WorldWideScience

Sample records for water md simulations

  1. Water at silica/liquid water interfaces investigated by DFT-MD simulations

    Science.gov (United States)

    Gaigeot, Marie-Pierre

    This talk is dedicated to probing the microscopic structural organization of water at silica/liquid water interfaces including electrolytes by first principles DFT-based molecular dynamics simulations (DFT-MD). We will present our very recent DFT-MD simulations of electrolytic (KCl, NaCl, NaI) silica/liquid water interfaces in order to unravel the intertwined structural properties of water and electrolytes at the crystalline quartz/liquid water and amorphous silica/liquid water interfaces. DFT-MD simulations provide direct knowledge of the structural organization of water and the H-Bond network formed between the water molecules within the different water layers above the silica surface. One can furthermore extract vibrational signatures of the water molecules within the interfacial layers from the DFT-MD simulations, especially non-linear SFG (Sum Frequency generation) signatures that are active at solid/liquid interfaces. The strength of the simulated spectra is that a detailed analysis of the signatures in terms of the water/water H-Bond networks formed within the interfacial water layers and in terms of the water/silica or water/electrolytes H-Bond networks can be given. Comparisons of SFG spectra between quartz/water/electrolytes and amorphous silica/water/electrolytes interfaces allow us to definitely conclude on how the structural arrangements of liquid water at these electrolytic interfaces modulate the final spectroscopic signatures. Invited speaker.

  2. Exploring the conserved water site and hydration of a coiled-coil trimerisation motif: a MD simulation study.

    Science.gov (United States)

    Dolenc, Jozica; Baron, Riccardo; Missimer, John H; Steinmetz, Michel O; van Gunsteren, Wilfred F

    2008-07-21

    The solvent structure and dynamics around ccbeta-p, a 17-residue peptide that forms a parallel three-stranded alpha-helical coiled coil in solution, was analysed through 10 ns explicit solvent molecular dynamics (MD) simulations at 278 and 330 K. Comparison with two corresponding simulations of the monomeric form of ccbeta-p was used to investigate the changes of hydration upon coiled-coil formation. Pronounced peaks in the solvent density distribution between residues Arg8 and Glu13 of neighbouring helices show the presence of water bridges between the helices of the ccbeta-p trimer; this is in agreement with the water sites observed in X-ray crystallography experiments. Interestingly, this water site is structurally conserved in many three-stranded coiled coils and, together with the Arg and Glu residues, forms part of a motif that determines three-stranded coiled-coil formation. Our findings show that little direct correlation exists between the solvent density distribution and the temporal ordering of water around the trimeric coiled coil. The MD-calculated effective residence times of up to 40 ps show rapid exchange of surface water molecules with the bulk phase, and indicate that the solvent distribution around biomolecules requires interpretation in terms of continuous density distributions rather than in terms of discrete molecules of water. Together, our study contributes to understanding the principles of three-stranded coiled-coil formation.

  3. Assessment of hydrogen bonding effect on ionization of water from ambient to supercritical region–MD simulation approach

    International Nuclear Information System (INIS)

    Swiatla-Wojcik, D.; Mozumder, A.

    2014-01-01

    We present a novel, molecular dynamics (MD) simulation based, strategy to analyze how the degree of hydrogen bonding may influence the ionization and dissociation of water upon heating from ambient to supercritical temperatures. Calculations show a negligible change in the ionization energy up to 200 °C. At higher temperatures the ionization energy increases due to the decreasing degree of hydrogen bonding. The influence of density (pressure) is pronounced in the supercritical region. The ionization is more energy consuming in the less dense fluid. We also show that high temperature and low density may promote dissociation of the electronically excited water molecules. Implications on the initial radiation chemical yields of the hydrated electron, hydrogen atom and hydroxyl radical are discussed. - Highlights: • Up to 200 °C changes in the vertical and adiabatic ionization potentials are negligible. • At higher temperatures ionization is more energy consuming. • Ionization potential increases with decreasing density of supercritical water. • High temperature and low density promote dissociation of the excited molecules

  4. 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

  5. Harvesting graphics power for MD simulations

    NARCIS (Netherlands)

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

    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

  6. MD simulation of cluster formation during sputtering

    International Nuclear Information System (INIS)

    Muramoto, T.; Okai, M.; Yamashita, Y.; Yorizane, K.; Yamamura, Y.

    2001-01-01

    The cluster ejection due to cluster impact on a solid surface is studied through molecular dynamics (MD) simulations. Simulations are performed for Cu cluster impacts on the Cu(1 1 1) surface for cluster energy 100 eV/atom, and for clusters of 6, 13, 28 and 55 atoms. Interatomic interactions are described by the AMLJ-EAM potential. The vibration energy spectrum is independent of the incident cluster size and energy. This comes from the fact that sputtered clusters become stable through the successive fragmentation of nascent large sputtered clusters. The vibration energy spectra for large sputtered clusters have a peak, whose energy corresponds to the melting temperature of Cu. The exponent of the power-law fit of the abundance distribution and the total sputtering yield for the cluster impacts are higher than that for the monatomic ion impacts with the same total energy, where the exponent δ is given by Y n ∝n δ and Y n is the yield of sputtered n-atom cluster. The exponent δ follows a unified function of the total sputtering yield, which is a monotonic increase function, and it is nearly equal to δ ∼ -3 for larger yield

  7. Oil-soluble and water-soluble BTPhens and their europium complexes in octanol/water solutions: interface crossing studied by MD and PMF simulations.

    Science.gov (United States)

    Benay, G; Wipff, G

    2013-01-31

    Bistriazinyl-phenantroline "BTPhen" ligands L display the remarkable feature to complex trivalent lanthanide and actinide ions, with a marked selectivity for the latter. We report on molecular dynamics studies of tetrasubstituted X(4)BTPhens: L(4+) (X = (+)Et(3)NCH(2)-), L(4-) (X = (-)SO(3)Ph-), and L(0) (X = CyMe(4)) and their complexes with Eu(III) in binary octanol/water solutions. Changes in free energies upon interface crossing are also calculated for typical solutes by potential of mean force PMF simulations. The ligands and their complexes partition, as expected, to either the aqueous or the oil phase, depending on the "solubilizing" group X. Furthermore, most of them are found to be surface active. The water-soluble L(4+) and L(4-) ligands and their (L)Eu(NO(3))(3) complexes adsorb at the aqueous side of the interface, more with L(4-) than with L(4+). The oil soluble ligand L(0) is not surface active in its endo-endo form but adsorbs on the oil side of the interface in its most polar endo-exo form, as well as in its protonated L(0)H(+) and complexed (L(0))Eu(NO(3))(3) states. Furthermore, comparing PMFs of the Eu(III) complexes with and without nitric acid shows that acidifying the aqueous phase has different effects, depending on the ligand charge. In particular, acid promotes the Eu(III) extraction by L(0) via the (L(0))(2)Eu(NO(3))(2+) complex, as observed experimentally. Overall, the results point to the importance of interfacial adsorption for the liquid-liquid extraction of trivalent lanthanide and actinide cations by BTPhens and analogues.

  8. 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)

  9. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

    International Nuclear Information System (INIS)

    Kylasa, S.B.; Aktulga, H.M.; Grama, A.Y.

    2014-01-01

    We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors

  10. PuReMD-GPU: A reactive molecular dynamics simulation package for GPUs

    Energy Technology Data Exchange (ETDEWEB)

    Kylasa, S.B., E-mail: skylasa@purdue.edu [Department of Elec. and Comp. Eng., Purdue University, West Lafayette, IN 47907 (United States); Aktulga, H.M., E-mail: hmaktulga@lbl.gov [Lawrence Berkeley National Laboratory, 1 Cyclotron Rd, MS 50F-1650, Berkeley, CA 94720 (United States); Grama, A.Y., E-mail: ayg@cs.purdue.edu [Department of Computer Science, Purdue University, West Lafayette, IN 47907 (United States)

    2014-09-01

    We present an efficient and highly accurate GP-GPU implementation of our community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD and its incorporation into LAMMPS (Reax/C) is used by a large number of research groups worldwide for simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail. The sub-femtosecond time-steps associated with ReaxFF strongly motivate significant improvements to per-timestep simulation time through effective use of GPUs. This paper presents, in detail, the design and implementation of PuReMD-GPU, which enables ReaxFF simulations on GPUs, as well as various performance optimization techniques we developed to obtain high performance on state-of-the-art hardware. Comprehensive experiments on model systems (bulk water and amorphous silica) are presented to quantify the performance improvements achieved by PuReMD-GPU and to verify its accuracy. In particular, our experiments show up to 16× improvement in runtime compared to our highly optimized CPU-only single-core ReaxFF implementation. PuReMD-GPU is a unique production code, and is currently available on request from the authors.

  11. A molecular dynamics (MD simulation on tire-aggregate friction

    Directory of Open Access Journals (Sweden)

    Fengyan Sun

    2017-07-01

    Full Text Available The friction between tire and road surface is fundamentally depending on the molecular forces. In this paper, the nanoscale 3D contact model is employed to investigate the tire-aggregate friction mechanism. The tire and aggregate micro-structure are both constructed to evaluate the microscopic performance of tire-aggregate friction influence. Simulation results show for a high velocity, the energy dissipation of sliding on crystal structure is small, which results in a small friction coefficient; temperature will have influences on the friction coefficient, and with the increasing of velocity, the effect will gradually reduce. Keywords: Tire, Aggregate, Friction coefficient, Microscopic mechanism, MD simulation

  12. 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.

  13. Applicability of effective fragment potential version 2 - Molecular dynamics (EFP2-MD) simulations for predicting excess properties of mixed solvents

    Science.gov (United States)

    Kuroki, Nahoko; Mori, Hirotoshi

    2018-02-01

    Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.

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

    Science.gov (United States)

    Hofer, Thomas S.; Hünenberger, Philippe H.

    2018-06-01

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

  15. Analysis of MD5 authentication in various routing protocols using simulation tools

    Science.gov (United States)

    Dinakaran, M.; Darshan, K. N.; Patel, Harsh

    2017-11-01

    Authentication being an important paradigm of security and Computer Networks require secure paths to make the flow of the data even more secure through some security protocols. So MD-5(Message Digest 5) helps in providing data integrity to the data being sent through it and authentication to the network devices. This paper gives a brief introduction to the MD-5, simulation of the networks by including MD-5 authentication using various routing protocols like OSPF, EIGRP and RIPv2. GNS3 is being used to simulate the scenarios. Analysis of the MD-5 authentication is done in the later sections of the paper.

  16. 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

  17. 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 (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.

  18. 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.

  19. MD and BCA simulations of He and H bombardment of fuzz in bcc elements

    Science.gov (United States)

    Klaver, T. P. C.; Zhang, S.; Nordlund, K.

    2017-08-01

    We present results of MD simulations of low energy He ion bombardment of low density fuzz in bcc elements. He ions can penetrate several micrometers into sparse fuzz, which allows for a sufficient He flux through it to grow the fuzz further. He kinetic energy falls off exponentially with penetration depth. A BCA code was used to carry out the same ion bombardment on the same fuzz structures as in MD simulations, but with simpler, 10 million times faster calculations. Despite the poor theoretical basis of the BCA at low ion energies, and the use of somewhat different potentials in MD and BCA calculations, the ion penetration depths predicted by BCA are only ∼12% less than those predicted by MD. The MD-BCA differences are highly systematic and trends in the results of the two methods are very similar. We have carried out more than 200 BCA calculation runs of ion bombardment of fuzz, in which parameters in the ion bombardment process were varied. For most parameters, the results show that the ion bombardment process is quite generic. The ion species (He or H), ion mass, fuzz element (W, Ta, Mo, Fe) and fuzz element lattice parameter turned out to have a modest influence on ion penetration depths at most. An off-normal angle of incidence strongly reduces the ion penetration depth. Increasing the ion energy increases the ion penetration, but the rate by which ion energy drops off at high ion energies follows the same exponential pattern as at lower energies.

  20. Interaction and dynamics of homologous pairing protein 2 (HOP2) and DNA studied by MD simulation

    Science.gov (United States)

    Moktan, Hem; Pezza, Roberto; Zhou, Donghua

    2015-03-01

    The homologous pairing protein 2 (Hop2) plays an important role in meiosis and DNA repair. Together with protein Mnd1, Hop2 enhances the strand invasion activity of recombinase Dmc1 by over 30 times, facilitating proper synapsis of homologous chromosomes. We recently determined the NMR structure of the N-terminal domain of Hop2 and proposed a model of Protein-DNA complex based on NMR chemical shift perturbations and mutagenesis studies (Moktan, J Biol Chem 2014 10.1074/jbc.M114.548180). However structure and dynamics of the complex have not been studied at the atomic level yet. Here, we used classical MD simulations to study the interactions between the N-terminal HOP2 and DNA. The simulated results indicate that helix3 (H3) interacts with DNA in major groove and wing1 (W1) interacts mostly in minor groove mainly via direct hydrogen bonds. Also it is found that binding leads to reduced fluctuations in both protein and DNA. Several water bridge interactions have been identified. The residue-wise contributions to the interaction energy were evaluated. Also the functional motion of the protein is analyzed using principal component analysis. The results confirmed the importance of H3 and W1 for the stability of the complex, which is consistent with our previous experimental studies.

  1. Hybrid classical/quantum simulation for infrared spectroscopy of water

    Science.gov (United States)

    Maekawa, Yuki; Sasaoka, Kenji; Ube, Takuji; Ishiguro, Takashi; Yamamoto, Takahiro

    2018-05-01

    We have developed a hybrid classical/quantum simulation method to calculate the infrared (IR) spectrum of water. The proposed method achieves much higher accuracy than conventional classical molecular dynamics (MD) simulations at a much lower computational cost than ab initio MD simulations. The IR spectrum of water is obtained as an ensemble average of the eigenvalues of the dynamical matrix constructed by ab initio calculations, using the positions of oxygen atoms that constitute water molecules obtained from the classical MD simulation. The calculated IR spectrum is in excellent agreement with the experimental IR spectrum.

  2. Investigation on single carbon atom transporting through the single-walled carbon nanotube by MD simulation

    International Nuclear Information System (INIS)

    Ding Yinfeng; Zhang Zhibin; Ke Xuezhi; Zhu Zhiyuan; Zhu Dezhang; Wang Zhenxia; Xu Hongjie

    2005-01-01

    The single carbon atom transporting through the single-walled carbon nanotube has been studied by molecular-dynamics (MD) simulation. We got different trajectories of the carbon atom by changing the input parameters. The simulation results indicate that the single carbon atom with low energy can transport through the carbon nanotube under some input conditions and result in different trajectories being straight line or 'rosette' or circular. (authors)

  3. Parallel Object Oriented MD Simulation Program for Long Time Simulations of Metallic Glasses and Undercooled Liquids

    Science.gov (United States)

    Böddeker, B.; Teichler, H.

    The MD simulation program TABB is motivated by the need of long time simulations for the investigation of slow processes near the glass transition of glass forming alloys. TABB is written in C++ with a high degree of flexibility: TABB allows the use of any short ranged pair potentials or EAM potentials, by generating and using a spline representation of all functions and their derivatives. TABB supports several numerical integration algorithms like the Runge-Kotta or the modified Gear-predictor-corrector algorithm of order five. The boundary conditions can be chosen to resemble the geometry of bulk materials or films. The simulation box length or the pressure can be fixed for each dimension separately. TABB may be used in isokinetic, isoenergeric or canonic (with random forces) mode. TABB contains a simple instruction interpreter to easily control the parameters and options during the simulation. The same source code can be compiled either for workstations or for parallel computers. The main optimization goal of TABB is to allow long time simulations of medium or small sized systems. To make this possible, much attention is spent on the optimized communication between the nodes. TABB uses a domain decomposition procedure. To use many nodes with a small system, the domain size has to be small compared to the range of particle interactions. In the limit of many nodes for only few atoms, the bottle neck of communication is the latency time. TABB minimizes the number of pairs of domains containing atoms that interact between these domains. This procedure minimizes the need of communication calls between pairs of nodes. TABB decides automatically, to how many, and to which directions the decomposition shall be applied. E.g., in the case of one dimensional domain decomposition, the simulation box is only split into "slabs" along a selected direction. The three dimensional domain decomposition is best with respect to the number of interacting domains only for simulations

  4. 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.

  5. PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations.

    Science.gov (United States)

    Scheurer, Maximilian; Rodenkirch, Peter; Siggel, Marc; Bernardi, Rafael C; Schulten, Klaus; Tajkhorshid, Emad; Rudack, Till

    2018-02-06

    Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X 3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex. Copyright © 2017 Biophysical Society

  6. Microsecond MD Simulations of Nano-patterned Polymer Brushes on Self-Assembled Monolayers

    Science.gov (United States)

    Buie, Creighton; Qiu, Liming; Cheng, Kwan; Park, Soyeun

    2010-03-01

    Nano-patterned polymer brushes end-grafted onto self-assembled monolayers have gained increasing research interests due to their unique thermodynamic properties and their chemical and biomedical applications in colloids, biosensing and tissue engineering. So far, the interactions between the polymer brushes with the surrounding environments such as the floor and solvent at the nanometer length scale and microsecond time scale are still difficult to obtained experimentally and computationally. Using a Coarse-Grained MD approach, polymer brushes of different monomeric lengths, grafting density and hydrophobicity of the monomers grafted on self-assembled monolayers and in explicit solvent were studied. Molecular level information, such as lateral diffusion, transverse height and volume contour of the brushes, were calculated from our microsecond-MD simulations. Our results demonstrated the significance of the hydration of the polymer in controlling the conformational arrangement of the polymer brushes.

  7. MD simulation: determination of the physical properties and surface vaporization analysis of beryllium armours

    International Nuclear Information System (INIS)

    Prinzio, M. Di; Aquaro, D.

    2006-01-01

    The erosion of the divertor and of the first wall determined on the base of the anticipated operating conditions, is a critical issue that could affect the performance and the operating schedule of the nuclear fusion reactor ITER. This paper deals with the analysis of beryllium thermal properties by means of MD simulations, in order to better predict thermal behaviour of beryllium armoured PFCs in fusion devices. The importance of this analysis is clearly connected to thermal response evaluation of PFCs to high heat flux exposure, during off-normal events and Edge Localized Modes. The ensuing strong over-heating, in fact, produces material ablation through vaporization of surface material layers and possible loss of melting material. The overall PFCs erosion has bearings on plasma contamination, due to eroded material transport, and components lifetime, due to armour thickness reduction. An important feature of beryllium is its high vapour pressure. During thermal transients the strong vaporization keeps surface temperature relatively low but eroded thickness results high as well. Small changes in beryllium vapour pressure produce not negligible differences in thermal analyses results. On the basis of available force fields, classical Molecular Dynamics simulations have been carried out in order to better understand surface vaporization in tokamak conditions and to evaluate the effect of beryllium oxides formation. This effect has been successfully modelled by MD simulation, carried out with Moldy code. Morse stretching and bending potential for Be-O bond simulation have been used, and partial charges method, accounting for molecular polarity, has been employed. Since during short thermal transients, such as ELMs, only a few microns of Be armour will be overheated and reach melting threshold, the effective thermal conductivity is very important in determining the temperature evolution of surface layers and the ensuing erosion. Thermal conductivity can be evaluated

  8. Prediction of Osmotic Pressure of Ionic Liquids Inside a Nanoslit by MD Simulation and Continuum Approach

    Science.gov (United States)

    Moon, Gi Jong; Yang, Yu Dong; Oh, Jung Min; Kang, In Seok

    2017-11-01

    Osmotic pressure plays an important role in the processes of charging and discharging of lithium batteries. In this work, osmotic pressure of the ionic liquids confined inside a nanoslit is calculated by using both MD simulation and continuum approach. In the case of MD simulation, an ionic liquid is modeled as singly charged spheres with a short-ranged repulsive Lennard-Jones potential. The radii of the spheres are 0.5nm, reflecting the symmetry of ion sizes for simplicity. The simulation box size is 11nm×11nm×7.5nm with 1050 ion pairs. The concentration of ionic liquid is about 1.922mol/L, and the total charge on an individual wall varies from +/-60e(7.944 μm/cm2) to +/-600e(79.44 μm/cm2) . In the case of continuum approach, we classify the problems according to the correlation length and steric factor, and considered the four separate cases: 1) zero correlation length and zero steric factor, 2) zero correlation length and non-zero steric factor, 3) non-zero correlation length and zero steric factor, and 4) non-zero correlation and non-zero steric factor. Better understanding of the osmotic pressure of ionic liquids confined inside a nanoslit can be achieved by comparing the results of MD simulation and continuum approach. This research was supported by the National Research Foundation of Korea (NRF) Grant funded by the Korea government (MSIP: Ministry of Science, ICT & Future Planning) (No. 2017R1D1A1B05035211).

  9. 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.

  10. 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.

  11. 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. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. 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.

  13. Structural and dynamical aspects of Streptococcus gordonii FabH through molecular docking and MD simulations.

    Science.gov (United States)

    Shamim, Amen; Abbasi, Sumra Wajid; Azam, Syed Sikander

    2015-07-01

    β-Ketoacyl-ACP-synthase III (FabH or KAS III) has become an attractive target for the development of new antibacterial agents which can overcome the multidrug resistance. Unraveling the fatty acid biosynthesis (FAB) metabolic pathway and understanding structural coordinates of FabH will provide valuable insights to target Streptococcus gordonii for curing oral infection. In this study, we designed inhibitors against therapeutic target FabH, in order to block the FAB pathway. As compared to other targets, FabH has more interactions with other proteins, located on the leading strand with higher codon adaptation index value and associated with lipid metabolism category of COG. Current study aims to gain in silico insights into the structural and dynamical aspect of S. gordonii FabH via molecular docking and molecular dynamics (MD) simulations. The FabH protein is catalytically active in dimerization while it can lock in monomeric state. Current study highlights two residues Pro88 and Leu315 that are close to each other by dimerization. The active site of FabH is composed of the catalytic triad formed by residues Cys112, His249, and Asn279 in which Cys112 is involved in acetyl transfer, while His249 and Asn279 play an active role in decarboxylation. Docking analysis revealed that among the studied compounds, methyl-CoA disulfide has highest GOLD score (82.75), binding affinity (-11 kcal/mol) and exhibited consistently better interactions. During MD simulations, the FabH structure remained stable with the average RMSD value of 1.7 Å and 1.6 Å for undocked protein and docked complex, respectively. Further, crucial hydrogen bonding of the conserved catalytic triad for exhibiting high affinity between the FabH protein and ligand is observed by RDF analysis. The MD simulation results clearly demonstrated that binding of the inhibitor with S. gordonii FabH enhanced the structure and stabilized the dimeric FabH protein. Therefore, the inhibitor has the potential to become

  14. Electroreduction Property and MD Simulation of Nitrobenzene in Ionic Liquid [BMim][Tf2N]/[BMim][BF4

    International Nuclear Information System (INIS)

    Zeng, Jianping; Zhang, Yinxu; Sun, Ruyao; Chen, Song

    2014-01-01

    Highlights: • The two different common accessible ionic liquids are mixed in a simple and economic way. • In some compound ratios, the dynamic performance of nitrobenzene is superior to either of ionic liquids. • Modification and functionalization of ionic liquids in electrochemical field is feasible. • The mass transfer of diffusion of nitrobenzene in ionic liquids can be simulated with molecular dynamics. • Molecular dynamics explains the improvement of nitrobenzene in composite ionic liquids. - Abstract: The two different common accessible ionic liquids [BMim][BF 4 ] and [BMim][Tf 2 N] were mixed each other in a simple and economic way. In some compound ratios, the dynamic performance of nitrobenzene in electric reduction was superior to that of any single kind of ionic liquid has been appeared. The interaction and mass transfer of diffusion of nitrobenzene in composite ionic liquids with different volume ratios were studied with molecular dynamics (MD) simulation. The improvement of the electroreduction performance of nitrobenzene in composite ionic liquids was verified and was tried to explain. This provides a new idea for the modification and functionalization of ionic liquids in electrochemical field. The experimental results showed that kinematic viscosity and electroconductibility of different ionic liquid systems display a regular change. And the change law has been basically unchanged after adding water. The two different functional ionic liquids were complemented each other in a simple and economic way, which has compensated for the disadvantage of mono-component ionic liquids. At 25 °C, electroreduction property of V [BMim][BF4] :V [BMim][Tf2N] = 1:1 is the best in cyclic voltammetry experiments of nitrobenzene in different composite ionic liquids. Its electrochemical behavior is significantly affected by scan rate, temperature, concentration of nitrobenzene and concentration of water. The MD simulation results showed most of interaction

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

    KAUST Repository

    Han, Gang; Zuo, Jian; Wan, Chunfeng; Chung, Neal Tai-Shung

    2015-01-01

    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

  16. 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.

  17. A green process for recovery of 1-propanol/2-propanol from their aqueous solutions: Experimental and MD simulation studies

    International Nuclear Information System (INIS)

    Gupta, Bhupender S.; Taha, Mohamed; Lee, Ming-Jer

    2017-01-01

    Highlights: • A green conceptual design for separating propanols from their aqueous solutions is proposed. • TRIS is biocompatible and non-volatile and can be used as an auxiliary agent for the separation. • Isobaric VLE data for 1-propanol/2-propanol + water + TRIS were measured at 101.3 kPa. • The azeotropic compositions are significantly shifted in the presence of TRIS. • Intermolecular interactions were studied with fluorescence, COSMO-RS, and MD simulation. - Abstract: In the present study, we have found that a common and relatively inexpensive biological buffer tris(hydroxymethyl)aminomethane (TRIS) is potentially applicable to shift the azeotrope compositions of aqueous solutions of 1-propanol and 2-propanol. By taking the advantage of our findings, we are proposing a green process for the recovery of these organics from their respective aqueous solutions. In order to confirm the effect of TRIS buffer on vapor–liquid equilibrium behavior of the aqueous propanol systems, we measured the isobaric vapor–liquid equilibrium (VLE) data at 101.3 kPa for the 1-proponol + water + TRIS and 2-propanol + water + TRIS systems over the azeotropic range with various concentrations of TRIS (0.02, 0.04, 0.08, and 0.12 in mole fraction). The binary interaction parameters were obtained for TRIS with water, TRIS with 1-propanol, and TRIS with 2-propanol by correlating the new VLE data with the NRTL model. The isobaric VLE properties for the investigated propanol + water mixtures in the presence of various concentrations of TRIS were also predicted with the conductor-like screening model COSMO-RS. Based on the predicted excess molar enthalpies (H E m ) from the COSMO-RS, the interactions between all constituent pairs of molecules were estimated. To explore the mechanism of TRIS-based separation of 1-propanol/2-propanol from their aqueous solutions, the interactions between different pairs of molecules were also investigated by using fluorescence analysis and

  18. 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......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...

  19. Water vapor permeabilities through polymers: diffusivities from experiments and simulations

    International Nuclear Information System (INIS)

    Seethamraju, Sindhu; Ramamurthy, Praveen Chandrashekarapura; Madras, Giridhar

    2014-01-01

    This study experimentally determines water vapor permeabilities, which are subsequently correlated with the diffusivities obtained from simulations. Molecular dynamics (MD) simulations were used for determining the diffusion of water vapor in various polymeric systems such as polyethylene, polypropylene, poly (vinyl alcohol), poly (vinyl acetate), poly (vinyl butyral), poly (vinylidene chloride), poly (vinyl chloride) and poly (methyl methacrylate). Cavity ring down spectroscopy (CRDS) based methodology has been used to determine the water vapor transmission rates. These values were then used to calculate the diffusion coefficients for water vapor through these polymers. A comparative analysis is provided for diffusivities calculated from CRDS and MD based results by correlating the free volumes. (paper)

  20. 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.

  1. 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...

  2. 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

  3. A direct ab initio molecular dynamics (MD) study on the benzophenone-water 1 : 1 complex.

    Science.gov (United States)

    Tachikawa, Hiroto; Iyama, Tetsuji; Kato, Kohichi

    2009-07-28

    Direct ab initio molecular dynamics (MD) method has been applied to a benzophenone-water 1 : 1 complex Bp(H(2)O) and free benzophenone (Bp) to elucidate the effects of zero-point energy (ZPE) vibration and temperature on the absorption spectra of Bp(H(2)O). The n-pi transition of free-Bp (S(1) state) was blue-shifted by the interaction with a water molecule, whereas three pi-pi transitions (S(2), S(3) and S(4)) were red-shifted. The effects of the ZPE vibration and temperature of Bp(H(2)O) increased the intensity of the n-pi transition of Bp(H(2)O) and caused broadening of the pi-pi transitions. In case of the temperature effect, the intensity of n-pi transition increases with increasing temperature. The electronic states of Bp(H(2)O) were discussed on the basis of the theoretical results.

  4. 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

  5. Water hammer simulator

    International Nuclear Information System (INIS)

    Sinha, S.K.; Madia, J.; Dixon, S.

    1995-01-01

    The Consolidated Edison Company of New York, Inc. (Con Edison) has constructed a first-of-a-kind water hammer events simulator for use at its training center. The Learning Center, Con Edison's central training facility, intends to use the simulator as an educational tool to demonstrate the various mechanisms of the water hammer phenomenon to power plant designers, engineers and operators. The water hammer phenomenon has been studied extensively for the past 15 years for the nuclear industry. However, the acknowledge of the various water hammer mechanisms and the measures to prevent or mitigate water hammer have not been widely disseminated among the operators of fossil-fueled power plants. Con Edison personnel who operate the various generation stations and the New York City steam distribution systems are expected to benefit from the new simulator. Knowledge gained from interacting with the simulator will be very important in helping the Con Edison prevent, mitigate, or accommodate water hammer at its facilities. The water hammer simulator was fabricated in Con Edison's central machine shop. Details of the design and construction of the simulator were finalized in consultation with Creare, Inc., an engineering research firm, located in Hanover, New Hampshire. The simulator seeks to recreate the essential features of water hammer in steam mines following the buildup of cold (subcooled) water by condensation and steam-water interaction. This paper describes the fabrication, design, testing, and operation of the Con Edison water hammer simulator. A discussion of how Con Edison plans to use the facility at The Learning Center is included

  6. Alamethicin in lipid bilayers: combined use of X-ray scattering and MD simulations.

    Science.gov (United States)

    Pan, Jianjun; Tieleman, D Peter; Nagle, John F; Kucerka, Norbert; Tristram-Nagle, Stephanie

    2009-06-01

    We study fully hydrated bilayers of two di-monounsaturated phospholipids diC18:1PC (DOPC) and diC22:1PC with varying amounts of alamethicin (Alm). We combine the use of X-ray diffuse scattering and molecular dynamics simulations to determine the orientation of alamethicin in model lipids. Comparison of the experimental and simulated form factors shows that Alm helices are inserted transmembrane at high humidity and high concentrations, in agreement with earlier results. The X-ray scattering data and the MD simulations agree that membrane thickness changes very little up to 1/10 Alm/DOPC. In contrast, the X-ray data indicate that the thicker diC22:1PC membrane thins with added Alm, a total decrease in thickness of 4 A at 1/10 Alm/diC22:1PC. The different effect of Alm on the thickness changes of the two bilayers is consistent with Alm having a hydrophobic thickness close to the hydrophobic thickness of 27 A for DOPC; Alm is then mismatched with the 7 A thicker diC22:1PC bilayer. The X-ray data indicate that Alm decreases the bending modulus (K(C)) by a factor of approximately 2 in DOPC and a factor of approximately 10 in diC22:1PC membranes (P/L approximately 1/10). The van der Waals and fluctuational interactions between bilayers are also evaluated through determination of the anisotropic B compressibility modulus.

  7. Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor

    Directory of Open Access Journals (Sweden)

    Sandra Posch

    2016-09-01

    Full Text Available We here give information for a deeper understanding of single molecule force spectroscopy (SMFS data through the example of the blood protein von Willebrand factor (VWF. It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK was used for this demonstration. Further, Brownian dynamics (BD simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, “Mutual A domain interactions in the force sensing protein von Willebrand Factor” (Posch et al., 2016 [1]. Keywords: Atomic force microscopy, Single molecule force spectroscopy, Molecular dynamics simulation, Brownian dynamics simulation, von Willebrand factor

  8. Coarse grained MD simulations of a fracture of filler-filled polymer nanocomposites under uniaxial elongation

    Science.gov (United States)

    Hagita, Katsumi; Morita, Hiroshi; Takano, Hiroshi

    We performed coarse grained molecular dynamics (MD) simulations based on Kremer-Grest model in order to investigate a fracture of polymer nanocomposites filled with spherical nanoparticles (NPs) under uniaxial elongation with a Poisson ratio of 0.4. In our model, the NP consists of 320 surface beads and one center bead. In order to make the NP spherical, a harmonic potential is applied to the surface particles from the center of the NP. Here, the initial volume fraction of the NPs is about 20%. The dependences of the fracture on the interactions between the NPs and polymers were examined. In order to observe the creation of nanovoids, the interaction among the polymers was set to be attractive. When the NP-polymer interaction is attractive, nanovoids appear in the bulk of polymers. On the other hand, for repulsive NP-polymer interaction, nanovoids are created at the surface between the polymers and NPs. At the same time, segregation of NPs is observed. We found that these behaviors depend on crosslink densities.

