within 10 % and the nucleation rate and cluster size distributions to within one order of magnitude. The sticking probability of the vapor molecules to the clusters was also determined from the growth rates of the clusters. The sticking probability rapidly increases with the supersaturation ratio S, which is similar to the ...

  15. Molecular dynamics simulations of water confined between matched pairs of hydrophobic and hydrophilic self-assembled monolayers.

    Energy Technology Data Exchange (ETDEWEB)

    Chandross, Michael Evan; Grest, Gary Stephen; Lane, J. Matthew D.; Lorenz, Christian Douglas (King' s College London, London, UK); Stevens, Mark Jackson

    2008-12-01

    We have conducted a molecular dynamics (MD) simulation study of water confined between methyl-terminated and carboxyl-terminated alkylsilane self-assembled monolayers (SAMs) on amorphous silica substrates. In doing so, we have investigated the dynamic and structural behavior of the water molecules when compressed to loads ranging from 20 to 950 MPa for two different amounts of water (27 and 58 water molecules/nm{sup 2}). Within the studied range of loads, we observe that no water molecules penetrate the hydrophobic region of the carboxyl-terminated SAMs. However, we observe that at loads larger than 150 MPa water molecules penetrate the methyl-terminated SAMs and form hydrogen-bonded chains that connect to the bulk water. The diffusion coefficient of the water molecules decreases as the water film becomes thinner and pressure increases. When compared to bulk diffusion coefficients of water molecules at the various loads, we found that the diffusion coefficients for the systems with 27 water molecules/nm{sup 2} are reduced by a factor of 20 at low loads and by a factor of 40 at high loads, while the diffusion coefficients for the systems with 58 water molecules/nm{sup 2} are reduced by a factor of 25 at all loads.

  16. 75 FR 32866 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

    Science.gov (United States)

    2010-06-10

    ... River, Solomons, MD AGENCY: Coast Guard, DHS. ACTION: Notice of proposed rulemaking. SUMMARY: The Coast... races, a marine event to be held on the waters of the Patuxent River, near Solomons, MD on October 3... Patuxent River near Solomons, MD. The event consists of offshore power boats racing in a counter-clockwise...

  17. 76 FR 52865 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

    Science.gov (United States)

    2011-08-24

    ... River, Solomons, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is... be held on the waters of the Patuxent River, near Solomons, MD on September 24 and 25, 2011. These... Marine Events; Patuxent River, Solomons, MD'' in the Federal Register (76 FR 118). We received no...

  18. 76 FR 35802 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

    Science.gov (United States)

    2011-06-20

    .... USCG-2011-0266] RIN 1625-AA08 Special Local Regulations for Marine Events; Patuxent River, Solomons, MD... be held on the waters of the Patuxent River, near Solomons, MD on September 24 and 25, 2011. These... boat races on the Patuxent River near Solomons, MD. The event consists of offshore power boats racing...

  19. 77 FR 47279 - Special Local Regulations for Marine Events, Patuxent River; Solomons, MD

    Science.gov (United States)

    2012-08-08

    ... River; Solomons, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is... be held on the waters of the Patuxent River, near Solomons, MD on September 15 and 16, 2012. These..., Solomons, MD'' in the Federal Register (77 FR 25649). We received no comments on the proposed rule. No...

  20. 75 FR 57388 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

    Science.gov (United States)

    2010-09-21

    ... River, Solomons, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is... be held on the waters of the Patuxent River, near Solomons, MD on October 1, 2010 and October 3, 2010... Marine Events; Patuxent River, Solomons, MD'' in the Federal Register (75 FR 32866). Additionally, on...

  1. Does consideration of water routing affect simulated water and carbon dynamics in terrestrial ecosystems?

    Directory of Open Access Journals (Sweden)

    G. Tang

    2013-10-01

    Full Text Available The cycling of carbon in terrestrial ecosystems is closely coupled with the cycling of water. An important mechanism connecting ecological and hydrological processes in terrestrial ecosystems is lateral flow of water along landscapes. Few studies, however, have examined explicitly how consideration of water routing affects simulated water and carbon dynamics in terrestrial ecosystems. The objective of this study is to explore how consideration of water routing in a process-based hydroecological model affects simulated water and carbon dynamics. To achieve that end, we rasterized the regional hydroecological simulation systems (RHESSys and employed the rasterized RHESSys (R-RHESSys in a forested watershed. We performed and compared two contrasting simulations, one with and another without water routing. We found that R-RHESSys is able to correctly simulate major hydrological and ecological variables regardless of whether water routing is considered. When water routing was neglected, however, soil water table depth and saturation deficit were simulated to be smaller and spatially more homogeneous. As a result, evaporation, forest productivity and soil heterotrophic respiration also were simulated to be spatially more homogeneous compared to simulation with water routing. When averaged for the entire watershed, however, differences in simulated water and carbon fluxes are not significant between the two simulations. Overall, the study demonstrated that consideration of water routing enabled R-RHESSys to better capture our preconception of the spatial patterns of water table depth and saturation deficit across the watershed. Because the spatial pattern of soil moisture is fundamental to water efflux from land to the atmosphere, forest productivity and soil microbial activity, ecosystem and carbon cycle models, therefore, need to explicitly represent water routing in order to accurately quantify the magnitudes and patterns of water and carbon fluxes

  2. Wettability of graphitic-carbon and silicon surfaces: MD modeling and theoretical analysis

    Science.gov (United States)

    Ramos-Alvarado, Bladimir; Kumar, Satish; Peterson, G. P.

    2015-07-01

    The wettability of graphitic carbon and silicon surfaces was numerically and theoretically investigated. A multi-response method has been developed for the analysis of conventional molecular dynamics (MD) simulations of droplets wettability. The contact angle and indicators of the quality of the computations are tracked as a function of the data sets analyzed over time. This method of analysis allows accurate calculations of the contact angle obtained from the MD simulations. Analytical models were also developed for the calculation of the work of adhesion using the mean-field theory, accounting for the interfacial entropy changes. A calibration method is proposed to provide better predictions of the respective contact angles under different solid-liquid interaction potentials. Estimations of the binding energy between a water monomer and graphite match those previously reported. In addition, a breakdown in the relationship between the binding energy and the contact angle was observed. The macroscopic contact angles obtained from the MD simulations were found to match those predicted by the mean-field model for graphite under different wettability conditions, as well as the contact angles of Si(100) and Si(111) surfaces. Finally, an assessment of the effect of the Lennard-Jones cutoff radius was conducted to provide guidelines for future comparisons between numerical simulations and analytical models of wettability.

  3. Integrating Water Supply Constraints into Irrigated Agricultural Simulations of California

    Science.gov (United States)

    Winter, Jonathan M.; Young, Charles A.; Mehta, Vishal K.; Ruane, Alex C.; Azarderakhsh, Marzieh; Davitt, Aaron; McDonald, Kyle; Haden, Van R.; Rosenzweig, Cynthia E.

    2017-01-01

    Simulations of irrigated croplands generally lack key interactions between water demand from plants and water supply from irrigation systems. We coupled the Water Evaluation and Planning system (WEAP) and Decision Support System for Agrotechnology Transfer (DSSAT) to link regional water supplies and management with field-level water demand and crop growth. WEAP-DSSAT was deployed and evaluated over Yolo County in California for corn, rice, and wheat. WEAP-DSSAT is able to reproduce the results of DSSAT under well-watered conditions and reasonably simulate observed mean yields, but has difficulty capturing yield interannual variability. Constraining irrigation supply to surface water alone reduces yields for all three crops during the 1987-1992 drought. Corn yields are reduced proportionally with water allocation, rice yield reductions are more binary based on sufficient water for flooding, and wheat yields are least sensitive to irrigation constraints as winter wheat is grown during the wet season.

  4. Simulation of water temperature distribution in Fenhe Reservoir

    Institute of Scientific and Technical Information of China (English)

    Shu-fang FAN; Min-quan FENG; Zhao LIU

    2009-01-01

    In order to evaluate the need of controlling the temperature of water discharged from the Fenhe Reservoir, the reservoir water temperature distribution was examined. A three-dimensional mathematical model was used to simulate the in-plane and vertical distribution of water temperature. The parameters of the model were calibrated with field data of the temperature distribution in the Fenhe Reservoir. The simulated temperature of discharged water is consistent with the measured data. The difference in temperature between the discharged water and the natural river channel is less than 3℃ under the current operating conditions. This will not significantly impact the environment of downstream areas.

  5. Simulation of water temperature distribution in Fenhe Reservoir

    Directory of Open Access Journals (Sweden)

    Shu-fang FAN

    2009-06-01

    Full Text Available Abstract: In order to evaluate the need of controlling the temperature of water discharged from the Fenhe Reservoir, the reservoir water temperature distribution was examined. A three-dimensional mathematical model was used to simulate the in-plane and vertical distribution of water temperature. The parameters of the model were calibrated with field data of the temperature distribution in the Fenhe Reservoir. The simulated temperature of discharged water is consistent with the measured data. The difference in temperature between the discharged water and the natural river channel is less than 3℃ under the current operating conditions. This will not significantly impact the environment of downstream areas.

  6. Data supporting beta-amyloid dimer structural transitions and protein–lipid interactions on asymmetric lipid bilayer surfaces using MD simulations on experimentally derived NMR protein structures

    Directory of Open Access Journals (Sweden)

    Sara Y. Cheng

    2016-06-01

    Full Text Available This data article supports the research article entitled “Maximally Asymmetric Transbilayer Distribution of Anionic Lipids Alters the Structure and interaction with Lipids of an Amyloidogenic Protein Dimer Bound to the Membrane Surface” [1]. We describe supporting data on the binding kinetics, time evolution of secondary structure, and residue-contact maps of a surface-absorbed beta-amyloid dimer protein on different membrane surfaces. We further demonstrate the sorting of annular and non-annular regions of the protein/lipid bilayer simulation systems, and the correlation of lipid-number mismatch and surface area per lipid mismatch of asymmetric lipid membranes.

  7. The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

    Science.gov (United States)

    Fang, Changming; Li, Wun-Fan; Koster, Rik S; Klimeš, Jiří; van Blaaderen, Alfons; van Huis, Marijn A

    2015-01-07

    Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

  8. Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores.

    Science.gov (United States)

    Burris, Paul C; Laage, Damien; Thompson, Ward H

    2016-05-21

    Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.

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

    NARCIS (Netherlands)

    BERENDSEN, HJC; MARRINK, SJ

    1993-01-01

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

  10. A close examination of the structure and dynamics of HC(NH2)2PbI3by MD simulations and group theory

    KAUST Repository

    Carignano, M. A.

    2016-06-22

    The formamidinium lead iodide hybrid perovskite is studied using first principles molecular dynamics simulations and further analyzed using group theory. The simulations are performed on large supercells containing 768 atoms under isothermal and fully anisotropic isobaric conditions. Two trajectories, one at 300 K and another at 450 K, were extended for over 50 ps in order to perform a detailed assessment of the rotational dynamics of organic cations. The characteristic rotations of the cation are analyzed by defining two rotation axes. It is found that the formamidinium molecules rotate preferentially around the direction parallel to the line connecting the two nitrogen atoms. The rotational dynamics shows some characteristics already observed in methylammonium lead iodide, like the heterogeneous dynamics at room temperature that disappears at 450 K. The orientational probability of the molecules is explored in terms of an expansion in cubic harmonics up to the 12th order. It reveals a strong directionality at room temperature that relaxes when increasing the temperature. These findings are further rationalized using Landau and group theories suggesting a mixed displacive/order-disorder structural instability at lower temperatures.

  11. Water Clarity Simulant for K East Basin Filtration Testing

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, Andrew J.

    2006-01-20

    This document provides a simulant formulation intended to mimic the behavior of the suspended solids in the K East (KE) Basin fuel storage pool. The simulant will be used to evaluate alternative filtration apparatus to improve Basin water clarity and to possibly replace the existing sandfilter. The simulant was formulated based on the simulant objectives, the key identified parameters important to filtration, the composition and character of the KE Basin suspended sludge particles, and consideration of properties of surrogate materials.

  12. Classification of functional d-metal/graphene interfaces according to a sorption mechanism and the resistance to thermoactivated disordering and melting. MD simulation

    Science.gov (United States)

    Polukhin, V. A.; Kurbanova, E. D.; Galashev, A. E.

    2014-08-01

    The thermally activated formation of a two-dimensional ring-cluster phase in the zone of contact of a transition metal (Ni, Pd, Cu) with graphene and its disordering and melting upon heating in the temperature range 850-3900 K are studied by molecular dynamics simulation with a correctly parameterized multiparticle potential. The diffusion mobilities in the interface plane and in the perpendicular direction are comprehensively analyzed with allowance for the character of interparticle interactions and a sorption mechanism, which are considered as the main factors that determine the thermal stability of the interface phase and the specific features of the order-disorder transition (which is an analog of melting in two-dimensional systems).

  13. Water Hammer Modelling and Simulation by GIS

    OpenAIRE

    Hariri Asli, K.; Haghi,A. K.; Hariri Asli, H.; E. Sabermaash Eshghi

    2012-01-01

    This work defined an Eulerian-based computational model compared with regression of the relationship between the dependent and independent variables for water hammer surge wave in transmission pipeline. The work also mentioned control of Unaccounted-for-Water (UFW) based on the Geography Information System (GIS) for water transmission pipeline. The experimental results of laboratory model and the field test results showed the validity of prediction achieved by computational model.

  14. Water Hammer Modelling and Simulation by GIS

    Directory of Open Access Journals (Sweden)

    K. Hariri Asli

    2012-01-01

    Full Text Available This work defined an Eulerian-based computational model compared with regression of the relationship between the dependent and independent variables for water hammer surge wave in transmission pipeline. The work also mentioned control of Unaccounted-for-Water (UFW based on the Geography Information System (GIS for water transmission pipeline. The experimental results of laboratory model and the field test results showed the validity of prediction achieved by computational model.

  15. Simulating structural response to water impact

    OpenAIRE

    Campbell, James C; Vignjevic, Rade

    2012-01-01

    Structural response to water impact is important for several areas, including the aerospace and marine industries. Aircraft must be designed to cope with ditching and offshore structures are subject to extreme wave impact and green water loading. The goal is a reliable technique for predicting the structural response to extreme water loading. This is a complex problem involving the interaction of non-linear fluid behaviour (breaking waves, fluid impact) with non-linear structural behaviour (l...

  16. The Plasmodium falciparum malaria M1 alanyl aminopeptidase (PfA-M1: insights of catalytic mechanism and function from MD simulations.

    Directory of Open Access Journals (Sweden)

    Peter M Jones

    Full Text Available Malaria caused by several species of Plasmodium is major parasitic disease of humans, causing 1-3 million deaths worldwide annually. The widespread resistance of the human parasite to current drug therapies is of major concern making the identification of new drug targets urgent. While the parasite grows and multiplies inside the host erythrocyte it degrades the host cell hemoglobin and utilizes the released amino acids to synthesize its own proteins. The P. falciparum malarial M1 alanyl-aminopeptidase (PfA-M1 is an enzyme involved in the terminal stages of hemoglobin digestion and the generation of an amino acid pool within the parasite. The enzyme has been validated as a potential drug target since inhibitors of the enzyme block parasite growth in vitro and in vivo. In order to gain further understanding of this enzyme, molecular dynamics simulations using data from a recent crystal structure of PfA-M1 were performed. The results elucidate the pentahedral coordination of the catalytic Zn in these metallo-proteases and provide new insights into the roles of this cation and important active site residues in ligand binding and in the hydrolysis of the peptide bond. Based on the data, we propose a two-step catalytic mechanism, in which the conformation of the active site is altered between the Michaelis complex and the transition state. In addition, the simulations identify global changes in the protein in which conformational transitions in the catalytic domain are transmitted at the opening of the N-terminal 8 Å-long channel and at the opening of the 30 Å-long C-terminal internal chamber that facilitates entry of peptides to the active site and exit of released amino acids. The possible implications of these global changes with regard to enzyme function are discussed.

  17. MD SIMULATION STUDIES TO INVESTIGATE ISO-ENERGETIC CONFORMATIONAL BEHAVIOUR OF MODIFIED NUCLEOSIDES M2G AND M22G PRESENT IN tRNA

    Directory of Open Access Journals (Sweden)

    Rohit S Bavi

    2013-02-01

    Full Text Available Modified nucleic acid bases are most commonly found in tRNA. These may contain modifications from simple methylation to addition of bulky groups. Methylation of the four canonical nucleotide bases at a wide variety of positions is particularly prominent among the known modification. Methylation of N2 group of guanine is a relatively common modification in tRNA and rRNA. N2-methylguanosine (m2G is the second most often encountered nucleoside in E. coli tRNAs. N2, N2-dimethylguanosine (m22G is found in the majority of eukaryotic tRNAs and involved in forming base pair interactions with adjacent bases. Hence, in order to understand the structural significance of these methylated nucleic acid bases we have carried out molecular dynamics simulation to see the salvation effect. The results obtained shows iso-energetic conformational behaviors for m2G and m22G. The simulation trajectory of m2G shows regular periodical fluctuations suggesting that m2G is equally stable as either s-cis or s-trans rotamers. The two rotamers of m2G may interact canonically or non-canonically with opposite base as s-trans m2G26:C/A/U44 and s-cis m2G26:A/U44. The free rotations around the C-N bond could be the possible reason for these iso-energetic conformations. Dimethylation of G has almost no influence on base pairing with either A or U. Thus, these results reveal that modified nucleosides m2G and m22G may play an important role to prevent tRNA from adopting the unusual mitochondrial like conformation.

  18. Revealing Surface Waters on an Antifreeze Protein by Fusion Protein Crystallography Combined with Molecular Dynamic Simulations.

    Science.gov (United States)

    Sun, Tianjun; Gauthier, Sherry Y; Campbell, Robert L; Davies, Peter L

    2015-10-01

    Antifreeze proteins (AFPs) adsorb to ice through an extensive, flat, relatively hydrophobic surface. It has been suggested that this ice-binding site (IBS) organizes surface waters into an ice-like clathrate arrangement that matches and fuses to the quasi-liquid layer on the ice surface. On cooling, these waters join the ice lattice and freeze the AFP to its ligand. Evidence for the generality of this binding mechanism is limited because AFPs tend to crystallize with their IBS as a preferred protein-protein contact surface, which displaces some bound waters. Type III AFP is a 7 kDa globular protein with an IBS made up two adjacent surfaces. In the crystal structure of the most active isoform (QAE1), the part of the IBS that docks to the primary prism plane of ice is partially exposed to solvent and has clathrate waters present that match this plane of ice. The adjacent IBS, which matches the pyramidal plane of ice, is involved in protein-protein crystal contacts with few surface waters. Here we have changed the protein-protein contacts in the ice-binding region by crystallizing a fusion of QAE1 to maltose-binding protein. In this 1.9 Å structure, the IBS that fits the pyramidal plane of ice is exposed to solvent. By combining crystallography data with MD simulations, the surface waters on both sides of the IBS were revealed and match well with the target ice planes. The waters on the pyramidal plane IBS were loosely constrained, which might explain why other isoforms of type III AFP that lack the prism plane IBS are less active than QAE1. The AFP fusion crystallization method can potentially be used to force the exposure to solvent of the IBS on other AFPs to reveal the locations of key surface waters.

  19. Morphometric methods for simulation of water flow.

    NARCIS (Netherlands)

    Booltink, H.W.G.

    1993-01-01

    Water flow in structured soils is strongly governed by the occurence of macropores. In this study emphasis was given to combined research of morphology of water- conducting macropores and soil physical measurements on bypass flow. Main research objectives were to: (i) develop and improve soil physic

  20. Mechanical properties of bamboo-like boron nitride nanotubes by in situ TEM and MD simulations: strengthening effect of interlocked joint interfaces.

    Science.gov (United States)

    Tang, Dai-Ming; Ren, Cui-Lan; Wei, Xianlong; Wang, Ming-Sheng; Liu, Chang; Bando, Yoshio; Golberg, Dmitri

    2011-09-27

    Understanding the influence of interfacial structures on the nanoarchitecture mechanical properties is of particular importance for its mechanical applications. Due to a small size of constituting nanostructural units and a consequently high volume ratio of such interfacial regions, this question becomes crucial for the overall mechanical performance. Boron nitride bamboo-like nanotubes, called hereafter boron nitride nanobamboos (BNNBs), are composed of short BN nanotubular segments with specific interfaces at the bamboo-shaped joints. In this work, the mechanical properties of such structures are investigated by using direct in situ transmission electron microscopy tensile tests and molecular dynamics simulations. The mechanical properties and deformation behaviors are correlated with the interfacial structure under atomic resolution, and a geometry strengthening effect is clearly demonstrated. Due to the interlocked joint interfacial structures and compressive interfacial stresses, the deformation mechanism is switched from an interplanar sliding mode to an in-plane tensile elongation mode. As a result of such a specific geometry strengthening effect, the BNNBs show high tensile fracture strength and Young's modulus up to 8.0 and 225 GPa, respectively.

  1. The Binding Mode Prediction and Similar Ligand Potency in the Active Site of Vitamin D Receptor with QM/MM Interaction, MESP, and MD Simulation.

    Science.gov (United States)

    Selvaraman, Nagamani; Selvam, Saravana Kumar; Muthusamy, Karthikeyan

    2016-08-01

    Non-secosteroidal ligands are well-known vitamin D receptor (VDR) agonists. In this study, we described a combined QM/MM to define the protein-ligand interaction energy a strong positive correlation in both QM-MM interaction energy and binding free energy against the biological activity. The molecular dynamics simulation study was performed, and specific interactions were extensively studied. The molecular docking results and surface analysis shed light on steric and electrostatic complementarities of these non-secosteroidal ligands to VDR. Finally, the drug likeness properties were also calculated and found within the acceptable range. The results show that bulky group substitutions in side chain decrease the VDR activity, whereas a small substitution increased it. Functional analyses of H393A and H301A mutations substantiate their roles in the VDR agonistic and antagonistic activities. Apart from the His393 and His301, two other amino acids in the hinge region viz. Ser233 and Arg270 acted as an electron donor/acceptor specific to the agonist in the distinct ligand potency. The results from this study disclose the binding mechanism of VDR agonists and structural modifications required to improve the selectivity.

  2. Structural, stability, dynamic and binding properties of the ALS-causing T46I mutant of the hVAPB MSP domain as revealed by NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Shixiong Lua

    Full Text Available T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS. Here using CD, NMR and molecular dynamics (MD simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1 unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2 Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3 T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4 EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5 As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.

  3. Water and heat fluxes in desert soils: 2. Numerical simulations

    Science.gov (United States)

    Scanlon, Bridget R.; Milly, P. C. D.

    1994-03-01

    Transient one-dimensional fluxes of soil water (liquid and vapor) and heat in response to 1 year of atmospheric forcing were simulated numerically for a site in the Chihuahuan Desert of Texas. The model was initialized and evaluated using the monitoring data presented in a companion paper (Scanlon, this issue). Soil hydraulic and thermal properties were estimated a priori from a combination of laboratory measurements, models, and other published information. In the first simulation, the main drying curves were used to describe soil water retention, and hysteresis was ignored. Remarkable consistency was found between computed and measured water potentials and temperatures. Attenuation and phase shift of the seasonal cycle of water potentials below the shallow subsurface active zone (0.0- to 0.3-m depth) were similar to those of temperatures, suggesting that water potential fluctuations were driven primarily by temperature changes. Water fluxes in the upper 0.3 m of soil were dominated by downward and upward liquid fluxes that resulted from infiltration of rain and subsequent evaporation from the surface. Upward flux was vapor dominated only in the top several millimeters of the soil during periods of evaporation. Below a depth of 0.3 m, water fluxes varied slowly and were dominated by downward thermal vapor flux that decreased with depth, causing a net accumulation of water. In a second simulation, nonhysteretic water retention was instead described by the estimated main wetting curves; the resulting differences in fluxes were attributed to lower initial water contents (given fixed initial water potential) and unsaturated hydraulic conductivities that were lower than they were in the first simulation. Below a depth of 0.3 m, the thermal vapor fluxes dominated and were similar to those in the first simulation. Two other simulations were performed, differing from the first only in the prescription of different (wetter) initial water potentials. These three simulations

  4. Simulation study of water and sugar dynamics in supercooled mixtures

    Science.gov (United States)

    Molinero, Valeria; Cagin, Tahir; Goddard, William A.

    2003-03-01

    Water dynamics in concentrated carbohydrate solutions is of utmost importance in food and pharmaceutical technology, where low water mobility is desirable to slow down chemical degradation and preserve biomolecules. We have studied the microscopic mechanism of water diffusion in binary and polydisperse malto-oligosaccharides and water mixtures by means of molecular dynamics simulations. The computations were performed with a coarse grain model (M3B), derived from atomistic simulations of water and malto-oligosaccharides. The use of the M3B model permits simulations of the order of 0.1 microsecond, thus allowing us to explore water dynamics from the liquid to the deep supercooled regime. The dynamics of water confined in the sugar matrix is slowed down with respect to bulk water. We found that at low moisture content and low temperature, ranslational diffusion of water and glucose rotation proceed through a hopping-diffusion mechanism. Moreover, we found water mobility to be heterogeneous: there is a broad distribution of time scales for different water molecules in the mixtures. We discuss whether there is a relationship between the heterogeneous structure of these mixtures in the sub-nanometer scale and the heterogeneous dynamics of water molecules.

  5. Theoretical investigation of loratadine reactivity in order to understand its degradation properties: DFT and MD study.

    Science.gov (United States)

    Armaković, Stevan; Armaković, Sanja J; Abramović, Biljana F

    2016-10-01

    Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding their fundamental reactive properties. In this study we have theoretically investigated reactive properties of LOR using both density functional theory (DFT) calculations and molecular dynamics (MD) simulations. DFT study is used for collecting information related to the molecule stability, structure, frontier molecular orbitals, quantum molecular descriptors, charge distribution, molecular electrostatic potential surfaces, charge polarization, and local reactivity properties according to average local ionization energy surfaces. Based on these results, N24 atom of pyridine ring and oxygen atom O1 were identified with nucleophilic nature. In order to collect the information necessary for the proposition of degradation compounds we also calculated bond dissociation energies (BDE) for hydrogen abstraction and single acyclic bonds as well. According to BDE, the oxidation is likely to occur in the piperidine and cycloheptane rings. MD simulations were used in order to understand the interactions with water through radial distribution functions (RDF). Based on RDFs the most important interactions with solvent are determined for carbon atom C5, chlorine atom Cl15, and oxygen atom O1. Collected results based on DFT calculations and MD simulations provided information important for suggestion of possible degradation compounds. Covalent and noncovalent interactions between LOR and (•)OH have also been investigated.

  6. Water Hammer Simulations of Monomethylhydrazine Propellant

    Science.gov (United States)

    Burkhardt, Zachary; Ramachandran, N.; Majumdar, A.

    2017-01-01

    Fluid Transient analysis is important for the design of spacecraft propulsion system to ensure structural stability of the system in the event of sudden closing or opening of the valve. Generalized Fluid System Simulation Program (GFSSP), a general purpose flow network code developed at NASA/MSFC is capable of simulating pressure surge due to sudden opening or closing of valve when thermodynamic properties of real fluid are available for the entire range of simulation. Specifically GFSSP needs an accurate representation of pressure density relationship in order to predict pressure surge during a fluid transient. Unfortunately, the available thermodynamic property programs such as REFPROP, GASP or GASPAK do not provide the thermodynamic properties of Monomethylhydrazine(MMH). This work illustrates the process used for building a customized table of properties of state variables from available properties and speed of sound that is required by GFSSP for simulation. Good agreement was found between the simulations and measured data. This method can be adopted for modeling flow networks and systems with other fluids whose properties are not known in detail in order to obtain general technical insight.

  7. High-resolution Structures of Protein-Membrane Complexes by Neutron Reflection and MD Simulation: Membrane Association of the PTEN Tumor Suppressor

    Science.gov (United States)

    Lösche, Matthias

    2012-02-01

    structure. The combination of binding studies and neutron reflection allows us to distinguish between PTEN mutant proteins and ultimately may identify the structural features required for membrane binding and activation of PTEN. Molecular dynamics simulations, currently in progress, refine this structural picture further.

  8. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

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

    2000-01-01

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

  9. Simulation of heavy metal contamination of fresh water bodies: Toxic ...

    African Journals Online (AJOL)

    Simulation of heavy metal contamination of fresh water bodies: Toxic effects in the catfish and its amelioration with co-contamination with glyphosate. ... Journal of Applied Sciences and Environmental Management. Journal Home · ABOUT ...

  10. Molecular Dynamics Simulations of Carbon Nanotubes in Water

    Science.gov (United States)

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

    2000-01-01

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

  11. Molecular Dynamics Simulation of Water Confined in Carbon Nanotubes

    Institute of Scientific and Technical Information of China (English)

    WANG Yan; YUAN Hong-Jun

    2007-01-01

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

  12. Continuum simulations of water flow past fullerene molecules

    Science.gov (United States)

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

    2015-09-01

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

  13. Effect of Cu2+ Activation on Interfacial Water Structure at the Sphalerite Surface as Studied by Molecular Dynamics Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Jiaqi; Miller, Jan D.; Dang, Liem X.; Wick, Collin D.

    2015-12-10

    In the first part of this paper, an experimental contact angle study of the fresh and Cu2+ activated sphalerite-ZnS surface as well as the covellite-CuS (001) surface is reported describing the increased hydrophobic character of the surface during Cu2+ activation. In addition to these experimental results, the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite- CuS2 (100), and covellite-CuS (001) surfaces were examined using Molecular Dynamics Simulation (MDS). Our MDS results on the behavior of interfacial water at the fresh sphalerite-ZnS (110), copper-zinc sulfide-CuZnS2 (110), villamaninite-CuS2 (100), and covellite-CuS (001) surfaces include simulated contact angles, water number density distribution, water dipole orientation, water residence time, and hydrogen-bonding considerations. The copper content at the Cu2+ activated sphalerite surface seems to account for the increased hydrophobicity as revealed by both experimental and MD simulated contact angle measurements. The relatively greater hydrophobic character developed at the Cu2+ activated sphalerite surface and at the copper-zinc sulfide surface has been described by MDS, based on the structure of interfacial water and its dynamic properties. L.X.D. acknowledges funding from the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences.

  14. Continuum simulations of water flow past fullerene molecules

    DEFF Research Database (Denmark)

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

    2015-01-01

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

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

    NARCIS (Netherlands)

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

    2011-01-01

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

  16. Variational approaches to water wave simulations

    NARCIS (Netherlands)

    Gagarina, Elena Vitalyevna

    2014-01-01

    This thesis starts with the study the theoretical aspects of water wave modelling using a variational framework, which is directly associated with phase space and energy conservation laws. In particular, we focus on a new variational model based on the work of Cotter and Bokhove. The new model inclu

  17. Three-Dimensional Simulations of Deep-Water Breaking Waves

    CERN Document Server

    Brucker, Kyle A; Dommermuth, Douglas G; Adams, Paul

    2014-01-01

    The formulation of a canonical deep-water breaking wave problem is introduced, and the results of a set of three-dimensional numerical simulations for deep-water breaking waves are presented. In this paper fully nonlinear progressive waves are generated by applying a normal stress to the free surface. Precise control of the forcing allows for a systematic study of four types of deep-water breaking waves, characterized herein as weak plunging, plunging, strong plunging, and very strong plunging.

  18. Molecular Dynamics Simulation Study of Parallel Telomeric DNA Quadruplexes at Different Ionic Strengths: Evaluation of Water and Ion Models.

    Science.gov (United States)

    Rebič, Matúš; Laaksonen, Aatto; Šponer, Jiří; Uličný, Jozef; Mocci, Francesca

    2016-08-04

    Most molecular dynamics (MD) simulations of DNA quadruplexes have been performed under minimal salt conditions using the Åqvist potential parameters for the cation with the TIP3P water model. Recently, this combination of parameters has been reported to be problematic for the stability of quadruplex DNA, especially caused by the ion interactions inside or near the quadruplex channel. Here, we verify how the choice of ion parameters and water model can affect the quadruplex structural stability and the interactions with the ions outside the channel. We have performed a series of MD simulations of the human full-parallel telomeric quadruplex by neutralizing its negative charge with K(+) ions. Three combinations of different cation potential parameters and water models have been used: (a) Åqvist ion parameters, TIP3P water model; (b) Joung and Cheatham ion parameters, TIP3P water model; and (c) Joung and Cheatham ion parameters, TIP4Pew water model. For the combinations (b) and (c), the effect of the ionic strength has been evaluated by adding increasing amounts of KCl salt (50, 100, and 200 mM). Two independent simulations using the Åqvist parameters with the TIP3P model show that this combination is clearly less suited for the studied quadruplex with K(+) as counterions. In both simulations, one ion escapes from the channel, followed by significant deformation of the structure, leading to deviating conformation compared to that in the reference crystallographic data. For the other combinations of ion and water potentials, no tendency is observed for the channel ions to escape from the quadruplex channel. In addition, the internal mobility of the three loops, torsion angles, and counterion affinity have been investigated at varied salt concentrations. In summary, the selection of ion and water models is crucial as it can affect both the structure and dynamics as well as the interactions of the quadruplex with its counterions. The results obtained with the TIP4Pew

  19. Root water uptake as simulated by three water flow models

    NARCIS (Netherlands)

    Willigen, de P.; Dam, van J.C.; Javaux, M.; Heinen, M.

    2012-01-01

    The objective of our study was to determine to what extent four root water uptake (RWU) models differed when tested under extreme conditions. Cumulative transpiration patterns were similar, contrary to the spatial extraction patterns. The analysis showed that both soil physical and root physiologica

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

    Science.gov (United States)

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

    2015-09-01

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

  1. A simulation of water call option prices

    OpenAIRE

    1994-01-01

    Ankara : The Department of Economics and the Institute of Economics and Social Sciences of Bilkent Univ., 1994. Thesis (Master's) -- Bilkent University, 1994. Includes bibliographical references. The popularity of iinancial derivatives and especially options is widespread in the last decade. Although various commodity options became popular nowadays, no form of water option happened to arise because there were no need. On the other hand, Turkey and the Middle East countries ...

  2. Water as a lubricant for graphite: a computer simulation study.

    Science.gov (United States)

    Pertsin, Alexander; Grunze, Michael

    2006-09-21

    The phase state and shear behavior of water confined between parallel graphite sheets are studied using the grand canonical Monte Carlo technique and TIP4P model for water. In describing the water-graphite interaction, two orientation-dependent potentials are tried. Both potentials are fitted to many-body polarizable model predictions for the binding energy and the equilibrium conformation of the water-graphite complex [K. Karapetian and K. D. Jordan in Water in Confining Geometries, edited by V. Buch and J. P. Devlin (Springer, Berlin, 2003), pp. 139-150]. Based on the simulation results, the property of water to serve as a lubricant between the rubbing surfaces of graphitic particles is associated, first, with the capillary condensation of water occurring in graphitic pores of monolayer width and, second, with the fact that the water monolayer compressed between graphite particles retains a liquidlike structure and offers only slight resistance to shear.

  3. Water management simulation games and the construction of knowledge

    Science.gov (United States)

    Rusca, M.; Heun, J.; Schwartz, K.

    2012-08-01

    In recent years, simulations have become an important part of teaching activities. The reasons behind the popularity of simulation games are twofold. On the one hand, emerging theories on how people learn have called for an experienced-based learning approach. On the other hand, the demand for water management professionals has changed. Three important developments are having considerable consequences for water management programmes, which educate and train these professionals. These developments are the increasing emphasis on integration in water management, the characteristics and speed of reforms in the public sector and the shifting state-society relations in many countries. In response to these developments, demand from the labour market is oriented toward water professionals who need to have both a specialist in-depth knowledge in their own field, as well as the ability to understand and interact with other disciplines and interests. In this context, skills in negotiating, consensus building and working in teams are considered essential for all professionals. In this paper, we argue that simulation games have an important role to play in (actively) educating students and training the new generation of water professionals to respond to the above-mentioned challenges. At the same time, simulations are not a panacea for learners and teachers. Challenges of using simulation games include the demands it places on the teacher. Setting up the simulation game, facilitating the delivery and ensuring that learning objectives are achieved require considerable knowledge and experience as well as considerable time-inputs of the teacher. Moreover, simulation games usually incorporate a case-based learning model, which may neglect or underemphasize theories and conceptualizations. For simulations to be effective, they have to be embedded in this larger theoretical and conceptual framework. Simulations, therefore, complement rather than substitute traditional teaching

  4. Water management simulation games and the construction of knowledge

    Directory of Open Access Journals (Sweden)

    M. Rusca

    2012-03-01

    Full Text Available In recent years simulations have become an important part of teaching activities. The reasons behind the popularity of simulation games are twofold. On the one hand, emerging theories on how people learn have called for an experienced-based learning approach. On the other hand, the demand for water management professionals has changed. Three important developments are having considerable consequences for water management programmes, which educate and train these professionals. These developments are the increasing emphasis on integration in water management, the characteristics and speed of reforms in the public sector and the shifting state-society relations in many countries. In response to these developments, demand from the labour market is oriented toward water professionals who need to have both a specialist in-depth knowledge in their own field, as well as the ability to understand and interact with other disciplines and interests. In this context, skills in negotiating, consensus building and working in teams are considered essential for all professionals. In this paper we argue that simulation games have an important role to play in (actively educating students and training the new generation of water professionals to respond to the above-mentioned challenges. At the same time, simulations are not a panacea for learners and teachers. Challenges of using simulations games include the demands it places on the teacher. Setting up the simulation game, facilitating the delivery and ensuring that learning objectives are achieved requires considerable knowledge and experience as well as considerable time-inputs of the teacher. Moreover, simulation games usually incorporate a case-based learning model, which may neglect or underemphasize theories and conceptualization. For simulations to be effective they have to be embedded in this larger theoretical and conceptual framework. Simulations, therefore, complement rather than substitute

  5. Water management simulation games and the construction of knowledge

    Directory of Open Access Journals (Sweden)

    M. Rusca

    2012-08-01

    Full Text Available In recent years, simulations have become an important part of teaching activities. The reasons behind the popularity of simulation games are twofold. On the one hand, emerging theories on how people learn have called for an experienced-based learning approach. On the other hand, the demand for water management professionals has changed. Three important developments are having considerable consequences for water management programmes, which educate and train these professionals. These developments are the increasing emphasis on integration in water management, the characteristics and speed of reforms in the public sector and the shifting state-society relations in many countries. In response to these developments, demand from the labour market is oriented toward water professionals who need to have both a specialist in-depth knowledge in their own field, as well as the ability to understand and interact with other disciplines and interests. In this context, skills in negotiating, consensus building and working in teams are considered essential for all professionals. In this paper, we argue that simulation games have an important role to play in (actively educating students and training the new generation of water professionals to respond to the above-mentioned challenges. At the same time, simulations are not a panacea for learners and teachers. Challenges of using simulation games include the demands it places on the teacher. Setting up the simulation game, facilitating the delivery and ensuring that learning objectives are achieved require considerable knowledge and experience as well as considerable time-inputs of the teacher. Moreover, simulation games usually incorporate a case-based learning model, which may neglect or underemphasize theories and conceptualizations. For simulations to be effective, they have to be embedded in this larger theoretical and conceptual framework. Simulations, therefore, complement rather than substitute

  6. Modeling Nanocomposites for Molecular Dynamics (MD) Simulations

    Science.gov (United States)

    2015-01-01

    Thermal Expansion and Diffusion Coefficients of Carbon Nanotube- Polymer Composites,” Nano Letters, Volume 2, Numbers 6, pp. 647-650, June 2002...are combined with an epoxy. Epoxy is a thermosetting polymer that, like the carbon fiber, has poor thermal conductivity; however, carbon fiber...a typical size for SWNTs [5]. PE is a simple hydrocarbon, yet it is applicable since polymers generally have low thermal conductivities. Its

  7. Simulation of Water Chemistry using and Geochemistry Code, PHREEQE

    Energy Technology Data Exchange (ETDEWEB)

    Chi, J.H. [Korea Electric Power Research Institute, Taejeon (Korea)

    2001-07-01

    This report introduces principles and procedures of simulation for water chemistry using a geochemistry code, PHREEQE. As and example of the application of this code, we described the simulation procedure for titration of an aquatic sample with strong acid to investigate the state of Carbonates in aquatic solution. Major contents of this report are as follows; Concepts and principles of PHREEQE, Kinds of chemical reactions which may be properly simulated by PHREEQE, The definition and meaning of each input data, An example of simulation using PHREEQE. (author). 2 figs., 1 tab.

  8. Structural and Dynamic Analysis on IDPs by Modified AWSEM-MD

    Science.gov (United States)

    Wu, Hao; Papoian, Garegin; Papoian Theoretical Biophysics Group Team

    Unlike globular proteins, intrinsically disordered proteins (IDPs) lack both secondary and tertiary structures and can play key roles in various biological processes, including transcriptional regulation, molecular recognition and cellular signaling. These functions can be potentially elucidated by structural heterogeneity of IDPs. Because of their flexibility and disordered nature, it has been difficult to investigate IDPs both computationally and experimentally. In particular, it is desirable to develop coarse-grained, yet accurate models of IDPs, such that simulations exploring sufficient conformational ensembles could be carried out within feasible times. To achieve this goal, we modified the associative memory, water mediated, structure and energy model (AWSEM-MD), which is typically used for folding of globular proteins or binding studies. We tested modified AWSEM-MD on several well-studied IDPs and found the transient secondary structure propensity is consistent with NMR experimental results. The rugged free energy landscapes obtained also show structural heterogeneity of these IDPs. Our proposed extension of AWSEM-MD may allow simulating a wider range of IDPs with high accuracy and computational efficiency.

  9. Water balance measurements and simulations of maize plants on lysimeters

    Science.gov (United States)

    Heinlein, Florian; Biernath, Christian; Klein, Christian; Thieme, Christoph; Priesack, Eckart

    2016-04-01

    In Central Europe expected major aspects of climate change are a shift of precipitation events and amounts towards winter months, and the general increase of extreme weather events like heat waves or summer droughts. This will lead to strongly changing regional water availability and will have an impact on future crop growth, water use efficiency and yields. Therefore, to estimate future crop yields by growth models accurate descriptions of transpiration as part of the water balance is important. In this study, maize was grown on weighing lysimeters (sowdate: 24 April 2013). Transpiration was determined by sap flow measurement devices (ICT International Pty Ltd, Australia) using the Heat-Ratio-Method: two temperature probes, 0.5 cm above and below a heater, detect a heat pulse and its speed which allows the calculation of sap flow. Water balance simulations were executed with different applications of the model framework Expert-N. The same pedotransfer and hydraulic functions and the same modules to simulate soil water flow, soil heat and nitrogen transport, nitrification, denitrification and mineralization were used. Differences occur in the chosen potential evapotranspiration ETpot (Penman-Monteith ASCE, Penman-Monteith FAO, Haude) and plant modules (SPASS, CERES). In all simulations ETpot is separated into a soil and a plant part using the leaf are index (LAI). In a next step, these parts are reduced by soil water availability. The sum of these parts is the actual evapotranspiration ETact which is compared to the lysimeter measurements. The results were analyzed from Mid-August to Mid-September 2013. The measured sap flow rates show clear diurnal cycles except on rainy days. The SPASS model is able to simulate these diurnal cycles, overestimates the measurements on rainy days and at the beginning of the analyzed period, and underestimates transpiration on the other days. The main reason is an overestimation of potential transpiration Tpot due to too high

  10. MD1228: Validation of Single Bunch Stability Threshold & MD1751: Instability Studies with a Single Beam

    CERN Document Server

    Carver, Lee Robert; Biancacci, Nicolo; Buffat, Xavier; Iadarola, Giovanni; Lasocha, Kacper; Li, Kevin Shing Bruce; Levens, Tom; Metral, Elias; Salvant, Benoit; Tambasco, Claudia; CERN. Geneva. ATS Department

    2017-01-01

    Instabilities were being routinely observed in B1V during ADJUST. The timing of the instabilities has been localised to shortly after the TOTEM bump has been implemented. The result is emittance blowup which can negatively effect the luminosity output of the fill. This MD aimed to rule out possible sources of the instability (i.e. beam-beam effects or electron cloud) by only taking one single beam to 6.5TeV and going through the full machine cycle. After the implementation of the TOTEM bump, a reduction of the octupole current was performed in order to determine if there was a discrepancy in the threshold between simulations and measurement. As a precursor, the results of the End of Fill MD: Validation of Single Bunch Stability Threshold will also be described.

  11. How processing digital elevation models can affect simulated water budgets.

    Science.gov (United States)

    Kuniansky, Eve L; Lowery, Mark A; Campbell, Bruce G

    2009-01-01

    For regional models, the shallow water table surface is often used as a source/sink boundary condition, as model grid scale precludes simulation of the water table aquifer. This approach is appropriate when the water table surface is relatively stationary. Since water table surface maps are not readily available, the elevation of the water table used in model cells is estimated via a two-step process. First, a regression equation is developed using existing land and water table elevations from wells in the area. This equation is then used to predict the water table surface for each model cell using land surface elevation available from digital elevation models (DEM). Two methods of processing DEM for estimating the land surface for each cell are commonly used (value nearest the cell centroid or mean value in the cell). This article demonstrates how these two methods of DEM processing can affect the simulated water budget. For the example presented, approximately 20% more total flow through the aquifer system is simulated if the centroid value rather than the mean value is used. This is due to the one-third greater average ground water gradients associated with the centroid value than the mean value. The results will vary depending on the particular model area topography and cell size. The use of the mean DEM value in each model cell will result in a more conservative water budget and is more appropriate because the model cell water table value should be representative of the entire cell area, not the centroid of the model cell.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

  13. Adaptive resolution simulation of an atomistic protein in MARTINI water

    Science.gov (United States)

    Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J.; Praprotnik, Matej

    2014-02-01

    We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

  14. Pump-stopping water hammer simulation based on RELAP5

    Science.gov (United States)

    Yi, W. S.; Jiang, J.; Li, D. D.; Lan, G.; Zhao, Z.

    2013-12-01

    RELAP5 was originally designed to analyze complex thermal-hydraulic interactions that occur during either postulated large or small loss-of-coolant accidents in PWRs. However, as development continued, the code was expanded to include many of the transient scenarios that might occur in thermal-hydraulic systems. The fast deceleration of the liquid results in high pressure surges, thus the kinetic energy is transformed into the potential energy, which leads to the temporary pressure increase. This phenomenon is called water hammer. Generally water hammer can occur in any thermal-hydraulic systems and it is extremely dangerous for the system when the pressure surges become considerably high. If this happens and when the pressure exceeds the critical pressure that the pipe or the fittings along the pipeline can burden, it will result in the failure of the whole pipeline integrity. The purpose of this article is to introduce the RELAP5 to the simulation and analysis of water hammer situations. Based on the knowledge of the RELAP5 code manuals and some relative documents, the authors utilize RELAP5 to set up an example of water-supply system via an impeller pump to simulate the phenomena of the pump-stopping water hammer. By the simulation of the sample case and the subsequent analysis of the results that the code has provided, we can have a better understand of the knowledge of water hammer as well as the quality of the RELAP5 code when it's used in the water-hammer fields. In the meantime, By comparing the results of the RELAP5 based model with that of other fluid-transient analysis software say, PIPENET. The authors make some conclusions about the peculiarity of RELAP5 when transplanted into water-hammer research and offer several modelling tips when use the code to simulate a water-hammer related case.

  15. MD 751: Train Instability Threshold

    CERN Document Server

    Carver, Lee Robert; Metral, Elias; Salvant, Benoit; Levens, Tom; Nisbet, David; Zobov, M; CERN. Geneva. ATS Department

    2016-01-01

    The purpose of this MD is to measure the octupole current thresholds for stability for a single bunch, and then make an immediate comparison (with the same operational settings) for a train of 72 bunches separated by 25ns. From theory, the expected thresholds should be similar. Any discrepancy between the two cases will be of great interest as it could indicate the presence of additional mechanisms that contribute to the instability threshold, for example electron cloud.

  16. Cycle Simulation of HotWater Fired Absorption Chiller

    Science.gov (United States)

    Esaki, Shuji; Iramina, Kazuyasu; Kobayashi, Takahiro; Ohnou, Masayuki; Kaneko, Toshiyuki; Soga, Takashi

    The design limits were examined to determine the lowest temperature for hot water that can be used as a heat source to drive a hot water fired absorption chiller. Advantage was taken of the fact that the cycle calculation method using the minimum temperature difference is quite effective. This minimum temperature difference was the lower of the two temperature differences used to get the logarithmic mean temperature difference that need to design the evaporator, absorber, condenser and generator in an absorption refrigerator. This report proposes a new solution algorithm employing this minimum temperature difference to make a cycle simulation of the hot water fired absorption chiller. It shows the lowest usable temperature for hot water and makes clear the chilled water and cooling water temperature conditions that can provide the lowest temperature.

  17. Simulation and Experimental Study on Cavitating Water Jet Nozzle

    Science.gov (United States)

    Zhou, Wei; He, Kai; Cai, Jiannan; Hu, Shaojie; Li, Jiuhua; Du, Ruxu

    2017-01-01

    Cavitating water jet technology is a new kind of water jet technology with many advantages, such as energy-saving, efficient, environmentally-friendly and so on. Based on the numerical simulation and experimental verification in this paper, the research on cavitating nozzle has been carried out, which includes comparison of the cleaning ability of the cavitating jet and the ordinary jet, and comparison of cavitation effects of different structures of cavitating nozzles.

  18. Thermodynamics of water modeled using ab initio simulations

    CERN Document Server

    Weber, Valéry

    2010-01-01

    We regularize the potential distribution framework to calculate the excess free energy of liquid water simulated with the BLYP-D density functional. The calculated free energy is in fair agreement with experiments but the excess internal energy and hence also the excess entropy are not. Our work emphasizes the importance of thermodynamic characterization in assessing the quality of electron density functionals in describing liquid water and hydration phenomena.

  19. Adsorption of Water on JSC-1A Lunar Simulant Samples

    Science.gov (United States)

    Goering, John; Sah, Shweta; Burghaus, Uwe; Street, Kenneth W.

    2008-01-01

    Remote sensing probes sent to the moon in the 1990s indicated that water may exist in areas such as the bottoms of deep, permanently shadowed craters at the lunar poles, buried under regolith. Water is of paramount importance for any lunar exploration and colonization project which would require self-sustainable systems. Therefore, investigating the interaction of water with lunar regolith is pertinent to future exploration. The lunar environment can be approximated in ultra-high vacuum systems such as those used in thermal desorption spectroscopy (TDS). Questions about water dissociation, surface wetting, degree of crystallization, details of water-ice transitions, and cluster formation kinetics can be addressed by TDS. Lunar regolith specimens collected during the Apollo missions are still available though precious, so testing with simulant is required before applying to use lunar regolith samples. Hence, we used for these studies JSC-1a, mostly an aluminosilicate glass and basaltic material containing substantial amounts of plagioclase, some olivine and traces of other minerals. Objectives of this project include: 1) Manufacturing samples using as little raw material as possible, allowing the use of surface chemistry and kinetics tools to determine the feasibility of parallel studies on regolith, and 2) Characterizing the adsorption kinetics of water on the regolith simulant. This has implications for the probability of finding water on the moon and, if present, for recovery techniques. For condensed water films, complex TDS data were obtained containing multiple features, which are related to subtle rearrangements of the water adlayer. Results from JSC-1a TDS studies indicate: 1) Water dissociation on JSC-1a at low exposures, with features detected at temperatures as high as 450 K and 2) The formation of 3D water clusters and a rather porous condensed water film. It appears plausible that the sub- m sized particles act as nucleation centers.

  20. Application of WEAP Simulation Model to Hengshui City Water Planning

    Institute of Scientific and Technical Information of China (English)

    OJEKUNLE Z O; ZHAO Lin; LI Manzhou; YANG Zhen; TAN Xin

    2007-01-01

    Like many river basins in China, water resources in the Fudong Pai River are almost fully allocated. This paper seeks to assess and evaluate water resource problems using water evaluation and planning (WEAP) model via its application to Hengshui Basin of Fudong Pai River. This model allows the simulation and analysis of various water allocation scenarios and, above all, scenarios of users' behavior. Water demand management is one of the options discussed in detail. Simulations are proposed for diverse climatic situations from dry years to normal years and results are discussed. Within the limits of data availability, it appears that most water users are not able to meet all their requirements from the river, and that even the ecological reserve will not be fully met during certain years. But the adoption of water demand management procedures offers opportunities for remedying this situation during normal hydrological years. However, it appears that demand management alone will not suffice during dry years. Nevertheless, the ease of use of the model and its user-friendly interfaces make it particularly useful for discussions and dialogue on water resources management among stakeholders.

  1. Simulation method for determining biodegradation in surface waters

    Energy Technology Data Exchange (ETDEWEB)

    Schoeberl, P.; Guhl, W. [Henkel KGaA, Duesseldorf (Germany). Hauptabteilung Oekologie; Scholz, N. [OXENO GmbH, Marl (Germany); Taeger, K. [BASF AG, Ludwigshafen am Rhein (Germany)

    1998-07-01

    OECD guidelines and EU directives on the biological testing of chemicals contain no methods able to simulate biodegradation in surface waters. The surface water simulation method presented in this paper is suitable for closing this gap. The species in the autochthonous biocoenosis used in the method form part of the food web in natural surface waters. The microbial degradation activity measured by the half-life is comparable with that in surface waters. The degrees of degradation measured in this surface water simulation method can be applied to natural surface waters. (orig.) [Deutsch] Die OECD- und EU-Richtlinien zur biologischen Pruefung von Chemikalien enthalten kein Verfahren, mit dem der biologische Abbau in Fliessgewaessern simuliert werden kann. Das in dieser Arbeit vorgestellte Fliessgewaesser-Simulationsmodell ist geeignet, diese Luecke zu schliessen. Die Arten der autochthonen Biocoenose des Modells sind Glieder im Nahrungsnetz natuerlicher Fliessgewaesser. Die an der Halbwertszeit gemessene mikrobielle Abbauaktivitaet ist mit derjenigen in Fliessgewaessern vergleichbar. Die im Fliessgewaesser-Simulationsmodell gemessenen Abbaugrade sind auf natuerliche Fliessgewaesser uebertragbar. (orig.)

  2. Simulation analysis of domestic water demand and its future uncertainty in water scarce areas

    Institute of Scientific and Technical Information of China (English)

    Shouke WEI; Albrecht GNAUCK; Alin LEI

    2009-01-01

    This paper demonstrates a practical simulation approach to analyze domestic water demand and its future uncertainty in water scarce areas through a case study of Beijing, China. Analytic models and a forecasting model were constructed using statistic and econometric regres-sion approaches. The analytic models were used to analyze the interrelationships between domestic water demand and some socio-economic factors of Beijing. The forecasting model was applied to predict domestic water demand from 2009 to 2015, and this model was validated by comparing the prediction values with the observations. Scenario analysis was applied to simulate uncertainty and risks in domestic water demand in the future. The simulation results proved that domestic water demand will increase from 13.9×108 m3 to 16.7×108 m3 from 2009 to 2015. Three more sustainable strategies were also found through scenario analysis. The simulation and modeling approaches and results would be very supportive for water decision makers in allocating water efficiently and making sustainable water strategies.

  3. Assessing water service coverage by placeholders: a social media simulation

    NARCIS (Netherlands)

    Mandara, C.G.; Lammeren, van R.J.A.; Niehof, A.

    2016-01-01

    This paper presents the simulation of a social media approach to assess village domestic water services coverage by using a combination of known methods to capture placeholders. Placeholder is location based information given by local people who are familiar with a specific area due to a longer

  4. Computational Simulation of a Water-Cooled Heat Pump

    Science.gov (United States)

    Bozarth, Duane

    2008-01-01

    A Fortran-language computer program for simulating the operation of a water-cooled vapor-compression heat pump in any orientation with respect to gravity has been developed by modifying a prior general-purpose heat-pump design code used at Oak Ridge National Laboratory (ORNL).

  5. Simulation of an anion in water: effect of ion polarizability

    Science.gov (United States)

    Karim, Omar A.

    1991-10-01

    A polarizable-polar water model is used to study the structure of wate near a chloride ion. A semi-classical description of ion polarizability is included. Significant changes in the solute-solvent distribution functions are observed. When compared with a simulation without ion polarizability, it is found that the hydration number is further decreased when ion polarizability is present.

  6. 76 FR 53346 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-08-26

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Jersey Avenue, SE., Washington, DC 20590. Hand Delivery: Deliver to Mail address above between 9 a.m. and...) This AD applies to The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD-83),...

  7. 76 FR 41651 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-07-15

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Ground Floor, Room W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590. FOR FURTHER INFORMATION...) This AD applies to The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD-83),...

  8. Direct Phase Equilibrium Simulations of NIPAM Oligomers in Water.

    Science.gov (United States)

    Boţan, Vitalie; Ustach, Vincent; Faller, Roland; Leonhard, Kai

    2016-04-07

    NIPAM (N-isopropylacrylamide)-based polymers in water show many interesting properties in experiments, including a lower critical solution temperature (LCST) at 305 K and a conformational transition of single chains at the same temperature. The results of many simulation studies suggest that standard force fields are able to describe the conformational transition and the phase equilibrium well. We show by performing long molecular dynamics simulations of the direct liquid-liquid phase equilibrium of NIPAM trimers in water that there is no LCST in the expected temperature range for any of the force fields under study. The results show further that the relaxation times of single-chain simulations are considerably longer than anticipated. Conformational transitions of single polymers can therefore not necessarily be used as surrogates for a real phase transition.

  9. Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.

    Science.gov (United States)

    Zavadlav, Julija; Marrink, Siewert J; Praprotnik, Matej

    2016-08-09

    The adaptive resolution scheme (AdResS) is a multiscale molecular dynamics simulation approach that can concurrently couple atomistic (AT) and coarse-grained (CG) resolution regions, i.e., the molecules can freely adapt their resolution according to their current position in the system. Coupling to supramolecular CG models, where several molecules are represented as a single CG bead, is challenging, but it provides higher computational gains and connection to the established MARTINI CG force field. Difficulties that arise from such coupling have been so far bypassed with bundled AT water models, where additional harmonic bonds between oxygen atoms within a given supramolecular water bundle are introduced. While these models simplify the supramolecular coupling, they also cause in certain situations spurious artifacts, such as partial unfolding of biomolecules. In this work, we present a new clustering algorithm SWINGER that can concurrently make, break, and remake water bundles and in conjunction with the AdResS permits the use of original AT water models. We apply our approach to simulate a hybrid SPC/MARTINI water system and show that the essential properties of water are correctly reproduced with respect to the standard monoscale simulations. The developed hybrid water model can be used in biomolecular simulations, where a significant speed up can be obtained without compromising the accuracy of the AT water model.

  10. Water Yield and Sediment Yield Simulations for Teba Catchment in Spain Using SWRRB Model: Ⅰ. Model Input and Simulation Experiment

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Water yield and sediment yield in the Teba catchment, Spain, were simulated using SWRRB (Simulator for Water Resources in Rural Basins) model. The model is composed of 198 mathematical equations. About 120 items (variables) were input for the simulation, including meteorological and climatic factors, hydrologic factors, topographic factors, parent materials, soils, vegetation, human activities, etc. The simulated results involved surface runoff, subsurface runoff, sediment, peak flow, evapotranspiration, soil water, total biomass,etc. Careful and thorough input data preparation and repeated simulation experiments are the key to get the accurate results. In this work the simulation accuracy for annual water yield prediction reached to 83.68%.``

  11. Design of virtual SCADA simulation system for pressurized water reactor

    Science.gov (United States)

    Wijaksono, Umar; Abdullah, Ade Gafar; Hakim, Dadang Lukman

    2016-02-01

    The Virtual SCADA system is a software-based Human-Machine Interface that can visualize the process of a plant. This paper described the results of the virtual SCADA system design that aims to recognize the principle of the Nuclear Power Plant type Pressurized Water Reactor. This simulation uses technical data of the Nuclear Power Plant Unit Olkiluoto 3 in Finland. This device was developed using Wonderware Intouch, which is equipped with manual books for each component, animation links, alarm systems, real time and historical trending, and security system. The results showed that in general this device can demonstrate clearly the principles of energy flow and energy conversion processes in Pressurized Water Reactors. This virtual SCADA simulation system can be used as instructional media to recognize the principle of Pressurized Water Reactor.

  12. Design of virtual SCADA simulation system for pressurized water reactor

    Energy Technology Data Exchange (ETDEWEB)

    Wijaksono, Umar, E-mail: umar.wijaksono@student.upi.edu; Abdullah, Ade Gafar; Hakim, Dadang Lukman [Electrical Power System Research Group, Department of Electrical Engineering Education, Jl. Dr. Setiabudi No. 207 Bandung, Indonesia 40154 (Indonesia)

    2016-02-08

    The Virtual SCADA system is a software-based Human-Machine Interface that can visualize the process of a plant. This paper described the results of the virtual SCADA system design that aims to recognize the principle of the Nuclear Power Plant type Pressurized Water Reactor. This simulation uses technical data of the Nuclear Power Plant Unit Olkiluoto 3 in Finland. This device was developed using Wonderware Intouch, which is equipped with manual books for each component, animation links, alarm systems, real time and historical trending, and security system. The results showed that in general this device can demonstrate clearly the principles of energy flow and energy conversion processes in Pressurized Water Reactors. This virtual SCADA simulation system can be used as instructional media to recognize the principle of Pressurized Water Reactor.

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

    Science.gov (United States)

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

    1996-04-01

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

  14. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters.

    Science.gov (United States)

    Joung, In Suk; Cheatham, Thomas E

    2009-10-01

    The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.

  15. Simulation of water quantity exchange between groundwater and the Platte River water, central Nebraska

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The authors demonstrate the importance of the simulation of the water quantity exchange between river water and groundwater to a better understanding of the hydrologic relations between a river and nearby aquifer where groundwater is pumped extensively but only seasonally. And MODFLOW is used to design the stream-aquifer model in which the pumpage of more than 1000 wells was simulated. The river gaining and river losing processes were analyzed. Simulation results suggest that continuation of over-extraction of groundwater will gradually increase the depletion volume in the river year after year and more depletion will occur in later years. The exchange manner between groundwater and the Platte River differs from place to place. The Platte River loses water to the adjacent aquifer in the west part of the study area, and gains water from the adjacent aquifer in the east part of the study area.

  16. Irrigation water policy analysis using a business simulation game

    Science.gov (United States)

    Buchholz, M.; Holst, G.; Musshoff, O.

    2016-10-01

    Despite numerous studies on farmers' responses to changing irrigation water policies, uncertainties remain about the potential of water pricing schemes and water quotas to reduce irrigation. Thus far, policy impact analysis is predominantly based upon rational choice models that assume behavioral assumptions, such as a perfectly rational profit-maximizing decision maker. Also, econometric techniques are applied which could lack internal validity due to uncontrolled field data. Furthermore, such techniques are not capable of identifying ill-designed policies prior to their implementation. With this in mind, we apply a business simulation game for ex ante policy impact analysis of irrigation water policies at the farm level. Our approach has the potential to reveal the policy-induced behavioral change of the participants in a controlled environment. To do so, we investigate how real farmers from Germany, in an economic experiment, respond to a water pricing scheme and a water quota intending to reduce irrigation. In the business simulation game, the participants manage a "virtual" cash-crop farm for which they make crop allocation and irrigation decisions during several production periods, while facing uncertain product prices and weather conditions. The results reveal that a water quota is able to reduce mean irrigation applications, while a water pricing scheme does not have an impact, even though both policies exhibit equal income effects for the farmers. However, both policies appear to increase the variation of irrigation applications. Compared to a perfectly rational profit-maximizing decision maker, the participants apply less irrigation on average, both when irrigation is not restricted and when a water pricing scheme applies. Moreover, the participants' risk attitude affects the irrigation decisions.

  17. H5MD: a structured, efficient, and portable file format for molecular data

    CERN Document Server

    de Buyl, Pierre; Höfling, Felix

    2013-01-01

    We propose a new open file format named "H5MD" for storing molecular simulation data such as trajectories of particle positions and velocities as well as thermodynamic observables that are tracked during the course of the simulation. H5MD files are HDF5 (Hierarchical Data Format) files with a specific hierarchy and naming scheme. Thus, H5MD inherits many benefits of HDF5, e.g., structured layout of multi-dimensional data sets, data compression, fast and parallel I/O, and portability across many programming languages and hardware platforms. H5MD files are self-contained, and foster the reproducibility of scientific data and the interchange of data between researchers using different simulation programs and analysis software. In addition, the H5MD specification can serve for other kinds of data (e.g. experimental data) and is extensible to supplemental data without breaking the compliance of the file to the specification.

  18. Simulation study on structure of water in aqueous solutions confined between graphene electrodes under very high applied electric field

    Science.gov (United States)

    Leuty, Gary; Tsige, Mesfin; Talapatra, Saikat

    2011-03-01

    Arising from questions regarding electric double-layer capacitors utilizing graphene electrodes and aqueous electrolyte (KOH solution), atomistic MD simulations of electrolyte confined between graphene electrodes were performed to understand the behavior of electrolyte as a function of electric field strength and solution concentration, from pure water to 6M KOH. It was noted that the strength of the electric field had a demonstrable effect on the structure of pure water between the electrodes (as has previously been seen in highly confined multilayer water systems), creating regularly spaced channels and densely packed sheets of highly ordered molecules. We also saw a clear effect due to the presence of electrolyte ions and their separation from the water due to the action of the field; different field strengths appear to greatly alter the distribution of ions, which in turn affects the structure and ordering of the water. Time dependence in the strength of the electric field was also studied to determine what effect, if any, it has on induced structure. Authors gratefully acknowledge support from the ACS Petroleum Research Fund and the National Science Foundation.

  19. CoMD Implementation Suite in Emerging Programming Models

    Energy Technology Data Exchange (ETDEWEB)

    2014-09-23

    CoMD-Em is a software implementation suite of the CoMD [4] proxy app using different emerging programming models. It is intended to analyze the features and capabilities of novel programming models that could help ensure code and performance portability and scalability across heterogeneous platforms while improving programmer productivity. Another goal is to provide the authors and venders with some meaningful feedback regarding the capabilities and limitations of their models. The actual application is a classical molecular dynamics (MD) simulation using either the Lennard-Jones method (LJ) or the embedded atom method (EAM) for primary particle interaction. The code can be extended to support alternate interaction models. The code is expected ro run on a wide class of heterogeneous hardware configurations like shard/distributed/hybrid memory, GPU's and any other platform supported by the underlying programming model.