  9. MD simulations of onset of tungsten fuzz formation under helium irradiation

    International Nuclear Information System (INIS)

    Lasa, A.; Henriksson, K.O.E.; Nordlund, K.

    2013-01-01

    When helium (He) escapes a fusion reactor plasma, a tungsten (W)-based divertor may, under some conditions, form a fuzz-like nano-morphology. This is a highly undesired phenomenon for the divertor, and is not well understood. We performed molecular dynamics simulations of high fluence He and also C-seeded He (He+C) irradiation on W, focusing on the effect of the high fluence, the temperature and the impurities on the onset of the structure formation. We concluded that MD reproduces the experimentally found square root of time dependence of the surface growth. The He atomic density decreases when increasing the number of He atoms in the cell. A higher temperature causes a larger bubble growth and desorption activity, specially for the pure He irradiation cases. It also it leads to W recrystallization for the He+C irradiation cases. Carbon acts as a local He trap for small clusters or single atoms and causes a larger loss of crystallinity of the W surface

  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. 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

    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...... dynamics (MD) simulations of a hydrophilic air-water-silica system using the MD package FASTTUBE. We employ quantum chemistry calculation to obtain air-silica interaction parameters for the simulations. Our simulations are based in the following force fields: i) The silica-silica interaction is based...... 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. For hydrophobic systems the static and dynamic properties of the fluid-solid interface are influenced by the presence of air. Hence...

  12. Distinct solvent- and temperature-dependent packing arrangements of anti-parallel β-sheet polyalanines studied with solid-state 13C NMR and MD simulation.

    Science.gov (United States)

    Kametani, Shunsuke; Tasei, Yugo; Nishimura, Akio; Asakura, Tetsuo

    2017-08-09

    Polyalanine (polyA) sequences are well known as the simplest sequence that naturally forms anti-parallel β-sheets and constitute a key element in the structure of spider and wild silkworm silk fibers. We have carried out a systematic analysis of the packing of anti-parallel β-sheets for (Ala) n , n = 5, 6, 7 and 12, using primarily 13 C solid-state NMR and MD simulation. HFIP and TFA are frequently used as the dope solvents for recombinant silks, and polyA was solidified from both HFIP and TFA solutions by drying. An analysis of Ala Cβ peaks in the 13 C CP/MAS NMR spectra indicated that polyA from HFIP was mainly rectangular but polyA from TFA was mainly staggered. The transition from the rectangular to the staggered arrangement in (Ala) 6 was observed for the first time from the change in the Ala Cβ peak through heat treatment at 200 °C for 4 h. The removal of the bound water was confirmed by thermal analysis. This transition could be reproduced by MD simulation of (Ala) 6 molecules at 200 °C after removal of the bound water molecules. In this way, the origin of the stability of the different packing arrangements of polyA was clarified.

  13. Md Naimuddin

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics. Md Naimuddin. Articles written in Pramana – Journal of Physics. Volume 79 Issue 5 November 2012 pp 1255-1258 Poster Presentations. Model unspecific search for new physics in collision at s = 7 TeV · Shivali Malhotra Md Naimuddin Thomas Hebbeker Arnd Meyer ...

  14. Nanotribological behavior analysis of graphene/metal nanocomposites via MD simulations: New concepts and underlying mechanisms

    Science.gov (United States)

    Montazeri, A.; Mobarghei, A.

    2018-04-01

    In this article, we report a series of MD-based nanoindentation tests aimed to examine the nanotribological characteristics of metal-based nanocomposites in the presence of graphene sheets. To evaluate the effects of graphene/matrix interactions on the results, nickel and copper are selected as metals having strong and weak interactions with graphene, respectively. Consequently, the influence of graphene layers sliding and their distance from the sample surface on the nanoindentation outputs is thoroughly examined. Additionally, the temperature dependence of the results is deeply investigated with emphasis on the underlying mechanisms. To verify the accuracy of nanoindentation outputs, results of this method are compared with the data obtained via the tensile test. It is concluded that the nanoindentation results are closer to the values obtained by means of experimental setups. Employing these numerical-based experiments enables us to perform parametric studies to find out the dominant factors affecting the nanotribological behavior of these nanocomposites at the atomic-scale.

  15. Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC

    International Nuclear Information System (INIS)

    Landman, I.S.

    2005-01-01

    For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O x W y at the surface, and the retained H-atoms form the volatile complexes H x O y , which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated

  16. MD simulations to evaluate effects of applied tensile strain on irradiation-induced defect production at various PKA energies

    International Nuclear Information System (INIS)

    Miyashiro, S.; Fujita, S.; Okita, T.; Okuda, H.

    2012-01-01

    Highlights: ► Strain effects on defect formation were evaluated at various PKA energies by MD. ► Radiation-induced defects were increased numerically by external strain. ► Enhanced formation of larger clusters causes the numerical increase of defects. ► Strain influence on the number of defects was greatest at about 20 keV PKA. ► Cluster size, which is mostly affected by strain, was greater with higher PKA energy. - Abstract: Molecular Dynamics (MD) simulations were conducted to investigate the influence of applied tensile strain on defect production during cascade damages at various Primary Knock-on Atom (PKA) energies of 1–30 keV. When 1% strain was applied, the number of surviving defects increased at PKA energies higher than 5 keV, although they did not increase at 1 keV. The rate of increase by strain application was higher with higher PKA energy, and attained the maximum at 20 keV PKA energy with a subsequent gradual decrease at 30 keV PKA energy The cluster size, mostly affected by strain, was larger with higher PKA energy, although clusters with fewer than seven interstitials did not increase in number at any PKA energy.

  17. Designing of phenol-based β-carbonic anhydrase1 inhibitors through QSAR, molecular docking, and MD simulation approach.

    Science.gov (United States)

    Ahamad, Shahzaib; Hassan, Md Imtaiyaz; Dwivedi, Neeraja

    2018-05-01

    Tuberculosis (Tb) is an airborne infectious disease caused by Mycobacterium tuberculosis. Beta-carbonic anhydrase 1 ( β-CA1 ) has emerged as one of the potential targets for new antitubercular drug development. In this work, three-dimensional quantitative structure-activity relationships (3D-QSAR), molecular docking, and molecular dynamics (MD) simulation approaches were performed on a series of natural and synthetic phenol-based β-CA1 inhibitors. The developed 3D-QSAR model ( r 2  = 0.94, q 2  = 0.86, and pred_r 2  = 0.74) indicated that the steric and electrostatic factors are important parameters to modulate the bioactivity of phenolic compounds. Based on this indication, we designed 72 new phenolic inhibitors, out of which two compounds (D25 and D50) effectively stabilized β-CA1 receptor and, thus, are potential candidates for new generation antitubercular drug discovery program.

  18. 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

    International Nuclear Information System (INIS)

    Blanco, Jose L. Jimenez; Rooijen, Johannes J.M. van; Erbel, Paul J.A.; Leeflang, Bas R.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.

    2000-01-01

    The conformational behaviour of the spacer-linked synthetic Sd a tetrasaccharide β-d-GalpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (1) and the two mimics β-d-Galp-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O)(CH 2 ) 5 NH 2 (2) and β-d-GlcpNAc-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp-(1 → 4)-β-d-GlcpNAc-(1 → O) (CH 2 ) 5 NH 2 (3) were investigated by 1 H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. Experimental 2D 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 β-d-Hex(NAc)-(1 → 4)-[α-Neu5Ac-(2 → 3)]-β-d-Galp fragments. The α- Neu5-Ac-(2 → 3)-β-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.

  19. Solid state NMR investigations and MD simulations of triblock copolymers in lipid bilayers

    Czech Academy of Sciences Publication Activity Database

    Baerenwald, R.; Ferreira, T. M.; Ollila, Samuli; Saalwaechter, K.

    2017-01-01

    Roč. 46, Suppl 1 (2017), S117 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : solid state NMR * molecular dynamic simulations Subject RIV: BO - Biophysics

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

    International Nuclear Information System (INIS)

    Tikhonchev, M.; Svetukhin, V.; Gaganidze, E.

    2013-01-01

    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

  1. 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.

  2. 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

    TMCL. Coarse grain molecular dynamics simulations confirm the experimental thickening of 2 Å for 20 mol% TMCL and locate the TMCL headgroups near the glycerol-carbonyl region of DMPC; i.e., they are sequestered below the DMPC phosphocholine headgroup. Our results suggest that TMCL plays a role similar...... 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......Cardiolipins (CLs) are important biologically for their unique role in biomembranes that couple phosphorylation and electron transport like bacterial plasma membranes, chromatophores, chloroplasts and mitochondria. CLs are often tightly coupled to proteins involved in oxidative phosphorylation...

  3. Low-energy oxygen bombardment of silicon by MD simulations making use of a reactive force field

    International Nuclear Information System (INIS)

    Philipp, P.; Briquet, L.; Wirtz, T.; Kieffer, J.

    2011-01-01

    In the field of Secondary Ion Mass Spectrometry (SIMS), ion-matter interactions have been largely investigated by numerical simulations. For MD simulations related to inorganic samples, mostly classical force fields assuming stable bonding structure have been used. In materials science, level-three force fields capable of simulating the breaking and formation of chemical bonds have recently been conceived. One such force field has been developed by John Kieffer . This potential includes directional covalent bonds, Coulomb and dipolar interaction terms, dispersion terms, etc. Important features of this force field for simulating systems that undergo significant structural reorganization are (i) the ability to account for the redistribution of electron density upon ionization, formation, or breaking of bonds, through a charge transfer term, and (ii) the fact that the angular constraints dynamically adjust when a change in the coordination number of an atom occurs. In this paper, the modification of the force field to allow for an exact description of the sputtering process, the influence of this modification on previous results obtained for phase transitions in glasses as well as properties of particles sputtered at 250-1000 eV from a mono-crystalline silicon sample will be presented. The simulation results agree qualitatively with predictions from experiments or models. Most atoms are sputtered from the first monolayer: for an impact energy of 250 eV up to 86% of the atoms are sputtered from the first monolayer and for 750 eV, this percentage drops to 61%, with 89% of the atoms being sputtered from the first two monolayers. For sputtering yields, 250 and 500 eV results agree with experimental data, but for 750 eV sub-channelling in the pristine sample becomes more important than in experiments where samples turn amorphous under ion bombardment.

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

    Directory of Open Access Journals (Sweden)

    V. Buchard

    2014-02-01

    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 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.

  5. 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.

  6. 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...... of the virtual sites used in GROMACS while the other uses a new definition of the virtual sites of the CH2 groups. Our methods is tested on a DPPC (no unsaturated chain), a POPC (one unsaturated chain), and a DOPC (two unsaturated chains) lipid bilayers. We calculate various physical properties of the membrane...... of our simulations with and without virtual sites and explain the differences and similarity observed. The best agreements are obtained for the GROMACS original virtual sites on the DOPC bilayer where we get an area per lipid of 67.3 ± 0.3 A˚2 without virtual sites and 67.6 ± 0.3 A˚2 with virtual sites...

  7. Simulation of multi-atomic interactions in H-O-W system with the MD code CADAC

    Energy Technology Data Exchange (ETDEWEB)

    Landman, I.S. [Forschungszentrum Karlsruhe, Institute for Pulsed Power and Microwave Technology, P.O. Box 3640, 76021 Karlsruhe (Germany)]. E-mail: igor.landman@ihm.fzk.de

    2005-11-15

    For future tokamak reactors, chemical erosion of tungsten armour surfaces under impact of hot deuterium-tritium plasma that contains impurities, for instance oxygen, is an important issue. Oxygen can form volatile molecular complexes O {sub x}W {sub y} at the surface, and the retained H-atoms form the volatile complexes H {sub x}O {sub y}, which mitigates the erosion (H states for hydrogen isotopes). The plasma impact can substantially destroy the complexes. To describe this H-O-W system, the molecular dynamics (MD) code CADAC was earlier developed using only pair-atomic interactions. Now CADAC is extended for multi-body forces to simulate molecular organization of atoms near the tungsten surface. The approach uses the Abell's model of empirical bond-order potentials in addition combined, for the first time, with a valence concept. CADAC simulates chemical features using atomic valences and the Morse potentials. The new model is introduced and model parameters are estimated.

  8. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    Energy Technology Data Exchange (ETDEWEB)

    Kamiyama, H. (Aomori Public College, 153-4 Yamazaki, Goushi-zawa, Aomori 030-01 (Japan)); Rafii-Tabar, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Kawazoe, Y. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan)); Matsui, H. (Institute for Materials Research, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980 (Japan))

    1994-09-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  9. An MD simulation of interactions between self-interstitial atoms and edge dislocation in bcc transition metals

    International Nuclear Information System (INIS)

    Kamiyama, H.; Rafii-Tabar, H.; Kawazoe, Y.; Matsui, H.

    1994-01-01

    According to our model on the mechanism of dislocation bias reduction based on the interaction of dumbbell self-interstitial atoms (SIAs) with dislocation, the bias is significantly different depending on the dumbbell configuration in the dislocation strain field. A large-scale molecular dynamics (MD) simulation is performed to reveal the stability and the mechanism of diffusion of dumbbell SIAs near the edge dislocation core in bcc iron. Most SIAs take the crowdion configuration parallel to the Burgers vector in the expansion side of the dislocation. Such crowdions are stable in the temperature range of this simulation, i.e. between 373 and 473 K, making one-dimensional random to-and-fro motion parallel to the dislocation Burgers vector staying at several atomic layers ''below'' the dislocation core. This means that the SIA does not approach the dislocation core. These results suggest that the stable configuration of SIAs is seriously affected by the dislocation resulting in a reduction of bias factor. ((orig.))

  10. MD simulation of plastic deformation nucleation in stressed crystallites under irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Korchuganov, A. V., E-mail: avkor@ispms.tsc.ru; Zolnikov, K. P., E-mail: kost@ispms.tsc.ru; Kryzhevich, D. S., E-mail: kryzhev@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation); Chernov, V. M., E-mail: VMChernov@bochvar.ru [National Research Tomsk State University (Russian Federation); Psakhie, S. G., E-mail: sp@ispms.tsc.ru [Russian Academy of Sciences, Institute of Strength Physics and Materials Science, Siberian Branch (Russian Federation)

    2016-12-15

    The investigation of plastic deformation nucleation in metals and alloys under irradiation and mechanical loading is one of the topical issues of materials science. Specific features of nucleation and evolution of the defect system in stressed and irradiated iron, vanadium, and copper crystallites were studied by molecular dynamics simulation. Mechanical loading was performed in such a way that the modeled crystallite volume remained unchanged. The energy of the primary knock-on atom initiating a cascade of atomic displacements in a stressed crystallite was varied from 0.05 to 50 keV. It was found that atomic displacement cascades might cause global structural transformations in a region far larger than the radiation-damaged area. These changes are similar to the ones occurring in the process of mechanical loading of samples. They are implemented by twinning (in iron and vanadium) or through the formation of partial dislocation loops (in copper).

  11. Bicelles and Other Membrane Mimics: Comparison of Structure, Properties, and Dynamics from MD Simulations

    DEFF Research Database (Denmark)

    Vestergaard, Mikkel; Kraft, Johan Frederik; Vosegaard, Thomas

    2015-01-01

    present molecular dynamics simulations to elucidate structural and dynamic properties of small bicelles and compare them to a large alignable bicelle, a small nanodisc, and a lipid bilayer. Properties such as lipid packing and properties related to embedding both an α-helical peptide and a transmembrane...... protein are investigated. The small bicelles are found to be very dynamic and mainly assume a prolate shape substantiating that small bicelles cannot be regarded as well-defined disclike structures. However, addition of a peptide results in an increased tendency to form disc-shaped bicelles. The small......The increased interest in studying membrane proteins has led to the development of new membrane mimics such as bicelles and nanodiscs. However, only limited knowledge is available of how these membrane mimics are affected by embedded proteins and how well they mimic a lipid bilayer. Herein, we...

  12. 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.

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

    KAUST Repository

    Ghaffour, NorEddine; Francis, Lijo; Li, Zhenyu; Valladares, Rodrigo; Alsaadi, Ahmad S.; Ghdaib, Muhannad Abu; Amy, Gary L.

    2016-01-01

    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.

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

    International Nuclear Information System (INIS)

    Tikhonchev, M.; Svetukhin, V.; Kadochkin, A.; Gaganidze, E.

    2009-01-01

    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 ∼0.2 NRT that is slightly higher than for pure α-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.

  15. 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.

  16. 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.

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

    Science.gov (United States)

    Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul

    2015-01-01

    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. PMID:26545107

  18. MD simulation of atomic displacements in metals and metallic bilayers under low energy ion bombardment at 300 K

    International Nuclear Information System (INIS)

    Kornich, G.V.; Betz, G.; Bazhin, A.I.

    1999-01-01

    MD simulations of 100 eV Ar ion bombardment of (1 0 0) Ni and Al as well as Al/Ni bilayer crystals at 300 K have been performed and compared to previous calculations at 0 K. The Al/Ni bilayer crystal consisted of one Al layer on a (1 0 0) Ni substrate. Sputtering yields for Ni and Al/Ni show no temperature dependence, while for Al a pronounced increase with temperature was observed. The contributions of different mechanisms to the production of surface and bulk defects are discussed. The mean square displacement (MSD) of atoms is in all cases larger at 300 K as compared to 0 K. The larger MSD at 300 K is mainly due to an increase in lateral (perpendicular to the ion beam) motion of displaced atoms. Similar the number of atomic jumps, in which an atom leaves its original Wigner-Seitz cell, increases in all cases with temperature. For the pure elements the production of bulk vacancies and interstitials decreases with temperature, but the number of surface vacancies and ad-atoms increases with temperature. For the bilayer system practically no temperature dependence for defects was observed

  19. Theoretical investigation on the inclusion of TCDD with β-cyclodextrin by performing QM calculations and MD simulations

    International Nuclear Information System (INIS)

    Pan, Wenxiao; Zhang, Dongju; Zhan, Jinhua

    2011-01-01

    Highlights: → We study the inclusion mechanism of TCDD with β-CD by theoretical methods. → Clearly, the formation of inclusion complex is an energetically driven process. → The inclusion complex can be detected by IR and Raman techniques. → The results imply that β-CD may be used as a host molecule to enrich TCDD molecules. - Abstract: The rapid enrichment and detection of trace polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) are currently challenging issues in the field of environmental science. In this paper, by performing quantum chemistry (QM) calculations and molecular dynamics (MD) simulations, we studied the inclusion complexation of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a representative PCDD molecule, with β-cyclodextrin (β-CD), one of the widely used compounds in supramolecular chemistry. The calculated results reveal that the stable inclusion complex can be formed in both the gas phase and solvent, which proposes that β-CD may serve as a potential substrate enriching TCDD. The calculated vibrational spectra indicate that the infrared (IR) and Raman spectroscopy may be suitable for the detection of β-CD-modified TCDD. The present theoretical results may be informative to environmental scientists who are devoting themselves to developing effective methods for detection and treatment of POPs.

  20. Detailed regulatory mechanism of the interaction between ZO-1 PDZ2 and connexin43 revealed by MD simulations.

    Directory of Open Access Journals (Sweden)

    Fei Xiao

    Full Text Available The gap junction protein connexin43 (Cx43 binds to the second PDZ domain of Zonula occludens-1 (ZO-1 through its C-terminal tail, mediating the regulation of gap junction plaque size and dynamics. Biochemical study demonstrated that the very C-terminal 12 residues of Cx43 are necessary and sufficient for ZO-1 PDZ2 binding and phosphorylation at residues Ser (-9 and Ser (-10 of the peptide can disrupt the association. However, only a crystal structure of ZO-1 PDZ2 in complex with a shorter 9 aa peptide of connexin43 was solved experimentally. Here, the interactions between ZO-1 PDZ2 and the short, long and phosphorylated Cx43 peptides were studied using molecular dynamics (MD simulations and free energy calculation. The short peptide bound to PDZ2 exhibits large structural variations, while the extension of three upstream residues stabilizes the peptide conformation and enhanced the interaction. Phosphorylation at Ser(-9 significantly weakens the binding and results in conformational flexibility of the peptide. Glu210 of ZO-1 PDZ2 was found to be a key regulatory point in Cx43 binding and phosphorylation induced dissociation.

  1. Water simulation of sodium reactors

    International Nuclear Information System (INIS)

    Grewal, S.S.; Gluekler, E.L.

    1981-01-01

    The thermal hydraulic simulation of a large sodium reactor by a scaled water model is examined. The Richardson Number, friction coefficient and the Peclet Number can be closely matched with the water system at full power and the similarity is retained for buoyancy driven flows. The simulation of thermal-hydraulic conditions in a reactor vessel provided by a scaled water experiment is better than that by a scaled sodium test. Results from a correctly scaled water test can be tentatively extrapolated to a full size sodium system

  2. An apparatus to measure water optical attenuation length for LHAASO-MD

    Science.gov (United States)

    Li, Cong; Xiao, Gang; Feng, Shaohui; Wang, Lingyu; Li, Xiurong; Zuo, Xiong; Cheng, Ning; Wang, Hui; Gao, Bo; Duan, Zhihao; Liu, Jia; He, Huihai; Saeed, Mohsin; Lhaaso Collaboration

    2018-06-01

    The large high altitude air shower observatory (LHAASO) is being constructed at 4400 m a.s.l. in Daocheng, Sichuan Province, aiming to reveal the secrets of cosmic rays origin. And it has the largest surface muon detector array in the world. Due to the needs of calibration and construction of muon detector, we developed a water optical attenuation measurement device using an 8 m long water tank. The results are presented for filtered water at wavelength of 405 nm, which proves this apparatus can reach an accuracy of about 20% at 100 m. This apparatus has not only a high precision measurement of water attenuation length up to 100 m but is also very convenient to be used, which is crucial for water optical properties study during LHAASO detector construction.

  3. 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.

  4. Supramolecular architecture of 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole.3H2O: Synthesis, spectroscopic investigations, DFT computation, MD simulations and docking studies

    Science.gov (United States)

    Murthy, P. Krishna; Smitha, M.; Sheena Mary, Y.; Armaković, Stevan; Armaković, Sanja J.; Rao, R. Sreenivasa; Suchetan, P. A.; Giri, L.; Pavithran, Rani; Van Alsenoy, C.

    2017-12-01

    Crystal and molecular structure of newly synthesized compound 5-bromo-7-methoxy-1-methyl-1H-benzoimidazole (BMMBI) has been authenticated by single crystal X-ray diffraction, FT-IR, FT-Raman, 1H NMR, 13C NMR and UV-Visible spectroscopic techniques; compile both experimental and theoretical results which are performed by DFT/B3LYP/6-311++G(d,p) method at ground state in gas phase. Visualize nature and type of intermolecular interactions and crucial role of these interactions in supra-molecular architecture has been investigated by use of a set of graphical tools 3D-Hirshfeld surfaces and 2D-fingerprint plots analysis. The title compound stabilized by strong intermolecular hydrogen bonds N⋯Hsbnd O and O⋯Hsbnd O, which are envisaged by dark red spots on dnorm mapped surfaces and weak Br⋯Br contacts envisaged by red spot on dnorm mapped surface. The detailed fundamental vibrational assignments of wavenumbers were aid by with help of Potential Energy distribution (PED) analysis by using GAR2PED program and shows good agreement with experimental values. Besides frontier orbitals analysis, global reactivity descriptors, natural bond orbitals and Mullikan charges analysis were performed by same basic set at ground state in gas phase. Potential reactive sites of the title compound have been identified by ALIE, Fukui functions and MEP, which are mapped to the electron density surfaces. Stability of BMMBI have been investigated from autoxidation process and pronounced interaction with water (hydrolysis) by using bond dissociation energies (BDE) and radial distribution functions (RDF), respectively after MD simulations. In order to identify molecule's most important reactive spots we have used a combination of DFT calculations and MD simulations. Reactivity study encompassed calculations of a set of quantities such as: HOMO-LUMO gap, MEP and ALIE surfaces, Fukui functions, bond dissociation energies and radial distribution functions. To confirm the potential

  5. 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.

  6. 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...

  7. 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

    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...

  8. Prediction and analysis of the structure of hydrated Mn2+, V2+, Ti3 and Cr3 ions by means of the MD simulation methods

    International Nuclear Information System (INIS)

    Iglesias, Y.J.

    2002-01-01

    Classical Molecular dynamics (MD) and hybrid Quantum/Molecular Mechanics-Molecular Dynamics (QM/MM-MD) simulations have been performed to investigate structural properties of Mn(II), V(II), Cr(III) and Ti(III) cations in aqueous solution. The first hydration sphere in QM/MM-MD simulations is treated quantum mechanically, while the rest of the system is described by classical analytical two- and three-body potentials. The results obtained for the first hydration shell from this method are in agreement with experimental data, showing 100 % of 6 fold coordination around the ion in all cases. The results prove that non/additive contributions are mandatory for an accurate description of ion hydration. Within the QM/MM method, the inclusion of a perturbation field describing the remaining system was shown to be an accurate tool for evaluating the first shell structure, and thus to be a good alternative for systems, where the construction of a three-body correction function is difficult or too time-consuming. (author)

  9. Water adsorption on amorphous silica surfaces: a Car-Parrinello simulation study

    International Nuclear Information System (INIS)

    Mischler, Claus; Horbach, Juergen; Kob, Walter; Binder, Kurt

    2005-01-01

    A combination of classical molecular dynamics (MD) and ab initio Car-Parrinello molecular dynamics (CPMD) simulations is used to investigate the adsorption of water on a free amorphous silica surface. From the classical MD, SiO 2 configurations with a free surface are generated which are then used as starting configurations for the CPMD. We study the reaction of a water molecule with a two-membered ring at the temperature T = 300 K. We show that the result of this reaction is the formation of two silanol groups on the surface. The activation energy of the reaction is estimated and it is shown that the reaction is exothermic

  10. Homogeneous nucleation of water in argon : nucleation rate computation from molecular simulations of TIP4P and TIP4P/2005 water model

    NARCIS (Netherlands)

    Dumitrescu, Lucia R.; Smeulders, David M.J.; Dam, Jacques A.M.; Gaastra-Nedea, Silvia V.

    2017-01-01

    Molecular dynamics (MD) simulations were conducted to study nucleation of water at 350 K in argon using TIP4P and TIP4P/2005 water models. We found that the stability of any cluster, even if large, strongly depends on the energetic interactions with its vicinity, while the stable clusters change

  11. Enhanced Dynamics of Hydrated tRNA on Nanodiamond Surfaces: A Combined Neutron Scattering and MD Simulation Study.

    Science.gov (United States)

    Dhindsa, Gurpreet K; Bhowmik, Debsindhu; Goswami, Monojoy; O'Neill, Hugh; Mamontov, Eugene; Sumpter, Bobby G; Hong, Liang; Ganesh, Panchapakesan; Chu, Xiang-Qiang

    2016-09-14

    Nontoxic, biocompatible nanodiamonds (ND) have recently been implemented in rational, systematic design of optimal therapeutic use in nanomedicines. However, hydrophilicity of the ND surface strongly influences structure and dynamics of biomolecules that restrict in situ applications of ND. Therefore, fundamental understanding of the impact of hydrophilic ND surface on biomolecules at the molecular level is essential. For tRNA, we observe an enhancement of dynamical behavior in the presence of ND contrary to generally observed slow motion at strongly interacting interfaces. We took advantage of neutron scattering experiments and computer simulations to demonstrate this atypical faster dynamics of tRNA on ND surface. The strong attractive interactions between ND, tRNA, and water give rise to unlike dynamical behavior and structural changes of tRNA in front of ND compared to without ND. Our new findings may provide new design principles for safer, improved drug delivery platforms.

  12. Water Quality Analysis Simulation Program (WASP)

    Science.gov (United States)

    The Water Quality Analysis Simulation Program (WASP) model helps users interpret and predict water quality responses to natural phenomena and manmade pollution for various pollution management decisions.

  13. MD simulation of organics adsorption from aqueous solution in carbon slit-like pores. Foundations of the pore blocking effect

    International Nuclear Information System (INIS)

    Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester; Zieliński, Wojciech; Włoch, Jerzy; Kowalczyk, Piotr

    2014-01-01

    The results of systematic studies of organics adsorption from aqueous solutions (at the neutral pH level) in a system of slit-like carbon pores having different sizes and oxygen groups located at the pore mouth are reported. Using molecular dynamics simulations (GROMACS package) the properties of adsorbent–adsorbate (benzene, phenol or paracetamol) as well as adsorbent–water systems are discussed. After the introduction of surface oxygen functionalities, adsorption of organic compounds decreases (in accordance with experimental data) and this is caused by the accumulation of water molecules at pore entrances. The pore blocking effect decreases with the diameter of slits and practically vanishes for widths larger than approx. 0.68 nm. We observed the increase in phenol adsorption with the rise in temperature. Moreover, adsorbed molecules occupy the external surface of the slit pores (the entrances) in the case of oxidized adsorbents. Among the studied molecules benzene, phenol and paracetamol prefer an almost flat orientation and with the rise in the pore width the number of molecules oriented in parallel decreases. The decrease or increase in temperature (with respect to 298 K) leads to insignificant changes of angular orientation of adsorbed molecules. (paper)

  14. Molecular dynamics simulations of a flexible polyethylene: a protein-like behaviour in a water solvent

    International Nuclear Information System (INIS)

    Kretov, D.A.; Kholmurodov, Kh.T.

    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 general-purpose DL P OLY code and the generic DREIDING force field. The MD simulations were performed on the parallel computers and special-purpose MDGRAPE-2 machine

  15. MD simulation of the Tat/Cyclin T1/CDK9 complex revealing the hidden catalytic cavity within the CDK9 molecule upon Tat binding.

    Directory of Open Access Journals (Sweden)

    Kaori Asamitsu

    Full Text Available In this study, we applied molecular dynamics (MD simulation to analyze the dynamic behavior of the Tat/CycT1/CDK9 tri-molecular complex and revealed the structural changes of P-TEFb upon Tat binding. We found that Tat could deliberately change the local flexibility of CycT1. Although the structural coordinates of the H1 and H2 helices did not substantially change, H1', H2', and H3' exhibited significant changes en masse. Consequently, the CycT1 residues involved in Tat binding, namely Tat-recognition residues (TRRs, lost their flexibility with the addition of Tat to P-TEFb. In addition, we clarified the structural variation of CDK9 in complex with CycT1 in the presence or absence of Tat. Interestingly, Tat addition significantly reduced the structural variability of the T-loop, thus consolidating the structural integrity of P-TEFb. Finally, we deciphered the formation of the hidden catalytic cavity of CDK9 upon Tat binding. MD simulation revealed that the PITALRE signature sequence of CDK9 flips the inactive kinase cavity of CDK9 into the active form by connecting with Thr186, which is crucial for its activity, thus presumably recruiting the substrate peptide such as the C-terminal domain of RNA pol II. These findings provide vital information for the development of effective novel anti-HIV drugs with CDK9 catalytic activity as the target.

  16. Unique structure and dynamics of the EphA5 ligand binding domain mediate its binding specificity as revealed by X-ray crystallography, NMR and MD simulations.

    Directory of Open Access Journals (Sweden)

    Xuelu Huan

    Full Text Available The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD, which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J-K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity

  17. On the application of accelerated molecular dynamics to liquid water simulations.

    Science.gov (United States)

    de Oliveira, César Augusto F; Hamelberg, Donald; McCammon, J Andrew

    2006-11-16

    Our group recently proposed a robust bias potential function that can be used in an efficient all-atom accelerated molecular dynamics (MD) approach to simulate the transition of high energy barriers without any advance knowledge of the potential-energy landscape. The main idea is to modify the potential-energy surface by adding a bias, or boost, potential in regions close to the local minima, such that all transitions rates are increased. By applying the accelerated MD simulation method to liquid water, we observed that this new simulation technique accelerates the molecular motion without losing its microscopic structure and equilibrium properties. Our results showed that the application of a small boost energy on the potential-energy surface significantly reduces the statistical inefficiency of the simulation while keeping all the other calculated properties unchanged. On the other hand, although aggressive acceleration of the dynamics simulation increases the self-diffusion coefficient of water molecules greatly and dramatically reduces the correlation time of the simulation, configurations representative of the true structure of liquid water are poorly sampled. Our results also showed the strength and robustness of this simulation technique, which confirm this approach as a very useful and promising tool to extend the time scale of the all-atom simulations of biological system with explicit solvent models. However, we should keep in mind that there is a compromise between the strength of the boost applied in the simulation and the reproduction of the ensemble average properties.