  20. Multiphase simulation of mine waters and aqueous leaching processes

    Directory of Open Access Journals (Sweden)

    Pajarre Risto

    2016-01-01

    Full Text Available Managing of large amounts of water in mining and mineral processing sites remains a concern in both actively operated and closed mining areas. When the mining site with its metal or concentrate producing units is operational, the challenge is to find either ways for economical processing with maximum yields, while minimizing the environmental impact of the water usage and waste salt treatments. For safe closure of the site, the environmental control of possible drainage will be needed. For both challenges, the present-day multiphase process simulations tools can be used to provide improved accuracy and better economy in controlling the smooth and environmentally sound operation of the plant. One of the pioneering studies in using the multiphase thermodynamic software in simulation of hydrometallurgical processes was that of Koukkari et al. [1]. The study covered the use of Solgasmix equilibrium software for a number of practical acid digesters. The models were made for sulfuric acid treatments in titania pigment production and in NPK fertilizer manufacturing. During the past two decades the extensive data assessment has taken place particularly in geochemistry and a new versions of geochemical multiphase equilibrium software has been developed. On the other hand, there has been some progress in development of the process simulation software in all the aforementioned fields. Thus, the thermodynamic simulation has become a tool of great importance in development of hydrometallurgical processes. The presentation will cover three example cases of either true pilot or industrial systems including a South African acid mine water drainage treatment, hydrometallurgical extraction of rare earths from uranium leachate in Russia and a multistage process simulation of a Finnish heap leaching mine with its subsequent water treatment system.

  1. Numerical Simulations of Vertical Water Redistribution in Sand

    Science.gov (United States)

    Abhishek, A.

    2016-12-01

    Moisture redistribution process in porous media has a wide range of practical applications in petroleum industry, agriculture engineering, hydrology and carbon/CO2 sequestration. Recently, a vertical water redistribution experiment was designed. A thin column with dimensions of 50 (height) by 1.2 cm (inner diameter) was employed. Five water tensiometers were mounted along the column at distances of 1, 13, 25, 37 and 49 cm from the top. Two air tensiometers were mounted at 15 and 35 cm from the top to measure air pressure. The column was packed with saturated medium sand and was set up vertically. The bottom of the column was set open to the air to allow the sand to drain gradually under gravity. Once the flow completely ceased and equilibrium was reached, the column was reversed to let moisture in the sand redistribute. During both free drainage and redistribution processes, saturation was measured by gamma transmission method, and water and air pressure were measured by tensiometers. Numerical simulations were used to estimate saturation distribution over the whole column and the duration of experiments. We used both 1D and 2D models based on Richards equation to simulate this vertical redistribution process. Both COMSOL and HYDRUS-1D were used to solve 1D model, while COMSOL was employed to solve 2D model. In 1D simulations, equilibrium time was found to increase linearly during free drainage process, proportional to the length of the column. It was 1.4 days for the length of 50 cm, which is employed in experiments. In 2D simulations, water saturation profiles were non-uniform along the width of the domain at earlier time steps, while they become almost uniform when equilibrium was reached. The simulated results are compared with experimental results.

  2. Runoff simulation sensitivity to remotely sensed initial soil water content

    Science.gov (United States)

    Goodrich, D. C.; Schmugge, T. J.; Jackson, T. J.; Unkrich, C. L.; Keefer, T. O.; Parry, R.; Bach, L. B.; Amer, S. A.

    1994-05-01

    A variety of aircraft remotely sensed and conventional ground-based measurements of volumetric soil water content (SW) were made over two subwatersheds (4.4 and 631 ha) of the U.S. Department of Agriculture's Agricultural Research Service Walnut Gulch experimental watershed during the 1990 monsoon season. Spatially distributed soil water contents estimated remotely from the NASA push broom microwave radiometer (PBMR), an Institute of Radioengineering and Electronics (IRE) multifrequency radiometer, and three ground-based point methods were used to define prestorm initial SW for a distributed rainfall-runoff model (KINEROS; Woolhiser et al., 1990) at a small catchment scale (4.4 ha). At a medium catchment scale (631 ha or 6.31 km2) spatially distributed PBMR SW data were aggregated via stream order reduction. The impacts of the various spatial averages of SW on runoff simulations are discussed and are compared to runoff simulations using SW estimates derived from a simple daily water balance model. It was found that at the small catchment scale the SW data obtained from any of the measurement methods could be used to obtain reasonable runoff predictions. At the medium catchment scale, a basin-wide remotely sensed average of initial water content was sufficient for runoff simulations. This has important implications for the possible use of satellite-based microwave soil moisture data to define prestorm SW because the low spatial resolutions of such sensors may not seriously impact runoff simulations under the conditions examined. However, at both the small and medium basin scale, adequate resources must be devoted to proper definition of the input rainfall to achieve reasonable runoff simulations.

  3. Molecular Dynamics Simulation: The Behavior of Asphaltene in Crude Oil and at the Oil/Water Interface

    KAUST Repository

    Gao, Fengfeng

    2014-12-18

    Carboxyl asphaltene is commonly discussed in the petroleum industry. In most conditions, electroneutral carboxyl asphaltene molecules can be deprotonated to become carboxylate asphaltenes. Both in crude oil and at the oil/water interface, the characteristics of anionic carboxylate asphaltenes are different than those of the carboxyl asphaltenes. In this paper, molecular dynamics (MD) simulations are utilized to study the structural features of different asphaltene molecules, namely, C5 Pe and anionic C5 Pe, at the molecular level. In crude oil, the electroneutral C5 Pe molecules prefer to form a steady face-to-face stacking, while the anionic C5 Pe molecules are inclined to form face-to-face stacking and T-shaped II stacking because of the repulsion of the anionic headgroups. Anionic C5 Pe has a distinct affinity to the oil/water interface during the simulation, while the C5 Pe molecules persist in the crude oil domain. A three-stage model of anionic C5 Pe molecules adsorbed at the oil/water interface is finally developed.

  4. Water shortage risk assessment using spatiotemporal flow simulation

    Science.gov (United States)

    Hsieh, Hsin-I.; Su, Ming-Daw; Wu, Yii-Chen; Cheng, Ke-Sheng

    2016-12-01

    Paddy irrigation practices in Taiwan utilize complicated water conveyance networks which draw streamflows from different tributaries. Characterizing and simulating streamflow series is thus an essential task for irrigation risk assessment and planning mitigation measures. It generally involves modeling the temporal variation and spatial correlation of streamflow data at different sites. Like many other environmental variables, streamflows are asymmetric and non-Gaussian. Such properties exacerbate the difficulties in spatiotemporal modeling of streamflow data. A stochastic spatiotemporal simulation approach capable of generating non-Gaussian ten-day period streamflow data series at different sites is presented in this paper. Historical flow data from different flow stations in southern Taiwan were used to exemplify the application of the proposed model. Simulated realizations of the spatiotemporal anisotropic multivariate Pearson type III distribution were validated by comparing parameters and spatiotemporal correlation characteristics of the simulated data and the observed streamflow data. Risks of irrigation water shortage were estimated and the effect of mitigation measures was assessed using the simulated data.

  5. Control algorithm for multiscale flow simulations of water

    DEFF Research Database (Denmark)

    Kotsalis, E. M.; Walther, Jens Honore; Kaxiras, E.

    2009-01-01

    . The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid......We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions...... Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water....

  6. Control algorithm for multiscale flow simulations of water

    Science.gov (United States)

    Kotsalis, Evangelos M.; Walther, Jens H.; Kaxiras, Efthimios; Koumoutsakos, Petros

    2009-04-01

    We present a multiscale algorithm to couple atomistic water models with continuum incompressible flow simulations via a Schwarz domain decomposition approach. The coupling introduces an inhomogeneity in the description of the atomistic domain and prevents the use of periodic boundary conditions. The use of a mass conserving specular wall results in turn to spurious oscillations in the density profile of the atomistic description of water. These oscillations can be eliminated by using an external boundary force that effectively accounts for the virial component of the pressure. In this Rapid Communication, we extend a control algorithm, previously introduced for monatomic molecules, to the case of atomistic water and demonstrate the effectiveness of this approach. The proposed computational method is validated for the cases of equilibrium and Couette flow of water.

  7. A simulation of water pollution model parameter estimation

    Science.gov (United States)

    Kibler, J. F.

    1976-01-01

    A parameter estimation procedure for a water pollution transport model is elaborated. A two-dimensional instantaneous-release shear-diffusion model serves as representative of a simple transport process. Pollution concentration levels are arrived at via modeling of a remote-sensing system. The remote-sensed data are simulated by adding Gaussian noise to the concentration level values generated via the transport model. Model parameters are estimated from the simulated data using a least-squares batch processor. Resolution, sensor array size, and number and location of sensor readings can be found from the accuracies of the parameter estimates.

  8. Computer simulation study of water using a fluctuating charge model

    Indian Academy of Sciences (India)

    M Krishnan; A Verma; S Balasubramanian

    2001-10-01

    Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Rick et al (S W Rick, S J Stuart and B J Berne 1994 J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size of ten. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.

  9. Compressive spectral method for the simulation of the water waves

    CERN Document Server

    Bayindir, Cihan

    2015-01-01

    In this paper an approach for decreasing the computational effort required for the spectral simulations of the water waves is introduced. Signals with majority of the components zero, are known as the sparse signals. Like majority of the signals in the nature it can be realized that water waves are sparse either in time or in the frequency domain. Using the sparsity property of the water waves in the time or in the frequency domain, the compressive sampling algorithm can be used as a tool for improving the performance of the spectral simulation of the water waves. The methodology offered in this paper depends on the idea of using a smaller number of spectral components compared to the classical spectral method with a high number of components. After performing the time integration with a smaller number of spectral components and using the compressive sampling technique, it is shown that the water wave field can be reconstructed with a significantly better efficiency compared to the classical spectral method w...

  10. Water sensitive papers simulation to assess deposits on targets

    Directory of Open Access Journals (Sweden)

    Emanuele Cerruto

    2013-09-01

    Full Text Available Aim of the study is to assess the possibility to use water sensitive papers to estimate, beside the superficial coverage, also the amount of deposit on the target at varying the spray features. To point out the main quantities influencing the deposit, the behaviour of the water sensitive papers was simulated by assuming some simplifying hypotheses: log-normal distribution of the diameter population of the drops and circular spots. Several images (630 of water sensitive papers, sprayed with drops of different mean diameter (from 100 up to 500 μm, constant coefficient of variation (0.50, and theoretical percentage of covered surface ranging from 10 up to 100%, were produced by means of simulation. These images were considered as effective water sensitive paper images and then analysed by means of an image processing software. The correlations between measured and effective values were studied and they allowed for an estimate of deposit and spray features from the image data. This implies that the analysis of the water sensitive paper images allows the determination of more complex parameters such as the unitary deposit and the impact density, all data strictly related to the efficacy of a phytosanitary treatment.

  11. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Animesh, E-mail: animesh@zedat.fu-berlin.de; Delle Site, Luigi, E-mail: dellesite@fu-berlin.de [Institute for Mathematics, Freie Universität Berlin, Berlin (Germany)

    2015-09-07

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  12. Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water

    Science.gov (United States)

    Agarwal, Animesh; Delle Site, Luigi

    2015-09-01

    Quantum effects due to the spatial delocalization of light atoms are treated in molecular simulation via the path integral technique. Among several methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to investigate properties induced by spatial delocalization of atoms; however, computationally this technique is very demanding. The above mentioned limitation implies the restriction of PIMD applications to relatively small systems and short time scales. One of the possible solutions to overcome size and time limitation is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme (AdResS). AdResS requires a relatively small region treated at path integral level and embeds it into a large molecular reservoir consisting of generic spherical coarse grained molecules. It was previously shown that the realization of the idea above, at a simple level, produced reasonable results for toy systems or simple/test systems like liquid parahydrogen. Encouraged by previous results, in this paper, we show the simulation of liquid water at room conditions where AdResS, in its latest and more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of the most relevant PIMD techniques available in the literature. The comparison of our results with those reported in the literature and/or with those obtained from full PIMD simulations shows a highly satisfactory agreement.

  13. Simulation of Irrigation Water Loss Based on VSMB Model

    Institute of Scientific and Technical Information of China (English)

    Hongwen ZHOU; Luxin ZHAI; Wenxing LU; Dongxu LIU

    2016-01-01

    The low degree of development and utilization as well as the contradiction between supply and demand of water resources in Huangshui River basin are the main restricting factors of the local agricultural development. The study on the simulation of irrigation water loss based on the VSMB model has very important significance to strengthening regional water management and improving water resource utilization efficiency. Five groundwater wells were set up to carry out the farmland irrigation water infiltration and the experimental study on groundwater dynamic effect. Two soil moisture monitoring sites were set up in two typical plots of Daxia and Guanting irrigation area at the same time and TDR300 was used to monitor four kinds of deep soil moisture( 10 cm,30 cm,50 cm and 70 cm). On this basis,the VSMB model was used to study the irrigation water loss in the irrigation area of Yellow River valley of Qinghai Province,including soil moisture content,the actual evapotranspiration,infiltration,runoff,groundwater buried depth and so on. The results showed that the water consumption caused by soil evaporation and crop transpiration accounted for 46. 4% and 24. 1% of the total precipitation plus irrigation,respectively,and the leakage accounted for 30. 3% and 60. 6% of the total precipitation plus irrigation,respectively,from March 1,2013 to April 30,and from August 1 to September 30. The actual evaporation of the GT- TR1 and GT- TR2 sites in the whole year of 2013 was 632. 6 mm and 646. 9 mm,respectively,and the leakage accounted for 2. 6% and 1. 2% of the total precipitation plus irrigation,respectively. RMSE of the simulation results of the groundwater depth in Daxia irrigation area during the two periods was 92. 3 mm and 27. 7 mm,respectively. And RMSE of the simulation results of the water content of soil profile in the two monitoring sites of Guanting irrigation area was 2. 04% and 5. 81%,respectively,indicating that the simulation results were reliable.

  14. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA.

    Science.gov (United States)

    Karakas, Esra; Taveneau, Cyntia; Bressanelli, Stéphane; Marchi, Massimo; Robert, Bruno; Abel, Stéphane

    2017-01-01

    In this paper, we describe the derivation and the validation of original RESP atomic partial charges for the N, N-dimethyl-dodecylamine oxide (LDAO) surfactant. These charges, designed to be fully compatible with all the AMBER force fields, are at first tested against molecular dynamics simulations of pure LDAO micelles and with a fragment of the lipid kinase PIK4A (DI) modeled with the QUARK molecular modeling server. To model the micelle, we used two distinct AMBER force fields (i.e. Amber99SB and Lipid14) and a variety of starting conditions. We find that the micelle structural properties (such as the shape, size, the LDAO headgroup hydration, and alkyl chain conformation) slightly depend on the force field but not on the starting conditions and more importantly are in good agreement with experiments and previous simulations. We also show that the Lipid14 force field should be used instead of the Amber99SB one to better reproduce the C(sp3)C(sp3)C(sp3)C(sp3) conformation in the surfactant alkyl chain. Concerning the simulations with LDAO-DI protein, we carried out different runs at two NaCl concentrations (i.e. 0 and 300 mM) to mimic, in the latter case, the experimental conditions. We notice a small dependence of the simulation results with the LDAO parameters and the salt concentration. However, we find that in the simulations, three out of four tryptophans of the DI protein are not accessible to water in agreement with our fluorescence spectroscopy experiments reported in the paper.

  15. Water Yield and Sediment Yield Simulations for Teba Catchment in Spain Using SWRRB Model: Ⅱ.Simulation Results

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Simulated results of water yield, sediment yield, surface runoff, subsurface runoff, peak flow, evapotranspiration, etc., in the Teba catchment, Spain, using SWRRB (Simulator for Water Resources in Rural Basins) model are presented and the related problems are discussed. The results showed that water yield and sediment yield could be satisfactorily simulated using SWRRB model The accuracy of the annual water yield simulation in the Teba catchment was up to 83.68%, which implied that this method could be effectively used to predict the annual or inter-annual water yield and to realize the quantification of geographic elements and processes of a river basin.``

  16. Numerical Simulation and Water Analog of Mold Filling Processes

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper demonstrates the potential of a computer code, developed by the authors, in shaping gating systems by modeling the fluid flow phenomena through a complex gating system during mold filling. A plate casting with dimension 200 mm×200 mm×50 mm was chosen as the verifying problem. Water analog studies were carried out on this casting. The comparison indicates that computer simulation could be a powerful tool in shaping gating systems.

  17. Simulations of Time Reversing Arrays in Shallow Ocean Waters

    Science.gov (United States)

    2016-06-07

    using a customized version of RAM that allows us to recover the amplitude and phase of the computed field. We have also developed Monte-Carlo...Simulations of Time Reversing Arrays in Shallow Ocean Waters David R. Dowling Department of Mechanical Engineering and Applied Mechanics University...1-0628 http://www.personal.engin.umich.edu/~drd LONG-TERM GOAL The long term goals of this project are: i) to predict and understand time reversing

  18. Simulation of distribution of radiation energy density in water balls

    Institute of Scientific and Technical Information of China (English)

    TANG Shi-Biao; MA Qing-Li; YIN Ze-Jie; TANG Yu; HUANG Huan; RAO Nan-Xia; ZHU Da-Ming

    2005-01-01

    The distribution of energy deposition density in radiate region and its surrounding areas from γ-rays was simulated and analyzed for a water-ball model with Geant4 package ( Geant4.7.0,2005 ) developed by CERN (the Center of European Research of Nucleus). The results show that the distribution depends strongly on the collimating condition of radiation beam. A well-collimated beam would reduce radiation effects on surrounding areas.

  19. Effect of artesian water on the mine floor water inrush and significance of similitude simulation to it

    Institute of Scientific and Technical Information of China (English)

    ZHANG Wen-quan; REN Yang-hui; ZHANG Hong-ri; ZHU Zhi-qiang

    2007-01-01

    According to the in situ statistics data, indoor rock hydraulic fracturing experiments and numerical simulation results, the role of artesian water quantity was analyzed,emphasis was put on the analysis of the damage mechanics of artesian water to rocks under the floor and the softening, solution and scouring action of artesian water were also researched. At the end of the paper, practical significance of similar material simulation to the influence of artesian water on water inrush under the floor was discussed and hoped to provide references to the artesian water hydraulics simulation experiment devices design and test based on the indoor similar material simulation platform.

  20. 76 FR 39251 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-07-06

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Jersey Avenue, SE., Washington, DC 20590. FOR FURTHER INFORMATION CONTACT: Roger Durbin, Aerospace.... Applicability (c) This AD applies to all The Boeing Company Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83...

  1. 76 FR 1993 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-01-12

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Ground Floor, Room W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590. FOR FURTHER INFORMATION.... Applicability (c) This AD applies to The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83...

  2. 76 FR 13543 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-03-14

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Floor, Room W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590. Hand Delivery: Deliver to Mail... stabilizer is similar in design and loading to that of the Model DC-9-81 (MD-81), DC- 9-82 (MD-82),...

  3. 33 CFR 165.507 - Security Zone; Chesapeake Bay, between Sandy Point and Kent Island, MD.

    Science.gov (United States)

    2010-07-01

    ... south (eastbound) span of the William P. Lane Jr. Memorial Bridge, from the western shore at Sandy Point..., between Sandy Point and Kent Island, MD. 165.507 Section 165.507 Navigation and Navigable Waters COAST... Guard District § 165.507 Security Zone; Chesapeake Bay, between Sandy Point and Kent Island, MD. (a...

  4. 75 FR 41789 - Special Local Regulations for Marine Events; Patuxent River, Solomons, MD

    Science.gov (United States)

    2010-07-19

    ... River, Solomons, MD AGENCY: Coast Guard, DHS. ACTION: Supplemental notice of proposed rulemaking... Challenge'' power boat races, a marine event to be held on the waters of the Patuxent River, near Solomons... for Marine Events; Patuxent River, Solomons, MD'' in the Federal Register (75 FR 111). The NPRM stated...

  5. Numerical Simulation of a Solar Domestic Hot Water System

    Science.gov (United States)

    Mongibello, L.; Bianco, N.; Di Somma, M.; Graditi, G.; Naso, V.

    2014-11-01

    An innovative transient numerical model is presented for the simulation of a solar Domestic Hot Water (DHW) system. The solar collectors have been simulated by using a zerodimensional analytical model. The temperature distributions in the heat transfer fluid and in the water inside the tank have been evaluated by one-dimensional models. The reversion elimination algorithm has been used to include the effects of natural convection among the water layers at different heights in the tank on the thermal stratification. A finite difference implicit scheme has been implemented to solve the energy conservation equation in the coil heat exchanger, and the energy conservation equation in the tank has been solved by using the finite difference Euler implicit scheme. Energy conservation equations for the solar DHW components models have been coupled by means of a home-made implicit algorithm. Results of the simulation performed using as input data the experimental values of the ambient temperature and the solar irradiance in a summer day are presented and discussed.

  6. Numerical simulation and analysis of water flow over stepped spillways

    Institute of Scientific and Technical Information of China (English)

    QIAN ZhongDong; HU XiaoQing; HUAI WenXin; AMADOR António

    2009-01-01

    Numerical simulation of water flow over the stepped spillway is conducted using Mixture multiphase flow model. Different turbulence models are chosen to enclose the controlling equations. The turbulence models investigated are realizable k-ε model, SST k-ω model, v2-f model and LES model. The computational results by the four turbulence models are compared with experimental ones in the following aspects: mean velocity, the spanwise vorticity and the growth of the turbulent boundary layer thickness in the streamwise direction. It is found from the comparison that the realizable k-ε model, in which the rotation tensor is included, shows good performance for simulation of flows involving rotation, boundary layer and recirculation. The realizable k-e model is the most efficient in simulating flow over stepped spillways. Further, the characteristics of water flow on the stepped spillway are studied in terms of the mean velocity profile normal to the pseudo-bottom and the pressure field on the steps based on the simulation results using realizable k-ε model.

  7. Numerical simulation and analysis of water flow over stepped spillways

    Institute of Scientific and Technical Information of China (English)

    AMADOR; António

    2009-01-01

    Numerical simulation of water flow over the stepped spillway is conducted using Mixture multiphase flow model. Different turbulence models are chosen to enclose the controlling equations. The turbulence models investigated are realizable k-ε model, SST k-ω model, v2-f model and LES model. The computational results by the four turbulence models are compared with experimental ones in the following aspects: mean velocity, the spanwise vorticity and the growth of the turbulent boundary layer thickness in the streamwise direction. It is found from the comparison that the realizable k-ε model, in which the rotation tensor is included, shows good performance for simulation of flows involving rotation, boundary layer and recirculation. The realizable k-ε model is the most efficient in simulating flow over stepped spillways. Further, the characteristics of water flow on the stepped spillway are studied in terms of the mean velocity profile normal to the pseudo-bottom and the pressure field on the steps based on the simulation results using realizable k-ε model.

  8. Cavity Voltage Phase Modulation MD

    CERN Document Server

    Mastoridis, Themistoklis; Molendijk, John; Timko, Helga; CERN. Geneva. ATS Department

    2016-01-01

    The LHC RF/LLRF system is currently configured for extremely stable RF voltage to minimize transient beam loading effects. The present scheme cannot be extended beyond nominal beam current since the demanded power would exceed the peak klystron power and lead to saturation. A new scheme has therefore been proposed: for beam currents above nominal (and possibly earlier), the cavity phase modulation by the beam will not be corrected (transient beam loading), but the strong RF feedback and One-Turn Delay feedback will still be active for loop and beam stability in physics. To achieve this, the voltage set point will be adapted for each bunch. The goal of this MD was to test a new algorithm that would adjust the voltage set point to achieve the cavity phase modulation that would minimize klystron forward power.

  9. Simulation of Water Movement through Unsaturated Infiltration- Redistribution System

    Directory of Open Access Journals (Sweden)

    T Bunsri

    2009-01-01

    Full Text Available This paper deals with the movement of water in a natural unsaturated zone, focusing on infiltration-redistribution system. Infiltration refers to the downward movement of water due to the gravitational force and redistribution defines the upward movement of water due to the capillary rise. Under natural conditions, the movement of water through an infiltrationredistribution depended upon the relations among water content, hydraulic conductivity and tension of soil pore. Various combinations of water balance concepts, Richards’ equation, soil-physics theory and capillary height concepts were applied to mathematically model the movement of water through infiltration-redistribution system. The accuracy and computational efficiency of the developed model were evaluated for the case study. Besides the laboratory scale sand/soil columns with the inner diameter of 10.4 cm were investigated in order to provide the supporting data for model calibration. Sand/soil layers were packed with a bulk density of 1.80 and 1.25 g/cm3, respectively. The infiltration was sprayed uniformly at the soil surface with the constant rate of 66.1 and 7.18 cm3/h for sand and soil columns, respectively. The redistribution process was developed by which water arriving at the column base enter to the sand/soil column due to capillary rise. The laboratory observations were simulated using the developed model. The results indicate that the developed model could well estimate the movement of water in the infiltration-redistribution system that observed in the case study and the experiments.

  10. STRUCTURAL-PROPERTIES OF 1,2-DIACYL-SN-GLYCEROL IN BULK AND AT THE WATER INTERFACE BY MOLECULAR-DYNAMICS

    NARCIS (Netherlands)

    VANBUUREN, AR; DEVLIEG, J; BERENDSEN, HJC

    1995-01-01

    We performed four different molecular dynamics (MD) simulations of 1,2-dilauroyl-sn-glycerol (DLG) systems at 300 and 360 K: a crystal simulation, a pure DLG oil phase, a DLG oil phase in contact with a water layer, and an oil/monolayer/water simulation. All these systems were simulated for several

  11. Molecular simulation of the magnetite-water interface

    Science.gov (United States)

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

    2003-03-01

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

  12. 散列算法MD5和SHA-1的比较%Comparison between MD5 and SHA-1

    Institute of Scientific and Technical Information of China (English)

    王泽; 曹莉莎

    2016-01-01

    MD5 and SHA-1 are the two known Hash Algorithm which are widely applied in information security, they are both developed from MD4.This paper introduces their algorithm logic in detail, compares them though simulation experiment ,soft-ware testing, etc. Finally, it draw a conclusion:The SHA-1 algorithm is more secure than the MD5 algorithm, but in the same hardware, SHA-1 is slower than MD5.%MD5和SHA-1是两个已知的广泛应用于信息安全的散列算法,均由MD4发展而来。详细介绍了它们的算法逻辑,并通过模拟实验、软件测试等方式对其在各个方面进行比较,最终得出结论:SHA-1算法比MD5算法的安全性更高,但在同一硬件上,SHA-1比MD5运行的要慢。

  13. Water at an electrochemical interface - a simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Willard, Adam; Reed, Stewart; Madden, Paul; Chandler, David

    2008-08-22

    The results of molecular dynamics simulations of the properties of water in an aqueous ionic solution close to an interface with a model metallic electrode are described. In the simulations the electrode behaves as an ideally polarizable hydrophilic metal, supporting image charge interactions with charged species, and it is maintained at a constant electrical potential with respect to the solution so that the model is a textbook representation of an electrochemical interface through which no current is passing. We show how water is strongly attracted to and ordered at the electrode surface. This ordering is different to the structure that might be imagined from continuum models of electrode interfaces. Further, this ordering significantly affects the probability of ions reaching the surface. We describe the concomitant motion and configurations of the water and ions as functions of the electrode potential, and we analyze the length scales over which ionic atmospheres fluctuate. The statistics of these fluctuations depend upon surface structure and ionic strength. The fluctuations are large, sufficiently so that the mean ionic atmosphere is a poor descriptor of the aqueous environment near a metal surface. The importance of this finding for a description of electrochemical reactions is examined by calculating, directly from the simulation, Marcus free energy profiles for transfer of charge between the electrode and a redox species in the solution and comparing the results with the predictions of continuum theories. Significant departures from the electrochemical textbook descriptions of the phenomenon are found and their physical origins are characterized from the atomistic perspective of the simulations.

  14. Humans running in place on water at simulated reduced gravity.

    Directory of Open Access Journals (Sweden)

    Alberto E Minetti

    Full Text Available BACKGROUND: On Earth only a few legged species, such as water strider insects, some aquatic birds and lizards, can run on water. For most other species, including humans, this is precluded by body size and proportions, lack of appropriate appendages, and limited muscle power. However, if gravity is reduced to less than Earth's gravity, running on water should require less muscle power. Here we use a hydrodynamic model to predict the gravity levels at which humans should be able to run on water. We test these predictions in the laboratory using a reduced gravity simulator. METHODOLOGY/PRINCIPAL FINDINGS: We adapted a model equation, previously used by Glasheen and McMahon to explain the dynamics of Basilisk lizard, to predict the body mass, stride frequency and gravity necessary for a person to run on water. Progressive body-weight unloading of a person running in place on a wading pool confirmed the theoretical predictions that a person could run on water, at lunar (or lower gravity levels using relatively small rigid fins. Three-dimensional motion capture of reflective markers on major joint centers showed that humans, similarly to the Basilisk Lizard and to the Western Grebe, keep the head-trunk segment at a nearly constant height, despite the high stride frequency and the intensive locomotor effort. Trunk stabilization at a nearly constant height differentiates running on water from other, more usual human gaits. CONCLUSIONS/SIGNIFICANCE: The results showed that a hydrodynamic model of lizards running on water can also be applied to humans, despite the enormous difference in body size and morphology.

  15. WATER BREAKTHROUGH SIMULATION IN NATURALLY FRACTURED GAS RESERVOIRS WITH WATER DRIVE

    Institute of Scientific and Technical Information of China (English)

    ZHANG Lie-hui; FENG Guo-qing; LI xiao-ping; LI Yun

    2005-01-01

    In the fractured water drive reservoirs of China, because of the complex geological conditions, almost all the active water invasions appear to be water breakthrough along fractures, especially along macrofractures. These seal the path of gas flow, thus the remaining gas in the pores mixes into water, and leads to gas-water interactive distribution in the fractured gas reservoir. These complicated fractured systems usually generate some abnormal flowing phenomena such as the crestal well produces water while the downdip well in the same gas reservoir produces gas, or the same gas well produces water intermittently. It is very difficult to explain these phenomena using existing fracture models because of their simple handling macrofractures without considering nonlinear flowing in the macrofractures and the low permeability matrix. Therefore, a nonlinear combined-flowing multimedia simulation model was successfully developed in this paper by introducing the equations of macrofractures and considering nonlinear flow in the macrofractures and the matrix. This model was then applied to actual fractured bottom water gas fields. Sensitivity studies of gas production by water drainage in fractured gas reservoirs were completed and the effect of different water drainage intensity and ways on actual gas production using this model were calculated. This model has been extensively used to predict the production performance in various fractured gas fields and proven to be reliable.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-07-01

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

  17. Simulation of Water Gas Shift Zeolite Membrane Reactor

    Science.gov (United States)

    Makertiharta, I. G. B. N.; Rizki, Z.; Zunita, Megawati; Dharmawijaya, P. T.

    2017-07-01

    The search of alternative energy sources keeps growing from time to time. Various alternatives have been introduced to reduce the use of fossil fuel, including hydrogen. Many pathways can be used to produce hydrogen. Among all of those, the Water Gas Shift (WGS) reaction is the most common pathway to produce high purity hydrogen. The WGS technique faces a downstream processing challenge due to the removal hydrogen from the product stream itself since it contains a mixture of hydrogen, carbon dioxide and also the excess reactants. An integrated process using zeolite membrane reactor has been introduced to improve the performance of the process by selectively separate the hydrogen whilst boosting the conversion. Furthermore, the zeolite membrane reactor can be further improved via optimizing the process condition. This paper discusses the simulation of Zeolite Membrane Water Gas Shift Reactor (ZMWGSR) with variation of process condition to achieve an optimum performance. The simulation can be simulated into two consecutive mechanisms, the reaction prior to the permeation of gases through the zeolite membrane. This paper is focused on the optimization of the process parameters (e.g. temperature, initial concentration) and also membrane properties (e.g. pore size) to achieve an optimum product specification (concentration, purity).

  18. Simulation of root water uptake. II. Non-uniform transient water stress using different reduction functions

    NARCIS (Netherlands)

    Homaee, M.; Feddes, R.A.; Dirksen, C.

    2002-01-01

    The macroscopic root water uptake approach was used in the numerical simulation model HYSWASOR to test four different pressure head-dependent reduction functions. The input parameter values were obtained from the literature and derived from extensive measurements under controlled conditions in the g

  19. Progress in numerical simulation of cavitating water jets

    Institute of Scientific and Technical Information of China (English)

    PENG Guoyi; SHMIZU Seiji

    2013-01-01

    This paper reviews recent progress made toward modeling of cavitation and numerical simulation of cavitating water jets.Properties of existing cavitation models are discussed and a compressible mixture flow method for the numerical simulation of highspeed water jets accompanied by intensive cavitation is introduced.Two-phase fluids media of cavitating flow are treated as a homogeneous bubbly mixture and the mean flow is computed by solving Reynolds-Averaged Navier-Stokes (RANS) equations for compressible fluid.The intensity of cavitation is evaluated by the gas volume fraction,which is governed by the compressibility of bubble-liquid mixture corresponding to the status of mean flow field.Numerical results of cavitating water jet issuing from an orifice nozzle are presented and its applicability to intensively cavitating jets is demonstrated.However,the effect of impact pressure caused by collapsing of bubbles is neglected,and effectively coupling of the present compressible mixture flow method with the dynamics of bubbles remains to be a challenge.

  20. Simulating future water temperatures in the North Santiam River, Oregon

    Science.gov (United States)

    Buccola, Norman; Risley, John C.; Rounds, Stewart A.