  18. Do SiO 2 and carbon-doped SiO 2 nanoparticles melt? Insights from QM/MD simulations and ramifications regarding carbon nanotube growth

    Science.gov (United States)

    Page, Alister J.; Chandrakumar, K. R. S.; Irle, Stephan; Morokuma, Keiji

    2011-05-01

    Quantum chemical molecular dynamics (QM/MD) simulations of pristine and carbon-doped SiO 2 nanoparticles have been performed between 1000 and 3000 K. At temperatures above 1600 K, pristine nanoparticle SiO 2 decomposes rapidly, primarily forming SiO. Similarly, carbon-doped nanoparticle SiO 2 decomposes at temperatures above 2000 K, primarily forming SiO and CO. Analysis of the physical states of these pristine and carbon-doped SiO 2 nanoparticles indicate that they remain in the solid phase throughout decomposition. This process is therefore one of sublimation, as the liquid phase is never entered. Ramifications of these observations with respect to presently debated mechanisms of carbon nanotube growth on SiO 2 nanoparticles will be discussed.

  19. 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...

  20. 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…

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

    Energy Technology Data Exchange (ETDEWEB)

    Jo, Ju-Yeon, E-mail: ju8879@kuchem.kyoto-u.ac.jp; Ito, Hironobu, E-mail: h.ito@kuchem.kyoto-u.ac.jp; Tanimura, Yoshitaka, E-mail: tanimura@kuchem.kyoto-u.ac.jp

    2016-12-20

    Frequency-domain two-dimensional (2D) 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 molecular dynamics (MD) simulation algorithm. An appropriate representation of the 2D Raman spectrum obtained from MD simulations provides an easy-to-understand depiction of structural and dynamical properties. We elucidate mechanisms governing the 2D signal profiles involving anharmonic mode–mode coupling and the nonlinearities of the polarizability for the intermolecular and intramolecular vibrational modes. The predicted signal profiles 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. Moreover, the MD simulation results allow us to visualize the molecular structure and dynamics by comparing the accurately calculated spectrum with experimental result.

  2. 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.

  3. 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.

  4. 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.

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

    International Nuclear Information System (INIS)

    2007-01-01

    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.

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

    International Nuclear Information System (INIS)

    Kritz, A.; Keyes, D.

    2007-01-01

    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

  7. QM/MM MD and Free Energy Simulation Study of Methyl Transfer Processes Catalyzed by PKMTs and PRMTs.

    Science.gov (United States)

    Chu, Yuzhuo; Guo, Hong

    2015-09-01

    Methyl transfer processes catalyzed by protein lysine methyltransferases (PKMTs) and protein arginine methyltransferases (PRMTs) control important biological events including transcriptional regulation and cell signaling. One important property of these enzymes is that different PKMTs and PRMTs catalyze the formation of different methylated product (product specificity). These different methylation states lead to different biological outcomes. Here, we review the results of quantum mechanics/molecular mechanics molecular dynamics and free energy simulations that have been performed to study the reaction mechanism of PKMTs and PRMTs and the mechanism underlying the product specificity of the methyl transfer processes.

  8. 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 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...

  9. Experimental analysis of solar thermal integrated MD system for cogeneration of drinking water and hot water for single family villa in dubai using flat plate and evacuated tube solar collectors

    DEFF Research Database (Denmark)

    Asim, Muhammad; Imran, Muhammad; Leung, Michael K.H.

    2017-01-01

    This paper presents the experimental analysis performed on solar thermal integrated membrane distillation (MD) system using flat plate and evacuated tube collectors. The system will be utilized for cogeneration of drinking water and domestic hot water for single family in Dubai comprising of four...... to five members. Experiments have been performed in Ras Al Khaimah Research and Innovation Centre (RAKRIC) facility. The experimental setup has been installed to achieve the required production of 15–25 L/d of drinking water and 250 L/d of hot water for domestic purposes. Experiments have been performed...

  10. MD Simulation on Collision Behavior Between Nano-Scale TiO₂ Particles During Vacuum Cold Spraying.

    Science.gov (United States)

    Yao, Hai-Long; Yang, Guan-Jun; Li, Chang-Jiu

    2018-04-01

    Particle collision behavior influences significantly inter-nano particle bonding formation during the nano-ceramic coating deposition by vacuum cold spraying (or aerosol deposition method). In order to illuminate the collision behavior between nano-scale ceramic particles, molecular dynamic simulation was applied to explore impact process between nano-scale TiO2 particles through controlling impact velocities. Results show that the recoil efficiency of the nano-scale TiO2 particle is decreased with the increase of the impact velocity. Nano-scale TiO2 particle exhibits localized plastic deformation during collision at low velocities, while it is intensively deformed by collision at high velocities. This intensive deformation promotes the nano-particle adhesion rather than rebounding off. A relationship between the adhesion energy and the rebound energy is established for the bonding formation of the nano-scale TiO2 particle. The adhesion energy required to the bonding formation between nano-scale ceramic particles can be produced by high velocity collision.

  11. 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.

  12. Injector MD Days 2017

    CERN Document Server

    Rumolo, G

    2017-01-01

    The Injector Machine Development (MD) days 2017 were held on 23-24 March, 2017, at CERN with thefollowing main goals:Give a chance to the MD users to present their results and show the relevant progress made in 2016 onseveral fronts.Provide the MD users and the Operation (OP) crews with a general overview on the outcome and theimpact of all ongoing MD activities.Identify the open questions and consequently define - with priorities - a list of machine studies in theinjectors for 2017 (covering the operational beams, LHC Injectors Upgrade, High Luminosity LHC,Physics Beyond Colliders, other projects).Create the opportunity to collect and document the highlights of the 2016 MDs and define the perspectivesfor 2017.Discuss how to make best use of the MD time, in particular let the main MD user express their wishesand see whether/how OP teams can contribute to their fulfilment.

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

    International Nuclear Information System (INIS)

    Bhattacharya, Debarati; Rao, T.V. Chandrasekhar; Bhushan, K.G.; Ali, Kawsar; Debnath, A.; Singh, S.; Arya, A.; Bhattacharya, S.; Basu, S.

    2015-01-01

    Monophasic and homogeneous Ni 10 Zr 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 10 Zr 7 alloy thin films deposited successfully by co-sputtering. • Creation of a crystalline alloy in a binary system with a tendency to amorphize. • Quantitative

  14. Boiling water reactor simulator. Workshop material

    International Nuclear Information System (INIS)

    2003-01-01

    The International Atomic Energy Agency (IAEA) has established an activity in nuclear reactor simulation computer programs to assist its Member States in education. The objective is to provide, for a variety of advanced reactor types, insight and practice in their operational characteristics and their response to perturbations and accident situations. To achieve this, the IAEA arranges for the development and distribution of simulation programs and workshop material and sponsors workshops. The workshops are in two parts: techniques and tools for reactor simulator development; and the use of reactor simulators in education. Workshop material for the first part is covered in the IAEA publication: Training Course Series No. 12, 'Reactor Simulator Development' (2001). Course material for workshops using a WWER- 1000 simulator from the Moscow Engineering and Physics Institute, Russian Federation is presented in the IAEA publication: Training Course Series No. 21 'WWER-1000 Reactor Simulator' (2002). Course material for workshops using a pressurized water reactor (PWR) simulator developed by Cassiopeia Technologies Incorporated, Canada, is presented in the IAEA publication: Training Course Series No. 22 'Pressurized Water Reactor Simulator' (2003). This report consists of course material for workshops using a boiling water reactor (BWR) simulator. Cassiopeia Technologies Incorporated, developed the simulator and prepared this report for the IAEA

  15. 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.

  16. Heterogeneous structure and solvation dynamics of DME/water binary mixtures: A combined spectroscopic and simulation investigation

    Science.gov (United States)

    Das Mahanta, Debasish; Rana, Debkumar; Patra, Animesh; Mukherjee, Biswaroop; Mitra, Rajib Kumar

    2018-05-01

    Water is often found in (micro)-heterogeneous environments and therefore it is necessary to understand their H-bonded network structure in such altered environments. We explore the structure and dynamics of water in its binary mixture with relatively less polar small biocompatible amphiphilic molecule 1,2-Dimethoxyethane (DME) by a combined spectroscopic and molecular dynamics (MD) simulation study. Picosecond (ps) resolved fluorescence spectroscopy using coumarin 500 as the fluorophore establishes a non-monotonic behaviour of the mixture. Simulation studies also explore the various possible H-bond formations between water and DME. The relative abundance of such different water species manifests the heterogeneity in the mixture.

  17. Pressurized water reactor simulator. Workshop material

    International Nuclear Information System (INIS)

    2003-01-01

    The International Atomic Energy Agency (IAEA) has established an activity in nuclear reactor simulation computer programs to assist its Member States in education. The objective is to provide, for a variety of advanced reactor types, insight and practice in their operational characteristics and their response to perturbations and accident situations. To achieve this, the IAEA arranges for the development and distribution of simulation programs and educational material and sponsors courses and workshops. The workshops are in two parts: techniques and tools for reactor simulator development; and the use of reactor simulators in education. Workshop material for the first part is covered in the IAEA Training Course Series No. 12, 'Reactor Simulator Development' (2001). Course material for workshops using a WWER- 1000 reactor department simulator from the Moscow Engineering and Physics Institute, the Russian Federation is presented in the IAEA Training Course Series No. 21 'WWER-1000 Reactor Simulator' (2002). Course material for workshops using a boiling water reactor simulator developed for the IAEA by Cassiopeia Technologies Incorporated of Canada (CTI) is presented in the IAEA publication: Training Course Series No.23 'Boiling Water Reactor Simulator' (2003). This report consists of course material for workshops using a pressurized water reactor simulator

  18. Enhancement Corrosion Resistance of (γ-Glycidyloxypropyl-Silsesquioxane-Titanium Dioxide Films and Its Validation by Gas Molecule Diffusion Coefficients Using Molecular Dynamics (MD Simulation

    Directory of Open Access Journals (Sweden)

    Haiyan Wang

    2014-01-01

    Full Text Available Based on silsesquioxanes (SSO derived from the hydrolytic condensation of (γ-glycidyloxypropyltrimethoxysilane (GPMS and titanium tetrabutoxide (TTB, hybrid films on aluminum alloy (AA, film-GPMS-SSO (f-GS and f-GS-TTBi% (f-GSTT5%–25%, i = 5, 10, 15, 20 and 25 wt%, were prepared and tested by electrochemical measurements with typical potentiodynamic polarization curves. The Icorr values of the samples were significantly lower, comparing with the Icorr values of the f-GS, AA and f-GS modified tetraethoxysilane (TEOS in the previous study, which implies that the TTB5%–25% (TiO2 additions in the coatings indeed enhance the electrochemical corrosion resistance. Correlations between the film structures and anticorrosion properties were discussed. To validate the corresponding anticorrosion experiment results, different 3D-amorphous cubic unit cells were employed as models to investigate the self-diffusion coefficient (SDC for SO2, NO2 and H2O molecules by molecular dynamics (MD simulation. All of the SDCs calculated for SO2, NO2 and H2O diffusing in f-GSTT5%–25% cells were less than the SDCs in f-GS. These results validated the corresponding anticorrosion experiment results.

  19. Integral Pressurized Water Reactor Simulator Manual

    International Nuclear Information System (INIS)

    2017-01-01

    This publication provides detailed explanations of the theoretical concepts that the simulator users have to know to gain a comprehensive understanding of the physics and technology of integral pressurized water reactors. It provides explanations of each of the simulator screens and various controls that a user can monitor and modify. A complete description of all the simulator features is also provided. A detailed set of exercises is provided in the Exercise Handbook accompanying this publication.

  20. Stormwater management impacts on urban stream water quality and quantity during and after development in Clarksburg, MD

    Science.gov (United States)

    Loperfido, J. V.; Noe, G. B.; Jarnagin, S.; Mohamoud, Y. M.; Van Ness, K.; Hogan, D. M.

    2012-12-01

    Urbanization and urban land use leads to degradation of local stream habitat and 'urban stream syndrome.' Best Management Practices (BMPs) are often used in an attempt to mitigate the impact of urban land use on stream water quality and quantity. Traditional development has employed stormwater BMPs that were placed in a centralized manner located either in the stream channel or near the riparian zone to treat stormwater runoff from large drainage areas; however, urban streams have largely remained impaired. Recently, distributed placement of BMPs throughout the landscape has been implemented in an attempt to detain, treat, and infiltrate stormwater runoff from smaller drainage areas near its source. Despite increasing implementation of distributed BMPs, little has been reported on the catchment-scale (1-10 km^2) performance of distributed BMPs and how they compare to centralized BMPs. The Clarksburg Special Protection Area (CSPA), located in the Washington, DC exurbs within the larger Chesapeake Bay watershed, is undergoing rapid urbanization and employs distributed BMPs on the landscape that treat small drainage areas with the goal of preserving high-quality stream resources in the area. In addition, the presence of a nearby traditionally developed (centralized BMPs) catchment and an undeveloped forested catchment makes the CSPA an ideal setting to understand how the best available stormwater management technology implemented during and after development affects stream water quality and quantity through a comparative watershed analysis. The Clarksburg Integrated Monitoring Partnership is a consortium of local and federal agencies and universities that conducts research in the CSPA including: monitoring of stream water quality, geomorphology, and biology; analysis of stream hydrological and water quality data; and GIS mapping and analysis of land cover, elevation change and BMP implementation data. Here, the impacts of urbanization on stream water quantity

  1. Identification of 253Md

    International Nuclear Information System (INIS)

    Kadkhodayan, B.; Czerwinski, K.R.; Kreek, S.A.; Hannink, N.J.; Gregorich, K.E.; Lee, D.M.; Nurmia, M.J.; Hoffman, D.C.; Hall, H.L.

    1992-01-01

    We have measured the half-life and production cross section of the new isotope 253 Md, produced via the 243 Am( 13 C,3n) reaction. Isolation of Md from other activities was accomplished using elution with ammonium α-hydroxyisobutyrate from a cation exchange resin column. Experiments were performed with different irradiation time intervals, but the chemical separation always began and ended at exactly the same length of time after the end of irradiation. All separations with the same irradation lengths were combined and analyzed for growth and decay of the 3.0-d 253 Fm daughter and 20.47-d 253 Es, granddaugther of 253 Md. The amount of 253 Es in each fraction depends on the length of each irradiation and the 253 Md half-life. An increase in the length of irradiation will cause a corresponding increase in the amount of the new isotope 253 Md and hence, in the amount of 253 Es produced, provided the length of irradiations are not very long compared to the half-life of 253 Md. In this way, the Md half-life was estimated to be about 6 minutes with a production cross section of the order of 50 nb. (orig.)

  2. Glass polymorphism in glycerol-water mixtures: I. A computer simulation study.

    Science.gov (United States)

    Jahn, David A; Wong, Jessina; Bachler, Johannes; Loerting, Thomas; Giovambattista, Nicolas

    2016-04-28

    We perform out-of-equilibrium molecular dynamics (MD) simulations of water-glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA-HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ(g) = 0-13% and find that, for the present mixture models and rates, the LDA-HDA transformation is detectable up to χ(g) ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ(g) ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ(g) > 5%. We present an analysis of the molecular-level changes underlying the LDA-HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA-HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA-HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the effects that

  3. Numerical simulation of sand jet in water

    Energy Technology Data Exchange (ETDEWEB)

    Azimi, A.H.; Zhu, D.; Rajaratnam, N. [Alberta Univ., Edmonton, AB (Canada). Dept. of Civil and Environmental Engineering

    2008-07-01

    A numerical simulation of sand jet in water was presented. The study involved a two-phase flow using two-phase turbulent jets. A literature review was also presented, including an experiment on particle laden air jet using laser doppler velocimetry (LDV); experiments on the effect of particle size and concentration on solid-gas jets; an experimental study of solid-liquid jets using particle image velocimetry (PIV) technique where mean velocity and fluctuations were measured; and an experimental study on solid-liquid jets using the laser doppler anemometry (LDA) technique measuring both water axial and radial velocities. Other literature review results included a photographic study of sand jets in water; a comparison of many two-phase turbulent flow; and direct numerical simulation and large-eddy simulation to study the effect of particle in gas jet flow. The mathematical model and experimental setup were also included in the presentation along with simulation results for sand jets, concentration, and kinetic energy. The presentation concluded with some proposed future studies including numerical simulation of slurry jets in water and numerical simulation of slurry jets in MFT. tabs., figs.

  4. 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.

  5. Toward a Rational Design of Bioactive Glasses with Optimal Structural Features: Composition–Structure Correlations Unveiled by Solid-State NMR and MD Simulations

    Science.gov (United States)

    2013-01-01

    The physiological responses of silicate-based bioactive glasses (BGs) are known to depend critically on both the P content (nP) of the glass and its silicate network connectivity (N̅BOSi). However, while the bioactivity generally displays a nonmonotonic dependence on nP itself, recent work suggest that it is merely the net orthophosphate content that directly links to the bioactivity. We exploit molecular dynamics (MD) simulations combined with 31P and 29Si solid-state nuclear magnetic resonance (NMR) spectroscopy to explore the quantitative relationships between N̅BOSi, nP, and the silicate and phosphate speciations in a series of Na2O–CaO–SiO2–P2O5 glasses spanning 2.1 ≤ N̅BOSi ≤ 2.9 and variable P2O5 contents up to 6.0 mol %. The fractional population of the orthophosphate groups remains independent of nP at a fixed N̅BOSi-value, but is reduced slightly as N̅BOSi increases. Nevertheless, P remains predominantly as readily released orthophosphate ions, whose content may be altered essentially independently of the network connectivity, thereby offering a route to optimize the glass bioactivity. We discuss the observed composition-structure links in relation to known composition-bioactivity correlations, and define how Na2O–CaO–SiO2–P2O5 compositions exhibiting an optimal bioactivity can be designed by simultaneously altering three key parameters: the silicate network connectivity, the (ortho)phosphate content, and the nNa/nCa molar ratio. PMID:24364818

  6. Characterization of the immersion properties of the peripheral membrane anchor of the FATC domain of the kinase "target of rapamycin" by NMR, oriented CD spectroscopy, and MD simulations.

    Science.gov (United States)

    Sommer, Lisa A M; Janke, J Joel; Bennett, W F Drew; Bürck, Jochen; Ulrich, Anne S; Tieleman, D Peter; Dames, Sonja A

    2014-05-08

    The multidomain ser/thr kinase "target of rapamycin" (TOR) centrally controls eukaryotic growth and metabolism. The C-terminal FATC domain is important for TOR regulation and was suggested to directly mediate TOR-membrane interactions. Here, we present a detailed characterization of the membrane immersion properties of the oxidized and reduced yeast TOR1 FATC domain (2438-2470 = y1fatc). The immersion depth was characterized by NMR-monitored interaction studies with DPC micelles containing paramagnetically tagged 5- or 16-doxyl stearic acid (5-/16-SASL) and by analyzing the paramagnetic relaxation enhancement (PRE) from Mn(2+) in the solvent. Complementary MD-simulations of micellar systems in the absence and presence of protein showed that 5-/16-SASL can move in the micelle and that 16-SASL can bend such that the doxyl group is close to the headgroup region and not deep in the interior as commonly assumed. Based on oriented CD (OCD) data, the single α-helix of oxidized/reduced y1fatc has an angle to the membrane normal of ∼30-60°/∼35-65° in neutral and ∼5-35°/∼0-30° in negatively charged bilayers. The presented experimentally well-founded models help to better understand how this redox-sensitive peripheral membrane anchor may be part of a network of protein-protein and protein-membrane interactions regulating TOR localization at different cellular membranes. Moreover, the presented work provides a good methodological reference for the structural characterization of other peripherally membrane associating proteins.

  7. Muscular Dystrophy (MD)

    Science.gov (United States)

    ... patients may need assisted ventilation to treat respiratory muscle weakness and a pacemaker for cardiac abnormalities. View Full Treatment Information Definition The muscular dystrophies (MD) are a group of more than 30 ...

  8. Glass polymorphism in glycerol–water mixtures: I. A computer simulation study

    Science.gov (United States)

    Jahn, David A.; Wong, Jessina; Bachler, Johannes; Loerting, Thomas

    2016-01-01

    We perform out-of-equilibrium molecular dynamics (MD) simulations of water–glycerol mixtures in the glass state. Specifically, we study the transformations between low-density (LDA) and high-density amorphous (HDA) forms of these mixtures induced by compression/decompression at constant temperature. Our MD simulations reproduce qualitatively the density changes observed in experiments. Specifically, the LDA–HDA transformation becomes (i) smoother and (ii) the hysteresis in a compression/decompression cycle decreases as T and/or glycerol content increase. This is surprising given the fast compression/decompression rates (relative to experiments) accessible in MD simulations. We study mixtures with glycerol molar concentration χ g = 0–13% and find that, for the present mixture models and rates, the LDA–HDA transformation is detectable up to χ g ≈ 5%. As the concentration increases, the density of the starting glass (i.e., LDA at approximately χ g ≤ 5%) rapidly increases while, instead, the density of HDA remains practically constant. Accordingly, the LDA state and hence glass polymorphism become inaccessible for glassy mixtures with approximately χ g > 5%. We present an analysis of the molecular-level changes underlying the LDA–HDA transformation. As observed in pure glassy water, during the LDA-to-HDA transformation, water molecules within the mixture approach each other, moving from the second to the first hydration shell and filling the first interstitial shell of water molecules. Interestingly, similar changes also occur around glycerol OH groups. It follows that glycerol OH groups contribute to the density increase during the LDA–HDA transformation. An analysis of the hydrogen bond (HB)-network of the mixtures shows that the LDA–HDA transformation is accompanied by minor changes in the number of HBs of water and glycerol. Instead, large changes in glycerol and water coordination numbers occur. We also perform a detailed analysis of the

  9. 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.

  10. Dynamics of water clusters confined in proteins: a molecular dynamics simulation study of interfacial waters in a dimeric hemoglobin.

    Science.gov (United States)

    Gnanasekaran, Ramachandran; Xu, Yao; Leitner, David M

    2010-12-23

    Water confined in proteins exhibits dynamics distinct from the dynamics of water in the bulk or near the surface of a biomolecule. We examine the water dynamics at the interface of the two globules of the homodimeric hemoglobin from Scapharca inaequivalvis (HbI) by molecular dynamics (MD) simulations, with focus on water-protein hydrogen bond lifetimes and rotational anisotropy of the interfacial waters. We find that relaxation of the waters at the interface of both deoxy- and oxy-HbI, which contain a cluster of 17 and 11 interfacial waters, respectively, is well described by stretched exponentials with exponents from 0.1 to 0.6 and relaxation times of tens to thousands of picoseconds. The interfacial water molecules of oxy-HbI exhibit slower rotational relaxation and hydrogen bond rearrangement than those of deoxy-HbI, consistent with an allosteric transition from unliganded to liganded conformers involving the expulsion of several water molecules from the interface. Though the interfacial waters are translationally and rotationally static on the picosecond time scale, they contribute to fast communication between the globules via vibrations. We find that the interfacial waters enhance vibrational energy transport across the interface by ≈10%.

  11. 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

  12. Ejection of solvated ions from electrosprayed methanol/water nanodroplets studied by molecular dynamics simulations.

    Science.gov (United States)

    Ahadi, Elias; Konermann, Lars

    2011-06-22

    The ejection of solvated small ions from nanometer-sized droplets plays a central role during electrospray ionization (ESI). Molecular dynamics (MD) simulations can provide insights into the nanodroplet behavior. Earlier MD studies have largely focused on aqueous systems, whereas most practical ESI applications involve the use of organic cosolvents. We conduct simulations on mixed water/methanol droplets that carry excess NH(4)(+) ions. Methanol is found to compromise the H-bonding network, resulting in greatly increased rates of ion ejection and solvent evaporation. Considerable differences in the water and methanol escape rates cause time-dependent changes in droplet composition. Segregation occurs at low methanol concentration, such that layered droplets with a methanol-enriched periphery are formed. This phenomenon will enhance the partitioning of analyte molecules, with possible implications for their ESI efficiencies. Solvated ions are ejected from the tip of surface protrusions. Solvent bridging prior to ion secession is more extensive for methanol/water droplets than for purely aqueous systems. The ejection of solvated NH(4)(+) is visualized as diffusion-mediated escape from a metastable basin. The process involves thermally activated crossing of a ~30 kJ mol(-1) free energy barrier, in close agreement with the predictions of the classical ion evaporation model.

  13. mdFoam+: Advanced molecular dynamics in OpenFOAM

    Science.gov (United States)

    Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

    2018-03-01

    This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

  14. Optimizing a Water Simulation based on Wavefront Parameter Optimization

    OpenAIRE

    Lundgren, Martin

    2017-01-01

    DICE, a Swedish game company, wanted a more realistic water simulation. Currently, most large scale water simulations used in games are based upon ocean simulation technology. These techniques falter when used in other scenarios, such as coastlines. In order to produce a more realistic simulation, a new one was created based upon the water simulation technique "Wavefront Parameter Interpolation". This technique involves a rather extensive preprocess that enables ocean simulations to have inte...

  15. 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%.

  16. Developing the MD Explorer

    Science.gov (United States)

    Howie, Philip V.

    1993-04-01

    The MD Explorer is an eight-seat twin-turbine engine helicopter which is being developed using integrated product definition (IPD) team methodology. New techniques include NOTAR antitorque system for directional control, a composite fuselage, an all-composite bearingless main rotor, and digital cockpit displays. Three-dimensional CAD models are the basis of the entire Explorer design. Solid models provide vendor with design clarification, removing much of the normal drawing interpretation errors.

  17. Elucidating adsorption mechanisms of phthalate esters upon carbon nanotubes/graphene and natural organic acid competitive effects in water by DFT and MD calculations

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhuang; Wang, Se; Chen, Min Dong; Xu, Defu [Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Jiangsu KeyLaboratory of Atmospheric Environment Monitoring and Pollution Control (AEMPC), School ofEnvironmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing (China); Tang, Lili [Jiangsu Environmental Monitoring Centre, Nanjing (China); Wang, Degao [Dept. of Environmental Science and Engineering, Dalian Maritime University, Dalian (China)

    2015-06-15

    Simulations at multiple levels were performed to investigate the aqueous adsorption of phthalate esters (PAEs) on carbon nanoparticles and to find the competitive effect of a low molecular weight natural organic acid (benzoic acid) on the adsorption process. Six PAEs of varying alkyl side chain lengths and three carbon-based nanomaterials including a single-walled carbon nanotube (SWNT), double-walled carbon nanotube (DWNT), and graphene (G) were studied. Results showed that the adsorption energies calculated using density functional theory increase with increasing length of the PAE alkyl chain. G exhibits higher adsorption capacity for the PAEs than SWNT and DWNT. The absolute adsorption energies of these systems also display a positive linear correlation with the hydrophobicity of the PAE molecules. Molecular dynamics simulations indicate that the presence of neutral/anionic benzoic acid in water alleviates the PAE adsorption. Furthermore, anionic benzoic acid exerts more impact on the PAE adsorption than the neutral form.

  18. Parallel Numerical Simulations of Water Reservoirs

    Science.gov (United States)

    Torres, Pedro; Mangiavacchi, Norberto

    2010-11-01

    The study of the water flow and scalar transport in water reservoirs is important for the determination of the water quality during the initial stages of the reservoir filling and during the life of the reservoir. For this scope, a parallel 2D finite element code for solving the incompressible Navier-Stokes equations coupled with scalar transport was implemented using the message-passing programming model, in order to perform simulations of hidropower water reservoirs in a computer cluster environment. The spatial discretization is based on the MINI element that satisfies the Babuska-Brezzi (BB) condition, which provides sufficient conditions for a stable mixed formulation. All the distributed data structures needed in the different stages of the code, such as preprocessing, solving and post processing, were implemented using the PETSc library. The resulting linear systems for the velocity and the pressure fields were solved using the projection method, implemented by an approximate block LU factorization. In order to increase the parallel performance in the solution of the linear systems, we employ the static condensation method for solving the intermediate velocity at vertex and centroid nodes separately. We compare performance results of the static condensation method with the approach of solving the complete system. In our tests the static condensation method shows better performance for large problems, at the cost of an increased memory usage. Performance results for other intensive parts of the code in a computer cluster are also presented.

  19. simulation of vertical water flow through vadose zone

    African Journals Online (AJOL)

    HOD

    Simulation of vertical water flow representing the release of water from the vadose zone to the aquifer of surroundings ... ground water pollution from agricultural, industrial and municipal .... Peak Flow Characteristics of Wyoming. Streams: US ...

  20. Conserved water-mediated H-bonding dynamics of catalytic Asn ...

    Indian Academy of Sciences (India)

    Prakash

    Extensive energy minimization and molecular dynamics simulation studies up to 2 ns ... Conserved water in molecular recognition; MD simulation; plant cysteine protease ..... Mustata G and Briggs J M 2004 Cluster analysis of water molecules.

  1. 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.

  2. Molecular dynamics simulations of structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces.

    Science.gov (United States)

    He, Guangzhi; Zhang, Meiyi; Zhou, Qin; Pan, Gang

    2015-09-01

    Concentration and salinity conditions are the dominant environmental factors affecting the behavior of perfluorinated compounds (PFCs) on the surfaces of a variety of solid matrices (suspended particles, sediments, and natural minerals). However, the mechanism has not yet been examined at molecular scales. Here, the structural transformation of perfluorooctane sulfonate (PFOS) at water/rutile interfaces induced by changes of the concentration level of PFOS and salt condition was investigated using molecular dynamics (MD) simulations. At low and intermediate concentrations all PFOS molecules directly interacted with the rutile (110) surface mainly by the sulfonate headgroups through electrostatic attraction, yielding a typical monolayer structure. As the concentration of PFOS increased, the molecules aggregated in a complex multi-layered structure, where an irregular assembling configuration was adsorbed on the monolayer structure by the van der Waals interactions between the perfluoroalkyl chains. When adding CaCl2 to the system, the multi-layered structure changed to a monolayer again, indicating that the addition of CaCl2 enhanced the critical concentration value to yield PFOS multilayer assemblies. The divalent Ca(2+) substituted for monovalent K(+) as the bridging counterion in PFOS adsorption. MD simulation may trigger wide applications in study of perfluorinated compounds (PFCs) from atomic/molecular scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    KAUST Repository

    Carignano, M. A.; Saeed, Y.; Aravindh, S. Assa; Roqan, Iman S.; Even, J.; Katan, C.

    2016-01-01

    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

  4. Pressure-induced transformations in glassy water: A computer simulation study using the TIP4P/2005 model

    Science.gov (United States)

    Wong, Jessina; Jahn, David A.; Giovambattista, Nicolas

    2015-08-01

    We study the pressure-induced transformations between low-density amorphous (LDA) and high-density amorphous (HDA) ice by performing out-of-equilibrium molecular dynamics (MD) simulations. We employ the TIP4P/2005 water model and show that this model reproduces qualitatively the LDA-HDA transformations observed experimentally. Specifically, the TIP4P/2005 model reproduces remarkably well the (i) structure (OO, OH, and HH radial distribution functions) and (ii) densities of LDA and HDA at P = 0.1 MPa and T = 80 K, as well as (iii) the qualitative behavior of ρ(P) during compression-induced LDA-to-HDA and decompression-induced HDA-to-LDA transformations. At the rates explored, the HDA-to-LDA transformation is less pronounced than in experiments. By studying the LDA-HDA transformations for a broad range of compression/decompression temperatures, we construct a "P-T phase diagram" for glassy water that is consistent with experiments and remarkably similar to that reported previously for ST2 water. This phase diagram is not inconsistent with the possibility of TIP4P/2005 water exhibiting a liquid-liquid phase transition at low temperatures. A comparison with previous MD simulation studies of SPC/E and ST2 water as well as experiments indicates that, overall, the TIP4P/2005 model performs better than the SPC/E and ST2 models. The effects of cooling and compression rates as well as aging on our MD simulations results are also discussed. The MD results are qualitatively robust under variations of cooling/compression rates (accessible in simulations) and are not affected by aging the hyperquenched glass for at least 1 μs. A byproduct of this work is the calculation of TIP4P/2005 water's diffusion coefficient D(T) at P = 0.1 MPa. It is found that, for T ≥ 210 K, D(T) ≈ (T - TMCT)-γ as predicted by mode coupling theory and in agreement with experiments. For TIP4P/2005 water, TMCT = 209 K and γ = 2.14, very close to the corresponding experimental values TMCT = 221 K

  5. 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.

  6. Molecular dynamics simulations of disjoining pressure effects in ultra-thin water films on a metal surface

    Science.gov (United States)

    Hu, Han; Sun, Ying

    2013-11-01

    Disjoining pressure, the excess pressure in an ultra-thin liquid film as a result of van der Waals interactions, is important in lubrication, wetting, flow boiling, and thin film evaporation. The classic theory of disjoining pressure is developed for simple monoatomic liquids. However, real world applications often utilize water, a polar liquid, for which fundamental understanding of disjoining pressure is lacking. In the present study, molecular dynamics (MD) simulations are used to gain insights into the effect of disjoining pressure in a water thin film. Our MD models were firstly validated against Derjaguin's experiments on gold-gold interactions across a water film and then verified against disjoining pressure in an argon thin film using the Lennard-Jones potential. Next, a water thin film adsorbed on a gold surface was simulated to examine the change of vapor pressure with film thickness. The results agree well with the classic theory of disjoining pressure, which implies that the polar nature of water molecules does not play an important role. Finally, the effects of disjoining pressure on thin film evaporation in nanoporous membrane and on bubble nucleation are discussed.