    2016-01-01

    A previously calibrated two-dimensional hydrodynamic and water-quality model (CE-QUAL-W2) of Detroit Lake in western Oregon was used in conjunction with inflows derived from Precipitation-Runoff Modeling System (PRMS) hydrologic models to examine in-lake and downstream water temperature effects under future climate conditions. Current and hypothetical operations and structures at Detroit Dam were imposed on boundary conditions derived from downscaled General Circulation Models in base (1990–1999) and future (2059–2068) periods. Compared with the base period, future air temperatures were about 2 °C warmer year-round. Higher air temperature and lower precipitation under the future period resulted in a 23% reduction in mean annual PRMS-simulated discharge and a 1 °C increase in mean annual estimated stream temperatures flowing into the lake compared to the base period. Simulations incorporating current operational rules and minimum release rates at Detroit Dam to support downstream habitat, irrigation, and water supply during key times of year resulted in lower future lake levels. That scenario results in a lake level that is above the dam’s spillway crest only about half as many days in the future compared to historical frequencies. Managing temperature downstream of Detroit Dam depends on the ability to blend warmer water from the lake’s surface with cooler water from deep in the lake, and the spillway is an important release point near the lake’s surface. Annual average in-lake and release temperatures from Detroit Lake warmed 1.1 °C and 1.5 °C from base to future periods under present-day dam operational rules and fill schedules. Simulated dam operations such as beginning refill of the lake 30 days earlier or reducing minimum release rates (to keep more water in the lake to retain the use of the spillway) mitigated future warming to 0.4 and 0.9 °C below existing operational scenarios during the critical autumn spawning period for endangered

  1. Simulating future water temperatures in the North Santiam River, Oregon

    Science.gov (United States)

    Buccola, Norman L.; Risley, John C.; Rounds, Stewart A.

    2016-04-01

    A previously calibrated two-dimensional hydrodynamic and water-quality model (CE-QUAL-W2) of Detroit Lake in western Oregon was used in conjunction with inflows derived from Precipitation-Runoff Modeling System (PRMS) hydrologic models to examine in-lake and downstream water temperature effects under future climate conditions. Current and hypothetical operations and structures at Detroit Dam were imposed on boundary conditions derived from downscaled General Circulation Models in base (1990-1999) and future (2059-2068) periods. Compared with the base period, future air temperatures were about 2 °C warmer year-round. Higher air temperature and lower precipitation under the future period resulted in a 23% reduction in mean annual PRMS-simulated discharge and a 1 °C increase in mean annual estimated stream temperatures flowing into the lake compared to the base period. Simulations incorporating current operational rules and minimum release rates at Detroit Dam to support downstream habitat, irrigation, and water supply during key times of year resulted in lower future lake levels. That scenario results in a lake level that is above the dam's spillway crest only about half as many days in the future compared to historical frequencies. Managing temperature downstream of Detroit Dam depends on the ability to blend warmer water from the lake's surface with cooler water from deep in the lake, and the spillway is an important release point near the lake's surface. Annual average in-lake and release temperatures from Detroit Lake warmed 1.1 °C and 1.5 °C from base to future periods under present-day dam operational rules and fill schedules. Simulated dam operations such as beginning refill of the lake 30 days earlier or reducing minimum release rates (to keep more water in the lake to retain the use of the spillway) mitigated future warming to 0.4 and 0.9 °C below existing operational scenarios during the critical autumn spawning period for endangered salmonids. A

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-04-07

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

  3. On spurious water flow during numerical simulation of steam injection into water-saturated soil.

    Science.gov (United States)

    Gudbjerg, J; Trötschler, O; Färber, A; Sonnenborg, T O; Jensen, K H

    2004-12-01

    Numerical simulation of steam injection into a water-saturated porous medium may be hindered by unphysical behavior causing the model to slow down. We show how spurious water flow may arise on the boundary between a steam zone and a saturated zone, giving rise to dramatic pressure drops. This is caused by the discretization of the temperature gradient coupled with the direct relation between pressure and temperature in the steam zone. The problem may be a severe limitation to numerical modeling. A solution is presented where the spurious water flow is blocked and this widely enhances the performance of the model. This new method is applied to a previously reported example exhibiting numerical problems. Furthermore, it is applied to the simulation of 2-D sandbox experiments where LNAPL is remediated from a smearing zone by steam injection. These experiments would have been difficult to analyze numerically without the adjustment to prevent spurious flow.

  4. Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface.

    Science.gov (United States)

    Lin, Huifang; Fan, Jianfen; Weng, Peipei; Si, Xialan; Zhao, Xin

    2017-09-08

    In this work, nine kinds of amino acid residues, i.e., alanine (A), leucine (L), valine (V), isoleucine (I), tryptophan (W), glutamine (Q), threonine (T), serine (S), and cysteine (C), were selected to construct seven cyclic peptide nanotubes (CPNTs) with diverse hydrophilic/hydrophobic external surfaces, which were further separately inserted at the water/hexane interface to investigate their microstructures and interfacial properties. Molecular dynamics (MD) simulations reveal that all the CPNTs except the QT- and VL-CPNTs have different degrees of tilt, fracture, and shedding at the interface. The end-CPs are more susceptible to the effect of the surroundings than the mid-CPs. The interactions of individual CP subunits with the neighborings disclose the firmness of the mid-CPs and the dissociation of the end-CPs. The results indicate that a hydrophobic CPNT is prone to stay at the interface, while a hydrophilic CPNT easily enters the water phase, resulting in many H-bonds with water. Results in this work enrich the dynamic properties of a hydrophilic/hydrophobic CPNT at the biphase interface at the atomic level.

  5. New quinolone derivative: Spectroscopic characterization and reactivity study by DFT and MD approaches

    Science.gov (United States)

    Ranjith, P. K.; Mary, Y. Sheena; Panicker, C. Yohannan; Anto, P. L.; Armaković, Stevan; Armaković, Sanja J.; Musiol, Robert; Jampilek, Josef; Van Alsenoy, C.

    2017-05-01

    The spectral characterization of ethyl-4-hydroxy-2-oxo-1, 2-dihydroquinoline-3-carboxylate (EHODQ3C) was performed by FT-IR and FT-Raman spectroscopic techniques and density functional theory computations have been carried using B3LYP/6-311++G(d,p) method. On the basis of potential energy distribution the vibrational assignments of the wavenumbers were proposed. Splitting of the Nsbnd H stretching mode and downshifted from the computed value which indicates the weakening of the Nsbnd H bond. NBO analysis was performed to study donor acceptor interactions. DFT calculations and molecular dynamics (MD) simulations have been combined in order to investigate fundamental reactive properties of the title molecule. To determine important reactive molecule sites we have calculated average local ionization energies (ALIE) and Fukui functions. Sensitivity towards autoxidation mechanism has been investigated by calculation of bond dissociation energies, while stability of title molecule in water has been investigated by calculation of radial distribution functions (RDF) after (MD) simulations. EHODQ3C exhibits inhibitory activity against ACP reductase and appears to be highly selective.

  6. Numerical simulation of photoexcited polaron states in water

    Energy Technology Data Exchange (ETDEWEB)

    Zemlyanaya, E. V., E-mail: elena@jinr.ru; Volokhova, A. V.; Amirkhanov, I. V.; Puzynin, I. V.; Puzynina, T. P.; Rikhvitskiy, V. S. [Laboratory of Information Technologies, Joint Institute for Nuclear Research, Dubna 141980 (Russian Federation); Lakhno, V. D. [Institute of Mathematical Problems of Biology, Russian Academy of Science, Pushchino 142290 (Russian Federation); Atanasova, P. Kh. [Faculty of Mathematics and Informatics, Paisii Hilendarski University of Plovdiv 4003 (Bulgaria)

    2015-10-28

    We consider the dynamic polaron model of the hydrated electron state on the basis of a system of three nonlinear partial differential equations with appropriate initial and boundary conditions. A parallel numerical algorithm for the numerical solution of this system has been developed. Its effectiveness has been tested on a few multi-processor systems. A numerical simulation of the polaron states formation in water under the action of the ultraviolet range laser irradiation has been performed. The numerical results are shown to be in a reasonable agreement with experimental data and theoretical predictions.

  7. Fast Collision Attack on MD5

    NARCIS (Netherlands)

    M.M.J. Stevens (Marc)

    2006-01-01

    textabstractIn this paper, we present an improved attack algorithm to find two-block collisions of the hash function MD5. The attack uses the same differential path of MD5 and the set of sufficient conditions that was presented by Wang et al. We present a new technique which allows us to

  8. Fast Collision Attack on MD5

    NARCIS (Netherlands)

    Stevens, M.M.J.

    2006-01-01

    In this paper, we present an improved attack algorithm to find two-block collisions of the hash function MD5. The attack uses the same differential path of MD5 and the set of sufficient conditions that was presented by Wang et al. We present a new technique which allows us to deterministically fulfi

  9. CFD simulations to optimize the blade design of water wheels

    Science.gov (United States)

    Quaranta, Emanuele; Revelli, Roberto

    2017-05-01

    At low head sites and at low discharges, water wheels can be considered among the most convenient hydropower converters to install. The aim of this work is to improve the performance of an existing breastshot water wheel by changing the blade shape using computational fluid dynamic (CFD) simulations. Three optimal profiles are investigated: the profile of the existing blades, a circular profile and an elliptical profile. The results are validated by performing experimental tests on the wheel with the existing profile. The numerical results show that the efficiency of breastshot wheels is affected by the blade profile. The average increase in efficiency using the new circular profile is about 4 % with respect to the profile of the existing blades.

  10. Measurements and simulations of water transport in maize plants

    Science.gov (United States)

    Heinlein, Florian; Klein, Christian; Thieme, Christoph; Priesack, Eckart

    2017-04-01

    In Central Europe climate change will become manifest in the increase of extreme weather events like flash floods, heat waves and summer droughts, and in a shift of precipitation towards winter months. Therefore, regional water availability will alter which has an effect on future crop growth, water use efficiency and yields. To better estimate these effects accurate model descriptions of transpiration and other parts of the water balance are important. In this study, we determined transpiration of four maize plants on a field of the research station Scheyern (about 40km North of Munich) by means of sap flow measurement devices (ICQ International Pty Ltd, Australia) using the Heat-Ratio-Method: two temperature probes, 0.5 cm above and below a heater, detect a heat pulse and its speed which facilitates the calculation of sap flow. Additionally, high resolution changes of stem diameters were measured with dendrometers (DD-S, Ecomatik). The field was also situated next to an eddy covariance station which provided latent heat fluxes from the soil-plant system. We also performed terrestrial laser scans of the respective plants to extract the plant architectures. These structures serve as input for our mechanistic transpiration model simulating the water transport within the plant. This model, which has already been successfully applied to single Fagus sylvatica L. trees, was adapted to agricultural plants such as maize. The basic principle of this model is to solve a 1-D Richards equation along the graph of the single plants. A comparison between the simulations and the measurements is presented and discussed.

  11. Adsorption of Water on Simulated Moon Dust Samples

    Science.gov (United States)

    Goering, John P.; Sah, Shweta; Burghaus, Uwe; Street, Kenneth W., Jr.

    2008-01-01

    A lunar regolith simulant dust sample (JSC-1a) supported on a silica wafer (SiO2/Si(111)) has been characterized by scanning electron microscopy (SEM), energy dispersive x-ray spectroscopy (EDX), and Auger electron spectroscopy (AES). The adsorption kinetics of water has been studied primarily by thermal desorption spectroscopy (TDS) and also by collecting isothermal adsorption transients. The support has been characterized by water TDS. JSC-1a consists mostly of aluminosilicate glass and other minerals containing Fe, Na, Ca, and Mg. The particle sizes span the range from a few microns up to 100 microns. At small exposures, H2O TDS is characterized by broad (100 to 450 K) structures; at large exposures distinct TDS peaks emerge that are assigned to amorphous solid water (145 K) and crystalline ice (165 K). Water dissociates on JSC-1a at small exposures but not on the bare silica support. It appears that rather porous condensed ice layers form at large exposures. At thermal impact energies, the initial adsorption probability amounts to 0.92+/-0.05.

  12. First thoughts on MD priorities for 2012

    CERN Document Server

    Zimmermann, F; Assmann, R

    2012-01-01

    In 2012, 22 days of beam time will be allocated for LHC MDs. In this paper, after recalling the 2011 LHC MD experience, the MD rrequests for 2012 are reviewed. Three primary MD themes for 2012 can be identified: 1)pushing performance in 2012, 2)preparing for 2014/15, and 3)towards maximum luminosity. Example topics include emittance growth in collision or enhanced satellites for theme 1), 25 ns operation for 2), and ATS optics for 3). Structures lists of MD requests and topics for each theme as well as some initial thoughts on the MD priorities are presented. For certain topics, "start-of-fill MDs" are proposed in order to most efficiently use of the available beam time.

  13. 76 FR 52225 - Airworthiness Directives; The Boeing Company Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD...

    Science.gov (United States)

    2011-08-22

    ... Model DC-9-81 (MD- 81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87), and MD-88 Airplanes AGENCY... Ground Floor, Room W12-140, 1200 New Jersey Avenue, SE., Washington, DC 20590. FOR FURTHER INFORMATION... ADs (b) None. Applicability (c) This AD applies to The Boeing Company Model DC-9-81 (MD-81),...

  14. Influence of Soil Water Retention Properties on Hydrological Cycle and Water Budgeting Module Simulation

    Directory of Open Access Journals (Sweden)

    Hamid Čustović

    2011-03-01

    Full Text Available The complexity of water budgeting module as shown in this paper is represented in phases. By experimental measurement of precipitation and lysimetric measurement of percolation runoff the fi rst phase establishes monthly and annual soil-water budgets of skeletal and clayey soils, and hence the influence of soil water-retention potential on hydrologic cycle and water budget over a four year period in the area of Mostar. Then, a soil-water budget model is simulated in a simplified procedure in order to determine the corresponding soil productive water reserve (R for given soils.In this way, depending on R values, the output parameters of the simulated model may produce different results in: calculated surplus or percolation runoff, real evapotranspiration (RET and water deficit.The lysimetric measuring of the water input and output in skeletal and clayey soils determined significant differences in the water budgets of these, by physical properties, divergent soils. Such correlations indicate that there is a realistic possibility of computing new, relatively reliable and pragmatically significant agro-hydrological parameters using measured precipitation and calculated PET.Also, this paper addresses a correlative analysis between the apple and maize ET on one side, and evaporation measured by Piche and by Class A, as well as PET calculated by Thornthwaite, Turc and Penman, on the other side. The results show a reliable reaction between ET of apple and maize with E by Piche, while the same relation is even more reliable with Class A. Other methods in this correlative analysis are less reliable.

  15. Water exit pathways and proton pumping mechanism in B-type cytochrome c oxidase from molecular dynamics simulations.

    Science.gov (United States)

    Yang, Longhua; Skjevik, Åge A; Han Du, Wen-Ge; Noodleman, Louis; Walker, Ross C; Götz, Andreas W

    2016-09-01

    Cytochrome c oxidase (CcO) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. While proton uptake channels as well as water exit channels have been identified for A-type CcOs, the means by which water and protons exit B-type CcOs remain unclear. In this work, we investigate potential mechanisms for proton transport above the dinuclear center (DNC) in ba3-type CcO of Thermus thermophilus. Using long-time scale, all-atom molecular dynamics (MD) simulations for several relevant protonation states, we identify a potential mechanism for proton transport that involves propionate A of the active site heme a3 and residues Asp372, His376 and Glu126(II), with residue His376 acting as the proton-loading site. The proposed proton transport process involves a rotation of residue His376 and is in line with experimental findings. We also demonstrate how the strength of the salt bridge between residues Arg225 and Asp287 depends on the protonation state and that this salt bridge is unlikely to act as a simple electrostatic gate that prevents proton backflow. We identify two water exit pathways that connect the water pool above the DNC to the outer P-side of the membrane, which can potentially also act as proton exit transport pathways. Importantly, these water exit pathways can be blocked by narrowing the entrance channel between residues Gln151(II) and Arg449/Arg450 or by obstructing the entrance through a conformational change of residue Tyr136, respectively, both of which seem to be affected by protonation of residue His376.

  16. Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

    Energy Technology Data Exchange (ETDEWEB)

    Cipcigan, Flaviu S., E-mail: flaviu.cipcigan@ed.ac.uk [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Sokhan, Vlad P. [National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Crain, Jason [School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD (United Kingdom); National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW (United Kingdom); Martyna, Glenn J. [IBM T. J. Watson Research Center, Yorktown Heights, NY 10598 (United States)

    2016-12-01

    One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082–1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230–233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeler through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO-MD. - Highlights: • Electronic coarse graining unites many-body dispersion and polarisation beyond the dipole limit. • It consists of replacing the electrons of a molecule using a quantum harmonic oscillator, called a

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

    Science.gov (United States)

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

    2015-06-01

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

  18. Simulating shock-bubble interactions at water-gelatin interfaces

    Science.gov (United States)

    Adami, Stefan; Kaiser, Jakob; Bermejo-Moreno, Ivan; Adams, Nikolaus

    2016-11-01

    Biomedical problems are often driven by fluid dynamics, as in vivo organisms are usually composed of or filled with fluids that (strongly) affected their physics. Additionally, fluid dynamical effects can be used to enhance certain phenomena or destroy organisms. As examples, we highlight the benign potential of shockwave-driven kidney-stone lithotripsy or sonoporation (acoustic cavitation of microbubbles) to improve drug delivery into cells. During the CTR SummerProgram 2016 we have performed axisymmetric three-phase simulations of a shock hitting a gas bubble in water near a gelatin interface mimicking the fundamental process during sonoporation. We used our multi-resolution finite volume method with sharp interface representation (level-set), WENO-5 shock capturing and interface scale-separation and compared the results with a diffuse-interface method. Qualitatively our simulation results agree well with the reference. Due to the interface treatment the pressure profiles are sharper in our simulations and bubble collapse dynamics are predicted at shorter time-scales. Validation with free-field collapse (Rayleigh collapse) shows very good agreement. The project leading to this application has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No 667483).

  19. United polarizable multipole water model for molecular mechanics simulation

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-07-07

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

  20. Study of clathrate hydrates via equilibrium molecular-dynamics simulation employing polarisable and non-polarisable, rigid and flexible water models

    Science.gov (United States)

    Burnham, Christian J.; English, Niall J.

    2016-04-01

    Equilibrium molecular-dynamics (MD) simulations have been performed on metastable sI and sII polymorphs of empty hydrate lattices, in addition to liquid water and ice Ih. The non-polarisable TIP4P-2005, simple point charge model (SPC), and polarisable Thole-type models (TTM): TTM2, TTM3, and TTM4 water models were used in order to survey the differences between models and to see what differences can be expected when polarisability is incorporated. Rigid and flexible variants were used of each model to gauge the effects of flexibility. Power spectra are calculated and compared to density-of-states spectra inferred from inelastic neutron scattering (INS) measurements. Thermodynamic properties were also calculated, as well as molecular-dipole distributions. It was concluded that TTM models offer optimal fidelity vis-à-vis INS spectra, together with thermodynamic properties, with the flexible TTM2 model offering optimal placement of vibrational modes.

  1. Molecular simulation and macroscopic modeling of the diffusion of hydrogen, carbon monoxide and water in heavy n-alkane mixtures.

    Science.gov (United States)

    Makrodimitri, Zoi A; Unruh, Dominik J M; Economou, Ioannis G

    2012-03-28

    The self-diffusion coefficient of hydrogen (H(2)), carbon monoxide (CO) and water (H(2)O) in n-alkanes was studied by molecular dynamics simulation. Diffusion in a few pure n-alkanes (namely n-C(8), n-C(20), n-C(64) and n-C(96)) was examined. In addition, binary n-C(12)-n-C(96) mixtures with various compositions as well as more realistic five- and six-n-alkane component mixtures were simulated. In all cases, the TraPPE united atom force field was used for the n-alkane molecules. The force field for the mixture of n-alkanes was initially validated against experimental density values and was shown to be accurate. Moreover, macroscopic correlations for predicting diffusion coefficient of H(2), CO and H(2)O in n-alkanes and mixtures of n-alkanes were developed. The functional form of the correlation was based on the rough hard sphere theory (RHS). The correlation was applied to simulation data and an absolute average deviation (AAD) of 5.8% for pure n-alkanes and 3.4% for n-alkane mixtures was obtained. Correlation parameters vary in a systematic way with carbon number and so they can be used to provide predictions in the absence of any experimental or molecular simulation data. Finally, in order to reduce the number of adjustable parameters, for the n-alkane mixtures the "pseudo-carbon number" approach was used. This approach resulted in relatively higher deviation from MD simulation data (AAD of 18.2%); however, it provides a convenient and fast method to predict diffusion coefficients. The correlations developed here are expected to be useful for engineering calculations related to the design of the Gas-to-Liquid process.

  2. Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

    Science.gov (United States)

    Rosnik, Andreana M; Curutchet, Carles

    2015-12-08

    Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

  3. The Role of Water in Activation Mechanism of Human N-Formyl Peptide Receptor 1 (FPR1) Based on Molecular Dynamics Simulations

    Science.gov (United States)

    Yuan, Shuguang; Ghoshdastider, Umesh; Trzaskowski, Bartosz; Latek, Dorota; Debinski, Aleksander; Pulawski, Wojciech; Wu, Rongliang; Gerke, Volker; Filipek, Slawomir

    2012-01-01

    The Formyl Peptide Receptor 1 (FPR1) is an important chemotaxis receptor involved in various aspects of host defense and inflammatory processes. We constructed a model of FPR1 using as a novel template the chemokine receptor CXCR4 from the same branch of the phylogenetic tree of G-protein-coupled receptors. The previously employed template of rhodopsin contained a bulge at the extracellular part of TM2 which directly influenced binding of ligands. We also conducted molecular dynamics (MD) simulations of FPR1 in the apo form as well as in a form complexed with the agonist fMLF and the antagonist tBocMLF in the model membrane. During all MD simulation of the fMLF-FPR1 complex a water molecule transiently bridged the hydrogen bond between W2546.48 and N1083.35 in the middle of the receptor. We also observed a change in the cytoplasmic part of FPR1 of a rotamer of the Y3017.53 residue (tyrosine rotamer switch). This effect facilitated movement of more water molecules toward the receptor center. Such rotamer of Y3017.53 was not observed in any crystal structures of GPCRs which can suggest that this state is temporarily formed to pass the water molecules during the activation process. The presence of a distance between agonist and residues R2015.38 and R2055.42 on helix TM5 may suggest that the activation of FPR1 is similar to the activation of β-adrenergic receptors since their agonists are separated from serine residues on helix TM5. The removal of water molecules bridging these interactions in FPR1 can result in shrinking of the binding site during activation similarly to the shrinking observed in β-ARs. The number of GPCR crystal structures with agonists is still scarce so the designing of new ligands with agonistic properties is hampered, therefore homology modeling and docking can provide suitable models. Additionally, the MD simulations can be beneficial to outline the mechanisms of receptor activation and the agonist/antagonist sensing. PMID:23189124

  4. Simulations of water transport through carbon nanotubes: how different water models influence the conduction rate.

    Science.gov (United States)

    Liu, L; Patey, G N

    2014-11-14

    The conduction rate of water through (8,8) and (9,9) carbon nanotubes at 300 K and a pressure difference of 220 MPa is investigated using molecular dynamics simulations. The TIP3P, SPC/E, and TIP4P/2005 water models are considered. The pressure-driven flow rate is found to be strongly model dependent for both nanotubes. The fastest model (TIP3P) has a flow rate that is approximately five times faster than the slowest (TIP4P/2005). It is shown that the flow rate is significantly influenced by the structure taken on by the water molecules confined in the nanotube channels. The slower models, TIP4P/2005 and SPC/E, tend to favor stacked ring arrangements, with the molecules of a ring moving together through the nanotube, in what we term a "cluster-by-cluster" conduction mode. Confined TIP3P water has a much weaker tendency to form ring structures, and those that do form are fragile and break apart under flow conditions. This creates a much faster "diffusive" conduction mode where the water molecules mainly move through the tube as individual particles, rather than as components of a larger cluster. Our results demonstrate that water models developed to describe the properties of bulk water can behave very differently in confined situations.

  5. Simulation insights for graphene-based water desalination membranes.

    Science.gov (United States)

    Konatham, Deepthi; Yu, Jing; Ho, Tuan A; Striolo, Alberto

    2013-09-24

    Molecular dynamics simulations were employed to study the transport of water and ions through pores created on the basal plane of one graphene sheet (GS). Graphene pore diameters ranged from 7.5 to 14.5 Å. Different pore functionalities were considered, obtained by tethering various functional groups to the terminal carbon atoms. The ease of ion and water translocation across the pores was monitored by calculating the potential of mean force along the direction perpendicular to the GS pore. The results indicate that effective ion exclusion can be achieved only using nonfunctionalized (pristine) pores of diameter ~7.5 Å, whereas the ions can easily penetrate pristine pores of diameters ~10.5 and 14.5 Å. Carboxyl functional groups can enhance ion exclusion for all pores considered, but the effect becomes less pronounced as both the ion concentration and the pore diameter increase. When compared to a carbon nanotube of similar pore diameter, our results suggest that GS pores functionalized with COO(-) groups are more effective in excluding Cl(-) ions from passing through the membrane. Our results suggest that narrow graphene pores functionalized with hydroxyl groups remain effective at excluding Cl(-) ions even at moderate solution ionic strength. The results presented could be useful for the design of water desalination membranes.

  6. A Study of the Solvation Structure of L-Leucine in Alcohol-Water Binary Solvents through Molecular Dynamics Simulations and FTIR and NMR Spectroscopy.

    Science.gov (United States)

    Takamuku, Toshiyuki; Hatomoto, Yohei; Tonegawa, Junko; Tsutsumi, Youichi; Umecky, Tatsuya

    2015-10-26

    The solvation structures of l-leucine (Leu) in aliphatic-alcohol-water and fluorinated-alcohol-water solvents are elucidated for various alcohol contents by using molecular dynamics (MD) simulations and IR, and (1) H and (13) C NMR spectroscopy. The aliphatic alcohols included methanol, ethanol, and 2-propanol, whereas the fluorinated alcohols were 2,2,2-trifluoroethanol and 1,1,1,3,3,3-hexafluoro-2-propanol. The MD results show that the hydrophobic alkyl moiety of Leu is surrounded by the alkyl or fluoroalkyl groups of the alcohol molecules. In particular, TFE and HFIP significantly solvate the alkyl group of Leu. IR spectra reveal that the Leu C-H stretching vibration blueshifts in fluorinated alcohol solutions with increasing alcohol content, whereas the vibration redshifts in aliphatic alcohol solutions. When the C-H stretching vibration blueshifts in the fluorinated alcohol solutions, the hydrogen and carbon atoms of the Leu alkyl group are magnetically shielded. Consequently, TFE and HFIP molecules may solvate the Leu alkyl group through the blue-shifting hydrogen bonds.

  7. Semiquantal molecular dynamics simulations of hydrogen-bond dynamics in liquid water using multi-dimensional Gaussian wave packets.

    Science.gov (United States)

    Ono, Junichi; Ando, Koji

    2012-11-01

    A semiquantal (SQ) molecular dynamics (MD) simulation method based on an extended Hamiltonian formulation has been developed using multi-dimensional thawed gaussian wave packets (WPs), and applied to an analysis of hydrogen-bond (H-bond) dynamics in liquid water. A set of Hamilton's equations of motion in an extended phase space, which includes variance-covariance matrix elements as auxiliary coordinates representing anisotropic delocalization of the WPs, is derived from the time-dependent variational principle. The present theory allows us to perform real-time and real-space SQMD simulations and analyze nuclear quantum effects on dynamics in large molecular systems in terms of anisotropic fluctuations of the WPs. Introducing the Liouville operator formalism in the extended phase space, we have also developed an explicit symplectic algorithm for the numerical integration, which can provide greater stability in the long-time SQMD simulations. The application of the present theory to H-bond dynamics in liquid water is carried out under a single-particle approximation in which the variance-covariance matrix and the corresponding canonically conjugate matrix are reduced to block-diagonal structures by neglecting the interparticle correlations. As a result, it is found that the anisotropy of the WPs is indispensable for reproducing the disordered H-bond network compared to the classical counterpart with the use of the potential model providing competing quantum effects between intra- and intermolecular zero-point fluctuations. In addition, the significant WP delocalization along the out-of-plane direction of the jumping hydrogen atom associated with the concerted breaking and forming of H-bonds has been detected in the H-bond exchange mechanism. The relevance of the dynamical WP broadening to the relaxation of H-bond number fluctuations has also been discussed. The present SQ method provides the novel framework for investigating nuclear quantum dynamics in the many

  8. Hydration Simulations of a Carbon Nanotube, Immersed in Water, according to the 3-Attractor Water Model

    Directory of Open Access Journals (Sweden)

    Francis F. Muguet

    2005-04-01

    Full Text Available MC simulations of a set of zigzag ((9,0-(14,0 and armchair ((6,6-(10,10carbon nanotubes immersed in water have been carried out in an NpT-ensemble (512 watermolecules, p=1 bar, T=298 K. Intermolecular interactions were described by BMWpotential according to which, besides the well-known linear water dimer bifurcated andinverted water dimers are metastable. In all cases, it was found that there are large periodicfluctuations of water occupancy inside the nanotubes. Decrease in the size of the nanotubediameter leads to a significant destruction of the H-bond network, and to a bifucarted dimerpopulation increase. Inverted dimer concentration relationship with the nanotube diameter ismore complicated. Population maximum for inverted dimers occurs for diameters of 10-11 å. Water features different intermolecular structures not only inside carbon nanotubesbut also in the outer first hydration shells. The amount of bifurcated and inverted dimers issignificantly more important in the first hydration shell than in bulk water.

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

    NARCIS (Netherlands)

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

    1993-01-01

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

  10. Composite Simulation of Dynamic Water Content and Water Use Efficiency of Winter Wheat

    Institute of Scientific and Technical Information of China (English)

    Liming; WANG

    2014-01-01

    In order to forecast the effect of climate warming on agriculture,ENWATBAL model was used to simulate evapotranspiration of winter wheat due to the change of air temperature and precipitation in the coming decades.The effect of climate warming on winter wheat yield in the future decades was speculated by the past yield and climate data in last decades,and the possible water use efficiency in the future decades was calculated.The results indicate that climate warming would increase winter wheat evapotranspiration,and decrease yield and water use efficiency of winter wheat.It shows that climate warming would intensify the water shortage in agriculture,and it is necessary to develop watersaving agriculture.

  11. Free fall of water drops in laboratory rainfall simulations

    Science.gov (United States)

    Chowdhury, M. Nasimul; Testik, Firat Y.; Hornack, Mathew C.; Khan, Abdul A.

    2016-02-01

    Motivated by various hydrological and meteorological applications, this paper investigates the free fall of water drops to provide guidance in laboratory simulations of natural rainfall and to elucidate drop morphodynamics. Drop fall velocity and shape parameters such as axis ratio (ratio of the maximum vertical and horizontal chords of the drop), chord ratio [ratio of the two orthogonal chords where one chord (cl) is the longest chord in the drop and the other one (cs) is the longest chord that is orthogonal to cl], canting angle (angle between the longest chord of the drop and the horizontal axis), and relative fluctuation of chords (difference between vertical and horizontal chord fluctuations) were investigated for three selected water drop sizes (2.6, 3.7, and 5.1 mm spherical volume equivalent diameter) using high speed imaging. Based upon experimental observations, three distinct fall zones were identified: Zone I, in which source-induced oscillations and shape adjustment take place; Zone II, in which equilibrium-shaped drops accelerate to achieve terminal velocity; and Zone III, in which equilibrium-shaped drops fall at terminal velocity. Our results revealed that the fall distance values of approximately 6 m and 12 m can be used as conservative reference values for rainfall experiments with oscillation-free fall of drops (i.e. end of Zone I and onset of Zone II) and with equilibrium-shaped drops falling at terminal velocities (i.e. end of Zone II and onset of Zone III), respectively, for the entire raindrop size spectrum in natural rainfall. These required fall distance values are smaller than the distances discussed in the literature. Methodology and results presented here will facilitate optimum experimental laboratory simulations of natural rainfall.

  12. Linking Atomistic and Mesoscale Simulations of Water Soluble Polymers

    Science.gov (United States)

    Jones, J. L.

    2003-03-01

    There exist a range of techniques for studying surfactants and polymers in the mesoscale regime. One of the challenges is to link mesoscale theories and simulations to other calculation methods which address different length scales of the system. We introduce some mesoscale methods of calculation for polymers and surfactants and then present a case study of where mesoscale modelling is used for mechanistic understanding, by linking the method to high throughput in-silico screening methods. We look at the adsorption onto silica of ethylene oxide (EO)/ propylene oxide (PO) block copolymers (lutrols) which have been modified by end-grafting of short, cationic dimethylamino ethyl methacrylate (DMAEMA)chains. Given that the silica surface is negatively charged, it is remarkable that in some circumstances, polymers with longercationic chains have a lower adsorption. The effect is attributed to a competition between strong adsorption of the cationic DMAEMA groups driven by electrostatics, and weaker adsorption of the more numerous EO groups. This then raises the question of how we produce the values for the mesoscale parameters in these models and in the second part of the talk we describe a calculation method for doing this for water soluble polymers. The most promising route, but notoriously costly, is based on free energy calculations at the atomistic level. Free energy calculations are computationally intensive in general, but in an aqueous system one is also faced with the additional problem of using complex continuum models and/or accurate interaction potentials for water. Here we show how potential of mean force (PMF)calculations offer a practical alternative which avoids these drawbacks, though one is still faced with extremely long simulations.