  7. Homogeneous nucleation of water in argon. Nucleation rate computation from molecular simulations of TIP4P and TIP4P/2005 water model.

    Science.gov (United States)

    Dumitrescu, Lucia R; Smeulders, David M J; Dam, Jacques A M; Gaastra-Nedea, Silvia V

    2017-02-28

    Molecular dynamics (MD) simulations were conducted to study nucleation of water at 350 K in argon using TIP4P and TIP4P/2005 water models. We found that the stability of any cluster, even if large, strongly depends on the energetic interactions with its vicinity, while the stable clusters change their composition almost entirely during nucleation. Using the threshold method, direct nucleation rates are obtained. Our nucleation rates are found to be 1.08×10 27 cm -3 s -1 for TIP4P and 2.30×10 27 cm -3 s -1 for TIP4P/2005. The latter model prescribes a faster dynamics than the former, with a nucleation rate two times larger due to its higher electrostatic charges. The non-equilibrium water densities derived from simulations and state-of-art equilibrium parameters from Vega and de Miguel [J. Chem. Phys. 126, 154707 (2007)] are used for the classical nucleation theory (CNT) prediction. The CNT overestimates our results for both water models, where TIP4P/2005 shows largest discrepancy. Our results complement earlier data at high nucleation rates and supersaturations in the Hale plot [Phys. Rev. A 33, 4156 (1986)], and are consistent with MD data on the SPC/E and the TIP4P/2005 model.

  8. Effect of surface hydrophobicity on the dynamics of water at the nanoscale confinement: A molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Choudhury, Niharendu

    2013-01-01

    Highlights: • We present atomistic MD simulation of water confined between two paraffin-like plates. • Effect of plate hydrophobicity on the confined water dynamics is investigated. • Diffusivity of confined water is calculated from mean squared displacements. • Rotational dynamics of the confined water has bimodal nature of relaxation. • Monotonic dependence of translational and rotational dynamics on hydrophobicity. - Abstract: We present detailed molecular dynamics simulations of water in and around a pair of plates immersed in water to investigate the effect of degree of hydrophobicity or hydrophilicity of the plates on dynamics of water confined between the two plates. The nature of the plate has been tuned from hydrophobic to hydrophilic and vice versa by varying plate-water dispersion interaction. Analyses of the translational dynamics as performed by calculating mean squared displacements of the confined water reveal a monotonically decreasing trend of the diffusivity with increasing hydrophilicity of the plates. Orientational dynamics of the confined water also follows the same monotonic trend. Although orientational time constant almost does not change with the increase of plate-water dispersion interaction in the hydrophobic regime corresponding to the smaller plate-water attraction, it changes considerably in the hydrophilic regime corresponding to larger plate-water dispersion interactions

  9. 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

  10. Effect of water on methane adsorption on the kaolinite (0 0 1) surface based on molecular simulations

    Science.gov (United States)

    Zhang, Bin; Kang, Jianting; Kang, Tianhe

    2018-05-01

    CH4 adsorption isotherms of kaolinite with moisture contents ranging from 0 to 5 wt% water, the effects of water on maximum adsorption capacity, kaolinite swelling, and radial distribution function were modelled by the implementing combined Monte Carlo (MC) and molecular dynamics (MD) simulations at 293.15 K (20 °C) and a pressure range of 1-20 MPa. The simulation results showed that the absolute adsorption of CH4 on both dry and moist kaolinite followed a Langmuir isotherm within the simulated pressure range, and both the adsorption capacity and the rate of CH4 adsorption decreased with the water content increases. The adsorption isosteric heats of CH4 on kaolinite decreased linearly with increasing water content, indicating that at higher water contents, the interaction energy between the CH4 and kaolinite was weaker. The interaction between kaolinite and water dominates and was the main contributing factor to kaolinite clay swelling. Water molecules were preferentially adsorbed onto oxygen and hydrogen atoms in kaolinite, while methane showed a tendency to be adsorbed only onto oxygen. The simulation results of our study provide the quantitative analysis of effect of water on CH4 adsorption capacity, adsorption rate, and interaction energy from a microscopic perspective. We hope that our study will contribute to the development of strategies for the further exploration of coal bed methane and shale gas.

  11. Verina Morton Jones, MD.

    Science.gov (United States)

    Rishworth, Susan K

    2012-01-01

    The purpose of this historical article is to demonstrate, as the biography of Verina Morton Jones, MD, is uncovered, the difficulties inherent in researching original source material on the lives of 19th- and early 20th-century African American physicians as well as the great benefits derived from doing this research. The procedures used include basic archival research and close examination of published materials about her in the past, in conjunction with oral history. Original correspondence from Dr Morton Jones to her niece and nephew is used to illustrate events in her life and the thoughts and attitudes she expressed. Some of these thoughts and attitudes reflect those current situations in which African Americans found themselves, and others are quite unique, no doubt owing to her privileged position in the African American community. The principle conclusions reached include the great benefits derived from doing this kind of research, as difficult and time-consuming as that may be, with the enhanced knowledge and appreciation of the heritage of African American physicians, and insights into American social history during this period.

  12. Harold E. Varmus, MD.

    Science.gov (United States)

    Varmus, H E

    1995-06-01

    On November 19, 1993, the Senate approved the nomination of Harold E. Varmus, MD, as Director of the National Institutes of Health (NIH). Varmus, who received the 1989 Nobel Prize in Medicine, brought unquestioned credentials as a scientist to the NIH. Despite his limited background as an administrator, Varmus has received high marks from most observers for improving the morale of NIH staffers and implementing streamlined procedures in the grant review process. His tenure has not been free of controversy, however. Many clinical researchers have long felt there is a bias in NIH study sections against patient-oriented research. A recent study sponsored by the Division of Research Grants confirmed the lower success rate of patient-oriented research proposals, but the outcome of these findings remains unclear. Faced with mounting political pressure for a balanced budget, and the resultant reduction of funding to many branches of government, Varmus has been a strong voice for non-targeted investigator initiated research. Interviewed in his office in Building One on the NIH campus in Bethesda, Maryland, Varmus discussed the state of patient oriented research, the evolving role of the NIH in supporting science, and just where the money to pay for it should be found.

  13. 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 ...

  14. Structural dynamics of supercooled water from quasielastic neutron scattering and molecular simulations.

    Science.gov (United States)

    Qvist, Johan; Schober, Helmut; Halle, Bertil

    2011-04-14

    One of the outstanding challenges presented by liquid water is to understand how molecules can move on a picosecond time scale despite being incorporated in a three-dimensional network of relatively strong H-bonds. This challenge is exacerbated in the supercooled state, where the dramatic slowing down of structural dynamics is reminiscent of the, equally poorly understood, generic behavior of liquids near the glass transition temperature. By probing single-molecule dynamics on a wide range of time and length scales, quasielastic neutron scattering (QENS) can potentially reveal the mechanistic details of water's structural dynamics, but because of interpretational ambiguities this potential has not been fully realized. To resolve these issues, we present here an extensive set of high-quality QENS data from water in the range 253-293 K and a corresponding set of molecular dynamics (MD) simulations to facilitate and validate the interpretation. Using a model-free approach, we analyze the QENS data in terms of two motional components. Based on the dynamical clustering observed in MD trajectories, we identify these components with two distinct types of structural dynamics: picosecond local (L) structural fluctuations within dynamical basins and slower interbasin jumps (J). The Q-dependence of the dominant QENS component, associated with J dynamics, can be quantitatively rationalized with a continuous-time random walk (CTRW) model with an apparent jump length that depends on low-order moments of the jump length and waiting time distributions. Using a simple coarse-graining algorithm to quantitatively identify dynamical basins, we map the newtonian MD trajectory on a CTRW trajectory, from which the jump length and waiting time distributions are computed. The jump length distribution is gaussian and the rms jump length increases from 1.5 to 1.9 Å as the temperature increases from 253 to 293 K. The rms basin radius increases from 0.71 to 0.75 Å over the same range. The

  15. Simulation of dense colloids

    NARCIS (Netherlands)

    Herrmann, H.J.; Harting, J.D.R.; Hecht, M.; Ben-Naim, E.

    2008-01-01

    We present in this proceeding recent large scale simulations of dense colloids. On one hand we simulate model clay consisting of nanometric aluminum oxide spheres in water using realistic DLVO potentials and a combination of MD and SRD. We find pronounced cluster formation and retrieve the shear

  16. Equilibration and analysis of first-principles molecular dynamics simulations of water

    Science.gov (United States)

    Dawson, William; Gygi, François

    2018-03-01

    First-principles molecular dynamics (FPMD) simulations based on density functional theory are becoming increasingly popular for the description of liquids. In view of the high computational cost of these simulations, the choice of an appropriate equilibration protocol is critical. We assess two methods of estimation of equilibration times using a large dataset of first-principles molecular dynamics simulations of water. The Gelman-Rubin potential scale reduction factor [A. Gelman and D. B. Rubin, Stat. Sci. 7, 457 (1992)] and the marginal standard error rule heuristic proposed by White [Simulation 69, 323 (1997)] are evaluated on a set of 32 independent 64-molecule simulations of 58 ps each, amounting to a combined cumulative time of 1.85 ns. The availability of multiple independent simulations also allows for an estimation of the variance of averaged quantities, both within MD runs and between runs. We analyze atomic trajectories, focusing on correlations of the Kohn-Sham energy, pair correlation functions, number of hydrogen bonds, and diffusion coefficient. The observed variability across samples provides a measure of the uncertainty associated with these quantities, thus facilitating meaningful comparisons of different approximations used in the simulations. We find that the computed diffusion coefficient and average number of hydrogen bonds are affected by a significant uncertainty in spite of the large size of the dataset used. A comparison with classical simulations using the TIP4P/2005 model confirms that the variability of the diffusivity is also observed after long equilibration times. Complete atomic trajectories and simulation output files are available online for further analysis.

  17. Formulation and make-up of simulated cement modified water

    International Nuclear Information System (INIS)

    Gdowski, G.

    1997-01-01

    This procedure describes the formulation and make-up of Simulated Cement-Modified Waters (SCMW), which are aqueous solutions to be used for Activity E-20-50 Long-Term Corrosion Studies. These solutions simulate the changes to representative Yucca Mountain water chemistry because of prolonged contact with aged cement. The representative water was chosen as J-13 well water [Harrar, 1990]. J-13 well water is obtained from ground water that is in contact with the Topopah Spring tuff, which is the repository horizon rock

  18. Synergy between NMR measurements and MD simulations of protein/RNA complexes: application to the RRMs, the most common RNA recognition motifs

    Czech Academy of Sciences Publication Activity Database

    Krepl, Miroslav; Clery, A.; Blatter, M.; Allain, F.H.T.; Šponer, Jiří

    2016-01-01

    Roč. 44, č. 13 (2016), s. 6452-6470 ISSN 0305-1048 Institutional support: RVO:68081707 Keywords : molecular- dynamics simulations * particle mesh ewald * pre-ribosomal-rna Subject RIV: BO - Biophysics Impact factor: 10.162, year: 2016

  19. 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.

  20. 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.

  1. 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.

  2. Rotational dynamics in supercooled water from nuclear spin relaxation and molecular simulations.

    Science.gov (United States)

    Qvist, Johan; Mattea, Carlos; Sunde, Erik P; Halle, Bertil

    2012-05-28

    Structural dynamics in liquid water slow down dramatically in the supercooled regime. To shed further light on the origin of this super-Arrhenius temperature dependence, we report high-precision (17)O and (2)H NMR relaxation data for H(2)O and D(2)O, respectively, down to 37 K below the equilibrium freezing point. With the aid of molecular dynamics (MD) simulations, we provide a detailed analysis of the rotational motions probed by the NMR experiments. The NMR-derived rotational correlation time τ(R) is the integral of a time correlation function (TCF) that, after a subpicosecond librational decay, can be described as a sum of two exponentials. Using a coarse-graining algorithm to map the MD trajectory on a continuous-time random walk (CTRW) in angular space, we show that the slowest TCF component can be attributed to large-angle molecular jumps. The mean jump angle is ∼48° at all temperatures and the waiting time distribution is non-exponential, implying dynamical heterogeneity. We have previously used an analogous CTRW model to analyze quasielastic neutron scattering data from supercooled water. Although the translational and rotational waiting times are of similar magnitude, most translational jumps are not synchronized with a rotational jump of the same molecule. The rotational waiting time has a stronger temperature dependence than the translation one, consistent with the strong increase of the experimentally derived product τ(R) D(T) at low temperatures. The present CTRW jump model is related to, but differs in essential ways from the extended jump model proposed by Laage and co-workers. Our analysis traces the super-Arrhenius temperature dependence of τ(R) to the rotational waiting time. We present arguments against interpreting this temperature dependence in terms of mode-coupling theory or in terms of mixture models of water structure.

  3. Simulation of low pressure water hammer

    Science.gov (United States)

    Himr, D.; Habán, V.

    2010-08-01

    Numerical solution of water hammer is presented in this paper. The contribution is focused on water hammer in the area of low pressure, which is completely different than high pressure case. Little volume of air and influence of the pipe are assumed in water, which cause sound speed change due to pressure alterations. Computation is compared with experimental measurement.

  4. 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.

  5. 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.

  6. 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.

  7. Potential of mean force for ion pairs in non-aqueous solvents. Comparison of polarizable and non-polarizable MD simulations

    Science.gov (United States)

    Odinokov, A. V.; Leontyev, I. V.; Basilevsky, M. V.; Petrov, N. Ch.

    2011-01-01

    Potentials of mean force (PMF) are calculated for two model ion pairs in two non-aqueous solvents. Standard non-polarizable molecular dynamics simulation (NPMD) and approximate polarizable simulation (PMD) are implemented and compared as tools for monitoring PMF profiles. For the polar solvent (dimethylsulfoxide, DMSO) the PMF generated in terms of the NPMD reproduces fairly well the refined PMD-PMF profile. For the non-polar solvent (benzene) the conventional NPMD computation proves to be deficient. The validity of the correction found in terms of the approximate PMD approach is verified by its comparison with the result of the explicit PMD computation in benzene. The shapes of the PMF profiles in DMSO and in benzene are quite different. In DMSO, owing to dielectric screening, the PMF presents a flat plot with a shallow minimum positioned in the vicinity of the van der Waals contact of the ion pair. For the benzene case, the observed minimum proves to be unexpectedly deep, which manifests the formation of a tightly-binded contact ion pair. This remarkable effect arises owing to the strong electrostatic interaction that is incompletely screened by a non-polar medium. The PMFs for the binary benzene/DMSO mixtures display intermediate behaviour depending on the DMSO content.

  8. 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.

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

    International Nuclear Information System (INIS)

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

    2015-01-01

    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

  10. 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.

  11. 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.

  12. 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

  13. Water simulation for cell based sandbox games

    OpenAIRE

    Lundell, Christian

    2014-01-01

    This thesis work presents a new algorithm for simulating fluid based on the Navier-Stokes equations. The algorithm is designed for cell based sandbox games where interactivity and performance are the main priorities. The algorithm enforces mass conservation conservatively instead of enforcing a divergence free velocity field. A global scale pressure model that simulates hydrostatic pressure is used where the pressure propagates between neighboring cells. A prefix sum algorithm is used to only...

  14. Self-Radiolysis of Tritiated Water: Experimental Study and Simulation

    International Nuclear Information System (INIS)

    Heinze, Sylver; Stolz, Thibaut; Ducret, Didier; Colson, Jean-Claude

    2005-01-01

    Radioactive decay of tritium contained in tritiated water leads to the production of gaseous helium and, through self-radiolysis, to the formation of molecular hydrogen and oxygen. For safety management of tritiated water storage, it is essential to be able to predict pressure increase resulting from this phenomenon. The present study aims to identify the mechanisms that take place in self-radiolysis of chemically pure liquid tritiated water. The evolution of the concentration of hydrogen and oxygen in the gas phase of closed vessels containing tritiated water has been followed experimentally. Simulation of pure water radiolysis has been carried out using data from the literature. In order to fit experimental results, simulation should take into account gas phase recombination reaction between hydrogen and oxygen. A simplified system has been extracted from the complete chemical system used to simulate radiolysis. This system allows identifying the basic mechanisms that are responsible for tritiated water self-radiolysis

  15. 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

    2015-10-08

    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.

  16. Mass imbalances in EPANET water-quality simulations

    Science.gov (United States)

    Davis, Michael J.; Janke, Robert; Taxon, Thomas N.

    2018-04-01

    EPANET is widely employed to simulate water quality in water distribution systems. However, in general, the time-driven simulation approach used to determine concentrations of water-quality constituents provides accurate results only for short water-quality time steps. Overly long time steps can yield errors in concentration estimates and can result in situations in which constituent mass is not conserved. The use of a time step that is sufficiently short to avoid these problems may not always be feasible. The absence of EPANET errors or warnings does not ensure conservation of mass. This paper provides examples illustrating mass imbalances and explains how such imbalances can occur because of fundamental limitations in the water-quality routing algorithm used in EPANET. In general, these limitations cannot be overcome by the use of improved water-quality modeling practices. This paper also presents a preliminary event-driven approach that conserves mass with a water-quality time step that is as long as the hydraulic time step. Results obtained using the current approach converge, or tend to converge, toward those obtained using the preliminary event-driven approach as the water-quality time step decreases. Improving the water-quality routing algorithm used in EPANET could eliminate mass imbalances and related errors in estimated concentrations. The results presented in this paper should be of value to those who perform water-quality simulations using EPANET or use the results of such simulations, including utility managers and engineers.

  17. 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.

  18. A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A.

    Science.gov (United States)

    Sobieraj, M; Krzyśko, K A; Jarmuła, A; Kalinowski, M W; Lesyng, B; Prokopowicz, M; Cieśla, J; Gojdź, A; Kierdaszuk, B

    2015-04-01

    Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data. A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase (PNP) complexed with a fluorescent ligand - formycin A (FA). FRET occurs between an excited Tyr residue (D*) and FA (A). This study aims to interpret experimental data that, among others, suggests the absence of FRET for the PNPF159A mutant in complex with FA, based on novel theoretical methodology. MD simulations for the protein molecule containing D*, and complexed with A, are carried out. Interactions of D* with its molecular environment are accounted by including changes of the ESP charges in S1, compared to S0, and computed at the SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted emission, thus in consequence in the absence of FRET. These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wild-type PNP, which does not exist in the Ala159 mutant, and for the effective association of PNP with FA. In a more general context, our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state, which may undergo spontaneous deprotonation in the biomolecular systems, resulting further in unexpected physical and/or biological phenomena. Until now, this observation has not been widely discussed in the

  19. 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.

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

    KAUST Repository

    Yoon, Seyoon; Monteiro, Paulo J.M.

    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

  1. Pressurized water reactor simulator. Workshop material. 2. ed

    International Nuclear Information System (INIS)

    2005-01-01

    The International Atomic Energy Agency (IAEA) has established an activity in nuclear reactor simulation computer programs to assist its Member States in education. The objective is to provide, for a variety of advanced reactor types, insight and practice in their operational characteristics and their response to perturbations and accident situations. To achieve this, the IAEA arranges for the development and distribution of simulation programs and educational material and sponsors courses and workshops. The workshops are in two parts: techniques and tools for reactor simulator development. And the use of reactor simulators in education. Workshop material for the first part is covered in the IAEA Training Course Series No. 12, 'Reactor Simulator Development' (2001). Course material for workshops using a WWER- 1000 reactor department simulator from the Moscow Engineering and Physics Institute, the Russian Federation is presented in the IAEA Training Course Series No. 21, 2nd edition, 'WWER-1000 Reactor Simulator' (2005). Course material for workshops using a boiling water reactor simulator developed for the IAEA by Cassiopeia Technologies Incorporated of Canada (CTI) is presented in the IAEA publication: Training Course Series No.23, 2nd edition, 'Boiling Water Reactor Simulator' (2005). This report consists of course material for workshops using a pressurized water reactor simulator

  2. Cerenkov radiation simulation in the Auger water ground detector

    International Nuclear Information System (INIS)

    Le Van Ngoc; Vo Van Thuan; Dang Quang Thieu

    2003-01-01

    The simulation of response of the Auger water Cerenkov ground detector to atmospheric shower muons in practically needed for the experimental research of cosmic rays at extreme energies. We consider here a simulation model for the process of emission and diffusion of Cerenkov photons concerned with muons moving through the detector volume with the velocity greater than the phase velocity of light in the water on purpose to define photons producing signal in the detector. (author)

  3. Spontaneous fission of 259Md

    International Nuclear Information System (INIS)

    Hulet, E.K.; Wild, J.F.; Lougheed, R.W.; Baisden, P.A.; Landrum, J.H.; Dougan, R.J.; Mustafa, M.; Ghiorso, A.; Nitschke, J.M.

    1979-01-01

    The mass and kinetic energy distributions of fission fragments from the spontaneous fission of th newly discovered nuclide 259 Md were obtained. 259 Md was identified as the E. C. daughter of 259 No, and was found to decay entirely (> 95%) by spontaneous fission with a 95-min half-life. From the kinetic energies measured for 397 pairs of coincident fragments, a mass distribution was derived that is symmetric with sigma = 13 amu. 259 Md, together with 258 Fm and 259 Fm, form a select group of three nuclides whose mass division in spontaneous fission is highly symmetric. Unlike the total-kinetic-energy (TKE) distributions of 258 Fm and 259 Fm, which peak at approx. = to 240 MeV, this distribution for 259 Md is broad and is 50 MeV lower in energy. Analysis of the mass and energy distributions shows that events near mass symmetry also exhibit a broad TKE distribution, with one-third of the symmetric events having TKEs less than 200 MeV. The associated of low TKEs with symmetric mass division in the fission of very heavy actinides is anomalous and inconsistent with theories based upon the emergence of fragment shells near the scission point. Either three-body fragmentation or peculiar fragment shapes are assumed as the cause for the large consumption of Coulomb energy observed for a significant fraction of symmetric fissions in 259 Md. 6 figures

  4. Simulation of Water Transport through a Lipid Membrane

    NARCIS (Netherlands)

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

    1994-01-01

    To obtain insight in the process of water permeation through a lipid membrane, we performed molecular dynamics simulations on a phospholipid (DPPC)/water system with atomic detail. Since the actual process of permeation is too slow to be studied directly, we deduced the permeation rate indirectly

  5. GROWTH OF HETROTROPHIC BIOFILMS IN A WATER DISTRIBUTION SYSTEM SIMULATOR

    Science.gov (United States)

    The U.S. EPA has designed and constructed a distribution system simulator (DSS) to evaluate factors which influence water quality within water distribution systems. Six individual 25 meter lengths of 15 cm diameter ductile iron pipe are arranged into loop configurations. Each lo...

  6. Simulating water hammer with corrective smoothed particle method

    NARCIS (Netherlands)

    Hou, Q.; Kruisbrink, A.C.H.; Tijsseling, A.S.; Keramat, A.

    2012-01-01

    The corrective smoothed particle method (CSPM) is used to simulate water hammer. The spatial derivatives in the water-hammer equations are approximated by a corrective kernel estimate. For the temporal derivatives, the Euler-forward time integration algorithm is employed. The CSPM results are in

  7. Combining Rosetta with molecular dynamics (MD): A benchmark of the MD-based ensemble protein design.

    Science.gov (United States)

    Ludwiczak, Jan; Jarmula, Adam; Dunin-Horkawicz, Stanislaw

    2018-07-01

    Computational protein design is a set of procedures for computing amino acid sequences that will fold into a specified structure. Rosetta Design, a commonly used software for protein design, allows for the effective identification of sequences compatible with a given backbone structure, while molecular dynamics (MD) simulations can thoroughly sample near-native conformations. We benchmarked a procedure in which Rosetta design is started on MD-derived structural ensembles and showed that such a combined approach generates 20-30% more diverse sequences than currently available methods with only a slight increase in computation time. Importantly, the increase in diversity is achieved without a loss in the quality of the designed sequences assessed by their resemblance to natural sequences. We demonstrate that the MD-based procedure is also applicable to de novo design tasks started from backbone structures without any sequence information. In addition, we implemented a protocol that can be used to assess the stability of designed models and to select the best candidates for experimental validation. In sum our results demonstrate that the MD ensemble-based flexible backbone design can be a viable method for protein design, especially for tasks that require a large pool of diverse sequences. Copyright © 2018 Elsevier Inc. All rights reserved.

  8. Molecular dynamics simulation of a phospholipid membrane

    NARCIS (Netherlands)

    Egberts, Egbert; Marrink, Siewert-Jan; Berendsen, Herman J.C.

    We present the results of molecular dynamics (MD) simulations of a phospholipid membrane in water, including full atomic detail. The goal of the simulations was twofold: first we wanted to set up a simulation system which is able to reproduce experimental results and can serve as a model membrane in

  9. 33 CFR 110.70a - Northeast River, North East, Md.

    Science.gov (United States)

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Northeast River, North East, Md. 110.70a Section 110.70a Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY ANCHORAGES ANCHORAGE REGULATIONS Special Anchorage Areas § 110.70a Northeast River, North East, Md. The water...

  10. 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

  11. 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

  12. 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 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...

  13. 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.

  14. Local density inhomogeneities and dynamics in supercritical water: A molecular dynamics simulation approach.

    Science.gov (United States)

    Skarmoutsos, Ioannis; Samios, Jannis

    2006-11-02

    Molecular dynamics atomistic simulations in the canonical ensemble (NVT-MD) have been used to investigate the "Local Density Inhomogeneities and their Dynamics" in pure supercritical water. The simulations were carried out along a near-critical isotherm (Tr = T/Tc = 1.03) and for a wide range of densities below and above the critical one (0.2 rho(c) - 2.0 rho(c)). The results obtained reveal the existence of significant local density augmentation effects, which are found to be sufficiently larger in comparison to those reported for nonassociated fluids. The time evolution of the local density distribution around each molecule was studied in terms of the appropriate time correlation functions C(Delta)rhol(t). It is found that the shape of these functions changes significantly by increasing the density of the fluid. Finally, the local density reorganization times for the first and second coordination shell derived from these correlations exhibit a decreasing behavior by increasing the density of the system, signifying the density effect upon the dynamics of the local environment around each molecule.

  15. Kinetic Theory and Simulation of Single-Channel Water Transport

    Science.gov (United States)

    Tajkhorshid, Emad; Zhu, Fangqiang; Schulten, Klaus

    Water translocation between various compartments of a system is a fundamental process in biology of all living cells and in a wide variety of technological problems. The process is of interest in different fields of physiology, physical chemistry, and physics, and many scientists have tried to describe the process through physical models. Owing to advances in computer simulation of molecular processes at an atomic level, water transport has been studied in a variety of molecular systems ranging from biological water channels to artificial nanotubes. While simulations have successfully described various kinetic aspects of water transport, offering a simple, unified model to describe trans-channel translocation of water turned out to be a nontrivial task.

  16. Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species.

    Science.gov (United States)

    Medvedev, Kirill E; Alemasov, Nikolay A; Vorobjev, Yuri N; Boldyreva, Elena V; Kolchanov, Nikolay A; Afonnikov, Dmitry A

    2014-10-15

    The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures. The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified. The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

  17. Chemical durability of simulated nuclear glasses containing water

    International Nuclear Information System (INIS)

    Li, H.; Tomozawa, M.

    1995-04-01

    The chemical durability of simulated nuclear waste glasses having different water contents was studied. Results from the product consistency test (PCT) showed that glass dissolution increased with water content in the glass. This trend was not observed during MCC-1 testing. This difference was attributed to the differences in reactions between glass and water. In the PCT, the glass network dissolution controlled the elemental releases, and water in the glass accelerated the reaction rate. On the other hand, alkali ion exchange with hydronium played an important role in the MCC-1. For the latter, the amount of water introduced into a leached layer from ion-exchange was found to be much greater than that of initially incorporated water in the glass. Hence, the initial water content has no effect on glass dissolution as measured by the MCC-1 test

  18. MD 2179: Scraping of off-momentum halo after injection

    CERN Document Server

    Garcia Morales, Hector; Patecki, Marcin; Wretborn, Sven Joel; CERN. Geneva. ATS Department

    2018-01-01

    In this MD, a beam scraping was performed using the momentum primary collimator in IR3 where dispersion is high. A second scraping was performed using a TCSG in IR7 where dispersion is almost negligible. In such a way, we aim to disentangle the contribution of off-momentum particles to halo population. These scrapings will provide useful information to better understand the usual off-momentum losses we see at the start of the ramp. The MD results would also be used to benchmark simulations of off-momentum beam losses in order to gain confidence in simulation models.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1994-12-31

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

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

    International Nuclear Information System (INIS)

    Wei Gu; Garcia, A.E.; Schoenborn, B.P.

    1994-01-01

    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

  1. Solubility studies of Np(V) in simulated underground water

    International Nuclear Information System (INIS)

    Zhang Yingjie; Ren Lilong; Jiao Haiyang; Yao Jun; Su Xiguang; Fan Xianhua

    2004-01-01

    The solubility of Np(V) in simulated underground water has been measured with the variation of pH, storage time (0-100 days). All experiments were performed in an Ar glove box which contained high purity Ar, with an oxygen content of less than 5ppm. Experimental results show that the solubility of Np(V) in simulated underground water decreased with increasing pH value of solution; the solubility of Np(V) in simulated underground water determined at different pH is : pH=6.96, [Np(V)]=(3.52±0.37) x 10 -4 mol/L; pH=8.04, [Np(V)]=(8.24±0.32) x 10 -5 mol/L; pH=9.01, [Np(V)]=(3.04±0.48) x 10'- 5 mol/L, respectively. (author)

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

    Science.gov (United States)

    Kuniansky, E.L.; Lowery, M.A.; Campbell, B.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.

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

    International Nuclear Information System (INIS)

    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 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

  4. Pump-stopping water hammer simulation based on RELAP5

    International Nuclear Information System (INIS)

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

    2013-01-01

    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

  5. 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.

  6. Simulations of Water Migration in the Lunar Exosphere

    Science.gov (United States)

    Hurley, D.; Benna, M.; Mahaffy, P. R.; Elphic, R. C.; Goldstein, D. B.

    2014-12-01

    We perform modeling and analysis of water in the lunar exosphere. There were two controlled experiments of water interactions with the surface of the Moon observed by the Lunar Atmosphere and Dust Environment Explorer (LADEE) Neutral Mass Spectrometer (NMS). The Chang'e 3 landing on the Moon on 14 Dec 2013 putatively sprayed ~120 kg of water on the surface on the Moon at a mid-morning local time. Observations by LADEE near the noon meridian on six of the orbits in the 24 hours following the landing constrain the propagation of water vapor. Further, on 4 Apr 2014, LADEE's Orbital Maintenance Manuever (OMM) #21 sprayed the surface of the Moon with an estimated 0.73 kg of water in the pre-dawn sector. Observations of this maneuver and later in the day constrain the adsorption and release at dawn of adsorbed materials. Using the Chang'e 3 exhaust plume and LADEE's OMM-21 as control experiments, we set limits to the adsorption and thermalization of water with lunar regolith. This enables us to predict the efficiency of the migration of water as a delivery mechanism to the lunar poles. Then we simulate the migration of water through the lunar exosphere using the rate of sporadic inputs from meteoritic sources (Benna et al., this session). Simulations predict the amount of water adsorbed to the surface of the Moon and the effective delivery rate to the lunar polar cold traps.

  7. Atomic Force Microscopy and MD Simulations Reveal Pore-Like Structures of All-D-Enantiomer of Alzheimer’s β-Amyloid Peptide: Relevance to the Ion Channel Mechanism of AD Pathology

    Science.gov (United States)

    Connelly, Laura; Arce, Fernando Teran; Jang, Hyunbum; Capone, Ricardo; Kotler, Samuel A.; Ramachandran, Srinivasan; Kagan, Bruce L.; Nussinov, Ruth; Lal, Ratnesh

    2012-01-01

    Alzheimer’s disease (AD) is a protein misfolding disease characterized by a build-up of β-amyloid (Aβ) peptide as senile plaques, uncontrolled neurodegeneration, and memory loss. AD pathology is linked to the destabilization of cellular ionic homeostasis and involves Aβ peptide-plasma membrane interactions. In principle, there are two possible ways through which disturbance of the ionic homeostasis can take place: directly, where the Aβ peptide either inserts into the membrane and creates ion-conductive pores or destabilizes the membrane organization; or, indirectly, where the Aβ peptide interacts with existing cell membrane receptors. To distinguish between these two possible types of Aβ-membrane interactions, we took advantage of the biochemical tenet that ligand-receptor interactions are stereospecific; L-amino acid peptides, but not their D-counterparts, bind to cell membrane receptors. However, with respect to the ion channel-mediated mechanism, like L-amino acids, D-amino acid peptides will also form ion channel-like structures. Using atomic force microscopy (AFM) we imaged the structures of both D- and L-enantiomers of the full length Aβ1-42 when reconstituted in lipid bilayers. AFM imaging shows that both L- and D-Aβ isomers form similar channel-like structures. Molecular dynamics (MD) simulations support the AFM imaged 3D structures. Earlier we have shown that D-Aβ1-42 channels conduct ions similarly to their L-counter parts. Taken together, our results support the direct mechanism of Aβ ion channel-mediated destabilization of ionic homeostasis rather than the indirect mechanism through Aβ interaction with membrane receptors. PMID:22217000

  8. Wetting and Diffusion of Water on Pristine and Strained Phosphorene

    OpenAIRE

    Zhang, Wei; Ye, Chao; Bi, Lin; Yang, Zaixing; Zhou, Ruhong

    2015-01-01

    Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, have exhibited promising application prospect in biology. Nonetheless, the wetting and diffusive properties of bio-fluids on phosphorene are still elusive. In this study, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on pristine and strained phosphorene. The MD simulations illustrated that the diffusion of water molecules on the phosphorene surface is anisotropic, whi...

  9. A MODFLOW Infiltration Device Package for Simulating Storm Water Infiltration.

    Science.gov (United States)

    Jeppesen, Jan; Christensen, Steen

    2015-01-01

    This article describes a MODFLOW Infiltration Device (INFD) Package that can simulate infiltration devices and their two-way interaction with groundwater. The INFD Package relies on a water balance including inflow of storm water, leakage-like seepage through the device faces, overflow, and change in storage. The water balance for the device can be simulated in multiple INFD time steps within a single MODFLOW time step, and infiltration from the device can be routed through the unsaturated zone to the groundwater table. A benchmark test shows that the INFD Package's analytical solution for stage computes exact results for transient behavior. To achieve similar accuracy by the numerical solution of the MODFLOW Surface-Water Routing (SWR1) Process requires many small time steps. Furthermore, the INFD Package includes an improved representation of flow through the INFD sides that results in lower infiltration rates than simulated by SWR1. The INFD Package is also demonstrated in a transient simulation of a hypothetical catchment where two devices interact differently with groundwater. This simulation demonstrates that device and groundwater interaction depends on the thickness of the unsaturated zone because a shallow groundwater table (a likely result from storm water infiltration itself) may occupy retention volume, whereas a thick unsaturated zone may cause a phase shift and a change of amplitude in groundwater table response to a change of infiltration. We thus find that the INFD Package accommodates the simulation of infiltration devices and groundwater in an integrated manner on small as well as large spatial and temporal scales. © 2014, National Ground Water Association.

  10. Thermodynamic simulation of ammonia-water absorption refrigeration system

    Directory of Open Access Journals (Sweden)

    Sathyabhama A.

    2008-01-01

    Full Text Available The ammonia-water absorption refrigeration system is attracting increasing research interests, since the system can be powered by waste thermal energy, thus reducing demand on electricity supply. The development of this technology demands reliable and effective system simulations. In this work, a thermodynamic simulation of the cycle is carried out to investigate the effects of different operating variables on the performance of the cycle. A computer program in C language is written for the performance analysis of the cycle.

  11. Numerical simulation of water quality in Yangtze Estuary

    Directory of Open Access Journals (Sweden)

    Xi Li

    2009-12-01

    Full Text Available In order to monitor water quality in the Yangtze Estuary, water samples were collected and field observation of current and velocity stratification was carried out using a shipboard acoustic Doppler current profiler (ADCP. Results of two representative variables, the temporal and spatial variation of new point source sewage discharge as manifested by chemical oxygen demand (COD and the initial water quality distribution as manifested by dissolved oxygen (DO, were obtained by application of the Environmental Fluid Dynamics Code (EFDC with solutions for hydrodynamics during tides. The numerical results were compared with field data, and the field data provided verification of numerical application: this numerical model is an effective tool for water quality simulation. For point source discharge, COD concentration was simulated with an initial value in the river of zero. The simulated increments and distribution of COD in the water show acceptable agreement with field data. The concentration of DO is much higher in the North Branch than in the South Branch due to consumption of oxygen in the South Branch resulting from discharge of sewage from Shanghai. The DO concentration is greater in the surface layer than in the bottom layer. The DO concentration is low in areas with a depth of less than 20 m, and high in areas between the 20-m and 30-m isobaths. It is concluded that the numerical model is valuable in simulation of water quality in the case of specific point source pollutant discharge. The EFDC model is also of satisfactory accuracy in water quality simulation of the Yangtze Estuary.

  12. Simulation Games: The Future of Water Resources Education and Management?

    Science.gov (United States)

    Castilla Rho, J. C.; Mariethoz, G.; Rojas, R. F.; Andersen, M. S.; Kelly, B. F.; Holley, C.

    2014-12-01

    Scientists rely on models of the water cycle to describe and predict problems of water scarcity in a changing climate, and to suggest adaptation strategies for securing future water needs. Yet these models are too often complicated for managers, the general public and for students to understand. Simpler modelling environments will help with finding solutions by engaging a broader segment of the population. Such environments will enable education at the earliest stages and collective action. I propose that simulation games can be an effective communication platform between scientists and 'non-experts' and that such games will shed light on problems of pollution and overuse of water resources. In the same way as pilots use flight simulators to become proficient at flying aircraft, simulation games—if underpinned by good science—can be used to educate the public, students and managers about how to best manage our water resources. I aim to motivate young scientists to think about using games to advance water education and management.

  13. Simulation of water quality for Salt Creek in northeastern Illinois

    Science.gov (United States)

    Melching, Charles S.; Chang, T.J.

    1996-01-01

    Water-quality processes in the Salt Creek watershed in northeastern Illinois were simulated with a computer model. Selected waste-load scenarios for 7-day, 10-year low-flow conditions were simulated in the stream system. The model development involved the calibration of the U.S. Environmental Protection Agency QUAL2E model to water-quality constituent concentration data collected by the Illinois Environmental Protection Agency (IEPA) for a diel survey on August 29-30, 1995, and the verification of this model with water-quality constituent concentration data collected by the IEPA for a diel survey on June 27-28, 1995. In-stream measurements of sediment oxygen demand rates and carbonaceous biochemical oxygen demand (CBOD) decay rates by the IEPA and traveltime and reaeration-rate coefficients by the U.S. Geological Survey facilitated the development of a model for simulation of water quality in the Salt Creek watershed. In general, the verification of the calibrated model increased confidence in the utility of the model for water-quality planning in the Salt Creek watershed. However, the model was adjusted to better simulate constituent concentrations measured during the June 27-28, 1995, diel survey. Two versions of the QUAL2E model were utilized to simulate dissolved oxygen (DO) concentrations in the Salt Creek watershed for selected effluent discharge and concentration scenarios for water-quality planning: (1) the QUAL2E model calibrated to the August 29-30, 1995, diel survey, and (2) the QUAL2E model adjusted to the June 27-28, 1995, diel survey. The results of these simulations indicated that the QUAL2E model adjusted to the June 27-28, 1995, diel survey simulates reliable information for water-quality planning. The results of these simulations also indicated that to maintain DO concentrations greater than 5 milligrams per liter (mg/L) throughout most of Salt Creek for 7-day, 10-year low-flow conditions, the sewage-treatment plants (STP's) must discharge

  14. SIMULATION OF NEGATIVE PRESSURE WAVE PROPAGATION IN WATER PIPE NETWORK

    Directory of Open Access Journals (Sweden)

    Tang Van Lam

    2017-11-01

    Full Text Available Subject: factors such as pipe wall roughness, mechanical properties of pipe materials, physical properties of water affect the pressure surge in the water supply pipes. These factors make it difficult to analyze the transient problem of pressure evolution using simple programming language, especially in the studies that consider only the magnitude of the positive pressure surge with the negative pressure phase being neglected. Research objectives: determine the magnitude of the negative pressure in the pipes on the experimental model. The propagation distance of the negative pressure wave will be simulated by the valve closure scenarios with the help of the HAMMER software and it is compared with an experimental model to verify the quality the results. Materials and methods: academic version of the Bentley HAMMER software is used to simulate the pressure surge wave propagation due to closure of the valve in water supply pipe network. The method of characteristics is used to solve the governing equations of transient process of pressure change in the pipeline. This method is implemented in the HAMMER software to calculate the pressure surge value in the pipes. Results: the method has been applied for water pipe networks of experimental model, the results show the affected area of negative pressure wave from valve closure and thereby we assess the largest negative pressure that may appear in water supply pipes. Conclusions: the experiment simulates the water pipe network with a consumption node for various valve closure scenarios to determine possibility of appearance of maximum negative pressure value in the pipes. Determination of these values in real-life network is relatively costly and time-consuming but nevertheless necessary for identification of the risk of pipe failure, and therefore, this paper proposes using the simulation model by the HAMMER software. Initial calibration of the model combined with the software simulation results and

  15. Molecular dynamics simulation of sodium aluminosilicate glass structures and glass surface-water reactions using the reactive force field (ReaxFF)

    Science.gov (United States)

    Dongol, R.; Wang, L.; Cormack, A. N.; Sundaram, S. K.

    2018-05-01

    Reactive potentials are increasingly used to study the properties of glasses and glass water reactions in a reactive molecular dynamics (MD) framework. In this study, we have simulated a ternary sodium aluminosilicate glass and investigated the initial stages of the glass surface-water reactions at 300 K using reactive force field (ReaxFF). On comparison of the simulated glass structures generated using ReaxFF and classical Buckingham potentials, our results show that the atomic density profiles calculated for the surface glass structures indicate a bond-angle distribution dependency. The atomic density profiles also show higher concentrations of non-bridging oxygens (NBOs) and sodium ions at the glass surface. Additionally, we present our results of formation of silanol species and the diffusion of water molecules at the glass surface using ReaxFF.

  16. 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).

  17. Simulation of heavy metal contamination of fresh water bodies: toxic ...

    African Journals Online (AJOL)

    Michael Horsfall

    www.bioline.org.br/ja. Simulation of heavy metal contamination of fresh water bodies: toxic effects in the ... 96 hours (though sampling was done at the 48th hour). Biochemical markers of ... silver, while enhancing the bioavailability of mercury in Ceriodaphnia ..... Biochemical and molecular disorders of bilirubin metabolism.

  18. Water Flow Simulation using Smoothed Particle Hydrodynamics (SPH)

    Science.gov (United States)

    Vu, Bruce; Berg, Jared; Harris, Michael F.

    2014-01-01

    Simulation of water flow from the rainbird nozzles has been accomplished using the Smoothed Particle Hydrodynamics (SPH). The advantage of using SPH is that no meshing is required, thus the grid quality is no longer an issue and accuracy can be improved.

  19. Control algorithm for multiscale flow simulations of water

    DEFF Research Database (Denmark)

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

    2009-01-01

    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...

  20. Mass imbalances in EPANET water-quality simulations

    Energy Technology Data Exchange (ETDEWEB)

    Davis, Michael J.; Janke, Robert; Taxon, Thomas N.

    2018-04-06

    EPANET is widely employed to simulate water quality in water distribution systems. However, the time-driven simulation approach used to determine concentrations of water-quality constituents provides accurate results, in general, only for small water-quality time steps; use of an adequately short time step may not be feasible. Overly long time steps can yield errors in concentrations and result in situations in which constituent mass is not conserved. Mass may not be conserved even when EPANET gives no errors or warnings. This paper explains how such imbalances can occur and provides examples of such cases; it also presents a preliminary event-driven approach that conserves mass with a water-quality time step that is as long as the hydraulic time step. Results obtained using the current approach converge, or tend to converge, to those obtained using the new approach as the water-quality time step decreases. Improving the water-quality routing algorithm used in EPANET could eliminate mass imbalances and related errors in estimated concentrations.

  1. A holistic water depth simulation model for small ponds

    Science.gov (United States)

    Ali, Shakir; Ghosh, Narayan C.; Mishra, P. K.; Singh, R. K.

    2015-10-01

    Estimation of time varying water depth and time to empty of a pond is prerequisite for comprehensive and coordinated planning of water resource for its effective utilization. A holistic water depth simulation (HWDS) and time to empty (TE) model for small, shallow ephemeral ponds have been derived by employing the generalized model based on the Green-Ampt equation in the basic water balance equation. The HWDS model includes time varying rainfall, runoff, surface water evaporation, outflow and advancement of wetting front length as external inputs. The TE model includes two external inputs; surface water evaporation and advancement of wetting front length. Both the models also consider saturated hydraulic conductivity and fillable porosity of the pond's bed material as their parameters. The solution of the HWDS model involved numerical iteration in successive time intervals. The HWDS model has successfully evaluated with 3 years of field data from two small ponds located within a watershed in a semi-arid region in western India. The HWDS model simulated time varying water depth in the ponds with high accuracy as shown by correlation coefficient (R2 ⩾ 0.9765), index of agreement (d ⩾ 0.9878), root mean square errors (RMSE ⩽ 0.20 m) and percent bias (PB ⩽ 6.23%) for the pooled data sets of the measured and simulated water depth. The statistical F and t-tests also confirmed the reliability of the HWDS model at probability level, p ⩽ 0.0001. The response of the TE model showed its ability to estimate the time to empty the ponds. An additional field calibration and validation of the HWDS and TE models with observed field data in varied hydro-climatic conditions could be conducted to increase the applicability and credibility of the models.

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

    International Nuclear Information System (INIS)

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

    2016-01-01

    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

  3. 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.

  4. Developing improved MD codes for understanding processive cellulases

    International Nuclear Information System (INIS)

    Crowley, M F; Nimlos, M R; Himmel, M E; Uberbacher, E C; Iii, C L Brooks; Walker, R C

    2008-01-01

    The mechanism of action of cellulose-degrading enzymes is illuminated through a multidisciplinary collaboration that uses molecular dynamics (MD) simulations and expands the capabilities of MD codes to allow simulations of enzymes and substrates on petascale computational facilities. There is a class of glycoside hydrolase enzymes called cellulases that are thought to decrystallize and processively depolymerize cellulose using biochemical processes that are largely not understood. Understanding the mechanisms involved and improving the efficiency of this hydrolysis process through computational models and protein engineering presents a compelling grand challenge. A detailed understanding of cellulose structure, dynamics and enzyme function at the molecular level is required to direct protein engineers to the right modifications or to understand if natural thermodynamic or kinetic limits are in play. Much can be learned about processivity by conducting carefully designed molecular dynamics (MD) simulations of the binding and catalytic domains of cellulases with various substrate configurations, solvation models and thermodynamic protocols. Most of these numerical experiments, however, will require significant modification of existing code and algorithms in order to efficiently use current (terascale) and future (petascale) hardware to the degree of parallelism necessary to simulate a system of the size proposed here. This work will develop MD codes that can efficiently use terascale and petascale systems, not just for simple classical MD simulations, but also for more advanced methods, including umbrella sampling with complex restraints and reaction coordinates, transition path sampling, steered molecular dynamics, and quantum mechanical/molecular mechanical simulations of systems the size of cellulose degrading enzymes acting on cellulose

  5. 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.

  6. Water desalination price from recent performances: Modelling, simulation and analysis

    International Nuclear Information System (INIS)

    Metaiche, M.; Kettab, A.

    2005-01-01

    The subject of the present article is the technical simulation of seawater desalination, by a one stage reverse osmosis system, the objectives of which are the recent valuation of cost price through the use of new membrane and permeator performances, the use of new means of simulation and modelling of desalination parameters, and show the main parameters influencing the cost price. We have taken as the simulation example the Seawater Desalting centre of Djannet (Boumerdes, Algeria). The present performances allow water desalting at a price of 0.5 $/m 3 , which is an interesting and promising price, corresponding with the very acceptable water product quality, in the order of 269 ppm. It is important to run the desalting systems by reverse osmosis under high pressure, resulting in further decrease of the desalting cost and the production of good quality water. Aberration in choice of functioning conditions produces high prices and unacceptable quality. However there exists the possibility of decreasing the price by decreasing the requirement on the product quality. The seawater temperature has an effect on the cost price and quality. The installation of big desalting centres, contributes to the decrease in prices. A very important, long and tedious calculation is effected, which is impossible to conduct without programming and informatics tools. The use of the simulation model has been much efficient in the design of desalination centres that can perform at very improved prices. (author)

  7. 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.

  8. Three-Dimensional Simulations of Oblique Asteroid Impacts into Water

    Science.gov (United States)

    Gisler, G. R.; Ferguson, J. M.; Heberling, T.; Plesko, C. S.; Weaver, R.

    2016-12-01

    Waves generated by impacts into oceans may represent the most significant danger from near-earth asteroids and comets. For impacts near populated shores, the crown splash and subsequent waves, accompanied by sediment lofting and high winds, could be more damaging than storm surges from the strongest hurricanes. For asteroids less than 500 m in diameter that impact into deep water far from shores, the waves produced will be detectable over large distances, but probably not significantly dangerous. We present new three-dimensional simulations of oblique impacts into deep water, with trajectory angles ranging from 20 degrees to 60 degrees (where 90 degrees is vertical). These simulations are performed with the Los Alamos Rage hydrocode, and include atmospheric effects including ablation and airbursts. These oblique impact simulations are specifically performed in order to help determine whether there are additional dangers from the obliquity of impact not covered by previous two-dimensional studies. Water surface elevation profiles, surface pressures, and depth-averaged mass fluxes within the water are prepared for use in propagation studies.

  9. 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.

  10. Computational fluid dynamics simulations of light water reactor flows

    International Nuclear Information System (INIS)

    Tzanos, C.P.; Weber, D.P.

    1999-01-01

    Advances in computational fluid dynamics (CFD), turbulence simulation, and parallel computing have made feasible the development of three-dimensional (3-D) single-phase and two-phase flow CFD codes that can simulate fluid flow and heat transfer in realistic reactor geometries with significantly reduced reliance, especially in single phase, on empirical correlations. The objective of this work was to assess the predictive power and computational efficiency of a CFD code in the analysis of a challenging single-phase light water reactor problem, as well as to identify areas where further improvements are needed

  11. Pressure-induced transformations in computer simulations of glassy water

    Science.gov (United States)

    Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas

    2013-11-01

    Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a "P-T phase diagram" for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water.

  12. 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.

  13. Hydration dynamics in water clusters via quantum molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Turi, László, E-mail: turi@chem.elte.hu [Department of Physical Chemistry, Eötvös Loránd University, Budapest 112, P. O. Box 32, H-1518 (Hungary)

    2014-05-28

    We have investigated the hydration dynamics in size selected water clusters with n = 66, 104, 200, 500, and 1000 water molecules using molecular dynamics simulations. To study the most fundamental aspects of relaxation phenomena in clusters, we choose one of the simplest, still realistic, quantum mechanically treated test solute, an excess electron. The project focuses on the time evolution of the clusters following two processes, electron attachment to neutral equilibrated water clusters and electron detachment from an equilibrated water cluster anion. The relaxation dynamics is significantly different in the two processes, most notably restoring the equilibrium final state is less effective after electron attachment. Nevertheless, in both scenarios only minor cluster size dependence is observed. Significantly different relaxation patterns characterize electron detachment for interior and surface state clusters, interior state clusters relaxing significantly faster. This observation may indicate a potential way to distinguish surface state and interior state water cluster anion isomers experimentally. A comparison of equilibrium and non-equilibrium trajectories suggests that linear response theory breaks down for electron attachment at 200 K, but the results converge to reasonable agreement at higher temperatures. Relaxation following electron detachment clearly belongs to the linear regime. Cluster relaxation was also investigated using two different computational models, one preferring cavity type interior states for the excess electron in bulk water, while the other simulating non-cavity structure. While the cavity model predicts appearance of several different hydrated electron isomers in agreement with experiment, the non-cavity model locates only cluster anions with interior excess electron distribution. The present simulations show that surface isomers computed with the cavity predicting potential show similar dynamical behavior to the interior clusters of

  14. 76 FR 51887 - Safety Zone; Patuxent River, Patuxent River, MD

    Science.gov (United States)

    2011-08-19

    ...-AA00 Safety Zone; Patuxent River, Patuxent River, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is establishing a temporary safety zone during the ``NAS Patuxent River... held over certain waters of the Patuxent River adjacent to Patuxent River, Maryland from September 1...

  15. Simulation of water movement and NaCl transport

    International Nuclear Information System (INIS)

    Li Xun; Zheng Zhihong; Yang Zeping

    2008-01-01

    Modeling of water flow and solute transport in the near-field of a high-level radioactive waste repository with TOUGH2 is done. The results show that salt accumulation in buffer material is not so significant, precipitation does not occur throughout the period covered by our simualtions. Further more, the changeable law of volumetric water content, liquid velocity and dissolved concentration of sodium chloride with simulated time or distance are attained, which is the base of understanding evolvement of near-field. (authors)

  16. Simulation of water hammer phenomena using the system code ATHLET

    Energy Technology Data Exchange (ETDEWEB)

    Bratfisch, Christoph; Koch, Marco K. [Bochum Univ. (Germany). Reactor Simulation and Safety Group

    2017-07-15

    Water Hammer Phenomena can endanger the integrity of structures leading to a possible failure of pipes in nuclear power plants as well as in many industrial applications. These phenomena can arise in nuclear power plants in the course of transients and accidents induced by the start-up of auxiliary feed water systems or emergency core cooling systems in combination with rapid acting valves and pumps. To contribute to further development and validation of the code ATHLET (Analysis of Thermalhydraulics of Leaks and Transients), an experiment performed in the test facility Pilot Plant Pipework (PPP) at Fraunhofer UMSICHT is simulated using the code version ATHLET 3.0A.

  17. Simulation of gas compressible flow by free surface water flow

    International Nuclear Information System (INIS)

    Altafini, C.R.; Silva Ferreira, R.T. da

    1981-01-01

    The analogy between the water flow with a free surface and the compressible fluid flow, commonly called hydraulic analogy, is analyzed and its limitations are identified. The water table is the equipment used for this simulation, which allows the quatitative analysis of subsonic and supersonic flow with a low cost apparatus. The hydraulic analogy is applied to subsonic flow around circular cylinders and supersonic flow around cones. The results are compared with available theoretical and experimental data and a good agreement is achieved. (Author) [pt

  18. Simulation of water hammer phenomena using the system code ATHLET

    International Nuclear Information System (INIS)

    Bratfisch, Christoph; Koch, Marco K.

    2017-01-01

    Water Hammer Phenomena can endanger the integrity of structures leading to a possible failure of pipes in nuclear power plants as well as in many industrial applications. These phenomena can arise in nuclear power plants in the course of transients and accidents induced by the start-up of auxiliary feed water systems or emergency core cooling systems in combination with rapid acting valves and pumps. To contribute to further development and validation of the code ATHLET (Analysis of Thermalhydraulics of Leaks and Transients), an experiment performed in the test facility Pilot Plant Pipework (PPP) at Fraunhofer UMSICHT is simulated using the code version ATHLET 3.0A.

  19. Growth Kinetics of the Homogeneously Nucleated Water Droplets: Simulation Results

    International Nuclear Information System (INIS)

    Mokshin, Anatolii V; Galimzyanov, Bulat N

    2012-01-01

    The growth of homogeneously nucleated droplets in water vapor at the fixed temperatures T = 273, 283, 293, 303, 313, 323, 333, 343, 353, 363 and 373 K (the pressure p = 1 atm.) is investigated on the basis of the coarse-grained molecular dynamics simulation data with the mW-model. The treatment of simulation results is performed by means of the statistical method within the mean-first-passage-time approach, where the reaction coordinate is associated with the largest droplet size. It is found that the water droplet growth is characterized by the next features: (i) the rescaled growth law is unified at all the considered temperatures and (ii) the droplet growth evolves with acceleration and follows the power law.

  20. 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.

  1. The Consortium for Advanced Simulation of Light Water Reactors

    International Nuclear Information System (INIS)

    Szilard, Ronaldo; Zhang, Hongbin; Kothe, Douglas; Turinsky, Paul

    2011-01-01

    The Consortium for Advanced Simulation of Light Water Reactors (CASL) is a DOE Energy Innovation Hub for modeling and simulation of nuclear reactors. It brings together an exceptionally capable team from national labs, industry and academia that will apply existing modeling and simulation capabilities and develop advanced capabilities to create a usable environment for predictive simulation of light water reactors (LWRs). This environment, designated as the Virtual Environment for Reactor Applications (VERA), will incorporate science-based models, state-of-the-art numerical methods, modern computational science and engineering practices, and uncertainty quantification (UQ) and validation against data from operating pressurized water reactors (PWRs). It will couple state-of-the-art fuel performance, neutronics, thermal-hydraulics (T-H), and structural models with existing tools for systems and safety analysis and will be designed for implementation on both today's leadership-class computers and the advanced architecture platforms now under development by the DOE. CASL focuses on a set of challenge problems such as CRUD induced power shift and localized corrosion, grid-to-rod fretting fuel failures, pellet clad interaction, fuel assembly distortion, etc. that encompass the key phenomena limiting the performance of PWRs. It is expected that much of the capability developed will be applicable to other types of reactors. CASL's mission is to develop and apply modeling and simulation capabilities to address three critical areas of performance for nuclear power plants: (1) reduce capital and operating costs per unit energy by enabling power uprates and plant lifetime extension, (2) reduce nuclear waste volume generated by enabling higher fuel burnup, and (3) enhance nuclear safety by enabling high-fidelity predictive capability for component performance.

  2. Numerical Simulation of a Solar Domestic Hot Water System

    International Nuclear Information System (INIS)

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

    2014-01-01

    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

  3. 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.

  4. Direct numerical simulation of water droplet coalescence in the oil

    International Nuclear Information System (INIS)

    Mohammadi, Mehdi; Shahhosseini, Shahrokh; Bayat, Mahmoud

    2012-01-01

    Highlights: ► VOF computational technique has been used to simulate coalescence of two water droplets in oil. ► The model was validated with the experimental data for binary droplet coalescence. ► Based on the CFD simulation results a correlation has been proposed to predict the coalescence time. - Abstract: Coalescence of two water droplets in the oil was simulated using Computational Fluid Dynamics (CFD) techniques. The finite volume numerical method was applied to solve the Navier–Stokes equations in conjunction with the Volume of Fluid (VOF) approach for interface tracking. The effects of some parameters consisting of the collision velocity, off-center collision parameter, oil viscosity and water–oil interfacial tension on the coalescence time were investigated. The simulation results were validated against the experimental data available in the literature. The results revealed that quicker coalescence could be achieved if the head-on collisions occur or the droplets approach each other with a high velocity. In addition, low oil viscosities or large water–oil interfacial tensions cause less coalescence time. Moreover, a correlation was developed to predict coalescence efficiency as a function of the mentioned parameters.

  5. Simulating liquid water for determining its structural and transport properties

    International Nuclear Information System (INIS)

    Arismendi-Arrieta, Daniel; Medina, Juan S.; Fanourgakis, George S.; Prosmiti, Rita; Delgado-Barrio, Gerardo

    2014-01-01

    Molecular dynamics simulations are carried out for calculating structural and transport properties of pure liquid water, such as radial distribution functions and self-diffusion and viscosity coefficients, respectively. We employed reparameterized versions of the ab initio water potential by Niesar, Clementi and Corongiu (NCC). In order to investigate the role of the electrostatic contribution, the partial charges of the NCC model are adjusted so that to reproduce the dipole moment values of the SPC/E, SPC/Fw and TIP4P/2005 water models. The single and collective transport coefficients are obtained by employing the Green–Kubo relations at various temperatures. Additionally, in order to overcome convergence difficulties arising from the long correlation times of the stress-tensor autocorrelation functions, a previously reported fitting scheme was employed. The present results indicate that there is a significant relationship between the dipole moment value of the model, and the calculated transport coefficients. We found that by adjusting the molecular dipole moment of the NCC to the value of the TIP4P/2005, the obtained values for the self-diffusion and viscosity coefficients are in better agreement with experiment, compared to the values obtained with the original NCC model. Even though the predictions of the present model exhibits an overall correct behavior, we conclude that further improvements are still required. In order to achieve that, a careful reparameterization of the repulsion–dispersion terms of the potential model is proposed. Also, the effect of the inclusion of many-body effects such as polarizability, should also be investigated. - Highlights: ► Transport properties of liquid water are important in bio-simulations. ► Self-diffusion coefficient, shear and bulk viscosities calculations from NVE molecular dynamics simulations. ► Their comparison with experimental data provides information on intermolecular forces, and serve to develop water

  6. A Water Temperature Simulation Model for Rice Paddies With Variable Water Depths

    Science.gov (United States)

    Maruyama, Atsushi; Nemoto, Manabu; Hamasaki, Takahiro; Ishida, Sachinobu; Kuwagata, Tsuneo

    2017-12-01

    A water temperature simulation model was developed to estimate the effects of water management on the thermal environment in rice paddies. The model was based on two energy balance equations: for the ground and for the vegetation, and considered the water layer and changes in the aerodynamic properties of its surface with water depth. The model was examined with field experiments for water depths of 0 mm (drained conditions) and 100 mm (flooded condition) at two locations. Daily mean water temperatures in the flooded condition were mostly higher than in the drained condition in both locations, and the maximum difference reached 2.6°C. This difference was mainly caused by the difference in surface roughness of the ground. Heat exchange by free convection played an important role in determining water temperature. From the model simulation, the temperature difference between drained and flooded conditions was more apparent under low air temperature and small leaf area index conditions; the maximum difference reached 3°C. Most of this difference occurred when the range of water depth was lower than 50 mm. The season-long variation in modeled water temperature showed good agreement with an observation data set from rice paddies with various rice-growing seasons, for a diverse range of water depths (root mean square error of 0.8-1.0°C). The proposed model can estimate water temperature for a given water depth, irrigation, and drainage conditions, which will improve our understanding of the effect of water management on plant growth and greenhouse gas emissions through the thermal environment of rice paddies.

  7. Supercritical water: On a road from CFD to NPP simulations

    International Nuclear Information System (INIS)

    Rintala, Lauri; Danielyan, Davit; Salomaa, Rainer

    2010-01-01

    The Fission and Radiation Physics Group at the Aalto University is contributing to the Finnish SCWR activities within the GEN4FIN-network. Our research involves reactor core thermal hydraulics, and in particular, heat transfer phenomena in supercritical water including both theoretical studies and simulations with APROS and OpenFOAM. APROS is a software applicable to full-scale power plant simulations and OpenFOAM an open source CFD code. The complicated heat transfer in the supercritical region is a very challenging problem for the design of SCWRs and their safety assessment. The steam tables of APROS have been extended to the supercritical region and their functionality has been tested with, e.g. blowdown simulations where the transient is rapid, hence mainly challenging for numerical stability whereas heat transfer has negligible effects. Numerous different heat correlations for supercritical water have been suggested , but simulations of benchmark experiments have shown that for instance fuel clad temperatures generally cannot be described sufficiently accurately. This discrepancy has been encountered in several process simulation codes. The largest errors occur near the pseudo critical line, during the heat transfer deterioration. It turns out that the physics in supercritical water is clearly more intricate than in ordinary boiling heat transfer where rather satisfactory heat transfer correlations are available. Full 3D CFD calculations allow a better description of various aspects of heat transfer in the supercritical region, i.e., effects arising from turbulence , buoyancy , varying material properties etc. On the other hand, CFD calculations are not feasible for plant-scale simulations. We have selected some simplified geometries and parameter ranges to study SCW heat transfer in a reactor. Old experiments have been calculated with satisfactory results with OpenFOAM to check its validity. A steady state case of heat transfer in a circular pipe with upward

  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. 77 FR 6708 - Special Local Regulations for Marine Events; Potomac River, Charles County, MD

    Science.gov (United States)

    2012-02-09

    ...-AA08 Special Local Regulations for Marine Events; Potomac River, Charles County, MD AGENCY: Coast Guard... River, Charles County, MD. (a) Regulated area. The following location is a regulated area: All waters of... local regulations during the ``Potomac River Sharkfest Swim'' amateur swim, a marine event to be held on...

  10. Simulation of gamma irradiation system for a ballast water treatment

    International Nuclear Information System (INIS)

    Faez, T. P.; Sarkar, S.

    2006-01-01

    Invasion by different kinds of ballast the water microorganisms is one of the most important marine environment problems around the world therefore preventing the invasion of these unwanted and harmful stowaways is one of the main strategies of responsible agencies. Some of these methods such as ocean exchange, heating, filtration, hydro cyclones, UV irradiation and chemical treatment, have various problems such as technical deficiency, high costs, lack of safety and environmental side effects. Materials and Methods: A novel system of treatment by Gamma irradiation is designed to irradiate the blast water uniformly and effectively. To determine the dose distribution as a function of distance from the irradiation source, the MCNP code was used. The systems used for source implant in this simulation were Paterson-Parker, Paris and Network systems. In each system, Sivert-integral and inverse square law were used in MATLAB program to determine the dose distribution. Results: Results of initial laboratory tests on offshore water samples of Siri Island indicated that the appropriate dose for deactivation of organisms of water samples is approximately one kGy. It has been demonstrated that the dose can be provided by twenty five 100,000 Ci line sources of ' 60 Co in a triangle implant arranged in a 1*1*1 m3 cubic shape water pipe. In order to increase efficiency and radiation safety, water passed from two other coaxial and bigger cubes, after passing from the first cube. A one meter thick wall of concrete around the cubes was adequate to shield the system completely. Conclusion: The main advantages of this system such as high efficiency, safety, reliability, minimum environmental adverse effects, proves that this novel method not only can be used for ballast water treatment, but is also effective for drinking water purification

  11. 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.