  13. Obituary of Philip H. Cooper, MD.

    Science.gov (United States)

    Patterson, James W; Wick, Mark R; Mills, Stacey E

    2015-08-01

    Dermatopathology lost a giant in the field with the death of Philip H. Cooper, MD, on Friday, January 30, 2015. The following obituary represents a celebration of his life and his contributions to our field.

  14. Hydrogeochemical Simulation of Water-Rock Interaction Under Water Flood Recovery in Renqiu Oilfield, Hebei Province, China

    Institute of Scientific and Technical Information of China (English)

    冯启言; 韩宝平

    2002-01-01

    Hydrogeochemical simulation is an effective method to study water-rock interaction.In this paper, PHREEQM was used for the simulation of water-rock interaction under water flooding in the Renqiu Oilfield. Calculated results revealed that when fresh water was injected into the reservoir, Cl- and Na+ would decrease without involvement in water-rock interaction.Erosion to dolomite will lead to an increase in Ca2 + , Mg2 + and CaHCO3+. Saturation index of calcite and aragonite decreased first and then increased. With fresh water accounting for up to 70 %, mixed water has the strongest erosion ability. Deoiled water has erosion ability under high temperature and high partial pressure of CO2. Pyrite and gypsum were sensitive to deoiled water, which can cause the dissolution of pyrite and the precipitation of gypsum. Micrographs revealed a great deal of information about water-rock interaction.

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

    Science.gov (United States)

    Sapay, Nicolas; Nurisso, Alessandra; Imberty, Anne

    2013-01-01

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

  16. Supercritical water oxidation of spent extraction solvent simulants

    Institute of Scientific and Technical Information of China (English)

    王帅; 秦强; 陈土方方; 夏晓彬; 马洪军; 乔延波; 何柳斌

    2015-01-01

    The rapid development of nuclear technology has led to more liquid organic radioactive wastes. Different from the regular aqueous radioactive wastes, these liquids possess a higher hazard potential and cannot be disposed through the conventional methods due to their radioactivity and chemical nature. Spent extraction solvent is a kind of common liquid organic radioactive wastes. In this work, tri-butyl phosphate (TBP), which is more difficult to degrade in the spent extraction solvent, was used as the model compound. Influences of reaction conditions on total organic carbon (TOC) removal and the volume percentage of each gas component under supercritical water oxidation (SCWO) were studied. The SCWO behaviors of spent extraction solvent simulants were studied under the optimal conditions derived from the TBP experiment. The SCWO experiments were studied at 400–550◦C, oxidant stoichiometric ratio of 0–200%, feed concentration of 1.5%–4%and pressure of 25 MPa for 15–75 s. The results show that the TOC removal of the simulants was greater than 99.7%and CH4, H2 and CO were not detected at 550◦C, 25 MPa, oxidant stoichiometric ratio of 150%, feed concentration of 3%, and residence time of 30 s.

  17. North Pacific Eastern Subtropical Mode Water simulation and future projection

    Institute of Scientific and Technical Information of China (English)

    XIA Ruibin; LIU Qinyu; XU Lixiao; LU Yiqun

    2015-01-01

    The present climate simulation and future projection of the Eastern Subtropical Mode Water (ESTMW) in the North Pacific are investigated based on the Geophysical Fluid Dynamics Laboratory Earth System Model (GFDL-ESM2M). Spatial patterns of the mixed layer depth (MLD) in the eastern subtropical North Pacific and the ESTMW are well simulated using this model. Compared with historical simulation, the ESTMW is produced at lighter isopycnal surfaces and its total volume is decreased in the RCP8.5 runs, because the subduction rate of the ESTMW decreases by 0.82×10−6 m/s during February–March. In addition, it is found that the lateral induction decreasing is approximately four times more than the Ekman pumping, and thus it plays a dominant role in the decreased subduction rate associated with global warming. Moreover, the MLD during February–March is banded shoaling in response to global warming, extending northeastward from the east of the Hawaii Islands (20°N, 155°W) to the west coast of North America (30°N, 125°W), with a max-imum shoaling of 50 m, and then leads to the lateral induction reduction. Meanwhile, the increased north-eastward surface warm current to the east of Hawaii helps strengthen of the local upper ocean stratification and induces the banded shoaling MLD under warmer climate. This new finding indicates that the ocean surface currents play an important role in the response of the MLD and the ESTMW to global warming.

  18. Dynamic compression of water to 700 GPa: single- and double shock experiments on Sandia's Z machine, first principles simulations, and structure of water planets

    Science.gov (United States)

    Mattsson, Thomas R.

    2011-11-01

    Significant progress has over the last few years been made in high energy density physics (HEDP) by executing high-precision multi-Mbar experiments and performing first-principles simulations for elements ranging from carbon [1] to xenon [2]. The properties of water under HEDP conditions are of particular importance in planetary science due to the existence of ice-giants like Neptune and Uranus. Modeling the two planets, as well as water-rich exoplanets, requires knowing the equation of state (EOS), the pressure as a function of density and temperature, of water with high accuracy. Although extensive density functional theory (DFT) simulations have been performed for water under planetary conditions [3] experimental validation has been lacking. Accessing thermodynamic states along planetary isentropes in dynamic compression experiments is challenging because the principal Hugoniot follows a significantly different path in the phase diagram. In this talk, we present experimental data for dynamic compression of water up to 700 GPa, including in a regime of the phase-diagram intersected by the Neptune isentrope and water-rich models for the exoplanet GJ436b. The data was obtained on the Z-accelerator at Sandia National Laboratories by performing magnetically accelerated flyer plate impact experiments measuring both the shock and re-shock in the sample. The high accuracy makes it possible for the data to be used for detailed model validation: the results validate first principles based thermodynamics as a reliable foundation for planetary modeling and confirm the fine effect of including nuclear quantum effects on the shock pressure. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. [4pt] [1] M.D. Knudson, D.H. Dolan, and M.P. Desjarlais, SCIENCE

  19. Simulations of dissociation constants in low pressure supercritical water

    Science.gov (United States)

    Halstead, S. J.; An, P.; Zhang, S.

    2014-09-01

    This article reports molecular dynamics simulations of the dissociation of hydrochloric acid and sodium hydroxide in water from ambient to supercritical temperatures at a fixed pressure of 250 atm. Corrosion of reaction vessels is known to be a serious problem of supercritical water, and acid/base dissociation can be a significant contributing factor to this. The SPC/e model was used in conjunction with solute models determined from density functional calculations and OPLSAA Lennard-Jones parameters. Radial distribution functions were calculated, and these show a significant increase in solute-solvent ordering upon forming the product ions at all temperatures. For both dissociations, rapidly decreasing entropy of reaction was found to be the controlling thermodynamic factor, and this is thought to arise due to the ions produced from dissociation maintaining a relatively high density and ordered solvation shell compared to the reactants. The change in entropy of reaction reaches a minimum at the critical temperature. The values of pKa and pKb were calculated and both increased with temperature, in qualitative agreement with other work, until a maximum value at 748 K, after which there was a slight decrease.

  20. Biofuels and water quality: challenges and opportunities for simulation modeling

    Energy Technology Data Exchange (ETDEWEB)

    Engel, Bernard A. [Purdue University; Chaubey, Indrajeet [Purdue University; Thomas, Mark [Purdue University; Saraswat, Dharmendra [University of Arkansas; Murphy, Patrick [Purdue University; Bhaduri, Budhendra L [ORNL

    2010-01-01

    Quantification of the various impacts of biofuel feedstock production on hydrology and water quality is complex. Mathematical models can be used to efficiently evaluate various what if scenarios related to biofeedstock production and their impacts on hydrology and water quality at various spatial and temporal scales. Currently available models, although having the potential to serve such purposes, have many limitations. In this paper, we review the strengths and weaknesses of such models in light of short- and long term biofeedstock production scenarios. The representation of processes in the currently available models and how these processes need to be modified to fully evaluate various complex biofeedstock production scenarios are discussed. Similarly, issues related to availability of data that are needed to parameterize and evaluate these models are presented. We have presented a vision for the development of decision support tools and ecosystem services that can be used to make watershed management decisions to minimize any potentially adverse environmental impacts while meeting biofeedstock demands. We also discuss a case study of biofeedstock impact simulation in relation to watershed management policy implications for various state and federal agencies in the USA.

  1. Collaborative Simulation Grid: Multiscale Quantum-Mechanical/Classical Atomistic Simulations on Distributed PC Clusters in the US and Japan

    Science.gov (United States)

    Kikuchi, Hideaki; Kalia, Rajiv; Nakano, Aiichiro; Vashishta, Priya; Iyetomi, Hiroshi; Ogata, Shuji; Kouno, Takahisa; Shimojo, Fuyuki; Tsuruta, Kanji; Saini, Subhash; Biegel, Bryan (Technical Monitor)

    2002-01-01

    A multidisciplinary, collaborative simulation has been performed on a Grid of geographically distributed PC clusters. The multiscale simulation approach seamlessly combines i) atomistic simulation backed on the molecular dynamics (MD) method and ii) quantum mechanical (QM) calculation based on the density functional theory (DFT), so that accurate but less scalable computations are performed only where they are needed. The multiscale MD/QM simulation code has been Grid-enabled using i) a modular, additive hybridization scheme, ii) multiple QM clustering, and iii) computation/communication overlapping. The Gridified MD/QM simulation code has been used to study environmental effects of water molecules on fracture in silicon. A preliminary run of the code has achieved a parallel efficiency of 94% on 25 PCs distributed over 3 PC clusters in the US and Japan, and a larger test involving 154 processors on 5 distributed PC clusters is in progress.

  2. General order parameter based correlation analysis of protein backbone motions between experimental NMR relaxation measurements and molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qing; Shi, Chaowei [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Yu, Lu [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China); Zhang, Longhua [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Xiong, Ying, E-mail: yxiong73@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); Tian, Changlin, E-mail: cltian@ustc.edu.cn [Hefei National Laboratory for Physical Sciences at The Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230026 (China); High Magnetic Field Laboratory, Chinese Academy of Science, Hefei, Anhui, 230031 (China)

    2015-02-13

    Internal backbone dynamic motions are essential for different protein functions and occur on a wide range of time scales, from femtoseconds to seconds. Molecular dynamic (MD) simulations and nuclear magnetic resonance (NMR) spin relaxation measurements are valuable tools to gain access to fast (nanosecond) internal motions. However, there exist few reports on correlation analysis between MD and NMR relaxation data. Here, backbone relaxation measurements of {sup 15}N-labeled SH3 (Src homology 3) domain proteins in aqueous buffer were used to generate general order parameters (S{sup 2}) using a model-free approach. Simultaneously, 80 ns MD simulations of SH3 domain proteins in a defined hydrated box at neutral pH were conducted and the general order parameters (S{sup 2}) were derived from the MD trajectory. Correlation analysis using the Gromos force field indicated that S{sup 2} values from NMR relaxation measurements and MD simulations were significantly different. MD simulations were performed on models with different charge states for three histidine residues, and with different water models, which were SPC (simple point charge) water model and SPC/E (extended simple point charge) water model. S{sup 2} parameters from MD simulations with charges for all three histidines and with the SPC/E water model correlated well with S{sup 2} calculated from the experimental NMR relaxation measurements, in a site-specific manner. - Highlights: • Correlation analysis between NMR relaxation measurements and MD simulations. • General order parameter (S{sup 2}) as common reference between the two methods. • Different protein dynamics with different Histidine charge states in neutral pH. • Different protein dynamics with different water models.

  3. RO、NF与MD去除水中五种微量药物的效能研究%Investigation on removal of five trace pharmaceuticals from pure water by RO, NF and MD

    Institute of Scientific and Technical Information of China (English)

    葛四杰; 曲丹; 封莉; 张立秋

    2013-01-01

    This paper investigated the removal efficiency of five trace pharmaceuticals,including carbamazepine (CBZ),ketoprofen (KEP),naproxene (NAP),diclofenac (DCF) and acetaminophen (ACE),which were detected frequently in aquatic environment,by reverse osmosis (RO),nanofiltration (NF) and membrane distillation (MD).The results show that RO and MD can remove these five selected drugs efficiently.During MD process,none of these pharmaceuticals was detected in the permeate; CBZ,KEP,NAP and DCF by RO process were not detected in the permeate neither.The removal efficiency of ACE was slightly lower,but it was also up to 96.5%.However,NF process had lower efficiency than MD and RO processes for removing drugs.The removal efficiency of KEP,NAP,DCF and ACE were 60.5%±0.5%,82.3%±0.7%,84.2%±0.4%,83.5%±1%,41.1%±0.2% respectively.%以水体中经常暴露的5种微量药物污染物:酰胺咪嗪(CBZ)、酮洛芬(KEP)、萘普生(NAP)、双氯芬酸(DCF)和扑热息痛(ACE)为研究对象,考察了反渗透(RO)、纳滤(NF)、膜蒸馏(MD)3种膜分离技术对5种目标药物的去除效果.试验结果表明:RO与MD两种膜分离技术对5种目标药物均能高效地去除,其中MD工艺出水中5种目标药物均未检出;RO工艺出水中,CBZ、KEP、NAP和DCF 4种药物也未检出,基本实现了完全去除,ACE的去除率略低,但也达到了96.5%;相对而言,NF工艺对5种目标药物的去除效果稍差,其对CBZ、KEP、NAP、DCF和ACE的去除率分别为60.5%±0.5%、82.3%±0.7%、84.2%±0.4%、83.5%±1%、41.1%±0.2%.

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

    Science.gov (United States)

    Ishiyama, Tatsuya; Takahashi, Hideaki; Morita, Akihiro

    2012-03-28

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

  5. PV HEAT - Simulation and Experimental Validation of a Photovoltaic Domestic Hot Water System

    OpenAIRE

    Kimmling, Mathias

    2016-01-01

    Presentation for Conference TRNSYS User Experience Days 2016 in Kaiserslautern, Germany.TRNSYS Simulation of SELACAL photovoltaic domestic hot water system. Further information on simulation results verification. 

  6. Numerical simulation of water flow in lysimeters; Numerische Simulation des Wasserflusses in Lysimetern

    Energy Technology Data Exchange (ETDEWEB)

    Honisch, M.; Klotz, D. [GSF - Forschungszentrum fuer Umwelt und Gesundheit GmbH, Neuherberg (Germany). Inst. fuer Hydrologie

    1999-02-01

    A small-scale lysimeter plant on the premises of GSF has been dedicated to the study of water movement in sediments of Quaternary and Tertiary origin. The purpose of the present study was to describe water transport and non-reactive transport in the lysimeters under transient conditions and test the suitability of the numerical simulation programme Hydrus-2D for the unsaturated zone. The hydraulic characteristics and dispersiveness parameters were derived from earlier studies. The validity of these values was determined on the basis of a tracer experiment using the ideal tracer tritium water. [Deutsch] Zur Charakterisierung der Wasserbewegung in Sedimenten quartaeren und tertiaeren Ursprungs wird auf dem Gelaende der GSF eine Kleinlysimeteranlage betrieben. Ziel der vorliegenden Untersuchung war es, den Wasserfluss und nicht-reaktiven Transport in den Saeulen unter transienten Bedingungen zu beschreiben und hierbei die Eignung des numerischen Simulationsprogramms Hydrus-2D fuer die ungesaettigte Zone zu ueberpruefen. Die hydraulischen Kenngroessen und Dispersivitaetsparameter waren aus frueheren Untersuchungen abzuleiten. Die offene Frage hinsichtlich der Validitaet dieser Werte sollte auf der Grundlage eines Tracerexperiments mit tritiiertem Wasser als idealem Tracer ueberprueft werden. (orig.)

  7. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway.

    Science.gov (United States)

    Harada, Ryuhei; Kitao, Akio

    2013-07-21

    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

  8. Modeling and simulation challenges pursued by the Consortium for Advanced Simulation of Light Water Reactors (CASL)

    Science.gov (United States)

    Turinsky, Paul J.; Kothe, Douglas B.

    2016-05-01

    The Consortium for the Advanced Simulation of Light Water Reactors (CASL), the first Energy Innovation Hub of the Department of Energy, was established in 2010 with the goal of providing modeling and simulation (M&S) capabilities that support and accelerate the improvement of nuclear energy's economic competitiveness and the reduction of spent nuclear fuel volume per unit energy, and all while assuring nuclear safety. To accomplish this requires advances in M&S capabilities in radiation transport, thermal-hydraulics, fuel performance and corrosion chemistry. To focus CASL's R&D, industry challenge problems have been defined, which equate with long standing issues of the nuclear power industry that M&S can assist in addressing. To date CASL has developed a multi-physics "core simulator" based upon pin-resolved radiation transport and subchannel (within fuel assembly) thermal-hydraulics, capitalizing on the capabilities of high performance computing. CASL's fuel performance M&S capability can also be optionally integrated into the core simulator, yielding a coupled multi-physics capability with untapped predictive potential. Material models have been developed to enhance predictive capabilities of fuel clad creep and growth, along with deeper understanding of zirconium alloy clad oxidation and hydrogen pickup. Understanding of corrosion chemistry (e.g., CRUD formation) has evolved at all scales: micro, meso and macro. CFD R&D has focused on improvement in closure models for subcooled boiling and bubbly flow, and the formulation of robust numerical solution algorithms. For multiphysics integration, several iterative acceleration methods have been assessed, illuminating areas where further research is needed. Finally, uncertainty quantification and data assimilation techniques, based upon sampling approaches, have been made more feasible for practicing nuclear engineers via R&D on dimensional reduction and biased sampling. Industry adoption of CASL's evolving M

  9. Agent-based Modeling to Simulate the Diffusion of Water-Efficient Innovations and the Emergence of Urban Water Sustainability

    Science.gov (United States)

    Kanta, L.; Giacomoni, M.; Shafiee, M. E.; Berglund, E.

    2014-12-01

    The sustainability of water resources is threatened by urbanization, as increasing demands deplete water availability, and changes to the landscape alter runoff and the flow regime of receiving water bodies. Utility managers typically manage urban water resources through the use of centralized solutions, such as large reservoirs, which may be limited in their ability balance the needs of urbanization and ecological systems. Decentralized technologies, on the other hand, may improve the health of the water resources system and deliver urban water services. For example, low impact development technologies, such as rainwater harvesting, and water-efficient technologies, such as low-flow faucets and toilets, may be adopted by households to retain rainwater and reduce demands, offsetting the need for new centralized infrastructure. Decentralized technologies may create new complexities in infrastructure and water management, as decentralization depends on community behavior and participation beyond traditional water resources planning. Messages about water shortages and water quality from peers and the water utility managers can influence the adoption of new technologies. As a result, feedbacks between consumers and water resources emerge, creating a complex system. This research develops a framework to simulate the diffusion of water-efficient innovations and the sustainability of urban water resources, by coupling models of households in a community, hydrologic models of a water resources system, and a cellular automata model of land use change. Agent-based models are developed to simulate the land use and water demand decisions of individual households, and behavioral rules are encoded to simulate communication with other agents and adoption of decentralized technologies, using a model of the diffusion of innovation. The framework is applied for an illustrative case study to simulate water resources sustainability over a long-term planning horizon.

  10. Soil water content and water balance simulation of Caragana korshinskii Kom. in the semiarid Chinese Loess Plateau

    Directory of Open Access Journals (Sweden)

    Jian Shengqi

    2014-06-01

    Full Text Available In this paper, to evaluate the hydrological effects of Caragana korshinskii Kom., measured data were combined with model-simulated data to assess the C. korshinskii soil water content based on water balance equation. With measured and simulated canopy interception, plant transpiration and soil evaporation, soil water content was modeled with the water balance equation. The monthly variations in the modeled soil water content by measured and simulated components (canopy interception, plant transpiration, soil evaporation were then compared with in situ measured soil water content. Our results shows that the modeled monthly water loss (canopy interception + soil evaporation + plant transpiration by measured and simulated components ranges from 43.78 mm to 113.95 mm and from 47.76 mm to 125.63 mm, respectively, while the monthly input of water (precipitation ranges from 27.30 mm to 108.30 mm. The relative error between soil water content modeled by measured and simulated components was 6.41%. To sum up, the net change in soil water (ΔSW is negative in every month of the growing season. The soil moisture is approaching to wilting coefficient at the end of the growth season, and the soil moisture recovered during the following season.

  11. Integrating the simulation of domestic water demand behaviour to an urban water model using agent based modelling

    Science.gov (United States)

    Koutiva, Ifigeneia; Makropoulos, Christos

    2015-04-01

    The urban water system's sustainable evolution requires tools that can analyse and simulate the complete cycle including both physical and cultural environments. One of the main challenges, in this regard, is the design and development of tools that are able to simulate the society's water demand behaviour and the way policy measures affect it. The effects of these policy measures are a function of personal opinions that subsequently lead to the formation of people's attitudes. These attitudes will eventually form behaviours. This work presents the design of an ABM tool for addressing the social dimension of the urban water system. The created tool, called Urban Water Agents' Behaviour (UWAB) model, was implemented, using the NetLogo agent programming language. The main aim of the UWAB model is to capture the effects of policies and environmental pressures to water conservation behaviour of urban households. The model consists of agents representing urban households that are linked to each other creating a social network that influences the water conservation behaviour of its members. Household agents are influenced as well by policies and environmental pressures, such as drought. The UWAB model simulates behaviour resulting in the evolution of water conservation within an urban population. The final outcome of the model is the evolution of the distribution of different conservation levels (no, low, high) to the selected urban population. In addition, UWAB is implemented in combination with an existing urban water management simulation tool, the Urban Water Optioneering Tool (UWOT) in order to create a modelling platform aiming to facilitate an adaptive approach of water resources management. For the purposes of this proposed modelling platform, UWOT is used in a twofold manner: (1) to simulate domestic water demand evolution and (2) to simulate the response of the water system to the domestic water demand evolution. The main advantage of the UWAB - UWOT model

  12. Conceptual model for simulating the water cycle of the Copenhagen area, Denmark

    DEFF Research Database (Denmark)

    Jeppesen, Jan; Christensen, Steen; Ladekarl, Ulla Lyngs

    2008-01-01

    A complete water cycle model has been constructed for the Copenhagen area (966 km2) in order to study the development of the water cycle during the period 1850-2003. The urban water cycle is quantified in terms of root zone water balance, water supply, waste water, storm water, groundwater flow......, and the interactions between these systems. The water cycle is simulated by combining a root-zone model, a grid distribution tool, and a modified Modflow-2000 model using existing flow packages and a new sewer package that simulates the interactions between ground water and sewers (or rain drains). Long time series...... cycle. It is also the hope that the model will provide a better and more complete overview of the consequences of different water management scenarios. The model concept and selected simulation results is presented....

  13. Structure of large nitrate-water clusters at ambient temperatures: simulations with effective fragment potentials and force fields with implications for atmospheric chemistry.

    Science.gov (United States)

    Miller, Yifat; Thomas, Jennie L; Kemp, Daniel D; Finlayson-Pitts, Barbara J; Gordon, Mark S; Tobias, Douglas J; Gerber, R Benny

    2009-11-19

    Structural properties of large NO(3)(-).(H(2)O)(n) (n = 15-500) clusters are studied by Monte Carlo simulations using effective fragment potentials (EFPs) and by classical molecular dynamics simulations using a polarizable empirical force field. The simulation results are analyzed with a focus on the description of hydrogen bonding and solvation in the clusters. In addition, a comparison between the electronic structure based EFP and the classical force field description of the 32 water cluster system is presented. The EFP simulations, which focused on the cases of n = 15 and 32, show an internal, fully solvated structure and a "surface adsorbed" structure for the 32 water cluster at 300 K, with the latter configuration being more probable. The internal solvated structure and the "surface adsorbed" structure differ considerably in their hydrogen bonding coordination numbers. The force field based simulations agree qualitatively with these results, and the local geometry of NO(3)(-) and solvation at the surface-adsorbed site in the force field simulations are similar to those predicted using EFPs. Differences and similarities between the description of hydrogen bonding of the anion in the two approaches are discussed. Extensive classical force field based simulations at 250 K predict that long time scale stability of "internal" NO(3)(-), which is characteristic of extended bulk aqueous interfaces, emerges only for n > 300. Ab initio Møller-Plesset perturbation theory is used to test the geometries of selected surface and interior anions for n = 32, and the results are compared to the EFP and MD simulations. Qualitatively, all approaches agree that surface structures are preferred over the interior structures for clusters of this size. The relatively large aqueous clusters of NO(3)(-) studied here are of comparable size to clusters that lead to new particle formation in air. Nitrate ions on the surface of such clusters may have significantly different photochemistry

  14. A super-high throughput implementation of MD5 algorithm on FPGA%超高吞吐量MD5算法的FPGA实现

    Institute of Scientific and Technical Information of China (English)

    王臣; 袁焱

    2011-01-01

    In this paper, a novel architecture is proposed to increase the performance of MD5 computing in FPGA , which can achieve a super-high throughput. The scheme is based on full-pipeline for MD5 implementation. Moreover, FIFO cache structure is used for data storage and cooperative computing. The results of simulation and implementation show that the scheme can achieve the theoretical upper bound on throughput. And based on the same platform of FPGA, it outperforms the published scheme with best performance in terms of 77% higher throughput.%为了提高MD5算法在FPGA中实现的运算效率,使之达到超高的数据吞吐量,提出了一种新的全流水线架构,用于实现MD5算法.架构中使用了FIFO缓存存储数据,以配合流水线的运算.实验验证其达到了单个MD5运算单元运算吞吐量的理论上限,在相同芯片平台上,超过已发表的MD5运算模块最高吞吐量的77%.

  15. Characteristics of hydration water around hen egg lysozyme as the protein model in aqueous solution. FTIR spectroscopy and molecular dynamics simulation.

    Science.gov (United States)

    Panuszko, Aneta; Wojciechowski, Marek; Bruździak, Piotr; Rakowska, Paulina W; Stangret, Janusz

    2012-12-05

    In this paper, the hydration of a model protein--hen egg white lysozyme in aqueous solution has been presented. The leading method used was FTIR spectroscopy with an application of a technique of semi-heavy water (HDO) isotope dilution. Analysis of spectra of HDO isotopically diluted in water solution of lysozyme allowed us to isolate HDO spectra affected by lysozyme, and thus to characterise the energetic state of water molecules and their arrangement around protein molecules. The number of water molecules and the shape of the affected HDO spectrum were obtained using a classical and a chemometric method. This shape showed that the HDO spectrum affected by lysozyme may be presented as a superposition of two spectra corresponding to HDO affected by N-methylacetamide and the carboxylate anion (of the formic acid). Moreover, based on the difference in intermolecular distances distribution of water molecules (obtained from spectral data), we demonstrated that the lysozyme molecule causes a decrease in population of weak hydrogen bonds, and concurrently increases the probability of an occurrence of short hydrogen bonds in water affected by lysozyme. This conclusion was also confirmed by the molecular dynamics (MD) simulation.

  16. Detailed atomistic simulation of the nano-sorption and nano-diffusivity of water, tyrosol, vanillic acid, and p-coumaric acid in single wall carbon nanotubes.

    Science.gov (United States)

    Anastassiou, Alexandros; Karahaliou, Elena K; Alexiadis, Orestis; Mavrantzas, Vlasis G

    2013-10-28

    We report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall carbon nanotubes (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for one of the molecules addressed here (water) were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on tube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the molecules simulated (phenolic), the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This is attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable

  17. Detailed atomistic simulation of the nano-sorption and nano-diffusivity of water, tyrosol, vanillic acid, and p-coumaric acid in single wall carbon nanotubes

    Science.gov (United States)

    Anastassiou, Alexandros; Karahaliou, Elena K.; Alexiadis, Orestis; Mavrantzas, Vlasis G.

    2013-10-01

    We report results from a detailed computer simulation study for the nano-sorption and mobility of four different small molecules (water, tyrosol, vanillic acid, and p-coumaric acid) inside smooth single-wall carbon nanotubes (SWCNTs). Most of the results have been obtained with the molecular dynamics (MD) method, but especially for the most narrow of the CNTs considered, the results for one of the molecules addressed here (water) were further confirmed through an additional Grand Canonical (μVT) Monte Carlo (GCMC) simulation using a value for the water chemical potential μ pre-computed with the particle deletion method. Issues addressed include molecular packing and ordering inside the nanotube for the four molecules, average number of sorbed molecules per unit length of the tube, and mean residence time and effective axial diffusivities, all as a function of tube diameter and tube length. In all cases, a strong dependence of the results on tube diameter was observed, especially in the way the different molecules are packed and organized inside the CNT. For water for which predictions of properties such as local structure and packing were computed with both methods (MD and GCMC), the two sets of results were found to be fully self-consistent for all types of SWCNTs considered. Water diffusivity inside the CNT (although, strongly dependent on the CNT diameter) was computed with two different methods, both of which gave identical results. For large enough CNT diameters (larger than about 13 Å), this was found to be higher than the corresponding experimental value in the bulk by about 55%. Surprisingly enough, for the rest of the molecules simulated (phenolic), the simulations revealed no signs of mobility inside nanotubes with a diameter smaller than the (20, 20) tube. This is attributed to strong phenyl-phenyl attractive interactions, also to favorable interactions of these molecules with the CNT walls, which cause them to form highly ordered, very stable

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

    Science.gov (United States)

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

    2014-07-01

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

  19. Numerical Simulation of Water/Al2O3 Nanofluid Turbulent Convection

    Directory of Open Access Journals (Sweden)

    Vincenzo Bianco

    2010-01-01

    Full Text Available Turbulent forced convection flow of a water-Al2O3 nanofluid in a circular tube subjected to a constant and uniform temperature at the wall is numerically analyzed. The two-phase mixture model is employed to simulate the nanofluid convection, taking into account appropriate thermophysical properties. Particles are assumed spherical with a diameter equal to 38 nm. It is found that convective heat transfer coefficient for nanofluids is greater than that of the base liquid. Heat transfer enhancement is increasing with the particle volume concentration and Reynolds number. Comparisons with correlations present in the literature are accomplished and a very good agreement is found with Pak and Cho (1998. As for the friction factor, it shows a good agreement with the classical correlation used for normal fluid, such as Blasius formula.

  20. Simulation of water flows in multiple columns with small outlets

    Energy Technology Data Exchange (ETDEWEB)

    Suh, Yong Kweon; Li, Zi Lu; Jeong, Jong Hyun; Lee, Jun Hee [Dong-A University, Busan (Korea, Republic of)

    2006-10-15

    High-pressure die casting such as thixocasting and rheocasting is an effective process in the manufacturing automotive parts. Following the recent trend in the automotive manufacturing technologies, the product design subject to the die casting becomes more and more complex. Simultaneously the injection speed is also designed to be very high to establish a short cycle-time. Thus, the requirement of the die design becomes more demanding than ever before. In some cases the product's shape can have multiple slender manifolds. In such cases, design of the inlet and outlet parts of the die is very important in the whole manufacturing process. The main issues required for the qualified products are to attain gentle and uniform flow of the molten liquid within the passages of the die. To satisfy such issues, the inlet cylinder ('bed cylinder' in this paper) must be as large as possible and simultaneously the outlet opening at the end of each passage must be as small as possible. However these in turn obviously bring additional manufacturing costs caused by re-melting of the bed cylinder and increased power due to the small outlet-openings. The purpose of this paper is to develop effective simulation methods of calculation for fluid flows in multiple columns, which mimic the actual complex design, and to get some useful information which can give some contributions to the die-casting industry. We have used a commercial code CFX in the numerical simulation. The primary parameter involved is the size of the bed cylinder. We will show how the very small opening of the outlet can be treated with the aid of the porous model provided in the code. To check the validity of the numerical results we have also conducted a simple experiment by using water.

  1. Modeling and simulation challenges pursued by the Consortium for Advanced Simulation of Light Water Reactors (CASL)

    Energy Technology Data Exchange (ETDEWEB)

    Turinsky, Paul J., E-mail: turinsky@ncsu.edu [North Carolina State University, PO Box 7926, Raleigh, NC 27695-7926 (United States); Kothe, Douglas B., E-mail: kothe@ornl.gov [Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6164 (United States)

    2016-05-15

    The Consortium for the Advanced Simulation of Light Water Reactors (CASL), the first Energy Innovation Hub of the Department of Energy, was established in 2010 with the goal of providing modeling and simulation (M&S) capabilities that support and accelerate the improvement of nuclear energy's economic competitiveness and the reduction of spent nuclear fuel volume per unit energy, and all while assuring nuclear safety. To accomplish this requires advances in M&S capabilities in radiation transport, thermal-hydraulics, fuel performance and corrosion chemistry. To focus CASL's R&D, industry challenge problems have been defined, which equate with long standing issues of the nuclear power industry that M&S can assist in addressing. To date CASL has developed a multi-physics “core simulator” based upon pin-resolved radiation transport and subchannel (within fuel assembly) thermal-hydraulics, capitalizing on the capabilities of high performance computing. CASL's fuel performance M&S capability can also be optionally integrated into the core simulator, yielding a coupled multi-physics capability with untapped predictive potential. Material models have been developed to enhance predictive capabilities of fuel clad creep and growth, along with deeper understanding of zirconium alloy clad oxidation and hydrogen pickup. Understanding of corrosion chemistry (e.g., CRUD formation) has evolved at all scales: micro, meso and macro. CFD R&D has focused on improvement in closure models for subcooled boiling and bubbly flow, and the formulation of robust numerical solution algorithms. For multiphysics integration, several iterative acceleration methods have been assessed, illuminating areas where further research is needed. Finally, uncertainty quantification and data assimilation techniques, based upon sampling approaches, have been made more feasible for practicing nuclear engineers via R&D on dimensional reduction and biased sampling. Industry adoption of CASL

  2. Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

    KAUST Repository

    Wang, Peng

    2015-11-01

    The incorporation of membrane distillation (MD) into forward osmosis (FO) provides process sustainability to regenerate the draw solution and to produce clean water simultaneously. However, the reverse salt flux is the major hurdle in the FO-MD system because it not only reduces the effective osmotic driving force across the membrane but also increases the replenishment cost and scaling issue. For the first time, a hydroacid complex with abundant hydrophilic groups and ionic species is evaluated as the draw solutes in the hybrid FO-MD system consisting of multi-bore PVDF MD membranes for seawater/brackish desalination. In order to evaluate the practicality of the hydroacid complex in the FO-MD system, FO and MD experiments were conducted at elevated temperatures and concentrations. The hydroacid complex has displayed desired properties such as high solubility, low viscosity, excellent thermal stability and minimal reverse salt flux suitable for FO and MD operations. FO-MD desalination process was demonstrated with a highest seawater desalination flux of 6/32 LMH (FO/MD). This study may open up the prospective of employing the hydroacid complex as the draw solute in FO-MD hybrid systems for seawater /brackish desalination. © 2015 Elsevier B.V.

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

    KAUST Repository

    Yoon, Seyoon

    2013-01-01

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

  4. Sulfur dioxide in water: structure and dynamics studied by an ab initio quantum mechanical charge field molecular dynamics simulation.

    Science.gov (United States)

    Moin, Syed Tarique; Lim, Len Herald V; Hofer, Thomas S; Randolf, Bernhard R; Rode, Bernd M

    2011-04-18

    An ab initio Quantum Mechanical Charge Field Molecular Dynamics Simulation (QMCF MD) was performed to investigate structure and dynamics behavior of hydrated sulfur dioxide (SO(2)) at the Hartree-Fock level of theory employing Dunning DZP basis sets for solute and solvent molecules. The intramolecular structural characteristics of SO(2), such as S═O bond lengths and O═S═O bond angle, are in good agreement with the data available from a number of different experiments. The structural features of the hydrated SO(2) were primarily evaluated in the form of S-O(wat) and O(SO(2))-H(wat) radial distribution functions (RDFs) which gave mean distances of 2.9 and 2.2 Å, respectively. The dynamical behavior characterizes the solute molecule to have structure making properties in aqueous solution or water aerosols, where the hydrated SO(2) can easily get oxidized to form a number of sulfur(VI) species, which are believed to play an important role in the atmospheric processes.

  5. Cold water immersion recovery after simulated collision sport exercise.

    Science.gov (United States)

    Pointon, Monique; Duffield, Rob

    2012-02-01

    This investigation examined the effects of cold water immersion (CWI) recovery after simulated collision sport exercise. Ten male rugby athletes performed three sessions consisting of a 2 × 30-min intermittent-sprint exercise (ISE) protocol with either tackling (T) or no tackling (CONT), followed by a 20-min CWI intervention (TCWI) or passive recovery (TPASS and CONT) in a randomized order. The ISE consisted of a 15-m sprint every minute separated by self-paced bouts of hard running, jogging, and walking for the remainder of the minute. Every sixth rotation, participants performed 5 × 10-m runs, receiving a shoulder-led tackle to the lower body on each effort. Sprint time and distance covered during ISE were recorded, with voluntary (maximal voluntary contraction; MVC) and evoked neuromuscular function (voluntary activation; VA), electromyogram (root mean square (RMS)), ratings of perceived muscle soreness (MS), capillary and venous blood markers for metabolites and muscle damage, respectively measured before and after exercise, immediately after recovery, and 2 and 24 h after recovery. Total distance covered during exercise was significantly greater in CONT (P = 0.01), without differences between TPASS and TCWI (P > 0.05). TCWI resulted in increased MVC, VA, and RMS immediately after recovery (P muscle damage (P > 0.05), lactate was significantly reduced after recovery compared with TPASS (P = 0.04). CWI also resulted in reduced MS 2 h after recovery compared with TPASS (P muscle contractile properties and perceptions of soreness after collision-based exercise.

  6. Water flow simulation and analysis in HMA microstructure

    Directory of Open Access Journals (Sweden)

    Can Chen

    2014-10-01

    Full Text Available This paper introduces a new method for reconstructing virtual two-dimensional (2-D microstructure of hot mix asphalt (HMA. Based on the method, the gradation of coarse aggregates and the film thickness of the asphalt binder can be defined by the user. The HMA microstructure then serves as the input to the computational fluid dynamic (CFD software (ANSYS-FLUENT to investigate the water flow pattern through it. It is found that the realistic flow fields can be simulated in the 2-D micro-structure and the flow patterns in some typical air void structures can be identified. These flow patterns can be used to explain the mechanism that could result in moisture damage in HMA pavement. The one-dimensional numerical permeability values are also derived from the flow fields of the 2-D HMA microstructure and compared with the measured values obtained by the Karol-Warner permeameter. Because the interconnected air voids channels in actual HMA samples cannot be fully represented in a 2-D model, some poor agreements need to be improved.

  7. MD5算法的分析和改进%Analysis and Improvement of .MD5 Algorithm

    Institute of Scientific and Technical Information of China (English)

    么丽颖

    2011-01-01

    首先研究了MD5算法,并总结了MD5算法的特点及性能,在研究MD5算法的基础之上,提出了MD5改进加密算法.最后,对MD5算法与MD5改进算法对应于相关数据、性能进行了比较.%At first , MD5 algorithm is researched, and the characteristic and capability of the MD5 are summaried in the paper. The improved MD5 algorithm is put forward based on the research of the MDS. At last, the contrast between MD5 algorithm and the improved MD5 algorithm in related datum and capability are put forward.

  8. New Message Differences for Collision Attacks on MD4 and MD5

    Science.gov (United States)

    Sasaki, Yu; Wang, Lei; Kunihiro, Noboru; Ohta, Kazuo

    In 2005, collision resistance of several hash functions was broken by Wang et al. The strategy of determining message differences is the most important part of collision attacks against hash functions. So far, many researchers have tried to analyze Wang et al.'s method and proposed improved collision attacks. Although several researches proposed improved attacks, all improved results so far were based on the same message differences proposed by Wang et al. In this paper, we propose new message differences for collision attacks on MD4 and MD5. Our message differences of MD4 can generate a collision with complexity of less than two MD4 computations, which is faster than the original Wang et al.'s attack, and moreover, than the all previous attacks. This is the first result that improves the complexity of collision attack by using different message differences from Wang et al.'s. Regarding MD5, so far, no other message difference from Wang et al.'s is known. Therefore, study for constructing method of other message differences on MD5 should be interesting. Our message differences of MD5 generates a collision with complexity of 242 MD5 computations, which is slower than the latest best attack. However, since our attack needs only 1 bit difference, it has some advantages in terms of message freedom of collision messages.

  9. Water Pollution Scrubber Activity Simulates Pollution Control Devices.

    Science.gov (United States)

    Kennedy, Edward C., III; Waggoner, Todd C.

    2003-01-01

    A laboratory activity caused students to think actively about water pollution. The students realized that it would be easier to keep water clean than to remove pollutants. They created a water scrubbing system allowing them to pour water in one end and have it emerge clean at the other end. (JOW)

  10. Water Pollution Scrubber Activity Simulates Pollution Control Devices.

    Science.gov (United States)

    Kennedy, Edward C., III; Waggoner, Todd C.

    2003-01-01

    A laboratory activity caused students to think actively about water pollution. The students realized that it would be easier to keep water clean than to remove pollutants. They created a water scrubbing system allowing them to pour water in one end and have it emerge clean at the other end. (JOW)

  11. Water scarcity and economic damage in Europe: regionally relevant simulations from 2000 to 2050

    Science.gov (United States)

    Bernhard, Jeroen; de Roo, Ad; Bisselink, Bernard; Gelati, Emiliano; Karssenberg, Derek; de Jong, Steven

    2017-04-01

    Water availability is unequally distributed across Europe. Where certain regions experience a surplus of water, other areas have limited water availability which causes economic damage to the water using sectors such as households, industries or agriculture. Future changes in climatic and socio-economic conditions are expected to further increase the competition for available water that is already present in Europe. This means there is an increasing need for models that are able to simulate this multi-sectorial system of water availability and demand and incorporate the socio-economic component required for robust decisions and policy support. We present our modelling study which is focused at providing regionally relevant pan-European water scarcity and economic damage simulations. First we developed regionally relevant pan-European water demand simulations for the household and industry sector from 2000 up to 2050. For the household sector we developed a model to simulate water use based on water price, income and several other relevant variables at NUTS-3 level (over 1200 regions in Europe). Alternatively, we modelled industrial water use based on regionally downscaled water productivity values at the national level for ten sub-sections of the NACE (Nomenclature of Economic Activities) classification for economic activities. Subsequently we used scenario projections of our explanatory variables to make scenario simulations of water demand from 2000 up to 2050 at pan-European scale with unprecedented spatial and sub-sectorial detail. In order to analyze the European water use system we integrated these water demand scenarios into the hydrological rainfall-runoff model called LISFLOOD (Distributed Water Balance and Flood Simulation Model), which incorporates a vegetation module for the simulation of crop yield and irrigation water demand of the agriculture sector. We simulated river discharge and groundwater availability for abstractions of water using sectors

  12. Daily Runoff Simulation at River Network by the WWASS (Watershed Water balance And Stream flow Simulation) Model

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyun Young; Hwang, Cheol Sang; Kang, Seok Man; Lee, Kwang Ya [Rural Development Corp., Seoul (Korea)

    1998-08-31

    When various elements of water balance are displayed at several points of a river network, the runoff amounts at an estuary especially tidal influenced are affected from the elements. This problem can be solved by a model that can generalize and formulate the elements and simulate daily runoff and water requirement. The WWASS model was built using DIROM for the simulation of daily runoff and water requirement, and the water balance elements were modeled to be balanced at the each control point of river network. The model was calibrated, verified and applied to the watershed for the Saemankeum tidal land reclamation development project. It showed that the results from the stream flow simulation at the Mankyung and Dongjin estuary were acceptable for the design of the Saemankeum estuary reservoir. (author). 7 refs., 3 tabs., 8 figs.

  13. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

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

    Science.gov (United States)

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

    2006-05-01

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

  15. Ground water/surface water responses to global climate simulations, Santa Clara-Calleguas Basin, Ventura, California

    Science.gov (United States)

    Hanson, R.T.; Dettinger, M.D.

    2005-01-01

    Climate variations can play an important, if not always crucial, role in successful conjunctive management of ground water and surface water resources. This will require accurate accounting of the links between variations in climate, recharge, and withdrawal from the resource systems, accurate projection or predictions of the climate variations, and accurate simulation of the responses of the resource systems. To assess linkages and predictability of climate influences on conjunctive management, global climate model (GCM) simulated precipitation rates were used to estimate inflows and outflows from a regional ground water model (RGWM) of the coastal aquifers of the Santa ClaraCalleguas Basin at Ventura, California, for 1950 to 1993. Interannual to interdecadal time scales of the El Nin??o Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) climate variations are imparted to simulated precipitation variations in the Southern California area and are realistically imparted to the simulated ground water level variations through the climate-driven recharge (and discharge) variations. For example, the simulated average ground water level response at a key observation well in the basin to ENSO variations of tropical Pacific sea surface temperatures is 1.2 m/??C, compared to 0.9 m/??C in observations. This close agreement shows that the GCM-RGWM combination can translate global scale climate variations into realistic local ground water responses. Probability distributions of simulated ground water level excursions above a local water level threshold for potential seawater intrusion compare well to the corresponding distributions from observations and historical RGWM simulations, demonstrating the combination's potential usefulness for water management and planning. Thus the GCM-RGWM combination could be used for planning purposes and - when the GCM forecast skills are adequate - for near term predictions.

  16. Numerical Simulation of Water Jet Flow Using Diffusion Flux Mixture Model

    Directory of Open Access Journals (Sweden)

    Zhi Shang

    2014-01-01

    Full Text Available A multidimensional diffusion flux mixture model was developed to simulate water jet two-phase flows. Through the modification of the gravity using the gradients of the mixture velocity, the centrifugal force on the water droplets was able to be considered. The slip velocities between the continuous phase (gas and the dispersed phase (water droplets were able to be calculated through multidimensional diffusion flux velocities based on the modified multidimensional drift flux model. Through the numerical simulations, comparing with the experiments and the simulations of traditional algebraic slip mixture model on the water mist spray, the model was validated.

  17. Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein

    NARCIS (Netherlands)

    van der Spoel, D.; Vogel, H.J.; Berendsen, H.J.C.

    Molecular dynamics (MD) simulations of N-terminal peptides from lactate dehydrogenase (LDH) with increasing length and individual secondary structure elements were used to study their stability in relation to folding, Ten simulations of 1-2 ns of different peptides in water starting from the

  18. Numerical simulation of high pressure water jet impacting concrete

    Science.gov (United States)

    Liu, Jialiang; Wang, Mengjin; Zhang, Di

    2017-08-01

    High pressure water jet technology is an unconventional concrete crushing technology. In order to reveal the mechanism of high pressure water jet impacting concrete, it built a three-dimensional numerical model of high pressure water jet impacting concrete based on fluid mechanics and damage mechanics. And the numerical model was verified by theoretical analysis and experiments. Based on this model, it studied the stress characteristics in concrete under high pressure water jet impacting at different time, and quantified the damage evolution rules in concrete along the water jet radial direction. The results can provide theoretical basis and guidance for the high pressure water jet crushing concrete technology.

  19. The numerical simulation of green water loading including vessel motions and the incoming wave field

    NARCIS (Netherlands)

    Kleefsman, K.M.Theresa; Loots, G. Erwin; Veldman, Arthur E.P.; Buchner, Bas; Bunnik, Tim; Falkenberg, Erik

    2005-01-01

    This paper presents results from simulation of green water loading including vessel motions. The simulation is performed through a domain decomposition: the far field and ship motions are calculated by potential theory and are used to simulate the local flow around the deck of an offshore floater us

  20. 76 FR 77579 - Maryland Disaster #MD-00017

    Science.gov (United States)

    2011-12-13

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Maryland Disaster MD-00017 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... INFORMATION CONTACT: A. Escobar, Office of Disaster Assistance, U.S. Small Business Administration, 409...

  1. 78 FR 2707 - Maryland Disaster # MD-00026

    Science.gov (United States)

    2013-01-14

    ... From the Federal Register Online via the Government Publishing Office SMALL BUSINESS ADMINISTRATION Maryland Disaster MD-00026 AGENCY: U.S. Small Business Administration. ACTION: Notice. SUMMARY... INFORMATION CONTACT: A. Escobar, Office of Disaster Assistance, U.S. Small Business Administration, 409...

  2. Simulation of water cluster assembly on a graphite surface.

    Science.gov (United States)

    Lin, C S; Zhang, R Q; Lee, S T; Elstner, M; Frauenheim, Th; Wan, L J

    2005-07-28

    The assembly of small water clusters (H2O)n, n = 1-6, on a graphite surface is studied using a density functional tight-binding method complemented with an empirical van der Waals force correction, with confirmation using second-order Møller-Plesset perturbation theory. It is shown that the optimized geometry of the water hexamer may change its original structure to an isoenergy one when interacting with a graphite surface in some specific orientation, while the smaller water cluster will maintain its cyclic or linear configurations (for the water dimer). The binding energy of water clusters interacting with graphite is dependent on the number of water molecules that form hydrogen bonds, but is independent of the water cluster size. These physically adsorbed water clusters show little change in their IR peak position and leave an almost perfect graphite surface.

  3. Liquid–liquid transition in supercooled water suggested by microsecond simulations

    OpenAIRE

    Li, Yaping; Li, Jicun; Wang, Feng

    2013-01-01

    The putative liquid–liquid phase transition in supercooled water has been used to explain many anomalous behaviors of water. However, no direct experimental verification of such a phase transition has been accomplished, and theoretical studies from different simulations contradict each other. We investigated the putative liquid–liquid phase transition using the Water potential from Adaptive Force Matching for Ice and Liquid (WAIL). The simulation reveals a first-order phase transition in the ...

  4. 33 CFR 110.70 - Chesapeake and Delaware Canal, easterly of Courthouse Point, Md.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Chesapeake and Delaware Canal, easterly of Courthouse Point, Md. 110.70 Section 110.70 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.70 Chesapeake and Delaware Canal, easterly of...

  5. Simulation of the ground-water-flow system in the Kalamazoo County area, Michigan

    Science.gov (United States)

    Luukkonen, Carol L.; Blumer, Stephen P.; Weaver, T.L.; Jean, Julie

    2004-01-01

    A ground-water-flow model was developed to investigate the ground-water resources of Kalamazoo County. Ground water is widely used as a source of water for drinking and industry in Kalamazoo County and the surrounding area. Additionally, lakes and streams are valued for their recreational and aesthetic uses. Stresses on the ground-water system, both natural and human-induced, have raised concerns about the long-term availability of ground water for people to use and for replenishment of lakes and streams. Potential changes in these stresses, including withdrawals and recharge, were simulated using a ground-water-flow model. Simulations included steady-state conditions (in which stresses remained constant and changes in storage were not included) and transient conditions (in which stresses changed in seasonal and monthly time scales and storage within the system was included). Steady-state simulations were used to investigate the long-term effects on water levels and streamflow of a reduction in recharge or an increase in pumping to projected 2010 withdrawal rates, withdrawal and application of water for irrigation, and a reduction in recharge in urban areas caused by impervious surfaces. Transient simulations were used to investigate changes in withdrawals to match seasonal and monthly patterns under various recharge conditions, and the potential effects of the use of water for irrigation over the summer months. With a reduction in recharge, simulated water levels declined over most of the model area in Kalamazoo County; with an increase in pumping, water levels declined primarily near pumping centers. Because withdrawals by wells intercept water that would have discharged possibly to a stream or lake, model simulations indicated that streamflow was reduced with increased withdrawals. With withdrawal and consumption of water for irrigation, simulated water levels declined. Assuming a reduction in recharge due to urbanization, water levels declined and flow to

  6. Evaluation of Crop-Water Consumption Simulation to Support Agricultural Water Resource Management using Satellite-based Water Cycle Observations

    Science.gov (United States)

    Gupta, M.; Bolten, J. D.; Lakshmi, V.

    2016-12-01

    Water scarcity is one of the main factors limiting agricultural development. Numerical models integrated with remote sensing datasets are increasingly being used operationally as inputs for crop water balance models and agricultural forecasting due to increasing availability of high temporal and spatial resolution datasets. However, the model accuracy in simulating soil water content is affected by the accuracy of the soil hydraulic parameters used in the model, which are used in the governing equations. However, soil databases are known to have a high uncertainty across scales. Also, for agricultural sites, the in-situ measurements of soil moisture are currently limited to discrete measurements at specific locations, and such point-based measurements do not represent the spatial distribution at a larger scale accurately, as soil moisture is highly variable both spatially and temporally. The present study utilizes effective soil hydraulic parameters obtained using a 1-km downscaled microwave remote sensing soil moisture product based on the NASA Advanced Microwave Scanning Radiometer (AMSR-E) using the genetic algorithm inverse method within the Catchment Land Surface Model (CLSM). Secondly, to provide realistic irrigation estimates for agricultural sites, an irrigation scheme within the land surface model is triggered when the root-zone soil moisture deficit reaches the threshold, 50% with respect to the maximum available water capacity obtained from the effective soil hydraulic parameters. An additional important criterion utilized is the estimation of crop water consumption based on dynamic root growth and uptake in root zone layer. Model performance is evaluated using MODIS land surface temperature (LST) product. The soil moisture estimates for the root zone are also validated with the in situ field data, for three sites (2- irrigated and 1- rainfed) located at the University of Nebraska Agricultural Research and Development Center near Mead, NE and monitored

  7. Electronic coarse graining enhances the predictive power of molecular simulation allowing challenges in water physics to be addressed

    Science.gov (United States)

    Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

    2016-12-01

    One key factor that limits the predictive power of molecular dynamics simulations is the accuracy and transferability of the input force field. Force fields are challenged by heterogeneous environments, where electronic responses give rise to biologically important forces such as many-body polarisation and dispersion. The importance of polarisation in the condensed phase was recognised early on, as described by Cochran in 1959 [Philosophical Magazine 4 (1959) 1082-1086] [32]. Currently in molecular simulation, dispersion forces are treated at the two-body level and in the dipole limit, although the importance of three-body terms in the condensed phase was demonstrated by Barker in the 1980s [Phys. Rev. Lett. 57 (1986) 230-233] [72]. One approach for treating both polarisation and dispersion on an equal basis is to coarse grain the electrons surrounding a molecular moiety to a single quantum harmonic oscillator (cf. Hirschfelder, Curtiss and Bird 1954 [The Molecular Theory of Gases and Liquids (1954)] [37]). The approach, when solved in strong coupling beyond the dipole limit, gives a description of long-range forces that includes two- and many-body terms to all orders. In the last decade, the tools necessary to implement the strong coupling limit have been developed, culminating in a transferable model of water with excellent predictive power across the phase diagram. Transferability arises since the environment automatically identifies the important long range interactions, rather than the modeller through a limited set of expressions. Here, we discuss the role of electronic coarse-graining in predictive multiscale materials modelling and describe the first implementation of the method in a general purpose molecular dynamics software: QDO_MD.

  8. Simulation of the Regional Ground-Water-Flow System and Ground-Water/Surface-Water Interaction in the Rock River Basin, Wisconsin

    Science.gov (United States)

    Juckem, Paul F.

    2009-01-01

    A regional, two-dimensional, areal ground-water-flow model was developed to simulate the ground-water-flow system and ground-water/surface-water interaction in the Rock River Basin. The model was developed by the U.S. Geological Survey (USGS), in cooperation with the Rock River Coalition. The objectives of the regional model were to improve understanding of the ground-water-flow system and to develop a tool suitable for evaluating the effects of potential regional water-management programs. The computer code GFLOW was used because of the ease with which the model can simulate ground-water/surface-water interactions, provide a framework for simulating regional ground-water-flow systems, and be refined in a stepwise fashion to incorporate new data and simulate ground-water-flow patterns at multiple scales. The ground-water-flow model described in this report simulates the major hydrogeologic features of the modeled area, including bedrock and surficial aquifers, ground-water/surface-water interactions, and ground-water withdrawals from high-capacity wells. The steady-state model treats the ground-water-flow system as a single layer with hydraulic conductivity and base elevation zones that reflect the distribution of lithologic groups above the Precambrian bedrock and a regionally significant confining unit, the Maquoketa Formation. In the eastern part of the Basin where the shale-rich Maquoketa Formation is present, deep ground-water flow in the sandstone aquifer below the Maquoketa Formation was not simulated directly, but flow into this aquifer was incorporated into the GFLOW model from previous work in southeastern Wisconsin. Recharge was constrained primarily by stream base-flow estimates and was applied uniformly within zones guided by regional infiltration estimates for soils. The model includes average ground-water withdrawals from 1997 to 2006 for municipal wells and from 1997 to 2005 for high-capacity irrigation, industrial, and commercial wells. In addition

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

    Science.gov (United States)

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

    2006-04-27

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

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  11. FUZZY MODEL FOR TWO-DIMENSIONAL RIVER WATER QUALITY SIMULATION UNDER SUDDEN POLLUTANTS DISCHARGED

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Based on the fuzziness and impreciseness of water environmental system, the fuzzy arithmetic was used to simulate the fuzzy and imprecise relations in modeling river water quality. By defining the parameters of water quality model as symmetrical triangular fuzzy numbers, a two-dimensional fuzzy water quality model for sudden pollutant discharge is established. From the fuzzy model, the pollutant concentrations, corresponding to the specified confidence level of α, can be obtained by means of the α-cut technique and arithmetic operations of triangular fuzzy numbers. Study results reveal that it is feasible in theory and reliable on calculation applying triangular fuzzy numbers to the simulation of river water quality.

  12. A Two-Continua Approach to Eulerian Simulation of Water Spray

    DEFF Research Database (Denmark)

    Nielsen, Michael Bang; Østerby, Ole

    2013-01-01

    Physics based simulation of the dynamics of water spray - water droplets dispersed in air - is a means to increase the visual plausibility of computer graphics modeled phenomena such as waterfalls, water jets and stormy seas. Spray phenomena are frequently encountered by the visual effects industry...

  13. Simulating yield response to water of Teff (Eragrostis tef) with FAO's AquaCrop model

    NARCIS (Netherlands)

    Araya, A.; Keesstra, S.D.; Stroosnijder, L.

    2010-01-01

    In a semi-arid environment, the main challenge for crop production is water deficit. FAO's AquaCrop model, which simulates yield response to water, has been calibrated to explore alternative water management strategies in teff crop. To calibrate and evaluate this model, we used independent data sets

  14. Geography in the Social Studies: High School Simulation on Water Supply

    Science.gov (United States)

    Dunn, James M.

    2009-01-01

    This is a ready-to-use simulation that has high school students portraying all of the key players that decide how water from the Colorado River will be allocated. Students act as judges, lobbyists, news analysts, and even protesters during a mock water conference. Water supply is promised beyond nature's delivery, so the problem is real and will…

  15. Direct simulation of liquid water dynamics in the gas channel of a polymer electrolyte fuel cell

    NARCIS (Netherlands)

    Qin, C.; Rensink, D.; Hassanizadeh, S.M.; Fell, S.

    2012-01-01

    For better water management in gas channels (GCs) of polymer electrolyte fuel cells (PEFCs), a profound understanding of the liquid water dynamics is needed. In this study, we propose a novel geometrical setup to conduct a series of direct simulations of the liquid water dynamics in a GC. The conduc

  16. Simulating yield response to water of Teff (Eragrostis tef) with FAO's AquaCrop model

    NARCIS (Netherlands)

    Araya, A.; Keesstra, S.D.; Stroosnijder, L.

    2010-01-01

    In a semi-arid environment, the main challenge for crop production is water deficit. FAO's AquaCrop model, which simulates yield response to water, has been calibrated to explore alternative water management strategies in teff crop. To calibrate and evaluate this model, we used independent data sets

  17. Behavior of solvent-exposed hydrophobic groove in the anti-apoptotic Bcl-XL protein: clues for its ability to bind diverse BH3 ligands from MD simulations.

    Directory of Open Access Journals (Sweden)

    Dilraj Lama

    Full Text Available Bcl-XL is a member of Bcl-2 family of proteins involved in the regulation of intrinsic pathway of apoptosis. Its overexpression in many human cancers makes it an important target for anti-cancer drugs. Bcl-XL interacts with the BH3 domain of several pro-apoptotic Bcl-2 partners. This helical bundle protein has a pronounced hydrophobic groove which acts as a binding region for the BH3 domains. Eight independent molecular dynamics simulations of the apo/holo forms of Bcl-XL were carried out to investigate the behavior of solvent-exposed hydrophobic groove. The simulations used either a twin-range cut-off or particle mesh Ewald (PME scheme to treat long-range interactions. Destabilization of the BH3 domain-containing helix H2 was observed in all four twin-range cut-off simulations. Most of the other major helices remained stable. The unwinding of H2 can be related to the ability of Bcl-XL to bind diverse BH3 ligands. The loss of helical character can also be linked to the formation of homo- or hetero-dimers in Bcl-2 proteins. Several experimental studies have suggested that exposure of BH3 domain is a crucial event before they form dimers. Thus unwinding of H2 seems to be functionally very important. The four PME simulations, however, revealed a stable helix H2. It is possible that the H2 unfolding might occur in PME simulations at longer time scales. Hydrophobic residues in the hydrophobic groove are involved in stable interactions among themselves. The solvent accessible surface areas of bulky hydrophobic residues in the groove are significantly buried by the loop LB connecting the helix H2 and subsequent helix. These observations help to understand how the hydrophobic patch in Bcl-XL remains stable in the solvent-exposed state. We suggest that both the destabilization of helix H2 and the conformational heterogeneity of loop LB are important factors for binding of diverse ligands in the hydrophobic groove of Bcl-XL.

  18. Improved Parameterization of Amine-Carboxyate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields

    CERN Document Server

    Yoo, Jejoong

    2015-01-01

    Over the past decades, molecular dynamics (MD) simulations of biomolecules have become a mainstream biophysics technique. As the length and time scales amenable to the MD method increase, shortcomings of the empirical force fields---which have been developed and validated using relatively short simulations of small molecules---become apparent. One common artifact is aggregation of water-soluble biomolecules driven by artificially strong charge--charge interactions. Here, we report a systematic refinement of Lennard-Jones parameters (NBFIX) describing amine--carboxylate and amine--phosphate interactions, which brings MD simulations of basic peptide-mediated nucleic acids assemblies and lipid bilayer membranes in better agreement with experiment. As our refinement neither affects the existing parameterization of bonded interaction nor does it alter the solvation free energies, it improves realism of an MD simulation without introducing additional artifacts.

  19. Uncertainty of Wheat Water Use: Simulated Patterns and Sensitivity to Temperature and CO2

    Science.gov (United States)

    Cammarano, Davide; Roetter, Reimund P.; Asseng, Senthold; Ewert, Frank; Wallach, Daniel; Martre, Pierre; Hatfield, Jerry L.; Jones, James W.; Rosenzweig, Cynthia E.; Ruane, Alex C.; Boote, Kenneth J.; Thorburn, Peter J.; Kersebaum, Kurt Christian; Aggarwal, Pramod K.; Angulo, Carlos; Basso, Bruno; Bertuzzi, Patrick; Biernath, Christian; Brisson, Nadine; Challinor, Andrew J.; Doltra, Jordi; Gayler, Sebastian; Goldberg, Richie; Heng, Lee; Steduto, Pasquale

    2016-01-01

    Projected global warming and population growth will reduce future water availability for agriculture. Thus, it is essential to increase the efficiency in using water to ensure crop productivity. Quantifying crop water use (WU; i.e. actual evapotranspiration) is a critical step towards this goal. Here, sixteen wheat simulation models were used to quantify sources of model uncertainty and to estimate the relative changes and variability between models for simulated WU, water use efficiency (WUE, WU per unit of grain dry mass produced), transpiration efficiency (Teff, transpiration per kg of unit of grain yield dry mass produced), grain yield, crop transpiration and soil evaporation at increased temperatures and elevated atmospheric carbon dioxide concentrations ([CO2]). The greatest uncertainty in simulating water use, potential evapotranspiration, crop transpiration and soil evaporation was due to differences in how crop transpiration was modelled and accounted for 50 of the total variability among models. The simulation results for the sensitivity to temperature indicated that crop WU will decline with increasing temperature due to reduced growing seasons. The uncertainties in simulated crop WU, and in particularly due to uncertainties in simulating crop transpiration, were greater under conditions of increased temperatures and with high temperatures in combination with elevated atmospheric [CO2] concentrations. Hence the simulation of crop WU, and in particularly crop transpiration under higher temperature, needs to be improved and evaluated with field measurements before models can be used to simulate climate change impacts on future crop water demand.

  20. Exploring intentions of physician-scientist trainees: factors influencing MD and MD/PhD interest in research careers.

    Science.gov (United States)

    Kwan, Jennifer M; Daye, Dania; Schmidt, Mary Lou; Conlon, Claudia Morrissey; Kim, Hajwa; Gaonkar, Bilwaj; Payne, Aimee S; Riddle, Megan; Madera, Sharline; Adami, Alexander J; Winter, Kate Quinn

    2017-07-11

    Prior studies have described the career paths of physician-scientist candidates after graduation, but the factors that influence career choices at the candidate stage remain unclear. Additionally, previous work has focused on MD/PhDs, despite many physician-scientists being MDs. This study sought to identify career sector intentions, important factors in career selection, and experienced and predicted obstacles to career success that influence the career choices of MD candidates, MD candidates with research-intense career intentions (MD-RI), and MD/PhD candidates. A 70-question survey was administered to students at 5 academic medical centers with Medical Scientist Training Programs (MSTPs) and Clinical and Translational Science Awards (CTSA) from the NIH. Data were analyzed using bivariate or multivariate analyses. More MD/PhD and MD-RI candidates anticipated or had experienced obstacles related to balancing academic and family responsibilities and to balancing clinical, research, and education responsibilities, whereas more MD candidates indicated experienced and predicted obstacles related to loan repayment. MD/PhD candidates expressed higher interest in basic and translational research compared to MD-RI candidates, who indicated more interest in clinical research. Overall, MD-RI candidates displayed a profile distinct from both MD/PhD and MD candidates. MD/PhD and MD-RI candidates experience obstacles that influence their intentions to pursue academic medical careers from the earliest training stage, obstacles which differ from those of their MD peers. The differences between the aspirations of and challenges facing MD, MD-RI and MD/PhD candidates present opportunities for training programs to target curricula and support services to ensure the career development of successful physician-scientists.

  1. Simulation of regional ground-water flow in the Upper Deschutes Basin, Oregon

    Science.gov (United States)

    Gannett, Marshall W.; Lite, Kenneth E.