  12. 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).

  13. 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.

  14. Simulation of water transport through a lipid membrane

    Energy Technology Data Exchange (ETDEWEB)

    Marrink, S.J.; Berendsen, H.J.C. (Univ. of Groningen (Netherlands))

    1994-04-14

    To obtain insight in the process of water permeation through a lipid membrane we performed molecular dynamics simulations on a phospholipid (DPPC)/water system with atomic detail. Since the actual process of permeation is too slow to be studied directly, we deduced the permeation rate indirectly via computation of the free energy and diffusion rate profiles of a water molecule across the bilayer. We concluded that the permeation of water through a lipid membrane cannot be described adequately by a simple homogeneous solubility-diffusion model. Both the excess free energy and the diffusion rate strongly depend on the position in the membrane, as a result from the inhomogeneous nature of the membrane. The calculated excess free energy profile has a shallow slope and a maximum height of 26 kJ/mol. The diffusion rate is highest in the middle of the membrane where the lipid density is low. In the interfacial region almost all water molecules are bound by the lipid headgroups, and the diffusion turns out to be 1 order of magnitude smaller. The total transport process is essentially determined by the free energy barrier. 78 refs., 12 figs.

  15. Laboratory simulation studies of uranium mobility in natural waters

    International Nuclear Information System (INIS)

    Giblin, A.M.; Swaine, D.J.; Batts, B.D.

    1981-01-01

    The effects of imposed variations of pH and Eh on aqueous uranium mobility at 25 0 C have been studied in three simulations of natural water systems. Constituents tested for their effect on uranium mobility were: (a) hydrous ferric oxide, to represent adsorptive solids which precipitate or dissolve in response to variations in pH and Eh; (b) kaolinite, representing minerals which, although modified by pH and Eh changes, are present as solids over the pH-Eh range of natural waters; and (c) carbonate, to represent a strong uranium-complexing species. Uranium mobility measurements from each simulation were regressed against pH and Eh within a range appropriate to natural waters. Hydrous ferric oxide and kaolinite each affected uranium mobility, but in separate pH-Eh domains. Aqueous carbonate increased mobility of uranium, and adsorption of UO 2 (CO 3 ) 3 4- caused colloidal dispersion of hydrous ferric oxide, possibly explaining the presence of 'hydrothermal hematite' in some uranium deposits. Enhanced uranium mobility observed in the pH-Eh domains of thermodynamically insoluble uranium oxides could be explained if the oxides were present as colloids. Uranium persisting as a mobile species, even after reduction, has implications for the near surface genesis of uranium ores. (author)

  16. 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

  17. Dynamic Simulation of Water Networks to Control and Reduce Physical Unaccounted-for Water

    Directory of Open Access Journals (Sweden)

    Nima Zorriasateyn

    2005-09-01

    Full Text Available A significant percentage of unaccounted-for water consists of leakage in water distribution networks in Iran. To detect leakage area with less costs and time spending and then identify the exact  place of it with special instruments, would be economical and a better water resource management. In this research, a real case has been selected and examined with dynamic simulation using MIKE NET. The method that has been carried out in this research based on maximizing the correlation coefficient and minimizing the sum of error squares between pressure measured inputs (observed data and calculated pressure (by model. According to the results, dynamic simulation of municipal water distribution system can be used as a guide to determine the place and the amount of leakage.Thereby the area of  large leakage can be simulated with appropriate accuracy through measured pressure. Therefor from management aspect, dynamic simulation can be used to decrease time consumption and to save costs for detecting leakage.

  18. 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

  19. 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

  20. Modeling and simulation of pressurized water reactor power plant

    International Nuclear Information System (INIS)

    Wang, S.J.

    1983-01-01

    Two kinds of balance of plant (BOP) models of a pressurized water reactor (PWR) system are developed in this work - the detailed BOP model and the simple BOP model. The detailed model is used to simulate the normal operational performance of a whole BOP system. The simple model is used to combine with the NSSS model for a whole plant simulation. The trends of the steady state values of the detailed model are correct and the dynamic responses are reasonable. The simple BOP model approach starts the modelling work from the overall point of view. The response of the normalized turbine power and the feedwater inlet temperature to the steam generator of the simple model are compared with those of the detailed model. Both the steady state values and the dynamic responses are close to those of the detailed model. The simple BOP model is found adequate to represent the main performance of the BOP system. The simple balance of plant model was coupled with a NSSS model for a whole plant simulation. The NSSS model consists of the reactor core model, the steam generator model, and the coolant temperature control system. A closed loop whole plant simulation for an electric load perturbation was performed. The results are plausible. The coupling effect between the NSSS system and the BOP system was analyzed. The feedback of the BOP system has little effect on the steam generator performance, while the performance of the BOP system is strongly affected by the steam flow rate from the NSSS

  1. Computer code for simulating pressurized water reactor core

    International Nuclear Information System (INIS)

    Serrano, A.M.B.

    1978-01-01

    A computer code was developed for the simulation of the steady-state and transient behaviour of the average channel of a Pressurizer Water Reactor core. Point kinetics equations were used with the reactivity calculated for average temperatures in the channel with the fuel and moderator temperature feedbacks. The radial heat conduction equation in the fuel was solved numerically. For calculating the thermodynamic properties of the coolant, the fundamental equations of conservation (mass, energy and momentum) were solved. The gap and clad were treated as a resistance added to the film coefficient. The fuel system equations were decoupled from the coolant equations. The program permitted the changes in the heat transfer correlations and the flow patterns along the coolant channel. Various test were performed to determine the steady-state and transient response employing the PWR core simulator developed, obtaining results with adequate precision. (author)

  2. Code for the core simulation in pressurized water reactors

    International Nuclear Information System (INIS)

    Serrano, M.A.B.

    1978-08-01

    A computer code was developed for the simulation of the steady-state and transient behaviour of the average channel of a Pressurizer Water Reactor core. Point kinetics equations were used with the reactivity calculated for average temperatures in the channel with the fuel and moderator temperature feedbacks. The radial heat conduction equation in the fuel was solved numericaly. For calculating the thermodynamic properties of the coolant, the fundamental equations of conservation (mass, energy and momentum) were solved. The gap and clad were treated as a resistence added to the film coeficient. The fuel system equations were decoupled from the coolant equations. The program permitted the changes in the heat transfer correlations and the flow patterns along the coolant channel. Various test were performed to determine the steady-state and transient response employing the PWR core simulator developed, obtaining results with adequate precision. (Author) [pt

  3. The Simulation Study of Horizontal Axis Water Turbine Using Flow Simulation Solidworks Application

    Science.gov (United States)

    Prasetyo, H.; Budiana, EP; Tjahjana, DDDP; Hadi, S.

    2018-02-01

    The design of Horizontal Axis Water Turbine in pico hydro power plants involves many parameters. To simplify that, usually using computer simulation is applied. This research performs simulation process variation on turbine blade number, turbine blade curvature angle, turbine bucket angle and blocking system tilt angle. Those four variations were combined in order to obtain the best design of turbine. The study used Flow Simulation Solidworks application, and obtain data on turbine speed, pressure, force, and torque. However, this research focused on turbine torque value. The best design of turbine was obtained in the turbine with 6 blades, blade curvature angle of 65° and bucket angle of 10°, and blocking system tilt angle of 40°. In the best turbine, the produced torque value was 8.464 Nm.

  4. Empowering stakeholders through simulation in water resources planning

    International Nuclear Information System (INIS)

    Palmer, R.N.; Keyes, A.M.; Fisher, S.

    1993-01-01

    During the past two years, researchers at the University of Washington (UW) have had the unique opportunity to facilitate and observe the development of drought planning activities associated with the National Drought Study (NDS) and its Drought Preparedness Studies (DPS) sites as sponsored by the Institute of Water Resources of the US Army Corps of Engineers. Each of the DPS sites is unique, with different study objectives and institutional constraints. However, one uniform requirement of the study is to develop tactical and strategic drought plans that can be successfully implemented within the study region. At the onset of the study, it was recognized that successful implementation is directly related to the active involvement of affected parties and agencies (denoted as stakeholders) and the degree to which they support the plan's conclusions. Their involvement is also necessary because the problems addressed by the DPS's require the experience and knowledge of a variety of water resource interests in order to arrive at effective alternatives. Their support of the plan conclusions enables regional implementation. Several techniques were used to encourage stakeholder participation in the planning process. Individuals representing the stakeholders had a wide range of professional backgrounds. This paper concentrates on one specific approach found useful in encouraging comprehensive and meaningful participation by a wide range of stakeholders; the development of object-oriented simulation models for the water resource systems under study. Simulation models were to develop tactical and strategic drought plans and to ensure the acceptance of the plans by building consensus among the stakeholders. The remainder of this paper describes: how simulation models became a part of the National Drought Study, procedures used to develop the DPS models, and how the model empowered stakeholders

  5. Simulation of water hammer experiments using RELAP5 code

    International Nuclear Information System (INIS)

    Kaliatka, A.; Vaisnoras, M.

    2005-01-01

    The rapid closing or opening of a valve causes pressure transients in pipelines. The fast deceleration of the liquid results in high pressure surges upstream the valve, thus the kinetic energy is transformed into the potential energy, which leads to the temporary pressure increases. This phenomenon is called water hammer. The intensity of water hammer effects will depend upon the rate of change in the velocity or momentum. Generally water hammer can occur in any thermal-hydraulic systems and it is extremely dangerous for the thermal-hydraulic system since, if the pressure induced exceeds the pressure range of a pipe given by the manufacturer, it can lead to the failure of the pipeline integrity. Due to its potential for damage of pipes, water hammer has been a subject of study since the middle of the nineteenth century. Many theoretical and experimental investigations were performed. The experimental investigation of the water hammer tests performed at Fraunhofer Institute for Environmental, Safety and Energy Technology (UMSICHT) [1] and Cold Water Hammer experiment performed by Forschungszentrum Rossendorf (CWHTF) [2] should be mentioned. The UMSICHT facility in Oberhausen was modified in order to simulate a piping system and associated supports that are typical for a nuclear power plant [3]. The Cold water hammer experiment is interesting and instructive because it covers a wide spectrum of particularities. One of them is sub-cooled water interaction with condensing steam at the closed end of the vertical pipe at room temperature and corresponding saturation pressure [4]. In the paper, the capabilities of RELAP5 code to correctly represent the water hammer phenomenon are presented. Paper presents the comparison of RELAP5 calculated and measured at UMSICHT and CWHTF test facilities pressure transient values after the fast closure (opening) of valves. The analyses of rarefaction wave travels inside the pipe and condensation of vapour bubbles in the liquid column

  6. Environmentally assisted cracking behaviour of copper in simulated ground water

    International Nuclear Information System (INIS)

    Hietanen, S.; Ehrnsten, U.; Saario, T.

    1996-05-01

    Environmentally assisted cracking (EAC) behaviour of pure oxygen free copper in simulated ground water with additions of sodium nitrite was studied. Low frequency corrosion fatigue tests with high positive load ratio values under crosshead speed control were performed using precracked diskshaped compact specimens C(T). The load ratio values were about 0.9 and the frequencies were between 0.0008 and 0.0017 Hz. Tests were performed under electrochemical potential control in an autoclave at room temperature and at 80 deg C. The aim of the study was to investigate the effects of repository environment on environmentally assisted cracking susceptibility of pure copper. (5 refs., 31 figs., 5 tabs.)

  7. Electrochemistry of lead in simulated ground water environments

    International Nuclear Information System (INIS)

    Joerg, E.A.; Devereux, O.F.

    1996-01-01

    Lead and lead alloys are used commonly as moisture barriers for underground cables. Lead exhibits excellent corrosion resistance in a variety of environments, but areas of localized attack have been found. These can result in able failures. The susceptibility of lead to pitting in several simulated ground water (SGW) environments was assessed using cyclic potentiodynamic pitting scans (PPS) and microscopy. Although general corrosion was observed, PPS demonstrated pitting did not occur in the same sense as in alloys known to be susceptible to pitting (i.e., very localized pit formation without general corrosion). However, areas of nonuniform general attack did occur, resulting in pitted surface morphologies

  8. Simulation of a pressurized-water nuclear power station

    International Nuclear Information System (INIS)

    Larminaux, Robert; Ourmann, Michel

    1978-01-01

    Faced with the large programme of fitting out PWR nuclear power stations, Electricite de France have undertaken a series of studies with a view to ensuring the best possible adaptation of the secondary part -particularly the feed water heating section- to the nuclear boiler. In order to undertake such studies it has been necessary to finalize simulation models of the entire power station. So as to verify the validity of the models, experiment-calculation comparisons were made during transient operating states recorded at the Ardennes power station as well as during starting up trials at the Tihange I power station [fr

  9. Molecular dynamics simulations of lysozyme in water/sugar solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lerbret, A. [Department of Food Science, Cornell University, 101 Stocking Hall, Ithaca, NY 14853 (United States); Affouard, F. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)], E-mail: frederic.affouard@univ-lille1.fr; Bordat, P. [Laboratoire de Chimie Theorique et de Physico-Chimie Moleculaire, UMR 5624, Universite de Pau et des Pays de l' Adour, 64000 Pau (France); Hedoux, A.; Guinet, Y.; Descamps, M. [Laboratoire de Dynamique et Structure des Materiaux Moleculaires, UMR CNRS 8024, Universite Lille I, 59655 Villeneuve d' Ascq Cedex (France)

    2008-04-18

    Structural and dynamical properties of the solvent at the protein/solvent interface have been investigated by molecular dynamics simulations of lysozyme in trehalose, maltose and sucrose solutions. Results are discussed in the framework of the bioprotection phenomena. The analysis of the relative concentration of water oxygen atoms around lysozyme suggests that lysozyme is preferentially hydrated. When comparing the three sugars, trehalose is seen more excluded than maltose and sucrose. The preferential exclusion of sugars from the protein surface induces some differences in the behavior of trehalose and maltose, particularly at 50 and 60 wt% concentrations, that are not observed experimentally in binary sugar/mixtures. The dynamical slowing down of the solvent is suggested to mainly arise from the homogeneity of the water/sugar matrices controlled by the percolation of the sugar hydrogen bonds networks. Furthermore, lysozyme strongly increases relaxation times of solvent molecules at the protein/solvent interface.

  10. Evaluating the Laplace pressure of water nanodroplets from simulations

    Science.gov (United States)

    Malek, Shahrazad M. A.; Sciortino, Francesco; Poole, Peter H.; Saika-Voivod, Ivan

    2018-04-01

    We calculate the components of the microscopic pressure tensor as a function of radial distance r from the centre of a spherical water droplet, modelled using the TIP4P/2005 potential. To do so, we modify a coarse-graining method for calculating the microscopic pressure (Ikeshoji et al 2003 Mol. Simul. 29 101) in order to apply it to a rigid molecular model of water. As test cases, we study nanodroplets ranging in size from 776 to 2880 molecules at 220 K. Beneath a surface region comprising approximately two molecular layers, the pressure tensor becomes approximately isotropic and constant with r. We find that the dependence of the pressure on droplet radius is that expected from the Young-Laplace equation, despite the small size of the droplets.

  11. Effect of arsenic on nitrification of simulated mining water.

    Science.gov (United States)

    Papirio, S; Zou, G; Ylinen, A; Di Capua, F; Pirozzi, F; Puhakka, J A

    2014-07-01

    Mining and mineral processing of gold-bearing ores often release arsenic to the environment. Ammonium is released when N-based explosives or cyanide are used. Nitrification of simulated As-rich mining waters was investigated in batch bioassays using nitrifying cultures enriched in a fluidized-bed reactor (FBR). Nitrification was maintained at 100mg AsTOT/L. In batch assays, ammonium was totally oxidized by the FBR enrichment in 48 h. As(III) oxidation to As(V) occurred during the first 3h attenuating arsenic toxicity to nitrification. At 150 and 200mg AsTOT/L, nitrification was inhibited by 25%. Candidatus Nitrospira defluvii and other nitrifying species mainly colonized the FBR. In conclusion, the FBR enriched cultures of municipal activated sludge origins tolerated high As concentrations making nitrification a potent process for mining water treatment. Copyright © 2014 Elsevier Ltd. All rights reserved.

  12. Molecular theory of mass transfer kinetics and dynamics at gas-water interface

    International Nuclear Information System (INIS)

    Morita, Akihiro; Garrett, Bruce C

    2008-01-01

    The mass transfer mechanism across gas-water interface is studied with molecular dynamics (MD) simulation. The MD results provide a robust and qualitatively consistent picture to previous studies about microscopic aspects of mass transfer, including interface structure, free energy profiles for the uptake, scattering dynamics and energy relaxation of impinging molecules. These MD results are quantitatively compared with experimental uptake measurements, and we find that the apparent inconsistency between MD and experiment could be partly resolved by precise decomposition of the observed kinetics into elemental steps. Remaining issues and future perspectives toward constructing a comprehensive multi-scale description of interfacial mass transfer are summarized.

  13. The discovery of 260Md and the decay properties of 258Fm, 258m,gMd and 259Md

    International Nuclear Information System (INIS)

    Lougheed, R.W.; Hulet, E.K.; Dougan, R.J.; Wild, J.F.; Dupzyk, R.J.; Henderson, C.M.; Moody, K.J.; Hahn, R.L.; Suemmerer, K.; Bethune, G.

    1986-01-01

    We have discovered a new neutron-rich isotope, 260 Md, from 18 O and 22 Ne bombardments of 254 Es. We observed a spontaneous-fission (SF) activity with a half-life of 32 days in electromagnetically separated fractions with mass number 260 from these bombardments and we measured the mass and kinetic energy distributions of this SF activity. The mass distribution was symmetric with the principal energy peak at a total kinetic energy (TKE) of 234 MeV, similar to previous observations for heavy fermium isotopes. Surprisingly, we also observed a smaller symmetric component with a TKE of 195 MeV. We interpret these two peaks in the TKE distribution as arising from two types of fission in the same nucleus, or bimodal fission. The observed fission activity may be either from the SF decay of 260 Md or from 260 Fm which would arise from electron-capture (EC) decay of 260 Md. We have eliminated the possible β - decay of 260 Md by measuring β - -SF time correlations for the decay of 260 Md and we plan to determine whether 260 Md decays by EC by measuring time correlations between fermium X-rays and SF events. We also measured various properties of the heavy fermium and mendelevium isotopes and obtained 1. more accurate cross-sections for the neutron-rich mendelevium isotopes which we use to predict the production rates of yet undiscovered nuclides, 2. improved half-life measurements for 258m,g Md and 259 Md, 3. confirmation of the EC decay of 258m Md by measurement of the fermium X-rays preceding the SF decay of 258 Fm and 4. very substantially improved mass and TKE distributions for the SF decay of 258 Fm and 259 Md. (orig.)

  14. Water Quality Assessment Simulation Program (WASP8): Upgrades to the Advanced Toxicant Module for Simulating Dissolved Chemicals, Nanomaterials, and Solids

    Science.gov (United States)

    The Water Quality Analysis Simulation Program (WASP) is a dynamic, spatially-resolved, differential mass balance fate and transport modeling framework. WASP is used to develop models to simulate concentrations of environmental contaminants in surface waters and sediments. As a mo...

  15. 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.

  16. 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).

  17. 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

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

    International Nuclear Information System (INIS)

    Cipcigan, Flaviu S.; Sokhan, Vlad P.; Crain, Jason; Martyna, Glenn J.

    2016-01-01

    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

  19. Structure and dynamics of hydrated Fe(II) and Fe(III) ions. Quantum mechanical and molecular mechanical simulations

    International Nuclear Information System (INIS)

    Remsungnen, T.

    2002-11-01

    Classical molecular dynamics (MD) and combined em ab initio quantum mechanical/molecular mechanical molecular dynamics (QM/MM-MD) simulations have been performed to investigate structural, dynamical and energetical properties of Fe(II), and Fe(III) transition metal ions in aqueous solution. In the QM/MM-MD simulations the ion and its first hydration sphere were treated at the Hartree-Fock ab initio quantum mechanical level, while ab initio generated pair plus three-body potentials were employed for the remaining system. For the classical MD simulation the pair plus three-body potential were employed for all ion-water interactions. The coordination number of the first hydration shell is 100 % of 6 in both cases. The number of waters in the second hydration shell obtained from classical simulations are 13.4 and 15.1 for Fe(II) and Fe(III), respectively, while QM/MM-MD gives the values of 12.4 and 13.4 for Fe(II) and Fe(III). The energies of hydration obtained from MD and QM/MM-MD for Fe(II) are 520 and 500 kcal/mol, and for Fe(III) 1160 and 1100 kcal/mol respectively. The mean residence times of water in the second shell obtained from QM/MM-MD are 24 and 48 ps for Fe(II) and Fe(III), respectively. In contrast to the data obtained from classical MD simulation, the QM/MM-MD values are all in good agreement with the experimental data available. These investigations and results clearly indicate that many-body effects are essential for the proper description of all properties of the aqueous solution of both Fe(II) and Fe(III) ions. (author)

  20. 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.

  1. Corrosion in the SCWR: insights from molecular dynamics simulations of the supercritical water - iron hydroxide interface

    Energy Technology Data Exchange (ETDEWEB)

    Kallikragas, D.; Plugatyr, A.; Svishchev, I.M., E-mail: dimitrioskallikragas@trentu.ca [Trent University, Peterborough, Ontario (Canada)

    2013-07-01

    The adsorption properties of supercritical water confined between parallel iron (II) hydroxide surfaces were determined through molecular dynamics simulations. Simulations were conducted at temperatures and water densities typically found in the heat transport system of the supercritical water cooled nuclear reactor (SCWR). Surface water layer densities were compared to those of the bulk water. Adsorption coverage was calculated as a function of the number of waters per surface OH group. Images of the water molecules configurations are provided along with the density profile of the adsorption layer. The observed localized adsorption and surface clustering of supercritical water, would likely produce more localized corrosion phenomena in the water bearing components of the SCWR. (author)

  2. 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

  3. Molecular Theory and Simulation of Water-Oil Contacts

    Science.gov (United States)

    Tan, Liang

    The statistical mechanical theory of hydrophobic interactions was initiated decades ago for purely repulsive hydrophobic species, in fact, originally for hard-sphere solutes in liquid water. Systems which treat only repulsive solute-water interactions obviously differ from the real world situation. The issue of the changes to be expected from inclusion of realistic attractive solute-water interactions has been of specific interest also for decades. We consider the local molecular field (LMF) theory for the effects of solute attractive forces on hydrophobic interactions. The principal result of LMF theory is outlined, then tested by obtaining radial distribution functions (rdfs) for Ar atoms in water, with and without attractive interactions distinguished by the Weeks-Chandler-Andersen (WCA) separation. Change from purely repulsive atomic solute interactions to include realistic attractive interactions substantially diminishes the strength of hydrophobic bonds. Since attractions make a big contribution to hydrophobic interactions, Pratt-Chandler theory, which did not include attractions, should not be naively compared to computer simulation results with general physical interactions, including attractions. Lack of general appreciation of this point has lead to mistaken comparisons throughout the history of this subject. The rdfs permit evaluation of osmotic second virial coefficients B2. Those B 2 are consistent with the conclusion that incorporation of attractive interactions leads to more positive (repulsive) values. In all cases here, B2 becomes more attractive with increasing temperature below T = 360K, the so-call inverse temperature behavior. In 2010, the Gulf of Mexico Macondo well (Deepwater Horizon) oil spill focused the attention of the world on water-oil phase equilibrium. In response to the disaster, chemical dispersants were applied to break oil slicks into droplets and thus to avoid large-scale fouling of beaches and to speed up biodegradation

  4. MD2036: UFO Dynamics Studies and UFO Fast Detection

    CERN Document Server

    Belanger, Philippe; Valette, Matthieu; Lindstrom, Bjorn Hans Filip; Grob, Laura Katharina; Schmidt, Rudiger; Wollmann, Daniel

    2017-01-01

    UFOs are one of the remaining unknown related to LHC operation. Therefore, improving the understanding of UFO dynamics and validating the developed models against direct beam measurements is of fundamental importance in view of LHC operation at 7 TeV and with HL-LHC beam intensities. If not understood, UFOs could also be a showstopper for future machines such as FCC. This MD demonstrates new methods to study the dynamic behaviour of a calibrated UFO, simulated by the interaction of wire scanners with the beam. The events created during the MD were monitored using diamond BLMs in IR7, providing bunch-by-bunch resolution measurements. The analysis presented herein shows that blown-up bunches can be used to identify the plane of movement of UFOs, that bunch profiles and bunch sizes can be measured with dBLMs with good precision, that simulation of expected losses are in good agreement with measurements for oscillating bunches and that the space resolution of the acquisition system used during the MD is about 10 ...

  5. Rotational dynamics of benzene and water in an ionic liquid explored via molecular dynamics simulations and NMR T1 measurements.

    Science.gov (United States)

    Yasaka, Yoshiro; Klein, Michael L; Nakahara, Masaru; Matubayasi, Nobuyuki

    2012-02-21

    The rotational dynamics of benzene and water in the ionic liquid (IL) 1-butyl-3-methylimidazolium chloride are studied using molecular dynamics (MD) simulation and NMR T(1) measurements. MD trajectories based on an effective potential are used to calculate the (2)H NMR relaxation time, T(1) via Fourier transform of the relevant rotational time correlation function, C(2R)(t). To compensate for the lack of polarization in the standard fixed-charge modeling of the IL, an effective ionic charge, which is smaller than the elementary charge is employed. The simulation results are in closest agreement with NMR experiments with respect to the temperature and Larmor frequency dependencies of T(1) when an effective charge of ±0.5e is used for the anion and the cation, respectively. The computed C(2R)(t) of both solutes shows a bi-modal nature, comprised of an initial non-diffusive ps relaxation plus a long-time ns tail extending to the diffusive regime. Due to the latter component, the solute dynamics is not under the motional narrowing condition with respect to the prevalent Larmor frequency. It is shown that the diffusive tail of the C(2R)(t) is most important to understand frequency and temperature dependencies of T(1) in ILs. On the other hand, the effect of the initial ps relaxation is an increase of T(1) by a constant factor. This is equivalent to an "effective" reduction of the quadrupolar coupling constant (QCC). Thus, in the NMR T(1) analysis, the rotational time correlation function can be modeled analytically in the form of aexp (-t/τ) (Lipari-Szabo model), where the constant a, the Lipari-Szabo factor, contains the integrated contribution of the short-time relaxation and τ represents the relaxation time of the exponential (diffusive) tail. The Debye model is a special case of the Lipari-Szabo model with a = 1, and turns out to be inappropriate to represent benzene and water dynamics in ILs since a is as small as 0.1. The use of the Debye model would result in

  6. Simulation models for water pollution in rivers and lakes; Suishitsu osen no simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hosomi, M. [Tokyo Univ. of Agriculture and Technology, Koganei (Japan). Faculty of Technology

    1996-11-05

    Rivers, lakes, and dam lakes are taken up as fields related to urban environment, and simulation models for water pollution control is introduced which are considered to be important for controlling water quality. In connection with rivers, a model showing the relationship between organic contamination and DO (dissolved oxygen) as well as an analyzed example of the use of continuous data of easy-to-measure DO are introduced. DO and pH in urban rivers sometimes exceed the environmental standards in the dry season. The cause is greater effect of biofilm adhesion at the river bed due to elongated staying time, and the establishment of the maintained river flow rate must be reviewed. One of the problems of ecological models is the deficiency of the data for the verification of the ecological models, and arrangement to solve the problem is required. Although it is admitted that simulation of phytoplankton in which neural network is employed has just started, it is expected to become an effective means for the study of phenomena which can not be elucidated by the modeling using normal numeric models. 7 refs., 13 figs.

  7. Multiscale modeling of a rectifying bipolar nanopore: explicit-water versus implicit-water simulations.

    Science.gov (United States)

    Ható, Zoltán; Valiskó, Mónika; Kristóf, Tamás; Gillespie, Dirk; Boda, Dezsö

    2017-07-21

    In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore at two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics technique. In a reduced model, we use implicit water and apply the Local Equilibrium Monte Carlo method together with the Nernst-Planck transport equation. This hybrid method makes the fast calculation of ion transport possible at the price of lost details. We show that the implicit-water model is an appropriate representation of the explicit-water model when we look at the system at the device (i.e., input vs. output) level. The two models produce qualitatively similar behavior of the electrical current for different voltages and model parameters. Looking at the details of concentration and potential profiles, we find profound differences between the two models. These differences, however, do not influence the basic behavior of the model as a device because they do not influence the z-dependence of the concentration profiles which are the main determinants of current. These results then address an old paradox: how do reduced models, whose assumptions should break down in a nanoscale device, predict experimental data? Our simulations show that reduced models can still capture the overall device physics correctly, even though they get some important aspects of the molecular-scale physics quite wrong; reduced models work because they include the physics that is necessary from the point of view of device function. Therefore, reduced models can suffice for general device understanding and device design, but more detailed models might be needed for molecular level understanding.

  8. Simulations of water nano-confined between corrugated planes

    Science.gov (United States)

    Zubeltzu, Jon; Artacho, Emilio

    2017-11-01

    Water confined to nanoscale widths in two dimensions between ideal planar walls has been the subject of ample study, aiming at understanding the intrinsic response of water to confinement, avoiding the consideration of the chemistry of actual confining materials. In this work, we study the response of such nanoconfined water to the imposition of a periodicity in the confinement by means of computer simulations, both using empirical potentials and from first-principles. For that we propose a periodic confining potential emulating the atomistic oscillation of the confining walls, which allows varying the lattice parameter and amplitude of the oscillation. We do it for a triangular lattice, with several values of the lattice parameter: one which is ideal for commensuration with layers of Ih ice and other values that would correspond to more realistic substrates. For the former, the phase diagram shows an overall rise of the melting temperature. The liquid maintains a bi-layer triangular structure, however, despite the fact that it is not favoured by the external periodicity. The first-principles liquid is significantly affected by the modulation in its layering and stacking even at relatively small amplitudes of the confinement modulation. Beyond some critical modulation amplitude, the hexatic phase present in flat confinement is replaced by a trilayer crystalline phase unlike any of the phases encountered for flat confinement. For more realistic lattice parameters, the liquid does not display higher tendency to freeze, but it clearly shows inhomogeneous behaviour as the strength of the rugosity increases. In spite of this expected inhomogeneity, the structural and dynamical response of the liquid is surprisingly insensitive to the external modulation. Although the first-principles calculations give a more triangular liquid than the one observed with empirical potentials (TIP4P/2005), both agree remarkably well for the main conclusions of the study.

  9. Simulation of sea water intrusion in coastal aquifers

    Indian Academy of Sciences (India)

    dependent miscible flow and transport modelling approach for simulation of seawater intrusion in coastal aquifers. A nonlinear optimization-based simulation methodology was used in this study. Various steady state simulations are performed for a ...

  10. MD study of pyrimidine base damage on DNA and its recognition by repair enzyme

    International Nuclear Information System (INIS)

    Pinak, M.

    2000-01-01

    The molecular dynamics (MD) simulation was used on the study of two specific damages of pyrimidine bases of DNA. Pyrimidine bases are major targets either of free radicals induced by ionizing radiation in DNA surrounding environment or UV radiation. Thymine dimer (TD) is UV induced damage, in which two neighboring thymines in one strand are joined by covalent bonds of C(5)-C(5) and C(6)-C(6) atoms of thymines. Thymine glycol (TG) is ionizing radiation induced damage in which the free water radical adds to unsaturated bond C(5)-C(6) of thymine. Both damages are experimentally suggested to be mutagenetic and carcinogenic unless properly repaired by repair enzymes. In the case of MD of TD, there is detected strong kink around the TD site that is not observed in native DNA. In addition there is observed the different value of electrostatic energy at the TD site - negative '-10 kcal/mol', in contrary to nearly neutral value of native thymine site. Structural changes and specific electrostatic energy - seems to be important for proper recognition of TD damaged site, formation of DNA-enzyme complex and thus for subsequent repair of DNA. In the case of TG damaged DNA there is major structural distortion at the TG site, mainly the increased distance between TG and the C5' of adjacent nucleotide. This enlarged gap between the neighboring nucleotides may prevent the insertion of complementary base during replication causing the replication process to stop. In which extend this structural feature together with energy properties of TG contributes to the proper recognition of TG by repair enzyme Endonuclease III is subject of further computational MD study. (author)

  11. 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; hide

    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.

  12. 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.)