    2004-01-01

    This report describes a numerical model that simulates regional ground-water flow in the upper Deschutes Basin of central Oregon. Ground water and surface water are intimately connected in the upper Deschutes Basin and most of the flow of the Deschutes River is supplied by ground water. Because of this connection, ground-water pumping and reduction of artificial recharge by lining leaking irrigation canals can reduce the amount of ground water discharging to streams and, consequently, streamflow. The model described in this report is intended to help water-management agencies and the public evaluate how the regional ground-water system and streamflow will respond to ground-water pumping, canal lining, drought, and other stresses. Ground-water flow is simulated in the model by the finite-difference method using MODFLOW and MODFLOWP. The finite-difference grid consists of 8 layers, 127 rows, and 87 columns. All major streams and most principal tributaries in the upper Deschutes Basin are included. Ground-water recharge from precipitation was estimated using a daily water-balance approach. Artificial recharge from leaking irrigation canals and on-farm losses was estimated from diversion and delivery records, seepage studies, and crop data. Ground-water pumpage for irrigation and public water supplies, and evapotranspiration are also included in the model. The model was calibrated to mean annual (1993-95) steady-state conditions using parameter-estimation techniques employing nonlinear regression. Fourteen hydraulic-conductivity parameters and two vertical conductance parameters were determined using nonlinear regression. Final parameter values are all within expected ranges. The general shape and slope of the simulated water-table surface and overall hydraulic-head distribution match the geometry determined from field measurements. The fitted standard deviation for hydraulic head is about 76 feet. The general magnitude and distribution of ground-water discharge to

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

    Science.gov (United States)

    Pérez-Hernández, Guillermo; Schmidt, Burkhard

    2013-04-14

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

  3. Humans Running in Place on Water at Simulated Reduced Gravity

    OpenAIRE

    Alberto E Minetti; Ivanenko, Yuri P.; Germana Cappellini; Nadia Dominici; Francesco Lacquaniti

    2012-01-01

    BACKGROUND: On Earth only a few legged species, such as water strider insects, some aquatic birds and lizards, can run on water. For most other species, including humans, this is precluded by body size and proportions, lack of appropriate appendages, and limited muscle power. However, if gravity is reduced to less than Earth's gravity, running on water should require less muscle power. Here we use a hydrodynamic model to predict the gravity levels at which humans should be able to run on wate...

  4. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  5. Prevention of IcaA regulated poly N-acetyl glucosamine formation in Staphylococcus aureus biofilm through new-drug like inhibitors: In silico approach and MD simulation study.

    Science.gov (United States)

    Gupta, Ayushi; Mishra, Swechha; Singh, Sangeeta; Mishra, Sonali

    2017-09-01

    The effectiveness of various ligands against the protein structure of IcaA of the IcaABCD gene locus of Staphylococcus aureus were examined using the approach of structure based drug designing in reference with the protein's efficiency to form biofilms. Four compounds CID42738592, CID90468752, CID24277882, and CID6435208 were secluded from a database of 31,242 inhibitory ligands on the justification of the evaluated values falling under the four - tier structure based virtual screening. Under this principle value of least binding energy, human oral absorption and ADME properties were taken into consideration. Using the Glide module of Schrödinger, the above mentioned ligands showed an effective action against the protein IcaA which showed reduced activity as a glucosaminyl transferase. The complex of protein and ligand with best docking score was chosen for simulation studies. Structure based drug designing for the protein IcaA has given us potential leads as anti - biofilm agents. These screened out ligands might enable the development of new therapeutic strategies aimed at disrupting Staphylococcus aureus biofilms. The complex was showing stability towards the end of time for which it has been put for simulation. Thus molecule could be considered for making of biofilms. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. MesoDyn Simulation Study on Phase Diagram of Aerosol OT/isooctane/water System

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A simple model, i.e. sodium di(2-ethylhexyl) sulfosuccinate (AOT) represented by one-head and two-tail beads tied together by a harmonic spring and water or isooctane by one bead, was put forward via Dissipative Particles Dynamics (DPD) simulation method. Using the changes of interfacial tension between water and oil phase, a ternary phase diagram of AOT/water/isooctane system was drawn. From the simulation, one conclusion is shown that DPD simulation can be considered as an adjunct to experiments.

  7. Comparison of simulations of land-use specific water demand and irrigation water supply by MF-FMP and IWFM

    Science.gov (United States)

    Schmid, Wolfgang; Dogural, Emin; Hanson, Randall T.; Kadir, Tariq; Chung, Francis

    2011-01-01

    Two hydrologic models, MODFLOW with the Farm Process (MF-FMP) and the Integrated Water Flow Model (IWFM), are compared with respect to each model’s capabilities of simulating land-use hydrologic processes, surface-water routing, and groundwater flow. Of major concern among the land-use processes was the consumption of water through evaporation and transpiration by plants. The comparison of MF-FMP and IWFM was conducted and completed using a realistic hypothetical case study. Both models simulate the water demand for water-accounting units resulting from evapotranspiration and inefficiency losses and, for irrigated units, the supply from surface-water deliveries and groundwater pumpage. The MF-FMP simulates reductions in evapotranspiration owing to anoxia and wilting, and separately considers land-use-related evaporation and transpiration; IWFM simulates reductions in evapotranspiration related to the depletion of soil moisture. The models simulate inefficiency losses from precipitation and irrigation water applications to runoff and deep percolation differently. MF-FMP calculates the crop irrigation requirement and total farm delivery requirement, and then subtracts inefficiency losses from runoff and deep percolation. In IWFM, inefficiency losses to surface runoff from irrigation and precipitation are computed and subtracted from the total irrigation and precipitation before the crop irrigation requirement is estimated. Inefficiency losses in terms of deep percolation are computed simultaneously with the crop irrigation requirement. The seepage from streamflow routing also is computed differently and can affect certain hydrologic settings and magnitudes ofstreamflow infiltration. MF-FMP assumes steady-state conditions in the root zone; therefore, changes in soil moisture within the root zone are not calculated. IWFM simulates changes in the root zone in both irrigated and non-irrigated natural vegetation. Changes in soil moisture are more significant for non

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

    DEFF Research Database (Denmark)

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

    2010-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    肖吉; 陆九芳; 陈健; 李以圭

    2001-01-01

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

  10. Simulation of Satellite Water Vapour Lidar Measurements: Performance Assessment under Real Atmospheric Conditions.

    OpenAIRE

    Di Girolamo, Paolo; Behrendt, Andreas; Kiemle, Christoph; Wulfmeyer, Volker; Bauer, Heinz; Summa, Donato; Dörnbrack, Andreas; Ehret, Gerhard

    2008-01-01

    A lidar simulator has been applied to assess the performances of a satellite water vapour differential absorption lidar (DIAL) system. Measurements performed by the airborne Deutsches Zentrum für Luft- und Raumfahrt (DLR) water vapour DIAL on 15 May 2002 during ESA’s Water Vapour Lidar Experiment (WALEX), in combination with MM5 mesoscale model output, were used to obtain backscatter and water vapour fields with high resolution and accuracy. These data and model output serve as input for the ...

  11. A decision support tool for sustainable planning of urban water systems: presenting the Dynamic Urban Water Simulation Model.

    Science.gov (United States)

    Willuweit, Lars; O'Sullivan, John J

    2013-12-15

    Population growth, urbanisation and climate change represent significant pressures on urban water resources, requiring water managers to consider a wider array of management options that account for economic, social and environmental factors. The Dynamic Urban Water Simulation Model (DUWSiM) developed in this study links urban water balance concepts with the land use dynamics model MOLAND and the climate model LARS-WG, providing a platform for long term planning of urban water supply and water demand by analysing the effects of urbanisation scenarios and climatic changes on the urban water cycle. Based on potential urbanisation scenarios and their effects on a city's water cycle, DUWSiM provides the functionality for assessing the feasibility of centralised and decentralised water supply and water demand management options based on forecasted water demand, stormwater and wastewater generation, whole life cost and energy and potential for water recycling. DUWSiM has been tested using data from Dublin, the capital of Ireland, and it has been shown that the model is able to satisfactorily predict water demand and stormwater runoff.

  12. Batch By Batch Longitudinal Emittance Blowup MD

    CERN Document Server

    Mastoridis, T; Butterworth, A; Jaussi, M; Molendijk, J

    2012-01-01

    The transverse bunch emittance increases significantly at 450 GeV from the time of injection till the ramp due to IBS. By selectively blowing up the longitudinal emittance of the incoming batch at each injection, it should be possible to reduce the transverse emittance growth rates due to IBS. An MD was conducted on April 22nd 2012 to test the feasibility and performance of the batch-by-batch longitudinal emittance blowup. There were three main goals during the MD. First, to test the developed hardware, firmware, and software for the batch-by-batch blowup. Then, to measure the transverse emittance growth rates of blown-up and "witness" batches to quantify any improvement, and finally to test the ALLInjectSequencer class, which deals with the complicated gymnastics of introducing or masking the new batch to various RF loops.

  13. MD on UFOs at MKIs and MKQs

    CERN Document Server

    Baer, T; Bartmann, W; Bracco, C; Carlier, E; Dehning, B; Garrel, N; Goddard, B; Jackson, S; Jimenez, M; Kain, V; Mertens, V; Misiowiec, M; Nordt, A; Papotti, G; Uythoven, J; Wenninger, J; Zerlauth, M; Zamantzas, C; Zimmermann, F

    2012-01-01

    UFOs ("Unidentified Falling Objects") are expected to be one of the major known performance limitation of the LHC. In this MD, the production mechanism and the dynamics of UFOs at the injection kicker magnets (MKIs) and the tune kicker magnets (MKQs) were studied. This was done by pulsing the MKIs and MKQs on a gap in the partly filled machine. During the MD, in total 58 UFO-type beam loss patterns were observed directly after pulsing the MKIs. None were observed after pulsing the MKQs, which provides important input for possible mitigation strategies. The temporal and spatial distribution of the UFO events could be determined by using a dedicated BLM Study Buffer, the implications for the UFO dynamics are discussed.

  14. MD5的Keygenme分析

    Institute of Scientific and Technical Information of China (English)

    Firebig

    2006-01-01

    闲来无事,抓出个不知何时下的Keygenme练练手,分析后可知.这个Keygenme有2张数据表,由注册名经MD5运算后进行查表,得出2个DWORD数据.然后再由注册码经过一个可逆循环得出2个DWORD数据.最后对比是否正确。(MD5的具体介绍黑防6期有说明)

  15. Algorithms for Model Calibration of Ground Water Simulators

    Science.gov (United States)

    2014-11-20

    cobian, and Jacobian-vector products are computed with a Monte Carlo simulation. This situation differs from the textbook case [5] in that one does not...Anderson acceleration is a natural method for multi-physics coupling (for example subsurface flow, chemistry , and heat transfer) when the individual physics...Online publication 7/12/2014. [11] J. Nance and C. T. Kelley, A sparse interpolation algorithm for dynamical simulations in compu- tational chemistry

  16. Classical MD calculations with parallel computers

    Energy Technology Data Exchange (ETDEWEB)

    Matsumoto, Mitsuhiro [Nagoya Univ. (Japan)

    1998-03-01

    We have developed parallel computation codes for a classical molecular dynamics (MD) method. In order to use them on work station clusters as well as parallel super computers, we use MPI (message passing interface) library for distributed-memory type computers. Two algorithms are compared: (1) particle parallelism technique: easy to install, effective for rather small number of processors. (2) region parallelism technique: take some time to install, effective even for many nodes. (J.P.N.)

  17. Photosynthetic efficiency of Pedunculate oak seedlings under simulated water stress

    Directory of Open Access Journals (Sweden)

    Popović Zorica

    2010-01-01

    Full Text Available Photosynthetic performance of seedlings of Quercus robur exposed to short-term water stress in the laboratory conditions was assessed through the method of induced fluorometry. The substrate for seedlings was clayey loam, with the dominant texture fraction made of silt, followed by clay and fine sand, with total porosity 68.2%. Seedlings were separated in two groups: control (C (soil water regime in pots was maintained at the level of field water capacity and treated (water-stressed, WS (soil water regime was maintained in the range of wilting point and lentocapillary capacity. The photosynthetic efficiency was 0.642±0.25 and 0.522±0.024 (WS and C, respectively, which was mostly due to transplantation disturbances and sporadic leaf chlorosis. During the experiment Fv/Fm decreased in both groups (0.551±0.0100 and 0.427±0.018 in C and WS, respectively. Our results showed significant differences between stressed and control group, in regard to both observed parameters (Fv/Fm and T½. Photosynthetic efficiency of pedunculate oak seedlings was significantly affected by short-term water stress, but to a lesser extent than by sufficient watering.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  19. Molecular Dynamics Simulations of Water Nanodroplets on Silica Surfaces

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  20. Water structure and dynamics in phosphate fluorosurfactant based reverse micelle: A computer simulation study

    Science.gov (United States)

    Senapati, Sanjib; Berkowitz, Max L.

    2003-01-01

    We performed a molecular dynamics simulation on a system containing a water pool inside the reverse micelle made up of an assembly of phosphate fluorosurfactant molecules dissolved in supercritical carbon dioxide. The water molecules in the first solvation shell of the headgroup lose the water to water tetrahedral hydrogen bonded network but are strongly bonded to the surfactant headgroups. This change in inter-water hydrogen bonding in connection with the confined geometry of the reverse micelle slows down the translational and especially the rotational dynamics of water.

  1. Simulation-based optimization framework for reuse of agricultural drainage water in irrigation.

    Science.gov (United States)

    Allam, A; Tawfik, A; Yoshimura, C; Fleifle, A

    2016-05-01

    A simulation-based optimization framework for agricultural drainage water (ADW) reuse has been developed through the integration of a water quality model (QUAL2Kw) and a genetic algorithm. This framework was applied to the Gharbia drain in the Nile Delta, Egypt, in summer and winter 2012. First, the water quantity and quality of the drain was simulated using the QUAL2Kw model. Second, uncertainty analysis and sensitivity analysis based on Monte Carlo simulation were performed to assess QUAL2Kw's performance and to identify the most critical variables for determination of water quality, respectively. Finally, a genetic algorithm was applied to maximize the total reuse quantity from seven reuse locations with the condition not to violate the standards for using mixed water in irrigation. The water quality simulations showed that organic matter concentrations are critical management variables in the Gharbia drain. The uncertainty analysis showed the reliability of QUAL2Kw to simulate water quality and quantity along the drain. Furthermore, the sensitivity analysis showed that the 5-day biochemical oxygen demand, chemical oxygen demand, total dissolved solids, total nitrogen and total phosphorous are highly sensitive to point source flow and quality. Additionally, the optimization results revealed that the reuse quantities of ADW can reach 36.3% and 40.4% of the available ADW in the drain during summer and winter, respectively. These quantities meet 30.8% and 29.1% of the drainage basin requirements for fresh irrigation water in the respective seasons.

  2. Ground water flow in a desert basin: challenges of simulating transport of dissolved chromium.

    Science.gov (United States)

    Andrews, Charles B; Neville, Christopher J

    2003-01-01

    A large chromium plume that evolved from chromium releases in a valley near the Mojave River was studied to understand the processes controlling fate and migration of chromium in ground water and used as a tracer to study the dynamics of a basin and range ground water system. The valley that was studied is naturally arid with high evapotranspiration such that essentially no precipitation infiltrates to the water table. The dominant natural hydrogeologic processes are recharge to the ground water system from the Mojave River during the infrequent episodes when there is flow in the river, and ground water flow toward a playa lake where the ground water evaporates. Agricultural pumping in the valley from the mid-1930s to the 1970s significantly altered ground water flow conditions by decreasing water levels in the valley by more than 20 m. This pumping declined significantly as a result of dewatering of the aquifer, and water levels have since recovered modestly. The ground water system was modeled using MODFLOW, and chromium transport was simulated using MT3D. Several innovative modifications were made to these modeling programs to simulate important processes in this ground water system. Modifications to MODFLOW include developing a new well package that estimates pumping rates from irrigation wells at each time step based on available drawdown. MT3D was modified to account for mass trapped above the water table when the water table declines beneath nonirrigated areas and to redistribute mass to the system when water levels rise.

  3. Surface-water hydrology and runoff simulations for three basins in Pierce County, Washington

    Science.gov (United States)

    Mastin, M.C.

    1996-01-01

    The surface-water hydrology in Clear, Clarks, and Clover Creek Basins in central Pierce County, Washington, is described with a conceptual model of the runoff processes and then simulated with the Hydrological Simulation Program-FORTRAN (HSPF), a continuous, deterministic hydrologic model. The study area is currently undergoing a rapid conversion of rural, undeveloped land to urban and suburban land that often changes the flow characteristics of the streams that drain these lands. The complex interactions of land cover, climate, soils, topography, channel characteristics, and ground- water flow patterns determine the surface-water hydrology of the study area and require a complex numerical model to assess the impact of urbanization on streamflows. The U.S. Geological Survey completed this investigation in cooperation with the Storm Drainage and Surface Water Management Utility within the Pierce County Department of Public Works to describe the important rainfall-runoff processes within the study area and to develop a simulation model to be used as a tool to predict changes in runoff characteristics resulting from changes in land use. The conceptual model, a qualitative representation of the study basins, links the physical characteristics to the runoff process of the study basins. The model incorporates 11 generalizations identified by the investigation, eight of which describe runoff from hillslopes, and three that account for the effects of channel characteristics and ground-water flow patterns on runoff. Stream discharge was measured at 28 sites and precipitation was measured at six sites for 3 years in two overlapping phases during the period of October 1989 through September 1992 to calibrate and validate the simulation model. Comparison of rainfall data from October 1989 through September 1992 shows the data-collection period beginning with 2 wet water years followed by the relatively dry 1992 water year. Runoff was simulated with two basin models-the Clover

  4. Numerical simulation of high-speed turbulent water jets in air

    CERN Document Server

    Guha, Anirban; Balachandar, Ram

    2010-01-01

    Numerical simulation of high-speed turbulent water jets in air and its validation with experimental data has not been reported in the literature. It is therefore aimed to simulate the physics of these high-speed water jets and compare the results with the existing experimental works. High-speed water jets diffuse in the surrounding atmosphere by the processes of mass and momentum transfer. Air is entrained into the jet stream and the entire process contributes to jet spreading and subsequent pressure decay. Hence the physical problem is in the category of multiphase flows, for which mass and momentum transfer is to be determined to simulate the problem. Using the Eulerian multiphase and the k-\\epsilon turbulence models, plus a novel numerical model for mass and momentum transfer, the simulation was achieved. The results reasonably predict the flow physics of high-speed water jets in air.

  5. Improving SWAT for simulating water and carbon fluxes of forest ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qichun; Zhang, Xuesong

    2016-11-01

    As a widely used watershed model for assessing impacts of anthropogenic and natural disturbances on water quantity and quality, the Soil and Water Assessment Tool (SWAT) has not been extensively tested in simulating water and carbon fluxes of forest ecosystems. Here, we examine SWAT simulations of evapotranspiration (ET), net primary productivity (NPP), net ecosystem exchange (NEE), and plant biomass at ten AmeriFlux forest sites across the U.S. We identify unrealistic radiation use efficiency (Bio_E), large leaf to biomass fraction (Bio_LEAF), and missing phosphorus supply from parent material weathering as the primary causes for the inadequate performance of the default SWAT model in simulating forest dynamics. By further revising the relevant parameters and processes, SWAT’s performance is substantially improved. Based on the comparison between the improved SWAT simulations and flux tower observations, we discuss future research directions for further enhancing model parameterization and representation of water and carbon cycling for forests.

  6. Wind and Water Power Modeling and Simulation at the NWTC (Fact Sheet)

    Energy Technology Data Exchange (ETDEWEB)

    2015-02-01

    Researchers and engineers at the National Wind Technology Center have developed a wide range of computer modeling and simulation tools to support the wind and water power industries with state-of-the-art design and analysis capabilities.

  7. Effects of optimized root water uptake parameterization schemes on water and heat flux simulation in a maize agroecosystem

    Science.gov (United States)

    Cai, Fu; Ming, Huiqing; Mi, Na; Xie, Yanbing; Zhang, Yushu; Li, Rongping

    2017-04-01

    As root water uptake (RWU) is an important link in the water and heat exchange between plants and ambient air, improving its parameterization is key to enhancing the performance of land surface model simulations. Although different types of RWU functions have been adopted in land surface models, there is no evidence as to which scheme most applicable to maize farmland ecosystems. Based on the 2007-09 data collected at the farmland ecosystem field station in Jinzhou, the RWU function in the Common Land Model (CoLM) was optimized with scheme options in light of factors determining whether roots absorb water from a certain soil layer ( W x ) and whether the baseline cumulative root efficiency required for maximum plant transpiration ( W c ) is reached. The sensibility of the parameters of the optimization scheme was investigated, and then the effects of the optimized RWU function on water and heat flux simulation were evaluated. The results indicate that the model simulation was not sensitive to W x but was significantly impacted by W c . With the original model, soil humidity was somewhat underestimated for precipitation-free days; soil temperature was simulated with obvious interannual and seasonal differences and remarkable underestimations for the maize late-growth stage; and sensible and latent heat fluxes were overestimated and underestimated, respectively, for years with relatively less precipitation, and both were simulated with high accuracy for years with relatively more precipitation. The optimized RWU process resulted in a significant improvement of CoLM's performance in simulating soil humidity, temperature, sensible heat, and latent heat, for dry years. In conclusion, the optimized RWU scheme available for the CoLM model is applicable to the simulation of water and heat flux for maize farmland ecosystems in arid areas.

  8. Large eddy simulation of water flow over series of dunes

    Directory of Open Access Journals (Sweden)

    Jun LU

    2011-12-01

    Full Text Available Large eddy simulation was used to investigate the spatial development of open channel flow over a series of dunes. The three-dimensional filtered Navier-Stokes (N-S equations were numerically solved with the fractional-step method in sigma coordinates. The subgrid-scale turbulent stress was modeled with a dynamic coherent eddy viscosity model proposed by the authors. The computed velocity profiles are in good agreement with the available experimental results. The mean velocity and the turbulent Reynolds stress affected by a series of dune-shaped structures were compared and analyzed. The variation of turbulence statistics along the flow direction affected by the wavy bottom roughness has been studied. The turbulent boundary layer in a complex geographic environment can be simulated well with the proposed large eddy simulation (LES model.

  9. Developed hydraulic simulation model for water pipeline networks

    Directory of Open Access Journals (Sweden)

    A. Ayad

    2013-03-01

    Full Text Available A numerical method that uses linear graph theory is presented for both steady state, and extended period simulation in a pipe network including its hydraulic components (pumps, valves, junctions, etc.. The developed model is based on the Extended Linear Graph Theory (ELGT technique. This technique is modified to include new network components such as flow control valves and tanks. The technique also expanded for extended period simulation (EPS. A newly modified method for the calculation of updated flows improving the convergence rate is being introduced. Both benchmarks, ad Actual networks are analyzed to check the reliability of the proposed method. The results reveal the finer performance of the proposed method.

  10. Dynamics simulation of bottom high-sediment sea water movement under waves

    Institute of Scientific and Technical Information of China (English)

    Xueyi YOU; Wei LIU; Houpeng XIAO

    2009-01-01

    The movement of bottom high-sediment sea water under water waves, especially that of the high-sediment water layer close to the sea bottom, is important to the resuspension and settlement of sediment. Supposing that the high-sediment sea water is a Newtonian fluid,based on Navier-Stokes (N-S) theory, the movement of the interfaces of air-water and water-sediment water was tracked by the volume of fluid (VOF) method. The velocity field of sediment water was simulated by considering the effect of water waves. The results show that the movement of sediment water is very different from that of sea water,which provides a solid basis for understanding the resuspension and settlement of sediment and the formation of bottom stripe, and the VOF method can trace the movement of the two interfaces simultaneously; the movement of the air-water interface has a strong effect on that of the water-sediment water interface, while the effect of the water-sediment water interface movement on the air-water interface is not obvious.

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

    Institute of Scientific and Technical Information of China (English)

    YIN Bing; DONG Shun-Le

    2009-01-01

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

  12. NUMERICAL SIMULATION ON 2-D WATER-AIR TWO-PHASE FLOW OVER TOP OUTLET

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Flood discharge over top outlet of dam is simu-lated by 2-dimension water-air two-phase mathematical model.Distribution of dynamic pressure, turbulent kinetic energy (k), turbulent dissipation rate (ε) , free water surface and veloci-ty field have been obtained. The simulated results were testedby physical model, which shows that the computed results areidentical with that of the physical model.

  13. A water market simulator considering pair-wise trades between agents

    Science.gov (United States)

    Huskova, I.; Erfani, T.; Harou, J. J.

    2012-04-01

    In many basins in England no further water abstraction licences are available. Trading water between water rights holders has been recognized as a potentially effective and economically efficient strategy to mitigate increasing scarcity. A screening tool that could assess the potential for trade through realistic simulation of individual water rights holders would help assess the solution's potential contribution to local water management. We propose an optimisation-driven water market simulator that predicts pair-wise trade in a catchment and represents its interaction with natural hydrology and engineered infrastructure. A model is used to emulate licence-holders' willingness to engage in short-term trade transactions. In their simplest form agents are represented using an economic benefit function. The working hypothesis is that trading behaviour can be partially predicted based on differences in marginal values of water over space and time and estimates of transaction costs on pair-wise trades. We discuss the further possibility of embedding rules, norms and preferences of the different water user sectors to more realistically represent the behaviours, motives and constraints of individual licence holders. The potential benefits and limitations of such a social simulation (agent-based) approach is contrasted with our simulator where agents are driven by economic optimization. A case study based on the Dove River Basin (UK) demonstrates model inputs and outputs. The ability of the model to suggest impacts of water rights policy reforms on trading is discussed.

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

    Science.gov (United States)

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

    2011-04-01

    We study the water-hexane interface using molecular dynamics (MD) and polarizable charge equilibration (CHEQ) force fields. Bulk densities for TIP4P-FQ water and hexane, 1.0086±0.0002 and 0.6378±0.0001 g/cm(3), demonstrate excellent agreement with experiment. Interfacial width and interfacial tension are consistent with previously reported values. The in-plane component of the dielectric permittivity (ɛ(||)) for water is shown to decrease from 81.7±0.04 to unity, transitioning longitudinally from bulk water to bulk hexane. ɛ(||) for hexane reaches a maximum in the interface, but this term represents only a small contribution to the total dielectric constant (as expected for a non-polar species). Structurally, net orientations of the molecules arise in the interfacial region such that hexane lies slightly parallel to the interface and water reorients to maximize hydrogen bonding. Interfacial potentials due to contributions of the water and hexane are calculated to be -567.9±0.13 and 198.7±0.01 mV, respectively, giving rise to a total potential in agreement with the range of values reported from previous simulations of similar systems. Potentials of mean force (PMF) calculated for methanol, ethanol, and 1-propanol for the transfer from water to hexane indicate an interfacial free energy minimum, corresponding to the amphiphilic nature of the molecules. The magnitudes of transfer free energies were further characterized from the solvation free energies of alcohols in water and hexane using thermodynamic integration. This analysis shows that solvation free energies for alcohols in hexane are 0.2-0.3 kcal/mol too unfavorable, whereas solvation of alcohols in water is approximately 1 kcal/mol too favorable. For the pure hexane-water interfacial simulations, we observe a monotonic decrease of the water dipole moment to near-vacuum values. This suggests that the electrostatic component of the desolvation free energy is not as severe for polarizable models than for

  15. Water savings potentials of irrigation systems: dynamic global simulation

    Science.gov (United States)

    Jägermeyr, J.; Gerten, D.; Heinke, J.; Schaphoff, S.; Kummu, M.; Lucht, W.

    2015-04-01

    Global agricultural production is heavily sustained by irrigation, but irrigation system efficiencies are often surprisingly low. However, our knowledge of irrigation efficiencies is mostly confined to rough indicative estimates for countries or regions that do not account for spatio-temporal heterogeneity due to climate and other biophysical dependencies. To allow for refined estimates of global agricultural water use, and of water saving and water productivity potentials constrained by biophysical processes and also non-trivial downstream effects, we incorporated a dynamic representation of the three major irrigation systems (surface, sprinkler, and drip) into a process-based bio- and agrosphere model, LPJmL. Based on this enhanced model we provide a gridded worldmap of dynamically retrieved irrigation efficiencies reflecting differences in system types, crop types, climatic and hydrologic conditions, and overall crop management. We find pronounced regional patterns in beneficial irrigation efficiency (a refined irrigation efficiency indicator accounting for crop-productive water consumption only), due to differences in these features, with lowest values (values (> 60%) in Europe and North America. We arrive at an estimate of global irrigation water withdrawal of 2396 km3 (2004-2009 average); irrigation water consumption is calculated to be 1212 km3, of which 511 km3 are non-beneficially consumed, i.e. lost through evaporation, interception, and conveyance. Replacing surface systems by sprinkler or drip systems could, on average across the world's river basins, reduce the non-beneficial consumption at river basin level by 54 and 76%, respectively, while maintaining the current level of crop yields. Accordingly, crop water productivity would increase by 9 and 15%, respectively, and by much more in specific regions such as in the Indus basin. This study significantly advances the global quantification of irrigation systems while providing a framework for assessing

  16. INTERVAL FINITE VOLUME METHOD FOR UNCERTAINTY SIMULATION OF TWO-DIMENSIONAL RIVER WATER QUALITY

    Institute of Scientific and Technical Information of China (English)

    HE Li; ZENG Guang-ming; HUANG Guo-he; LU Hong-wei

    2004-01-01

    Under the interval uncertainties, by incorporating the discretization form of finite volume method and interval algebra theory, an Interval Finite Volume Method (IFVM) was developed to solve water quality simulation issues for two-dimensional river when lacking effective data of flow velocity and flow quantity. The IFVM was practically applied to a segment of the Xiangjiang River because the Project of Hunan Inland Waterway Multipurpose must be started working after the environmental impact assessment for it. The simulation results suggest that there exist rather apparent pollution zones of BOD5 downstream the Dongqiaogang discharger and that of COD downstream Xiaoxiangjie discharger, but the pollution sources have no impact on the safety of the three water plants located in this river segment. Although the developed IFVM is to be perfected, it is still a powerful tool under interval uncertainties for water environmental impact assessment, risk analysis, and water quality planning, etc. besides water quality simulation studied in this paper.

  17. Integrated Water Flow Model (IWFM), A Tool For Numerically Simulating Linked Groundwater, Surface Water And Land-Surface Hydrologic Processes

    Science.gov (United States)

    Dogrul, E. C.; Brush, C. F.; Kadir, T. N.

    2006-12-01

    The Integrated Water Flow Model (IWFM) is a comprehensive input-driven application for simulating groundwater flow, surface water flow and land-surface hydrologic processes, and interactions between these processes, developed by the California Department of Water Resources (DWR). IWFM couples a 3-D finite element groundwater flow process and 1-D land surface, lake, stream flow and vertical unsaturated-zone flow processes which are solved simultaneously at each time step. The groundwater flow system is simulated as a multilayer aquifer system with a mixture of confined and unconfined aquifers separated by semiconfining layers. The groundwater flow process can simulate changing aquifer conditions (confined to unconfined and vice versa), subsidence, tile drains, injection wells and pumping wells. The land surface process calculates elemental water budgets for agricultural, urban, riparian and native vegetation classes. Crop water demands are dynamically calculated using distributed soil properties, land use and crop data, and precipitation and evapotranspiration rates. The crop mix can also be automatically modified as a function of pumping lift using logit functions. Surface water diversions and groundwater pumping can each be specified, or can be automatically adjusted at run time to balance water supply with water demand. The land-surface process also routes runoff to streams and deep percolation to the unsaturated zone. Surface water networks are specified as a series of stream nodes (coincident with groundwater nodes) with specified bed elevation, conductance and stage-flow relationships. Stream nodes are linked to form stream reaches. Stream inflows at the model boundary, surface water diversion locations, and one or more surface water deliveries per location are specified. IWFM routes stream flows through the network, calculating groundwater-surface water interactions, accumulating inflows from runoff, and allocating available stream flows to meet specified or

  18. Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; Schiøtt, Birgit

    2007-01-01

    used all-atom MD simulation and free energy calculations to study the initial phase of this process. We have calculated the free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine. We show that tetramer formation is indeed only...

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

    Science.gov (United States)

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

    2016-11-01

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

  20. Planning for Regional Water Resources in Northwest China Using a Dynamic Simulation Model

    Science.gov (United States)

    Chen, C.; Kalra, A.; Ahmad, S.

    2014-12-01

    Problem of water scarcity is prominent in northwest China due to its typical desert climate. Exceedence of sustainable yield of groundwater resources has resulted in groundwater depletion, which has raised a series of issues such as drying wells, increasing pumping costs and environmental damage. With a rapid agricultural and economic development, population increase has added extra stress on available water resources by increasing municipal, agricultural and industrial demands. This necessitates efficient water resources management strategies with better understanding of the causes of water stress and options for sustainable development of economy and management of environment. This study focuses on simulating the water supply and demand, under the influence of changing climate, for Shanshan County, located in northwest of China. A dynamic simulation model is developed using the modeling tool Stella for monthly water balance for the period ranging from 2000-2030. Different future water demand and supply scenarios are developed to represent: (1) base scenario- with current practices; (2) change of the primary water source; (3) improvement of irrigation efficiency; (4) reduction of irrigation area; and (5) reduction of industrial water demand. The results indicate that besides growing demand, the low water use efficiency and low level of water reuse are the primary concerns for water scarcity. Groundwater recharge and abstraction could be balanced by 2030, by reducing industrial demand by 50% and using high efficiency irrigation for agriculture. The model provided a better understanding of the effect of different policies and can help in identifying water resources management strategies.

  1. Research framework of integrated simulation on bilateral interaction between water cycle and socio-economic development

    Science.gov (United States)

    Hao, C. F.; Yang, X. L.; Niu, C. W.; Jia, Y. W.

    2016-08-01

    The mechanism of bilateral interaction between natural water cycle evolution and socio-economic development has been obscured in current research due to the complexity of the hydrological process and the socio-economic system. The coupling of economic model CGE (Computable General Equilibrium) and distributed hydrological model WEP (Water and Energy transfer Processes) provides a model-based tool for research on response and feedback of water cycle and social development, as well as economic prospects under the constraint of water resources. On one hand, water policies, such as water use limitation and water price adjustment under different levels of socio-economic development, are to be evaluated by CGE model as assumed conditions and corresponding results of water demand could be put into WEP model to simulate corresponding response during the whole process of water cycle. On the other hand, variation of available water resources quantity under different scenarios simulated by WEP model may provide proper limitation for water demand in CGE model, and corresponding change of economic factors could indicate the influence of water resources constraints on socio-economic development. The research is believed to be helpful for better understanding of bilateral interaction between water and society.

  2. Oxidation behavior of Incoloy 800 under simulated supercritical water conditions

    Energy Technology Data Exchange (ETDEWEB)

    Fulger, M. [Institute for Nuclear Research Pitesti, POB 78, Campului Street, No. 1, 115400 Mioveni (Romania)], E-mail: manuela.fulger@nuclear.ro; Ohai, D.; Mihalache, M.; Pantiru, M. [Institute for Nuclear Research Pitesti, POB 78, Campului Street, No. 1, 115400 Mioveni (Romania); Malinovschi, V. [University of Pitesti, Research Center for Advanced Materials, Targul din Vale Street, No. 1, 110040 Pitesti (Romania)

    2009-03-31

    For a correct design of supercritical water-cooled reactor (SCWR) components, data regarding the behavior of candidate materials in supercritical water are necessary. Corrosion has been identified as a critical problem because the high temperature and the oxidative nature of supercritical water may accelerate the corrosion kinetics. The goal of this paper is to investigate the oxidation behavior of Incoloy 800 exposed in autoclaves under supercritical water conditions for up to 1440 h. The exposure conditions (thermal deaerated water, temperatures of 723, 773, 823 and 873 K and a pressure of 25 MPa) have been selected as relevant for a supercritical power plant concept. To investigate the structural changes of the oxide films, X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray spectrometry (EDX) and electrochemical impedance spectroscopy (EIS) analyses were used. Results show changes in the oxides chemical composition, microstructure and thickness versus testing conditions (pressure, temperature and time). The oxide films are composed of two layers: an outer layer enriched in Fe oxide and an inner layer enriched in Cr and Ni oxides corresponding to small cavities supposedly due to internal oxidation.

  3. Water interaction with laboratory-simulated fossil fuel combustion particles.

    Science.gov (United States)

    Popovicheva, O B; Kireeva, E D; Shonija, N K; Khokhlova, T D

    2009-10-01

    To clarify the impact of fossil fuel combustion particles' composition on their capacity to take up water, we apply a laboratory approach in which the method of deposition of compounds, identified in the particulate coverage of diesel and aircraft engine soot particles, is developed. It is found that near-monolayer organic/inorganic coverage of the soot particles may be represented by three groups of fossil fuel combustion-derived particulate matter with respect to their Hansh's coefficients related to hydrophilic properties. Water adsorption measurements show that nonpolar organics (aliphatic and aromatic hydrocarbons) lead to hydrophobization of the soot surface. Acidic properties of organic compounds such as those of oxidized PAHs, ethers, ketones, aromatic, and aliphatic acids are related to higher water uptake, whereas inorganic acids and ionic compounds such as salts of organic acids are shown to be responsible for soot hydrophilization. This finding allows us to quantify the role of the chemical identity of soot surface compounds in water uptake and the water interaction with fossil fuel combustion particles in the humid atmosphere.

  4. Effects of sulphuric acid and acidifying ammonium deposition on water quality and vegetation of simulated soft water ecosystem

    Energy Technology Data Exchange (ETDEWEB)

    Schuurkes, J.A.A.R.; Heck, I.C.C; Hesen, P.L.G.M.; Leuven, R.S.E.W.; Roelofs, J.G.M.

    1986-11-01

    In a greenhouse, seven identical mini-ecosystems, simulating soft water ponds, were exposed to different types of artificial rain water. The effects of rain water containing H/sub 2/SO/sub 4/ and nitrate, and rain water containing ammonium sulphate on water quality and vegetation were studied and compared. Causal relations were established between rain water quality, water chemistry and changes in floristic composition. Ammonium sulphate deposition, particularly, strongly affected water quality and vegetation development. Although ammonium sulphate deposition was only slightly acid, due to nitrification it acted as an important acid source, causing acidification to pH 3.8. Under acidified conditions, ammonium sulphate deposition led to a luxuriant growth of Juncus bulbosus and Agrostis canina. In the mini-ecosystems, H/sub 2/SO/sub 4/ deposition with a pH of 3.5 only decreased the pH of the water to 5.1 within 1 yr, the acidification of water appeared to be coupled with changes in alkalinity, sulphate, Al, Cd, Ca, Mg, K and inorganic-N. It is concluded that in NH/sub 3/-affected regions in The Netherlands, the high atmospheric deposition of ammonium sulphate probably contributes to a large extent in the acidification, eutrophication and floristic changes of oligotrophic soft waters. 10 references.

  5. CHEMICAL REACTIONS SIMULATED BY GROUND-WATER-QUALITY MODELS.

    Science.gov (United States)

    Grove, David B.; Stollenwerk, Kenneth G.

    1987-01-01

    Recent literature concerning the modeling of chemical reactions during transport in ground water is examined with emphasis on sorption reactions. The theory of transport and reactions in porous media has been well documented. Numerous equations have been developed from this theory, to provide both continuous and sequential or multistep models, with the water phase considered for both mobile and immobile phases. Chemical reactions can be either equilibrium or non-equilibrium, and can be quantified in linear or non-linear mathematical forms. Non-equilibrium reactions can be separated into kinetic and diffusional rate-limiting mechanisms. Solutions to the equations are available by either analytical expressions or numerical techniques. Saturated and unsaturated batch, column, and field studies are discussed with one-dimensional, laboratory-column experiments predominating. A summary table is presented that references the various kinds of models studied and their applications in predicting chemical concentrations in ground waters.

  6. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

    Energy Technology Data Exchange (ETDEWEB)

    Jakobtorweihen, S., E-mail: jakobtorweihen@tuhh.de; Ingram, T.; Gerlach, T.; Smirnova, I. [Institute of Thermal Separation Processes, Hamburg University of Technology, Eissendorfer Str. 38, 21073 Hamburg (Germany); Zuniga, A. Chaides; Keil, F. J. [Institute of Chemical Reaction Engineering, Hamburg University of Technology, Eissendorfer Str. 38, 21073 Hamburg (Germany)

    2014-07-28

    Quantitative predictions of biomembrane/water partition coefficients are important, as they are a key property in pharmaceutical applications and toxicological studies. Molecular dynamics (MD) simulations are used to calculate free energy profiles for different solutes in lipid bilayers. How to calculate partition coefficients from these profiles is discussed in detail and different definitions of partition coefficients are compared. Importantly, it is shown that the calculated coefficients are in quantitative agreement with experimental results. Furthermore, we compare free energy profiles from MD simulations to profiles obtained by the recent method COSMOmic, which is an extension of the conductor-like screening model for realistic solvation to micelles and biomembranes. The free energy profiles from these molecular methods are in good agreement. Additionally, solute orientations calculated with MD and COSMOmic are compared and again a good agreement is found. Four different solutes are investigated in detail: 4-ethylphenol, propanol, 5-phenylvaleric acid, and dibenz[a,h]anthracene, whereby the latter belongs to the class of polycyclic aromatic hydrocarbons. The convergence of the free energy profiles from biased MD simulations is discussed and the results are shown to be comparable to equilibrium MD simulations. For 5-phenylvaleric acid the influence of the carboxyl group dihedral angle on free energy profiles is analyzed with MD simulations.

  7. Wettability-Water/brine Film Thickness Relationship and the Effect of Supercritical CO2 Pre-contact for CO2/brine/mineral Systems under Geologic CO2 Sequestration Conditions: Insights from Molecular Dynamics Simulations

    Science.gov (United States)

    Chen, C.; Song, Y.; Li, W.

    2016-12-01

    Injection CO2 into deep saline aquifers is one of the main options for geologic carbon sequestration (GCS). A successful GCS in saline aquifers requires full knowledge about CO2/brine/mineral systems under sequestration conditions to reduce uncertainties during subsurface storage of CO2. Adsorbed water film thickness and wettability on mineral surfaces are two key characteristics for CO2/brine/mineral systems. Wettability and water/brine film thickness have been measured experimentally and predicted by molecular simulation (MD) studies. However, these studies only consider the films apart from contact angles. Investigations on wettability for CO2/brine/mineral systems only consider contact angles without measurements on film thickness. The relationship between film thicknesses with water contact angles is open to questions. In this paper, MD simulations have been performed to investigate the interrelationship between water film thicknesses and water contact angles. Three silica surfaces with different silanol group number densities (Q3, Q3-50%, Q3/Q4) were selected to represent silica surfaces with different wettabilities. We found that as water contact angle increases, the film thickness decreases. We also studied the effect of CO2-mineral pre-contact and found that: on Q3 surface, if a CO2 bubble was pre-contacted with the surface, it can remain on the surface without forming a water film; however, if a CO2 bubble was placed certain distances away from the surface, it formed a water film. Wettability analysis revealed that on the same surface, water contact angle was larger when there was no water film. These findings show that on some silica surfaces, water film may be destroyed by supercritical CO2 even the silica surfaces are hydrophilic. A water film rupture mechanism was propsed for CO2 adhesion on mineral surfaces [Wang (2013) Environ. Sci. Technol. 47, 11858; Zhang (2016) Environ. Sci. Technol. Lett. 10.1021/acs.estlett.5b00359]. The rupture of water film

  8. Evaluation of measured and simulated cotton water use and yield under full and deficit irrigation

    Science.gov (United States)

    The AquaCrop model simulates crop growth, water use, yield, and water use efficiency of several crops including cotton. The model is intended to be useful for irrigation planning and management, and it attempts to balance simplicity and accuracy so that it can be applied in locations where weather a...

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

    NARCIS (Netherlands)

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

    1996-01-01

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

  10. An Integrated Model for Simulating Regional Water Resources Based on Total Evapotranspiration Control Approach

    Directory of Open Access Journals (Sweden)

    Jianhua Wang

    2014-01-01

    Full Text Available Total evapotranspiration and water consumption (ET control is considered an efficient method for water management. In this study, we developed a water allocation and simulation (WAS model, which can simulate the water cycle and output different ET values for natural and artificial water use, such as crop evapotranspiration, grass evapotranspiration, forest evapotranspiration, living water consumption, and industry water consumption. In the calibration and validation periods, a “piece-by-piece” approach was used to evaluate the model from runoff to ET data, including the remote sensing ET data and regional measured ET data, which differ from the data from the traditional hydrology method. We applied the model to Tianjin City, China. The Nash-Sutcliffe efficiency (Ens of the runoff simulation was 0.82, and its regression coefficient R2 was 0.92. The Nash-Sutcliffe Efficiency (Ens of regional total ET simulation was 0.93, and its regression coefficient R2 was 0.98. These results demonstrate that ET of irrigation lands is the dominant part, which accounts for 53% of the total ET. The latter is also a priority in ET control for water management.

  11. Modeling and Simulations in Photoelectrochemical Water Oxidation: From Single Level to Multiscale Modeling

    NARCIS (Netherlands)

    Zhang, X.; Bieberle, A.

    2016-01-01

    This review summarizes recent developments, challenges, and strategies in the field of modeling and simulations of photoelectrochemical (PEC) water oxidation. We focus on water splitting by metal-oxide semiconductors and discuss topics such as theoretical calculations of light absorption, band gap/b

  12. Evaluation of aqua crop simulation of early season evaporation and water flux in a semiarid environment

    Science.gov (United States)

    The AquaCrop model of crop growth, water use, yield and water use efficiency (WUE) is intended for use by extension personnel, farm and irrigation managers, planners and other less advanced users of simulation models in irrigation planning and scheduling. It could be useful in estimating changes in ...

  13. Modelling and simulation of a nitrification biofilter for drinking water ...

    African Journals Online (AJOL)

    2005-09-30

    Sep 30, 2005 ... surface area available for biofilm growth is 17 424 m². In the biofilter the total water volume for nitrification is 14.52 m³. The raw canal ... diffusion limitation. The major ..... First the effect of reducing the aeration of the biofilter was inves- tigated. ... day 200. Outside this period the DO ammonium ratio is higher.

  14. Transient water stress in a vegetation canopy - Simulations and measurements

    Science.gov (United States)

    Carlson, Toby N.; Belles, James E.; Gillies, Robert R.

    1991-01-01

    Consideration is given to observational and modeling evidence of transient water stress, the effects of the transpiration plateau on the canopy radiometric temperature, and the factors responsible for the onset of the transpiration plateau, such as soil moisture. Attention is also given to the point at which the transient stress can be detected by remote measurement of surface temperature.

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  16. Accelerated Monte Carlo simulation on the chemical stage in water radiolysis using GPU

    Science.gov (United States)

    Tian, Zhen; Jiang, Steve B.; Jia, Xun

    2017-04-01

    The accurate simulation of water radiolysis is an important step to understand the mechanisms of radiobiology and quantitatively test some hypotheses regarding radiobiological effects. However, the simulation of water radiolysis is highly time consuming, taking hours or even days to be completed by a conventional CPU processor. This time limitation hinders cell-level simulations for a number of research studies. We recently initiated efforts to develop gMicroMC, a GPU-based fast microscopic MC simulation package for water radiolysis. The first step of this project focused on accelerating the simulation of the chemical stage, the most time consuming stage in the entire water radiolysis process. A GPU-friendly parallelization strategy was designed to address the highly correlated many-body simulation problem caused by the mutual competitive chemical reactions between the radiolytic molecules. Two cases were tested, using a 750 keV electron and a 5 MeV proton incident in pure water, respectively. The time-dependent yields of all the radiolytic species during the chemical stage were used to evaluate the accuracy of the simulation. The relative differences between our simulation and the Geant4-DNA simulation were on average 5.3% and 4.4% for the two cases. Our package, executed on an Nvidia Titan black GPU card, successfully completed the chemical stage simulation of the two cases within 599.2 s and 489.0 s. As compared with Geant4-DNA that was executed on an Intel i7-5500U CPU processor and needed 28.6 h and 26.8 h for the two cases using a single CPU core, our package achieved a speed-up factor of 171.1-197.2.

  17. Simulations of structural and dynamic anisotropy in nano-confined water between parallel graphite plates.

    Science.gov (United States)

    Mosaddeghi, Hamid; Alavi, Saman; Kowsari, M H; Najafi, Bijan

    2012-11-14

    We use molecular dynamics simulations to study the structure, dynamics, and transport properties of nano-confined water between parallel graphite plates with separation distances (H) from 7 to 20 Å at different water densities with an emphasis on anisotropies generated by confinement. The behavior of the confined water phase is compared to non-confined bulk water under similar pressure and temperature conditions. Our simulations show anisotropic structure and dynamics of the confined water phase in directions parallel and perpendicular to the graphite plate. The magnitude of these anisotropies depends on the slit width H. Confined water shows "solid-like" structure and slow dynamics for the water layers near the plates. The mean square displacements (MSDs) and velocity autocorrelation functions (VACFs) for directions parallel and perpendicular to the graphite plates are calculated. By increasing the confinement distance from H = 7 Å to H = 20 Å, the MSD increases and the behavior of the VACF indicates that the confined water changes from solid-like to liquid-like dynamics. If the initial density of the water phase is set up using geometric criteria (i.e., distance between the graphite plates), large pressures (in the order of ~10 katm), and large pressure anisotropies are established within the water. By decreasing the density of the water between the confined plates to about 0.9 g cm(-3), bubble formation and restructuring of the water layers are observed.

  18. Simulating potential water grabbing from large-scale land acquisitions in Africa}

    Science.gov (United States)

    Li Johansson, Emma; Fader, Marianela; Seaquist, Jonathan W.; Nicholas, Kimberly A.

    2017-04-01

    The potential high level of water appropriation in Africa by foreign companies might pose high socioenvironmental challenges, including overconsumption of water and conflicts and tensions over water resources allocation. We will present a study published recently in the Proceedings of the National Academy of Sciences11 of the USA, where we simulated green and blue water demand and crop yields of large-scale land acquisitions in several African countries. Green water refers to precipitation stored in soils and consumed by plants through evapotranspiration, while blue water is extracted from rivers, lakes, aquifers, and dams. We simulated seven irrigation scenarios, and compared these data with two baseline scenarios of staple crops representing previous water demand. The results indicate that the green and blue water use is 39% and 76-86% greater, respectively, for crops grown on acquired land compared with the baseline of common staple crops, showing that land acquisitions substantially increase water demands. We also found that most land acquisitions are planted with crops such as sugarcane, jatropha, and eucalyptus, that demand volumes of water >9,000 m3ṡha-1. And even if the most efficient irrigation systems were implemented, 18% of the land acquisitions, totaling 91,000 ha, would still require more than 50% of water from blue water sources.

  19. Computation of shear viscosity of colloidal suspensions by SRD-MD

    Energy Technology Data Exchange (ETDEWEB)

    Laganapan, A. M. K.; Videcoq, A., E-mail: arnaud.videcoq@unilim.fr; Bienia, M. [SPCTS, UMR 7315, ENSCI, CNRS, Centre Européen de la Céramique, 12 rue Atlantis, 87068 Limoges Cedex (France); Ala-Nissila, T. [COMP CoE at the Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FIN-00076 Aalto, Espoo (Finland); Department of Physics, Brown University, Providence, Rhode Island 02912-1843 (United States); Bochicchio, D.; Ferrando, R. [Dipartimento di Fisica and CNR-IMEM, via Dodecaneso 33, Genova I-16146 (Italy)

    2015-04-14

    The behaviour of sheared colloidal suspensions with full hydrodynamic interactions (HIs) is numerically studied. To this end, we use the hybrid stochastic rotation dynamics-molecular dynamics (SRD-MD) method. The shear viscosity of colloidal suspensions is computed for different volume fractions, both for dilute and concentrated cases. We verify that HIs help in the collisions and the streaming of colloidal particles, thereby increasing the overall shear viscosity of the suspension. Our results show a good agreement with known experimental, theoretical, and numerical studies. This work demonstrates the ability of SRD-MD to successfully simulate transport coefficients that require correct modelling of HIs.

  20. Numerical simulation of the floor water-inrush in working face influenced by fault structure

    Institute of Scientific and Technical Information of China (English)

    CHENG Jiu-long; CAO Ji-sheng; XU Jin-peng; YU Shi-jian; TIAN Li

    2007-01-01

    Used numerical simulation method to study the floor water-inrush mechanism in working face which was influenced by fault structure, and set up many kinds of models and performs numerical calculation by fully using large finite element soft-ANSYS and element birth-death method. The results show that the more high the underground water pressure, the more big the floor displacement and possibility of water-inrush; the floor which has fault structure is more prone to water-inrush than the floor which not has fault structure, the floor which has multi-groups cracks is more prone to water-inrush than the floor which has single-group cracks. The numerical simulation result forecasts the water-inrush in working face preferably.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2016-01-15

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

  2. Molecular dynamics simulation of impact test

    Energy Technology Data Exchange (ETDEWEB)

    Akahoshi, Y. [Kyushu Inst. of Tech., Kitakyushu, Fukuoka (Japan); Schmauder, S.; Ludwig, M. [Stuttgart Univ. (Germany). Staatliche Materialpruefungsanstalt

    1998-11-01

    This paper describes an impact test by molecular dynamics (MD) simulation to evaluate embrittlement of bcc Fe at different temperatures. A new impact test model is developed for MD simulation. The typical fracture behaviors show transition from brittle to ductile fracture, and a history of the impact loads also demonstrates its transition. We conclude that the impact test by MD could be feasible. (orig.)

  3. Integrative Medicine Program- MD Anderson Cancer Center

    Directory of Open Access Journals (Sweden)

    Richard T Lee

    2012-06-01

    Full Text Available The Integrative Medicine Program at MD Anderson Cancer Center was first established in 1998.  Our mission is to empower patients with cancer and their families to become active partners in their own physical, psycho-spiritual, and social health through personalized education and evidenced-based clinical care to optimize health, quality of life, and clinical outcomes across the cancer continuum.  The program consists of three main components: clinical care, research, and education.  The Integrative Medicine Center provides clinical services to patients through individual and group programs.  The clinical philosophy of the center is to work collaboratively with the oncology teams to build comprehensive and integrative care plans that are personalized, evidence-based, and safe with the goal of improving clinical outcomes.  The individual services comprise of integrative oncology consultation, acupuncture, meditation, music therapy, nutrition, and oncology massage.  The center also provides a variety of group programs including meditation, yoga, tai chi, cooking classes and others.  Over the past 13 years, over 70,000 patients and families have participated in services and programs offered by the center.  The research portfolio focuses on three main areas: mind-body interventions, acupuncture, and meditation.  This lecture will focus on providing an overview of the Integrative Medicine Program at MD Anderson with a focus on the clinical services provided.  Participants will learn about the integrative clinical model and how this is applied to the care of cancer patients at MD Anderson Cancer Center.  Current and future research topics will be discussed as well as patient cases.

  4. Dawbeney Turbervile, MD (1612-1696).

    Science.gov (United States)

    Simunovic, Matthew P

    2012-03-01

    The year 2012 marks the quatercentenary of the birth of Dawbeney Turbervile,MD(1612-1696), one-time Royalist soldier and later ophthalmologist to England’s Princess Anne, the diarist Samuel Pepys, the natural philosopher Robert Boyle, and the astronomer Walter Pope. Turbervile is remarkable for many reasons: He specialized at a time when generalization was prized; though he was a qualified physician, he also practiced the trade of surgery. Furthermore, he provided in his communications with the Royal Society early descriptions of achromatopsia, ocular foreign body removal with a magnet, and tic doloreaux. He is a forebear worth remembering

  5. MD Test of a Ballistic Optics

    CERN Document Server

    Garcia-Tabares Valdivieso, Ana; Salvachua Ferrando, Belen Maria; Skowronski, Piotr Krzysztof; Solfaroli Camillocci, Matteo; Tomas Garcia, Rogelio; Wenninger, Jorg; Coello De Portugal - Martinez Vazquez, Jaime Maria; CERN. Geneva. ATS Department

    2016-01-01

    The ballistic optics is designed to improve the understanding of optical errors and BPM systematic effects in the critical triplet region. The particularity of that optics is that the triplet is switched off, effectively transforming the triplets on both sides of IR1 and IR5 into drift spaces. Advantage can be taken from that fact to localize better errors in the Q4-Q5-triplet region. During this MD this new optics was tested for the first time at injection with beam 2.

  6. Orlando C. Kirton, MD, FACS, FCCM, FCCP.

    Science.gov (United States)

    Pyrtek, Ludwig J

    2007-12-01

    The chair is named for Ludwig J. Pyrtek, MD, an esteemed surgeon at Hartford Hospital, who was devoted to the care of his patients and was an outstanding educator within his chosen field. A unique aspect of the chair is that its income is not used to support the salary of the director but is used to enhance the education activities of the department, such as the purchasing of state-of-the-art teaching devices, support of surgical resident research activities, educational travel for residents and honoraria for nationally/internationally known clinicians/scientists to speak at grand rounds.

  7. Operational simulation of continental water masses consistent with atmospheric and oceanic data.

    OpenAIRE

    Robert Dill; Walter, C.;  

    2008-01-01

    Operational global mass transport data of the atmosphere and the oceans are widely used for studies of earth rotation excitation and gravity field simulations and are essential for GRACE dealising purposes, too. Seasonal and short periodic variations are also caused by continental water mass redistributions. In order to account for the continental hydrology processes as well and to close the global water cycle, continental water mass storage fields and fluxes are needed in the same operationa...

  8. Hydration and Nanoconfined Water: Insights from Computer Simulations.

    Science.gov (United States)

    Alarcón, Laureano M; Rodríguez Fris, J A; Morini, Marcela A; Sierra, M Belén; Accordino, S A; Montes de Oca, J M; Pedroni, Viviana I; Appignanesi, Gustavo A

    2015-01-01

    The comprehension of the structure and behavior of water at interfaces and under nanoconfinement represents an issue of major concern in several central research areas like hydration, reaction dynamics and biology. From one side, water is known to play a dominant role in the structuring, the dynamics and the functionality of biological molecules, governing main processes like protein folding, protein binding and biological function. In turn, the same principles that rule biological organization at the molecular level are also operative for materials science processes that take place within a water environment, being responsible for the self-assembly of molecular structures to create synthetic supramolecular nanometrically-sized materials. Thus, the understanding of the principles of water hydration, including the development of a theory of hydrophobicity at the nanoscale, is imperative both from a fundamental and an applied standpoint. In this work we present some molecular dynamics studies of the structure and dynamics of water at different interfaces or confinement conditions, ranging from simple model hydrophobic interfaces with different geometrical constraints (in order to single out curvature effects), to self-assembled monolayers, proteins and phospholipid membranes. The tendency of the water molecules to sacrifice the lowest hydrogen bond (HB) coordination as possible at extended interfaces is revealed. This fact makes the first hydration layers to be highly oriented, in some situations even resembling the structure of hexagonal ice. A similar trend to maximize the number of HBs is shown to hold in cavity filling, with small subnanometric hydrophobic cavities remaining empty while larger cavities display an alternation of filled and dry states with a significant inner HB network. We also study interfaces with complex chemical and geometrical nature in order to determine how different conditions affect the local hydration properties. Thus, we show some

  9. Simulation of upward flux from shallow water-table using UPFLOW model

    Directory of Open Access Journals (Sweden)

    M. H. Ali

    2013-11-01

    Full Text Available The upward movement of water by capillary rise from shallow water-table to the root zone is an important incoming flux. For determining exact amount of irrigation requirement, estimation of capillary flux or upward flux is essential. Simulation model can provide a reliable estimate of upward flux under variable soil and climatic conditions. In this study, the performance of model UPFLOW to estimate upward flux was evaluated. Evaluation of model performance was performed with both graphical display and statistical criteria. In distribution of simulated capillary rise values against observed field data, maximum data points lie around the 1:1 line, which means that the model output is reliable and reasonable. The coefficient of determination between observed and simulated values was 0.806 (r = 0.93, which indicates a good inter-relation between observed and simulated values. The relative error, model efficiency, and index of agreement were found as 27.91%, 85.93% and 0.96, respectively. Considering the graphical display of observed and simulated upward flux and statistical indicators, it can be concluded that the overall performance of the UPFLOW model in simulating actual upward flux from a crop field under variable water-table condition is satisfactory. Thus, the model can be used to estimate capillary rise from shallow water-table for proper estimation of irrigation requirement, which would save valuable water from over-irrigation.

  10. A BOD-DO coupling model for water quality simulation by artificial neural network

    Institute of Scientific and Technical Information of China (English)

    郭劲松; LONG; Tengrui; 等

    2002-01-01

    A one-dimensional BOD-DO coupling model for water quality simulation is presented,which adopts Streeter-Phelps equations and the theory of back-propagation artificial neural network.The water quality data of Yangtze River in the Chongqing region in the year of 1989 are divided into 5 groups and used in the learning and testing courses of this model.The result shows that such model is feasible for water quality simulation and is more accurate than traditional models.

  11. 33 CFR 334.140 - Chesapeake Bay; U.S. Army Proving Ground Reservation, Aberdeen, Md.

    Science.gov (United States)

    2010-07-01

    ....140 Chesapeake Bay; U.S. Army Proving Ground Reservation, Aberdeen, Md. (a) Restricted area defined. The following indicates the limits of the waters of or adjacent to the Aberdeen Proving Ground, Maryland, and inside of which boundaries will lie the restricted area known as the Aberdeen Proving...

  12. Simulations of seasonal variations of stable water isotopes in land surface process model CLM

    Institute of Scientific and Technical Information of China (English)

    ZHANG XinPing; WANG XiaoYun; YANG ZongLiang; NIU GuoYue; Xie ZiChu

    2009-01-01

    In this study, we simulated and analyzed the monthly variations of stable water isotopes in different reservoirs at Manaus, Brazil, using the Community Land Model (CLM) that incorporates stable isotopic effects as a diagnostic tool for understanding stable water isotopic processes, filling the observational data gaps and predicting hydrometeorological processes. The simulation results show that the δO values in precipitation, vapor and surface runoff have distinct seasonality with the marked negative correlations with corresponding water amount. Compared with the survey results by the International Atomic Energy Agency (IAEA) in co-operation with the World Meteorological Organization (WMO), the simulations by CLM reveal the similar temporal distributions of the δO in precipitation. Moreover, the simulated amount effect between monthly δO and monthly precipitation amount, and MWL (meteoric water line) are all close to the measured values. However, the simulated seasonal difference in the δO in precipitation is distinctly smaller than observed one, and the simulated temporal distribution of the 8180 in precipitation displays the ideal bimodal seasonality rather than the observed single one. These mismatches are possibly related to the simulation capacity and the veracity in forcing data.

  13. Evaluating the performance of Lyzenga's water column correction in case-1 coral reef water using a simulated Wolrdview-2 imagery

    Science.gov (United States)

    Dwi Mandini Manessa, Masita; Haidar, Muhammad; Budhiman, Syarif; Winarso, Gatot; Kanno, Ariyo; Sagawa, Tatsuyuki; Sekine, Masahiko

    2016-11-01

    This study identified the performance of Lyzenga water column correction under controlled condition of noise, water quality, and bottom type diversity. We build a simulated multispectral imagery, represent the subsurface reflectance of coral reef environment that receives by Worldview-2 satellite. The evaluation was performed to two different subsurface reflectance: Lee et al.’s and Maritonia et al.’s radiative transfer model. As a result, in the case of simple Maritonia et al.’s reflectance model, it shows that the effect of the water column is removable. However, if the actual just above surface reflectance is as more complex as Lee et al.’s model, then the Lyzenga's water column method could reduce the effect of water attenuation but not removed. In fact, based on the mathematical presentation of Lyzenga's model on simulation reflectance formula the effect of depth and water attenuation are in multiplication function. Thus, even after the correction, the water column attenuation effect stillremain.

  14. Water and heat transport in hilly red soil of southern China: Ⅱ. Modeling and simulation

    Institute of Scientific and Technical Information of China (English)

    LU Jun; HUANG Zhi-zhen; HAN Xiao-fei

    2005-01-01

    Simulation models of heat and water transport have not been rigorously tested for the red soils of southern China.Based on the theory of nonisothermal water-heat coupled transfer, a simulation model, programmed in Visual Basic 6.0, was developed to predict the coupled transfer of water and heat in hilly red soil. A series of soil column experiments for soil water and heat transfer, including soil columns with closed and evaporating top ends, were used to test the simulation model. Results showed that in the closed columns, the temporal and spatial distribution of moisture and heat could be very well predicted by the model,while in the evaporating columns, the simulated soil water contents were somewhat different from the observed ones. In the heat flow equation by Taylor and Lary (1964), the effect of soil water evaporation on the heat flow is not involved, which may be the main reason for the differences between simulated and observed results. The predicted temperatures were not in agreement with the observed one with thermal conductivities calculated by de Vries and Wierenga equations, so that it is suggested that Kh, soil heat conductivity, be multiplied by 8.0 for the first 6.5 h and by 1.2 later on. Sensitivity analysis of soil water and heat coefficients showed that the saturated hydraulic conductivity, Ks, and the water diffusivity, D(θ), had great effects on soil water transport; the variation of soil porosity led to the difference of soil thermal properties, and accordingly changed temperature redistribution,which would affect water redistribution.

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

    Science.gov (United States)

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

    2012-07-01

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

  16. Global network of embodied water flow by systems input-output simulation

    Institute of Scientific and Technical Information of China (English)

    Zhanming CHEN; Guoqian CHEN; Xiaohua XIA; Shiyun XU

    2012-01-01

    The global water resources network is simulated in the present work for the latest target year with statistical data available and with the most detailed data disaggregation.A top-down approach of systems inputoutput simulation is employed to track the embodied water flows associated with economic flows for the globalized economy in 2004.The numerical simulation provides a database of embodied water intensities for all economic commodities from 4928 producers,based on which the differences between direct and indirect water using efficiencies at the global scale are discussed.The direct and embodied water uses are analyzed at continental level.Besides,the commodity demand in terms of monetary expenditure and the water demand in terms of embodied water use are compared for the world as well as for three major water using regions,i.e.,India,China,and the United States.Results show that food product contributes to a significant fraction for water demand,despite the value varies significantly with respect to the economic status of region.

  17. Eco-hydrological process simulations within an integrated surface water-groundwater model

    DEFF Research Database (Denmark)

    Butts, Michael; Loinaz, Maria Christina; Bauer-Gottwein, Peter

    2014-01-01

    . In the second, we examine ecological impacts related to the flows and temperatures in the Silver Creek ecosystem that are important for the fish habitat. The Silver Creek ecosystem is controlled by large-scale interactions of surface water and groundwater systems in the Lower Wood River Valley, USA......Integrated water resources management requires tools that can quantify changes in groundwater, surface water, water quality and ecosystem health, as a result of changes in catchment management. To address these requirements we have developed an integrated eco-hydrological modelling framework...... water and ground water are important for the ecosystem. In the first, simulations are performed to understand the importance of surface water-groundwater interactions for a restored riparian wetland on the Odense River in Denmark as part of a larger investigation of water quality and nitrate retention...

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

    DEFF Research Database (Denmark)

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

    2012-01-01

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