  13. 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

  14. 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

  15. Numerical simulation of water and sand blowouts when penetrating through shallow water flow formations in deep water drilling

    Science.gov (United States)

    Ren, Shaoran; Liu, Yanmin; Gong, Zhiwu; Yuan, Yujie; Yu, Lu; Wang, Yanyong; Xu, Yan; Deng, Junyu

    2018-02-01

    In this study, we applied a two-phase flow model to simulate water and sand blowout processes when penetrating shallow water flow (SWF) formations during deepwater drilling. We define `sand' as a pseudo-component with high density and viscosity, which can begin to flow with water when a critical pressure difference is attained. We calculated the water and sand blowout rates and analyzed the influencing factors from them, including overpressure of the SWF formation, as well as its zone size, porosity and permeability, and drilling speed (penetration rate). The obtained data can be used for the quantitative assessment of the potential severity of SWF hazards. The results indicate that overpressure of the SWF formation and its zone size have significant effects on SWF blowout. A 10% increase in the SWF formation overpressure can result in a more than 90% increase in the cumulative water blowout and a 150% increase in the sand blowout when a typical SWF sediment is drilled. Along with the conventional methods of well flow and pressure control, chemical plugging, and the application of multi-layer casing, water and sand blowouts can be effectively reduced by increasing the penetration rate. As such, increasing the penetration rate can be a useful measure for controlling SWF hazards during deepwater drilling.

  16. 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....

  17. Simulation of water flows in multiple columns with small outlets

    International Nuclear Information System (INIS)

    Suh, Yong Kweon; Li, Zi Lu; Jeong, Jong Hyun; Lee, Jun Hee

    2006-01-01

    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

  18. 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

  19. Improved simulation of river water and groundwater exchange in an alluvial plain using the SWAT model

    Science.gov (United States)

    Hydrological interaction between surface and subsurface water systems has a significant impact on water quality, ecosystems and biogeochemistry cycling of both systems. Distributed models have been developed to simulate this function, but they require detailed spatial inputs and extensive computati...

  20. 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.

  1. Formulation and make-up of simulated concentrated water, high ionic content aqueous solution

    International Nuclear Information System (INIS)

    Gdowski, G.

    1997-01-01

    This procedure describes the formulation and make-up of Simulated Concentrated Water (SCW), a high-ionic-content water to be used for Activity E-20-50 Long-Term Corrosion Studies. This water has an ionic content which is nominally a factor of a thousand higher than that of representative waters at or near Yucca Mountain. Representative waters were chosen as J-13 well water [Harrar, 1990] and perched water at Yucca Mountain [Glassley, 1996]. J-13 well water is obtained from ground water that is in contact with the Topopah Spring tuff, which is the repository horizon rock. The perched water is located in the Topopah Spring tuff, but below the repository horizon and above the water table. A nominal thousand times higher ionic content was chosen to simulate the water that would result from the wetting of salts which have been previously deposited on a container surface

  2. Formulation and make-up of simulate dilute water, low ionic content aqueous solution

    International Nuclear Information System (INIS)

    Gdowski, G.

    1997-01-01

    This procedure describes the formulation and make-up of Simulated Dilute Water (SOW), a low-ionic-content water to be used for Activity E-20-50, Long-Term Corrosion Studies. This water has an ionic content which is nominally a factor of ten higher than that of representative waters at or near Yucca Mountain. Representative waters were chosen as J-13 well water [Harrar, 1990] and perched water at Yucca Mountain [Glassley, 1996]. J-13 well water is obtained from ground water that is in contact with the Topopah Spring tuff, which is the repository horizon rock. The perched water is located in the Topopah Spring tuff, but below the repository horizon and above the water table. A nominal times ten higher ionic content was chosen to simulate the effect of ionic concentrating due to elevated temperature water flowing through fractures where salts and minerals have been deposited due to evaporation and boiling

  3. Large-eddy simulations of unidirectional water flow over dunes

    Science.gov (United States)

    Grigoriadis, D. G. E.; Balaras, E.; Dimas, A. A.

    2009-06-01

    The unidirectional, subcritical flow over fixed dunes is studied numerically using large-eddy simulation, while the immersed boundary method is implemented to incorporate the bed geometry. Results are presented for a typical dune shape and two Reynolds numbers, Re = 17,500 and Re = 93,500, on the basis of bulk velocity and water depth. The numerical predictions of velocity statistics at the low Reynolds number are in very good agreement with available experimental data. A primary recirculation region develops downstream of the dune crest at both Reynolds numbers, while a secondary region develops at the toe of the dune crest only for the low Reynolds number. Downstream of the reattachment point, on the dune stoss, the turbulence intensity in the developing boundary layer is weaker than in comparable equilibrium boundary layers. Coherent vortical structures are identified using the fluctuating pressure field and the second invariant of the velocity gradient tensor. Vorticity is primarily generated at the dune crest in the form of spanwise "roller" structures. Roller structures dominate the flow dynamics near the crest, and are responsible for perturbing the boundary layer downstream of the reattachment point, which leads to the formation of "horseshoe" structures. Horseshoe structures dominate the near-wall dynamics after the reattachment point, do not rise to the free surface, and are distorted by the shear layer of the next crest. The occasional interaction between roller and horseshoe structures generates tube-like "kolk" structures, which rise to the free surface and persist for a long time before attenuating.

  4. 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.

  5. X-Pol Potential: An Electronic Structure-Based Force Field for Molecular Dynamics Simulation of a Solvated Protein in Water.

    Science.gov (United States)

    Xie, Wangshen; Orozco, Modesto; Truhlar, Donald G; Gao, Jiali

    2009-02-17

    A recently proposed electronic structure-based force field called the explicit polarization (X-Pol) potential is used to study many-body electronic polarization effects in a protein, in particular by carrying out a molecular dynamics (MD) simulation of bovine pancreatic trypsin inhibitor (BPTI) in water with periodic boundary conditions. The primary unit cell is cubic with dimensions ~54 × 54 × 54 Å(3), and the total number of atoms in this cell is 14281. An approximate electronic wave function, consisting of 29026 basis functions for the entire system, is variationally optimized to give the minimum Born-Oppenheimer energy at every MD step; this allows the efficient evaluation of the required analytic forces for the dynamics. Intramolecular and intermolecular polarization and intramolecular charge transfer effects are examined and are found to be significant; for example, 17 out of 58 backbone carbonyls differ from neutrality on average by more than 0.1 electron, and the average charge on the six alanines varies from -0.05 to +0.09. The instantaneous excess charges vary even more widely; the backbone carbonyls have standard deviations in their fluctuating net charges from 0.03 to 0.05, and more than half of the residues have excess charges whose standard deviation exceeds 0.05. We conclude that the new-generation X-Pol force field permits the inclusion of time-dependent quantum mechanical polarization and charge transfer effects in much larger systems than was previously possible.

  6. Evaluation of hydroacid complex in the forward osmosis–membrane distillation (FO–MD) system for desalination

    KAUST Repository

    Wang, Peng; Cui, Yue; Ge, Qingchun; Fern Tew, Tjin; Chung, Neal Tai-Shung

    2015-01-01

    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.

  7. 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.

  8. 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.

  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. Irrigation of grapevines with saline water. II. Mathematical simulation of vine growth and yield

    NARCIS (Netherlands)

    Ben-Asher, J.; Dam, van J.C.; Feddes, R.A.; Jhorar, R.K.

    2006-01-01

    Soil, water, atmosphere and plant (SWAP) model simulates deterministic transport of water and solutes, incorporating a semi-analytical sink function. It enables one to simulate detailed (SAWPd) or simple (SWAPs) crop growth patterns in response to flow patterns in the root zone. The objectives of

  11. 33 CFR 334.155 - Severn River, Naval Station Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area.

    Science.gov (United States)

    2010-07-01

    ... Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area. 334.155 Section 334.155 Navigation and... RESTRICTED AREA REGULATIONS § 334.155 Severn River, Naval Station Annapolis, Small Boat Basin, Annapolis, MD; naval restricted area. (a) The area. The waters within the Naval Station Annapolis small boat basin and...

  12. Effect of salinity and temperature on treatment of concentrated wastewater from RO by FO-MD

    Science.gov (United States)

    Zhou, Yingru; Huang, Manhong; Deng, Qian

    2018-02-01

    In this study the appropriate temperature of the membrane distillation (MD) hot side (the permeation flux of MD was controlled by adjusting the hot side temperature) was selected according to the water flux of FO process so that the water transfer rate on both sides of FO and MD was consistent and the FO-MD process could be stable operation. When the salt concentration of feed solution was 30, 55, 80 and 100 g/L, the desalination rates changed little, which were 99.1%, 98.4%, 98.9% and 98.7%, respectively. The removal rate of COD was 93.8%, 94.2%, 91.6% and 92.7% which also changed little like the desalination rates. The removal rate of chromaticity increased with the increase of salinity, which attained 96.6%, 97.0%, 97.2% and 97.9%, respectively. This study proved that salinity of the feed solution affected little on the removal rate of contaminants but great on the water flux, with the increase of salinity from 30 to 100 g/L, the water flux was 6.05, 4.81, 4.33 and 3.87 LMH with the appropriate temperature (67.5±0.5, 64.5±0.5, 62.5±0.5 and 60.5±0.5 °C) of MD hot side. In a word, FO-MD was first used to treat the high salinity RO water with over 30 g/L total dissolved solids (TDS), FO-MD was a promising new process for high salinity wastewater treatment, and the hybrid system can solve the problem of lower draw solution concentration, and the high-quality production water will be obtained directly by this hybrid system with low membrane fouling tendency.

  13. 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

    Czech Academy of Sciences Publication Activity Database

    Havrila, Marek; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, Miroslav; Otyepka, M.; Šponer, Jiří

    2015-01-01

    Roč. 119, č. 49 (2015), s. 15176-15190 ISSN 1520-6106 R&D Projects: GA ČR(CZ) GBP305/12/G034 Institutional support: RVO:68081707 Keywords : MOLECULAR-DYNAMICS SIMULATIONS * DIMERIZATION INITIATION SITE * QUANTUM-CHEMICAL COMPUTATIONS Subject RIV: BO - Biophysics Impact factor: 3.187, year: 2015

  14. 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.

  15. Pressurized water reactor simulation in the training environment

    International Nuclear Information System (INIS)

    Wills, A.G.

    1990-01-01

    The paper gives a brief history of PWR Simulation within the DNST and an outline of the training courses leading to the requirement for the Display Array Simulation System. Focus is then placed upon the flexible use of real time simulation in the teaching of plant dynamics by the use of model generated data. The use of interactive consoles and a large scale colour graphic display has led to the success of the Display Array Simulation System within the DNST. Realisation of the potential of the system has led to many other proposed uses for the installed system and the paper concludes by discussing some of these. (orig./DG)

  16. 75 FR 47203 - Airworthiness Directives; McDonnell Douglas Corporation Model MD-11 and MD-11F Airplanes Equipped...

    Science.gov (United States)

    2010-08-05

    ... Airworthiness Directives; McDonnell Douglas Corporation Model MD- 11 and MD-11F Airplanes Equipped With General... Sec. 39.13 by adding the following new AD: 2010-16-03 McDonnell Douglas Corporation: Amendment 39... applies to McDonnell Douglas Corporation Model MD-11 and MD-11F airplanes, certified in any category...

  17. 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.

  18. MD2190: Q" Stabilization during injection

    CERN Document Server

    Schenk, Michael; Li, Kevin Shing Bruce; Malina, Lukas; Metral, Elias; Tomas Garcia, Rogelio; CERN. Geneva. ATS Department

    2018-01-01

    This MD is a follow-up study of MD1831, where single bunches were stabilized against impedance-driven instabilities at 6.5 TeV in the LHC with Q''. The goals are (i) to explore whether an amplitude detuning free Q'' knob can be implemented at injection energy, and (ii) whether Q'' can provide beam stability at injection, where the beams suffer mostly from electron cloud effects. Ideally, this would relax the use of the Landau octupoles and may help in preserving the beam quality by reducing dynamic aperture limitations originating from the octupoles. The MD has been split into two parts: First, optics corrections were put in place to minimize beta-beating and linear coupling introduced by the knobs. The corrections were achieved by means of orbit bumps and skew quadrupole knobs. Machine safety was then validated with loss maps. While the betatron loss maps were approved, the off-momentum maps showed a priori unexpected losses in several arcs and the MD was stopped at this point for reasons of machine protecti...

  19. MD2725: 16L2 aperture measurement

    CERN Document Server

    Mirarchi, Daniele; Rossi, Roberto; CERN. Geneva. ATS Department

    2018-01-01

    Dumps induced by sudden increase of losses in the half-cell 16L2 have been a serious machine limitation during the 2017 run. The aim of this MD was to perform local aperture measurements in order to assess differences after the beam screen regeneration, compared to first measurements in 2017.

  20. 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......Silicon dioxides-water systems are abundant in nature and play fundamental roles in a diversity of novel science and engineering applications. Although extensive research has been devoted to study the nature of the interaction between silica and water a complete understanding of the system has...... 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...

  1. Visualization of the collective vortex-like motions in liquid argon and water: Molecular dynamics simulation

    Science.gov (United States)

    Anikeenko, A. V.; Malenkov, G. G.; Naberukhin, Yu. I.

    2018-03-01

    We propose a new measure of collectivity of molecular motion in the liquid: the average vector of displacement of the particles, ⟨ΔR⟩, which initially have been localized within a sphere of radius Rsph and then have executed the diffusive motion during a time interval Δt. The more correlated the motion of the particles is, the longer will be the vector ⟨ΔR⟩. We visualize the picture of collective motions in molecular dynamics (MD) models of liquids by constructing the ⟨ΔR⟩ vectors and pinning them to the sites of the uniform grid which divides each of the edges of the model box into equal parts. MD models of liquid argon and water have been studied by this method. Qualitatively, the patterns of ⟨ΔR⟩ vectors are similar for these two liquids but differ in minor details. The most important result of our research is the revealing of the aggregates of ⟨ΔR⟩ vectors which have the form of extended flows which sometimes look like the parts of vortices. These vortex-like clusters of ⟨ΔR⟩ vectors have the mesoscopic size (of the order of 10 nm) and persist for tens of picoseconds. Dependence of the ⟨ΔR⟩ vector field on parameters Rsph, Δt, and on the model size has been investigated. This field in the models of liquids differs essentially from that in a random-walk model.

  2. 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...

  3. 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…

  4. 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.

  5. 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

  6. MD-11 PCA - Research flight team photo

    Science.gov (United States)

    1995-01-01

    On Aug. 30, 1995, a the McDonnell Douglas MD-11 transport aircraft landed equipped with a computer-assisted engine control system that has the potential to increase flight safety. In landings at NASA Dryden Flight Research Center, Edwards, California, on August 29 and 30, the aircraft demonstrated software used in the aircraft's flight control computer that essentially landed the MD-11 without a need for the pilot to manipulate the flight controls significantly. In partnership with McDonnell Douglas Aerospace (MDA), with Pratt & Whitney and Honeywell helping to design the software, NASA developed this propulsion-controlled aircraft (PCA) system following a series of incidents in which hydraulic failures resulted in the loss of flight controls. This new system enables a pilot to operate and land the aircraft safely when its normal, hydraulically-activated control surfaces are disabled. This August 29, 1995, photo shows the MD-11 team. Back row, left to right: Tim Dingen, MDA pilot; John Miller, MD-11 Chief pilot (MDA); Wayne Anselmo, MD-11 Flight Test Engineer (MDA); Gordon Fullerton, PCA Project pilot; Bill Burcham, PCA Chief Engineer; Rudey Duran, PCA Controls Engineer (MDA); John Feather, PCA Controls Engineer (MDA); Daryl Townsend, Crew Chief; Henry Hernandez, aircraft mechanic; Bob Baron, PCA Project Manager; Don Hermann, aircraft mechanic; Jerry Cousins, aircraft mechanic; Eric Petersen, PCA Manager (Honeywell); Trindel Maine, PCA Data Engineer; Jeff Kahler, PCA Software Engineer (Honeywell); Steve Goldthorpe, PCA Controls Engineer (MDA). Front row, left to right: Teresa Hass, Senior Project Management Analyst; Hollie Allingham (Aguilera), Senior Project Management Analyst; Taher Zeglum, PCA Data Engineer (MDA); Drew Pappas, PCA Project Manager (MDA); John Burken, PCA Control Engineer.

  7. 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.; hide

    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.

  8. 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...

  9. Transient Simulations of Gas-Oil-Water Separation Plants

    Directory of Open Access Journals (Sweden)

    Tor S. Schei

    1991-01-01

    Full Text Available A set of mathematical models for the dynamic simulation of offshore processing plants is developed. Each process unit is modeled separately, and the various models are integrated into a system for the simulation of an entire plant. The purpose of the simulation system is to study the effects of various disturbances and investigate appropriate control strategies. Important variables subject to control are pressure, flow rate, temperature, vessel liquid level and compressor speed. In separators the rate of interfacial mass transfer between the liquid and vapour phases at non-equilibrium is modeled as a first order time lag. The vapour liquid equilibrium ratio is linearized with respect to variations in pressure and temperature for each separator stage. A realistic scenario is chosen in order to demonstrate the capabilities of the simulation system.

  10. Process simulation of heavy water plants - a powerful analytical tool

    International Nuclear Information System (INIS)

    Miller, A.I.

    1978-10-01

    The commercially conscious designs of Canadian GS (Girdler-Sulphide) have proved sensitive to process conditions. That, combined with the large scale of our units, has meant that computer simulation of their behaviour has been a natural and profitable development. Atomic Energy of Canada Limited has developed a family of steady state simulations to describe all of the Canadian plants. Modelling of plant conditions has demonstrated that the simulation description is very precise and it has become an integral part of the industry's assessments of both plant operation and decisions on capital expenditures. The simulation technique has also found extensive use in detailed designing of both the rehabilitated Glace Bay and the new La Prade plants. It has opened new insights into plant design and uncovered a radical and significant flowsheet change for future designs as well as many less dramatic but valuable lesser changes. (author)

  11. Influence of root-water-uptake parameterization on simulated heat transport in a structured forest soil

    Science.gov (United States)

    Votrubova, Jana; Vogel, Tomas; Dohnal, Michal; Dusek, Jaromir

    2015-04-01

    Coupled simulations of soil water flow and associated transport of substances have become a useful and increasingly popular tool of subsurface hydrology. Quality of such simulations is directly affected by correctness of its hydraulic part. When near-surface processes under vegetation cover are of interest, appropriate representation of the root water uptake becomes essential. Simulation study of coupled water and heat transport in soil profile under natural conditions was conducted. One-dimensional dual-continuum model (S1D code) with semi-separate flow domains representing the soil matrix and the network of preferential pathways was used. A simple root water uptake model based on water-potential-gradient (WPG) formulation was applied. As demonstrated before [1], the WPG formulation - capable of simulating both the compensatory root water uptake (in situations when reduced uptake from dry layers is compensated by increased uptake from wetter layers), and the root-mediated hydraulic redistribution of soil water - enables simulation of more natural soil moisture distribution throughout the root zone. The potential effect on heat transport in a soil profile is the subject of the present study. [1] Vogel T., M. Dohnal, J. Dusek, J. Votrubova, and M. Tesar. 2013. Macroscopic modeling of plant water uptake in a forest stand involving root-mediated soil-water redistribution. Vadose Zone Journal, 12, 10.2136/vzj2012.0154. The research was supported by the Czech Science Foundation Project No. 14-15201J.

  12. Using CONFIG for Simulation of Operation of Water Recovery Subsystems for Advanced Control Software Evaluation

    Science.gov (United States)

    Malin, Jane T.; Flores, Luis; Fleming, Land; Throop, Daiv

    2002-01-01

    A hybrid discrete/continuous simulation tool, CONFIG, has been developed to support evaluation of the operability life support systems. CON FIG simulates operations scenarios in which flows and pressures change continuously while system reconfigurations occur as discrete events. In simulations, intelligent control software can interact dynamically with hardware system models. CONFIG simulations have been used to evaluate control software and intelligent agents for automating life support systems operations. A CON FIG model of an advanced biological water recovery system has been developed to interact with intelligent control software that is being used in a water system test at NASA Johnson Space Center

  13. Relationships between water table and model simulated ET

    Science.gov (United States)

    Prem B. Parajuli; Gretchen F. Sassenrath; Ying Ouyang

    2013-01-01

    This research was conducted to develop relationships among evapotranspiration (ET), percolation (PERC), groundwater discharge to the stream (GWQ), and water table fluctuations through a modeling approach. The Soil and Water Assessment Tool (SWAT) hydrologic and crop models were applied in the Big Sunflower River watershed (BSRW; 7660 km2) within the Yazoo River Basin...

  14. A one-dimensional model for simulating soil water movement ...

    African Journals Online (AJOL)

    ... regression analysis revealed the relati-onship to be exponential. The values of calculated and measured soil water content and total evapotranspiration decreased with number of days after rain or irrigation. The nodal soil water content also decreased with the soil depth. (Journal of Applied Science and Technology: 2001 ...

  15. Communication: Minimum in the thermal conductivity of supercooled water: A computer simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Bresme, F., E-mail: f.bresme@imperial.ac.uk [Chemical Physics Section, Department of Chemistry, Imperial College, London SW7 2AZ, United Kingdom and Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491 (Norway); Biddle, J. W.; Sengers, J. V.; Anisimov, M. A. [Institute for Physical Science and Technology, and Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742 (United States)

    2014-04-28

    We report the results of a computer simulation study of the thermodynamic properties and the thermal conductivity of supercooled water as a function of pressure and temperature using the TIP4P-2005 water model. The thermodynamic properties can be represented by a two-structure equation of state consistent with the presence of a liquid-liquid critical point in the supercooled region. Our simulations confirm the presence of a minimum in the thermal conductivity, not only at atmospheric pressure, as previously found for the TIP5P water model, but also at elevated pressures. This anomalous behavior of the thermal conductivity of supercooled water appears to be related to the maximum of the isothermal compressibility or the minimum of the speed of sound. However, the magnitudes of the simulated thermal conductivities are sensitive to the water model adopted and appear to be significantly larger than the experimental thermal conductivities of real water at low temperatures.

  16. Communication: Minimum in the thermal conductivity of supercooled water: A computer simulation study

    International Nuclear Information System (INIS)

    Bresme, F.; Biddle, J. W.; Sengers, J. V.; Anisimov, M. A.

    2014-01-01

    We report the results of a computer simulation study of the thermodynamic properties and the thermal conductivity of supercooled water as a function of pressure and temperature using the TIP4P-2005 water model. The thermodynamic properties can be represented by a two-structure equation of state consistent with the presence of a liquid-liquid critical point in the supercooled region. Our simulations confirm the presence of a minimum in the thermal conductivity, not only at atmospheric pressure, as previously found for the TIP5P water model, but also at elevated pressures. This anomalous behavior of the thermal conductivity of supercooled water appears to be related to the maximum of the isothermal compressibility or the minimum of the speed of sound. However, the magnitudes of the simulated thermal conductivities are sensitive to the water model adopted and appear to be significantly larger than the experimental thermal conductivities of real water at low temperatures

  17. 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.

  18. A global hydrological simulation to specify the sources of water used by humans

    Science.gov (United States)

    Hanasaki, Naota; Yoshikawa, Sayaka; Pokhrel, Yadu; Kanae, Shinjiro

    2018-01-01

    Humans abstract water from various sources to sustain their livelihood and society. Some global hydrological models (GHMs) include explicit schemes of human water abstraction, but the representation and performance of these schemes remain limited. We substantially enhanced the water abstraction schemes of the H08 GHM. This enabled us to estimate water abstraction from six major water sources, namely, river flow regulated by global reservoirs (i.e., reservoirs regulating the flow of the world's major rivers), aqueduct water transfer, local reservoirs, seawater desalination, renewable groundwater, and nonrenewable groundwater. In its standard setup, the model covers the whole globe at a spatial resolution of 0.5° × 0.5°, and the calculation interval is 1 day. All the interactions were simulated in a single computer program, and all water fluxes and storage were strictly traceable at any place and time during the simulation period. A global hydrological simulation was conducted to validate the performance of the model for the period of 1979-2013 (land use was fixed for the year 2000). The simulated water fluxes for water abstraction were validated against those reported in earlier publications and showed a reasonable agreement at the global and country level. The simulated monthly river discharge and terrestrial water storage (TWS) for six of the world's most significantly human-affected river basins were compared with gauge observations and the data derived from the Gravity Recovery and Climate Experiment (GRACE) satellite mission. It is found that the simulation including the newly added schemes outperformed the simulation without human activities. The simulated results indicated that, in 2000, of the 3628±75 km3 yr-1 global freshwater requirement, 2839±50 km3 yr-1 was taken from surface water and 789±30 km3 yr-1 from groundwater. Streamflow, aqueduct water transfer, local reservoirs, and seawater desalination accounted for 1786±23, 199±10, 106±5, and 1.8

  19. Improving SWAT for simulating water and carbon fluxes of forest ecosystems

    International Nuclear Information System (INIS)

    Yang, Qichun; Zhang, Xuesong

    2016-01-01

    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. - Graphical abstract: Evaluating and improving SWAT simulations of water and carbon cycling over ten AmeriFlux sites across the United States. - Highlights: • The default forest parameterization in SWAT results in inadequate simulations of water and carbon. • Radiation use efficiency, leaf to biomass fraction, and parent material weathering processes are modified. • Revised SWAT provides improved simulations of evapotranspiration and net ecosystem exchange

  20. Improving SWAT for simulating water and carbon fluxes of forest ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Qichun [Joint Global Change Research Institute, Pacific Northwest National Lab, College Park, MD 20740 (United States); Zhang, Xuesong, E-mail: xuesong.zhang@pnnl.gov [Joint Global Change Research Institute, Pacific Northwest National Lab, College Park, MD 20740 (United States); Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 (United States)

    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. - Graphical abstract: Evaluating and improving SWAT simulations of water and carbon cycling over ten AmeriFlux sites across the United States. - Highlights: • The default forest parameterization in SWAT results in inadequate simulations of water and carbon. • Radiation use efficiency, leaf to biomass fraction, and parent material weathering processes are modified. • Revised SWAT provides improved simulations of evapotranspiration and net ecosystem exchange.

  1. Simulations of water and solute movement in the buried waste repository at Vaalputs

    International Nuclear Information System (INIS)

    Hutson, J.L.

    1987-01-01

    A previous series of simulations examined the movement of water through trench cap configurations of several types. The objectives of this series are i) to extent the simulations from the surface to the bottom of the repository, accounting for the placement of drums, ii) to examine the magnitude and direction of water fluxes throughout this depth and iii) to simulate the movement of solutes, using various assumptions regarding solute adsorption. Two models were used. The first was an adaptation of a solute transport model which incorporates the transient water flow model used in previous simulations. This was used primarily to estimate the likely water fluxes in the drum placement region. Since it requires large amounts of computer time this model was used to simulate periods of one or two years only. The second model was a very simple steady state solute transport model which was used to simulate Cs distribution after a 100 year period, using flux data obtained from the transient model simulations. The most important conclusion reached from this series of simulations is that the movement of Cs in the soil under the likely water regime is extremely slow. 'Worst case' situations were simulated. Some of these situations are unlikely in reality but provide a useful indication of the rates of movement of solute under various conditions. For this reason it was assumed that plants were absent in cases when maximum percolation was simulated and present when maximum upward flow was simulated. In no case was a 'wick' (a textural barrier to unsaturated water flow) assumed to be present

  2. 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.

  3. Empirical method for simulation of water tables by digital computers

    International Nuclear Information System (INIS)

    Carnahan, C.L.; Fenske, P.R.

    1975-09-01

    An empirical method is described for computing a matrix of water-table elevations from a matrix of topographic elevations and a set of observed water-elevation control points which may be distributed randomly over the area of interest. The method is applicable to regions, such as the Great Basin, where the water table can be assumed to conform to a subdued image of overlying topography. A first approximation to the water table is computed by smoothing a matrix of topographic elevations and adjusting each node of the smoothed matrix according to a linear regression between observed water elevations and smoothed topographic elevations. Each observed control point is assumed to exert a radially decreasing influence on the first approximation surface. The first approximation is then adjusted further to conform to observed water-table elevations near control points. Outside the domain of control, the first approximation is assumed to represent the most probable configuration of the water table. The method has been applied to the Nevada Test Site and the Hot Creek Valley areas in Nevada

  4. Turbulence modeling for Francis turbine water passages simulation

    International Nuclear Information System (INIS)

    Maruzewski, P; Munch, C; Mombelli, H P; Avellan, F; Hayashi, H; Yamaishi, K; Hashii, T; Sugow, Y

    2010-01-01

    The applications of Computational Fluid Dynamics, CFD, to hydraulic machines life require the ability to handle turbulent flows and to take into account the effects of turbulence on the mean flow. Nowadays, Direct Numerical Simulation, DNS, is still not a good candidate for hydraulic machines simulations due to an expensive computational time consuming. Large Eddy Simulation, LES, even, is of the same category of DNS, could be an alternative whereby only the small scale turbulent fluctuations are modeled and the larger scale fluctuations are computed directly. Nevertheless, the Reynolds-Averaged Navier-Stokes, RANS, model have become the widespread standard base for numerous hydraulic machine design procedures. However, for many applications involving wall-bounded flows and attached boundary layers, various hybrid combinations of LES and RANS are being considered, such as Detached Eddy Simulation, DES, whereby the RANS approximation is kept in the regions where the boundary layers are attached to the solid walls. Furthermore, the accuracy of CFD simulations is highly dependent on the grid quality, in terms of grid uniformity in complex configurations. Moreover any successful structured and unstructured CFD codes have to offer a wide range to the variety of classic RANS model to hybrid complex model. The aim of this study is to compare the behavior of turbulent simulations for both structured and unstructured grids topology with two different CFD codes which used the same Francis turbine. Hence, the study is intended to outline the encountered discrepancy for predicting the wake of turbine blades by using either the standard k-ε model, or the standard k-ε model or the SST shear stress model in a steady CFD simulation. Finally, comparisons are made with experimental data from the EPFL Laboratory for Hydraulic Machines reduced scale model measurements.

  5. Turbulence modeling for Francis turbine water passages simulation

    Energy Technology Data Exchange (ETDEWEB)

    Maruzewski, P; Munch, C; Mombelli, H P; Avellan, F [Ecole polytechnique federale de Lausanne, Laboratory of Hydraulic Machines Avenue de Cour 33 bis, CH-1007 Lausanne (Switzerland); Hayashi, H; Yamaishi, K; Hashii, T; Sugow, Y, E-mail: pierre.maruzewski@epfl.c [Nippon KOEI Power Systems, 1-22 Doukyu, Aza, Morijyuku, Sukagawa, Fukushima Pref. 962-8508 (Japan)

    2010-08-15

    The applications of Computational Fluid Dynamics, CFD, to hydraulic machines life require the ability to handle turbulent flows and to take into account the effects of turbulence on the mean flow. Nowadays, Direct Numerical Simulation, DNS, is still not a good candidate for hydraulic machines simulations due to an expensive computational time consuming. Large Eddy Simulation, LES, even, is of the same category of DNS, could be an alternative whereby only the small scale turbulent fluctuations are modeled and the larger scale fluctuations are computed directly. Nevertheless, the Reynolds-Averaged Navier-Stokes, RANS, model have become the widespread standard base for numerous hydraulic machine design procedures. However, for many applications involving wall-bounded flows and attached boundary layers, various hybrid combinations of LES and RANS are being considered, such as Detached Eddy Simulation, DES, whereby the RANS approximation is kept in the regions where the boundary layers are attached to the solid walls. Furthermore, the accuracy of CFD simulations is highly dependent on the grid quality, in terms of grid uniformity in complex configurations. Moreover any successful structured and unstructured CFD codes have to offer a wide range to the variety of classic RANS model to hybrid complex model. The aim of this study is to compare the behavior of turbulent simulations for both structured and unstructured grids topology with two different CFD codes which used the same Francis turbine. Hence, the study is intended to outline the encountered discrepancy for predicting the wake of turbine blades by using either the standard k-{epsilon} model, or the standard k-{epsilon} model or the SST shear stress model in a steady CFD simulation. Finally, comparisons are made with experimental data from the EPFL Laboratory for Hydraulic Machines reduced scale model measurements.

  6. Turbulence modeling for Francis turbine water passages simulation

    Science.gov (United States)

    Maruzewski, P.; Hayashi, H.; Munch, C.; Yamaishi, K.; Hashii, T.; Mombelli, H. P.; Sugow, Y.; Avellan, F.

    2010-08-01

    The applications of Computational Fluid Dynamics, CFD, to hydraulic machines life require the ability to handle turbulent flows and to take into account the effects of turbulence on the mean flow. Nowadays, Direct Numerical Simulation, DNS, is still not a good candidate for hydraulic machines simulations due to an expensive computational time consuming. Large Eddy Simulation, LES, even, is of the same category of DNS, could be an alternative whereby only the small scale turbulent fluctuations are modeled and the larger scale fluctuations are computed directly. Nevertheless, the Reynolds-Averaged Navier-Stokes, RANS, model have become the widespread standard base for numerous hydraulic machine design procedures. However, for many applications involving wall-bounded flows and attached boundary layers, various hybrid combinations of LES and RANS are being considered, such as Detached Eddy Simulation, DES, whereby the RANS approximation is kept in the regions where the boundary layers are attached to the solid walls. Furthermore, the accuracy of CFD simulations is highly dependent on the grid quality, in terms of grid uniformity in complex configurations. Moreover any successful structured and unstructured CFD codes have to offer a wide range to the variety of classic RANS model to hybrid complex model. The aim of this study is to compare the behavior of turbulent simulations for both structured and unstructured grids topology with two different CFD codes which used the same Francis turbine. Hence, the study is intended to outline the encountered discrepancy for predicting the wake of turbine blades by using either the standard k-epsilon model, or the standard k-epsilon model or the SST shear stress model in a steady CFD simulation. Finally, comparisons are made with experimental data from the EPFL Laboratory for Hydraulic Machines reduced scale model measurements.

  7. Digitization and simulation realization of full range control system for steam generator water level

    International Nuclear Information System (INIS)

    Qian Hong; Ye Jianhua; Qian Fei; Li Chao

    2010-01-01

    In this paper, a full range digital control system for the steam generator water level is designed by a control scheme of single element control and three-element cascade feed-forward control, and the method to use the software module configuration is proposed to realize the water level control strategy. This control strategy is then applied in the operation of the nuclear power simulation machine. The simulation result curves indicate that the steam generator water level maintains constant at the stable operation condition, and when the load changes, the water level changes but finally maintains the constant. (authors)

  8. Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes MdSAUR37, MdPP2CH and MdALMTII.

    Science.gov (United States)

    Jia, Dongjie; Shen, Fei; Wang, Yi; Wu, Ting; Xu, Xuefeng; Zhang, Xinzhong; Han, Zhenhai

    2018-05-11

    Many efforts have been made to map quantitative trait loci (QTLs) to facilitate practical marker-assisted selection (MAS) in plants. In the present study, we identified four genome-wide major QTLs responsible for apple fruit acidity by MapQTL and BSA-seq analyses using two independent pedigree-based populations. Candidate genes were screened in major QTL regions, and three functional gene markers, including a non-synonymous A/G single nucleotide polymorphism (SNP) in the coding region of MdPP2CH, a 36-bp insertion in the promoter of MdSAUR37, and a previously reported SNP in MdALMTII, were validated to influence the malate content of apple fruits. In addition, MdPP2CH inactivated three vacuolar H + -ATPases (MdVHA-A3, MdVHA-B2 and MdVHA-D2) and one aluminium-activated malate transporter (MdALMTII) via dephosphorylation and negatively influenced fruit malate accumulation. The dephosphotase activity of MdPP2CH was suppressed by MdSAUR37, which implied a higher hierarchy of genetic interaction. Therefore, the MdSAUR37/MdPP2CH/MdALMTII chain cascaded hierarchical epistatic genetic effects to precisely determine apple fruit malate content. An A/G SNP (-1010) on MdMYB44 promoter region from a major QTL (qtl08.1) was closely associated with fruit malate content. The predicted phenotype values (PPVs) were estimated using the tentative genotype values of the gene markers, and the PPVs were significantly correlated with the observed phenotype values. Our findings provide an insight into plant genome-based selection in apples and will aid in conducting research to understand the physiological fundamentals of quantitative genetics. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

  9. Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Larsen, Anders Støttrup; Rantanen, Jukka; Johansson, Kristoffer E

    2017-01-01

    Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach...... to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration....... The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure...

  10. 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.

  11. 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

    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...... that allows hydrologists and ecologists to represent the complex and dynamic interactions occurring between surface water, ground water, water quality and freshwater ecosystems within a catchment. We demonstrate here the practical application of this tool to two case studies where the interaction of surface...... 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...

  12. Simulation of water quality parameters from the treatment of ...

    African Journals Online (AJOL)

    Michael Horsfall

    ABSTRACT: Today, discharging the wastewaters into the river is the main factor of water pollution and ... Ecological condition and wastewater properties affect the efficiency of WSP. ... 1 cubic meter domestic wastewater can pollute about.

  13. 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.

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

    KAUST Repository

    Lardhi, Sheikha F.

    2013-01-01

    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

  15. LOGOS. HX: a core simulator for high conversion boiling water reactors

    International Nuclear Information System (INIS)

    Tsuiki, Makoto; Sakurada, Koichi; Yoshida, Hiroyuki.

    1988-01-01

    A three-dimensional physics simulator 'LOGOS. HX' has been developed for the designing analysis of high conversion boiling water reactor (HCBWR) cores. Its functions, calculational methods, and verification results will briefly be discussed. (author)

  16. 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.

  17. LWR [Light Water Reactor] power plant simulations using the AD10 and AD100 systems

    International Nuclear Information System (INIS)

    Wulff, W.; Cheng, H.S.; Chien, C.J.; Jang, J.Y.; Lin, H.C.; Mallen, A.N.; Wang, S.J.

    1989-01-01

    Boiling (BWR) and Pressurized (PWR) Water Reactor Power Plants are being simulated at BNL with the AD10 and AD100 Peripheral Processor Systems. The AD10 system has been used for BWR simulations since 1984 for safety analyses, emergency training and optimization studies. BWR simulation capabilities have been implemented recently on the AD100 system and PWR simulation capabilities are currently being developed under the auspices of international cooperation. Modeling and simulation methods are presented with emphasis on the simulation of the Nuclear Steam Supply System. Results are presented for BWR simulation and performance characteristics are compared of the AD10 and AD100 systems. It will be shown that the AD100 simulates two times faster than two AD10 processors operating in parallel and that the computing capacity of one AD100 (with FMU processor) is twice as large as that of two AD10 processors. 9 refs., 5 figs., 1 tab

  18. Identification and simulation for steam generator water level based on Kalman Filter

    International Nuclear Information System (INIS)

    Deng Chen; Zhang Qinshun

    2008-01-01

    In order to effectively control the water level of the steam generator (SG), this paper has set about the state-observer theory in modern control and put forward a method to detect the 'false water level' based on Kalman Filter. Kalman Filter is a efficient tool to estimate state-variable by measured value including noise. For heavy measurement noise of steam flow, constructing a 'false water level' observer by Kalman Filter could availably obtain state variable of 'false water level'. The simulation computing for the dynamics characteristic of nuclear SG water level process under several typically running power was implemented by employing the simulation model. The result shows that the simulation model accurately identifies the 'false water level' produced in the reverse thermal-dynamic effects of nuclear SG water level process. The simulation model can realize the precise analysis of dynamics characteristic for the nuclear SG water level process. It can provide a kind of new ideas for the 'false water level' detecting of SG. (authors)

  19. 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.

  20. Evaluation of a simulation model for predicting soil-water ...

    African Journals Online (AJOL)

    The soils particle size distribution (specifically, percent clay and sand) and organic matter contents were inputted into the model to simulate soil moisture status at saturation, field capacity and wilting point, soil bulk density and saturated hydraulic conductivity. The model outputs were statistically compared with observed ...

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

    Indian Academy of Sciences (India)

    Unknown

    Typically, the simulated diffusion constants are larger, and relaxation times smaller than .... where λi is the Lagrange multiplier for the charge neutrality constraint. As the .... For a geometrically rigid model such as SPC, the integral turns out to ...

  2. Environmental Systems Simulations for Carbon, Energy, Nitrogen, Water, and Watersheds: Design Principles and Pilot Testing

    NARCIS (Netherlands)

    Lant, C.; Pérez Lapena, B.; Xiong, W.; Kraft, S.; Kowalchuk, R.; Blair, M.

    2016-01-01

    Guided by the Next Generation Science Standards and elements of problem-based learning, four human-environment systems simulations are described in brief—carbon, energy, water, and watershed—and a fifth simulation on nitrogen is described in more depth. These science, technology, engineering, and

  3. Development and implementation of an empirical frequency map for use in MD simulations of isotope-edited proteins, and, Development, implementation, and evaluation of an online student portal as a textbook replacement in an advanced general chemistry course

    Science.gov (United States)

    Shorb, Justin Matthew

    The first portion of this thesis describes an extension of work done in the Skinner group to develop an empirical frequency map for N-methylacetamide (NMA) in water. NMA is a peptide bond capped on either side by a methyl group and is therefore a common prototypical molecule used when studying complicated polypeptides and proteins. This amide bond is present along the backbone of every protein as it connects individual component amino acids. This amide bond also has a strong observable frequency in the IR due to the Amide-I mode (predominantly carbon-oxygen stretching motion). This project describes the simplification of the prior model for mapping the frequency of the Amide-I mode from the electric field due to the environment and develops a parallel implementation of this algorithm for use in larger biological systems, such as the trans-membrane portion of the tetrameric polypeptide bundle protein CD3zeta. The second portion of this thesis describes the development, implementation and evaluation of an online textbook within the context of a cohesive theoretical framework. The project begins by describing what is meant when discussing a digital textbook, including a survey of various types of digital media being used to deliver textbook-like content. This leads into the development of a theoretical framework based on constructivist pedagogical theory, hypertext learning theory, and chemistry visualization and representation frameworks. The implementation and design of ChemPaths, the general chemistry online text developed within the Chemistry Education Digital Library (ChemEd DL) is then described. The effectiveness of ChemPaths being used as a textbook replacement in an advanced general chemistry course is evaluated within the developed theoretical framework both qualitatively and quantitatively.

  4. 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.

  5. G189A analytical simulation of the RITE Integrated Waste Management-Water System

    Science.gov (United States)

    Coggi, J. V.; Clonts, S. E.

    1974-01-01

    This paper discusses the computer simulation of the Integrated Waste Management-Water System Using Radioisotopes for Thermal Energy (RITE) and applications of the simulation. Variations in the system temperature and flows due to particular operating conditions and variations in equipment heating loads imposed on the system were investigated with the computer program. The results were assessed from the standpoint of the computed dynamic characteristics of the system and the potential applications of the simulation to system development and vehicle integration.

  6. Phase-Transfer Energetics of Small-Molecule Alcohols Across the Water-Hexane Interface: Molecular Dynamics Simulation Using Charge Equilibration Models

    Science.gov (United States)

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

    2010-01-01

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

  7. 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.

  8. Effects of sulphuric acid and acidifying ammonium deposition on water quality and vegetation of simulated soft water ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Schuurkes, J.A.; Heck, I.C.; Hesen, P.L.; Leuven, R.S.; Roelofs, J.G.

    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 sulfate 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 sulfate deposition, particularly, strongly affected water quality and vegetation development. Although ammonium sulfate 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 sulfate deposition lead 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, sulfate, 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 sulfate probably contributes to a large extent in the acidification, eutrophication and floristic changes of oligotrophic soft waters. 10 refs.

  9. 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.

  10. Modelling and simulation of a nitrification biofilter for drinking water ...

    African Journals Online (AJOL)

    For the purification of pure and microbiologically safe drinking water, different treatment steps are necessary. One of those steps is the removal of ammonium, which can, e.g. be accomplished through nitrification in a biofilter. In this study, a model for such a nitrifying biofilter was developed and the model was ...

  11. Global sensitivity analysis for UNSATCHEM simulations of crop production with degraded waters

    Science.gov (United States)

    One strategy for maintaining irrigated agricultural productivity in the face of diminishing resource availability is to make greater use of marginal quality waters and lands. A key to sustaining systems using degraded irrigation waters is salinity management. Advanced simulation models and decision ...

  12. Steel corrosion products solubility under conditions simulating various water chemistry parameters in power plants

    International Nuclear Information System (INIS)

    Slobodov, A.A.; Kritskij, V.G.; Zarembo, V.I.; Puchkov, L.V.

    1988-01-01

    To simulate construction material corrosion product mass transfer model in power plant circuits calculation of iron oxide and hydroxide solubility, depending on water chemistry parameters: temperature, pH-value, content of dissolved in water hydrogen and oxygen, is carried out

  13. Water balance versus land surface model in the simulation of Rhine river discharges

    NARCIS (Netherlands)

    Hurkmans, R.T.W.L.; Moel, de H.; Aerts, J.C.J.H.; Troch, P.A.

    2008-01-01

    Accurate streamflow simulations in large river basins are crucial to predict timing and magnitude of floods and droughts and to assess the hydrological impacts of climate change. Water balance models have been used frequently for these purposes. Compared to water balance models, however, land

  14. Combined spectroscopic, DFT, TD-DFT and MD study of newly synthesized thiourea derivative

    Science.gov (United States)

    Menon, Vidya V.; Sheena Mary, Y.; Shyma Mary, Y.; Panicker, C. Yohannan; Bielenica, Anna; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, Christian

    2018-03-01

    A novel thiourea derivative, 1-(3-bromophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea (ANF-22) is synthesized and characterized by FTIR, FT-Raman and NMR spectroscopy experimentally and theoretically. A detailed conformational analysis of the title molecule has been conducted in order to locate the lowest energy geometry, which was further subjected to the detailed investigation of spectroscopic, reactive, degradation and docking studies by density functional theory (DFT) calculations and molecular dynamics (MD) simulations. Time dependent DFT (TD-DFT) calculations have been used also in order to simulate UV spectra and investigate charge transfer within molecule. Natural bond orbital analysis has been performed analyzing the charge delocalization and using HOMO and LUMO energies the electronic properties are analyzed. Molecular electrostatic potential map is used for the quantitative measurement of active sites in the molecule. In order to determine the locations possibly prone to electrophilic attacks we have calculated average local ionization energies and mapped them to the electron density surface. Further insight into the local reactivity properties have been obtained by calculation of Fukui functions, also mapped to the electron density surface. Possible degradation properties by the autoxidation mechanism have been assessed by calculations of bond dissociation energies for hydrogen abstraction. Atoms of title molecule with significant interactions with water molecules have been determined by calculations of radial distribution functions. The title compound can be a lead compound for developing new analgesic drug.

  15. 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...

  16. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

    Science.gov (United States)

    Jakobtorweihen, S.; Zuniga, A. Chaides; Ingram, T.; Gerlach, T.; Keil, F. J.; Smirnova, I.

    2014-07-01

    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.

  17. Predicting solute partitioning in lipid bilayers: Free energies and partition coefficients from molecular dynamics simulations and COSMOmic

    International Nuclear Information System (INIS)

    Jakobtorweihen, S.; Ingram, T.; Gerlach, T.; Smirnova, I.; Zuniga, A. Chaides; Keil, F. J.

    2014-01-01

    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

  18. 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.

  19. Water erosion under simulated rainfall in different soil management systems during soybean growth

    OpenAIRE

    Engel,Fernando Luis; Bertol,Ildegardis; Mafra,Álvaro Luiz; Cogo,Neroli Pedro

    2007-01-01

    Soil management influences soil cover by crop residues and plant canopy, affecting water erosion. The objective of this research was to quantify water and soil losses by water erosion under different soil tillage systems applied on a typical aluminic Hapludox soil, in an experiment carried out from April 2003 to May 2004, in the Santa Catarina highland region, Lages, southern Brazil. Simulated rainfall was applied during five soybean cropstages, at the constant intensity of 64.0 mm h-1. Treat...

  20. Advanced Hydroinformatic Techniques for the Simulation and Analysis of Water Supply and Distribution Systems

    OpenAIRE

    Herrera, Manuel; Meniconi, Silvia; Alvisi, Stefano; Izquierdo, Joaquin

    2018-01-01

    This document is intended to be a presentation of the Special Issue “Advanced Hydroinformatic Techniques for the Simulation and Analysis of Water Supply and Distribution Systems”. The final aim of this Special Issue is to propose a suitable framework supporting insightful hydraulic mechanisms to aid the decision-making processes of water utility managers and practitioners. Its 18 peer-reviewed articles present as varied topics as: water distribution system design, optimization of network perf...

  1. A mathematical model for the simulation of thermal transients in the water loop of IPEN

    International Nuclear Information System (INIS)

    Pontedeiro, A.C.

    1980-01-01

    A mathematical model for simulation of thermal transients in the water loop at the Instituto de Pesquisas Energeticas e Nucleares, Sao Paulo, Brasil, is developed. The model is based on energy equations applied to the components of the experimental water loop. The non-linear system of first order diferencial equations and of non-linear algebraic equations obtained through the utilization of the IBM 'System/360-Continous System Modeling Program' (CSMP) is resolved. An optimization of the running time of the computer is made and a typical simulation of the water loop is executed. (Author) [pt

  2. A molecular dynamics simulation of sodium pentadecyl sulphonate (SPDS)/water system

    International Nuclear Information System (INIS)

    Arsenyan, L.H.; Poghosyan, A.H.; Shahinyan, A.A.

    2008-07-01

    We have carried out a molecular dynamics simulation of a sodium pentadecylsulfonate (SPDS)/water system consisting of 64PDS/1200water and 512PDS/9000water molecules, correspondingly. The overall simulation time for both cases reaches up to 60ns and the simulation was performed using the NAMD code with CHARMM27 force field. The main parameters of the system have been calculated and compared with available X-ray diffraction findings. For large system, after a couple of ns, we receive the molecule's hydrocarbon chains tilt in the opposite sense in layers and reducing the system size leads to the decrease of the average angle between bilayer normal and chain vector. At the end of 50ns of a simulation run we achieve the crystalline-like structure of hydrocarbon packing. For both cases, we obtain tilted hydrocarbon chains packing and the average angle between bilayer normal and chain vector is estimated to be about 13 deg. and 10 deg. (author)

  3. Molecular dynamics simulation of impact test

    International Nuclear Information System (INIS)

    Akahoshi, Y.; Schmauder, S.; Ludwig, M.

    1998-01-01

    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.)

  4. 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.)

  5. Simulation of steam-water and binary geothermal power plants

    International Nuclear Information System (INIS)

    Popel', O.S.; Frid, S.E.; Shpil'rajn, Eh.Eh.

    2004-01-01

    The generalized scheme of the geothermal power plant (GeoPP), assuming the possibility of the electric power production in the steam-water turbine or in the turbine on the low-boiling working body, is considered. The GeoPP mathematical model, making it possible to carry out the comparison of the power indices of various GeoPP schemes and analysis of the calculational indices sensitivity of these schemes to the mode parameters change, is presented [ru

  6. Simulation of Integrated Qualitative and Quantitative Allocation of Surafce and Underground Water Resources to Drinking Water Demand in Mashhad

    Directory of Open Access Journals (Sweden)

    Mansoureh Atashi

    2015-12-01

    Full Text Available Despite the fact that both surface and groundwater resources inside and outside the city of Mashhad have been already exploited to their maximum capacity and that the large water transfer Doosti Dam Project has been already implemented to transfer a considerable quanity of water to Mashhad, the city will be encountering a daily water shortage of about 1.7 m3/s by 2021. The problem would be even worse if the quality of the water resources are taken into account, in which case, the shortage would start even sooner in 2011 when the water deficit will be about 0.9 m3/s. As a result, it is essential to develop short- and medium-term strategies for secure adequate water supplies for the city's domestic water demand. The present study aims to carry out a qualitative and quantitative modeling of surface and groundwater resources supplying Mashhad domestic water. The qualitative model is based on the quality indices of surface and groundwater resources according to which the resources are classified in the three quality categories of resources with no limitation, those with moderate limitations, and those with high limitations for use as domestic water supplies. The pressure zones are then examined with respect to the potable water demand and supply to be simulated in the MODSIM environment. The model thus developed is verified for the 2012 data based on the measures affecting water resources in the region and various scenarios are finally evaluated for a long-term 30-year period. Results show that the peak hourdaily water shortage in 2042for the zone supplied from no limitation resources will be 38%. However, this value will drop to 28% if limitations due to resource quality are also taken into account. Finally, dilution is suggested as a solution for exploiting the maximum quantitative and qualitative potential of the resources used as domestic water supplies. In this situation, the daily peak hour water shortage will be equal to 31%.

  7. Methane hydrate dissociation using inverted five-spot water flooding method in cubic hydrate simulator

    International Nuclear Information System (INIS)

    Li, Gang; Li, Xiao-Sen; Li, Bo; Wang, Yi

    2014-01-01

    The combination forms of the hydrate dissociation methods in different well systems are divided into 6 main patterns. Dissociation processes of methane hydrate in porous media using the inverted five-spot water flooding method (Pattern 4) are investigated by the experimental observation and numerical simulation. In situ methane hydrate is synthesized in the Cubic Hydrate Simulator (CHS), a 5.832-L cubic reactor. A center vertical well is used as the hot water injection well, while the four vertical wells at the corner are the gas and water production wells. The gas production begins simultaneously with the hot water injection, while after approximately 20 min of compression, the water begins to be produced. One of the common characteristics of the inverted five-spot water flooding method is that both the gas and water production rates decrease with the reduction of the hydrate dissociation rate. The evaluation of the energy efficiency ratio might indicate the inverted five-spot water flooding as a promising gas producing method from the hydrate reservoir. - Highlights: • A three-dimensional 5.8-L cubic pressure vessel is developed. • Gas production of hydrate using inverted five-spot flooding method is studied. • Water/gas production rate and energy efficiency ratio are evaluated. • Temperature distributions of numerical simulation and experiment agree well. • Hydrate dissociation process is a moving boundary problem in this study

  8. Simulation experiments for a large leak sodium-water reaction analysis. Volume 4. IHTS/relief system simulation tests

    International Nuclear Information System (INIS)

    Ploeger, D.W.

    1978-09-01

    Tests were performed in which a simplified 1/8-scale model of the intermediate heat transfer system and relief system of a LMFBR was subjected to a simulated sodium-water reaction in a steam generator. Pressures in the intermediate heat exchanger (IHX) and in the pipe were measured. The flow of water through the relief system was photographed and its velocity was measured. The forces on the relief system elbows resulting from the fluid flow were also measured. The tests were performed primarily to validate pulse propagation codes used for design and for direct use as design data

  9. Molecular simulation of water removal from simple gases with zeolite NaA.

    Science.gov (United States)

    Csányi, Eva; Ható, Zoltán; Kristóf, Tamás

    2012-06-01

    Water vapor removal from some simple gases using zeolite NaA was studied by molecular simulation. The equilibrium adsorption properties of H(2)O, CO, H(2), CH(4) and their mixtures in dehydrated zeolite NaA were computed by grand canonical Monte Carlo simulations. The simulations employed Lennard-Jones + Coulomb type effective pair potential models, which are suitable for the reproduction of thermodynamic properties of pure substances. Based on the comparison of the simulation results with experimental data for single-component adsorption at different temperatures and pressures, a modified interaction potential model for the zeolite is proposed. In the adsorption simulations with mixtures presented here, zeolite exhibits extremely high selectivity of water to the investigated weakly polar/non-polar gases demonstrating the excellent dehydration ability of zeolite NaA in engineering applications.

  10. Water Hammer Simulations of MMH Propellant - New Capability Demonstration of the Generalized Fluid Flow Simulation Program

    Science.gov (United States)

    Burkhardt, Z.; 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 does not provide the thermodynamic properties of Monomethylhydrazine (MMH). This paper will illustrate 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. Rigorous code validation of this approach will be done and reported at a future date.

  11. 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.

  12. Comparison of tritium concentrations in rainwater, simulated infiltrating water, and groundwater

    International Nuclear Information System (INIS)

    Ishii, Yoshiyuki; Saito, Masaaki; Imaizumi, Hiroshi; Kato, Norio; Kitaoka, Koichi

    2014-01-01

    The tritium concentration in initial groundwater(i.e., freshly infiltrating rainwater) is necessary for groundwater dating. We collected simulated infiltrating water as the initial groundwater and examined its characteristics for tritium concentration. First, in Tokyo, the tritium concentration of simulated infiltrating water was compared with that of rainwater, atmospheric moisture, groundwater, spring water, and sap water. While rainwater, atmospheric moisture, and simulated infiltrating water remarkably changed month-to-month or with every rainfall event, groundwater and spring water were nearly constant throughout the year. Second, we collected the simulated infiltrating water monthly at four sampling sites widely dispersed across Japan(i.e., Sapporo, Niigata, Tokyo, and Matsuyama) from 2004 to 2010. Sapporo and Niigata showed high tritium concentrations as compared with the relatively low concentrations in Tokyo and Matsuyama. These results indicate that we can obtain annual maximum and minimum concentrations at each site, and that we can estimate the tritium concentration in initial groundwater at each site by using a mixing model composed of these maximum and minimum concentrations. (author)

  13. Geant4-DNA simulation of electron slowing-down spectra in liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Incerti, S., E-mail: sebastien.incerti@tdt.edu.vn [Division of Nuclear Physics, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Univ. Bordeaux, CENBG, UMR 5797, F-33170, Gradignan (France); CNRS, IN2P3, CENBG, UMR 5797, F-33170 Gradignan (France); Kyriakou, I. [Medical Physics Laboratory, University of Ioannina Medical School, 45110 Ioannina (Greece); Tran, H.N. [Division of Nuclear Physics, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam); Faculty of Applied Sciences, Ton Duc Thang University, Tan Phong Ward, District 7, Ho Chi Minh City (Viet Nam)

    2017-04-15

    This work presents the simulation of monoenergetic electron slowing-down spectra in liquid water by the Geant4-DNA extension of the Geant4 Monte Carlo toolkit (release 10.2p01). These spectra are simulated for several incident energies using the most recent Geant4-DNA physics models, and they are compared to literature data. The influence of Auger electron production is discussed. For the first time, a dedicated Geant4-DNA example allowing such simulations is described and is provided to Geant4 users, allowing further verification of Geant4-DNA track structure simulation capabilities.

  14. Interpretation of Water Tracer Simulation in the H-1 Segment of the Gullfaks Field

    Energy Technology Data Exchange (ETDEWEB)

    Moid, Farrukh

    2000-07-01

    This thesis describes the water tracer simulation in the H-1 segment of the Gullfaks field. Three passive water tracer slugs were injected from the two producing wells during water flooding, pressure maintenance and reservoir monitoring program in the Gullfaks field. The same program is considered in this thesis. Computer Modelling Group's (CMG) simulator STARS is used for the general reservoir simulation and a separate module for tracer flow (ITRC-SIM) which is incorporated in the STARS and developed at Institute For Energy (IFE) is used for the tracer simulation. Water cut and tracer concentration data are used in history matching of the field. History matching is performed by changing the transmissibility and permeability of different layers; also the effect of changing saturations near the well bore on history matching is examined. It is noted that water cut is sensitive to transmissibility of the layers and the saturation around the well bore. Tracers are found to be moving in the most permeable layers. The corresponding history matching of water and tracer production shows a severe loss of first tracer injected because of imbibition process. Water phase velocity and areal communication between different wells are determined. Advance numerical features of tracer module ITRC-SIM such as flux limiting scheme and grid refinement scheme are evaluated and are found to be an important tool for reducing the numerical smearing. The effects of dispersion and diffusion on tracer response curve are also evaluated. Dispersion makes the tracer concentration curve smeared. Simulation results of water cut and tracer concentration show a good history match for this reservoir. The improved simulation model and the tracer module for this reservoir can be used for the prediction of future performance of the reservoir and interpretation of the tracer behaviour in the reservoir. (author)

  15. Multiscale network model for simulating liquid water and water vapour transfer properties of porous materials

    NARCIS (Netherlands)

    Carmeliet, J.; Descamps, F.; Houvenaghel, G.

    1999-01-01

    A multiscale network model is presented to model unsaturated moisture transfer in hygroscopic capillary-porous materials showing a broad pore-size distribution. Both capillary effects and water sorption phenomena, water vapour and liquid water transfer are considered. The multiscale approach is

  16. Simulation of the water-table altitude in the Biscayne Aquifer, southern Dade County, Florida, water years 1945-89

    Science.gov (United States)

    Merritt, M.L.

    1995-01-01

    A digital model of the flow system in the highly permeable surficial aquifer of southern Dade County, Florida, was constructed for the purposes of better understanding processes that influence the flow system and of supporting the construction of a subregional model of the transport of brackish water from a flowing artesian well. Problems that needed resolution in this endeavor included the development of methods to represent the influence of flowing surface water in seasonally inundated wetlands and the influence of a network of controlled canals developed in stages during the simulation time period (water years 1945-89). An additional problem was the general lack of natural aquifer boundaries near the boundaries of the study area. The model construction was based on a conceptual description of the Biscayne aquifer developed from the results of previous U.S. Geological Survey investigations. Modifications were made to an existing three- dimensional finite-difference simulator of ground- water flow to enable an upper layer of the grid to represent seasonally occurring overland sheetflow in a series of transient simulations of water levels from 1945 to 1989. A rewetting procedure was developed for the simulator that permitted resaturation of cells in this layer when the wet season recurred. An "equivalent hydraulic conductivity" coefficient was assigned to the overland flow layer that was analogous, subject to various approximations, to the use of the Manning equation. The surficial semiconfining peat and marl layers, levees, canals, and control structures were also represented as part of the model grid with the appropriate choices of hydraulic coefficient values. For most of the Biscayne aquifer grid cells, the value assigned to hydraulic conductivity for model calibration was 30,000 feet per day and the value assigned to porosity was 20 percent. Boundary conditions were specified near data sites having long-term records of surface-water stages or water

  17. Structure and dynamics of solvated Ba(II) in dilute aqueous solution - an ab initio QM/MM MD approach

    International Nuclear Information System (INIS)

    Hofer, Thomas S.; Rode, Bernd M.; Randolf, Bernhard R.

    2005-01-01

    Structural properties of the hydrated Ba(II) ion have been investigated by ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations at double zeta HF quantum mechanical level. The first shell coordination number was found to be 9.3, and several other structural parameters such as angular distribution functions, radial distribution functions and tilt- and θ-angle distributions allowed the full characterization of the hydration structure of the Ba(II) ion in dilute aqueous solution. Velocity autocorrelation functions were used to calculate librational and vibrational motions, ion-ligand motions as well as reorientation times. Different dynamical parameters such as water reorientation, mean ligand residence time, the number of ligand exchange processes and rate constants were also analyzed and the ligand exchange rate constant for the first shell was determined as k = 5.3 x 10 10 s -1

  18. Mathematical simulation of water distillation column for decreasing volume of tritiated water

    International Nuclear Information System (INIS)

    Kinoshita, Masahiro; Naruse, Yuji

    1981-12-01

    Water distillation is an attractive method for decreasing volume of the tritiated water produced by operation of tritium facilities. The tritiated water is continuously fed to a column and it is separated into two streams. The top stream is discarded to the environment after addition of sufficient amount of uncontaminated water. The bottom stream is further treated for solidification and capsulation. The tridiagonal matrix method proved to provide surprisingly rapid convergences of the calculations. The concentration of deuterium naturally contained in the tritiated water is higher than the tritium concentration, but it was verified that presence of HDO can be ignored in the calculation. (author)

  19. Simulation of pressurized water reactor in accidental state

    International Nuclear Information System (INIS)

    Chakir, E.

    1994-01-01

    The aim of this work is to develop the 1300 MWe 4 loops 'PWR' simulator called 'SATRAPE', witch the adopted physics modelisation allows a simplified neutronic calculation, and focus essentially on the reactor thermal hydraulic behavior in the case of the following accidents: - Loss of Coolant Accident (LOCA). - Steam Generator Tube Failure (SGTF). - Steam Line Break (SLB). In case of the 'LOCA' or 'SLB' accident, this modelisation enables the calculation of the pressure and the temperature in the containment building, and also the debit of the released dose in this latter in case of the 'LOCA' accident. The adopted models are relatively simple so as to allow an explicit resolve. In SATRAPE, two graphical interfaces enables to launch orders, whereas the other permits to visualize, the principal state variables of installations. The results obtained show a very good consistency with the envisaged commonly scenario at the time of the considered accidents. 33 refs., 52 figs., 1 tab. (author)

  20. 75 FR 53574 - Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD

    Science.gov (United States)

    2010-09-01

    ...-AA00 Safety Zone; Fireworks Displays, Potomac River, National Harbor, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during five fireworks displays launched from a discharge barge located... necessary to protect persons and vessels against the hazards associated with a fireworks display on...

  1. 78 FR 68002 - Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD

    Science.gov (United States)

    2013-11-13

    ... 1625-AA00 Safety Zone for Fireworks Display, Baltimore Harbor, Baltimore, MD AGENCY: Coast Guard, DHS... safety of life on navigable waters during a fireworks display launched from a barge located in Baltimore... rule involves a fireworks display associated with a New Year's Eve event that will take place in...

  2. Remote sensing reflectance simulation of coastal optical complex water in the East China Sea

    Science.gov (United States)

    He, Shuo; Lou, Xiulin; Zhang, Huaguo; Zheng, Gang

    2018-02-01

    In this work, remote sensing reflectance (Rrs) spectra of the Zhejiang coastal water in the East China Sea (ECS) were simulated by using the Hydrolight software with field data as input parameters. The seawater along the Zhejiang coast is typical Case II water with complex optical properties. A field observation was conducted in the Zhejiang coastal region in late May of 2016, and the concentration of ocean color constituents (pigment, SPM and CDOM), IOPs (absorption and backscattering coefficients) and Rrs were measured at 24 stations of 3 sections covering the turbid to clear inshore coastal waters. Referring to these ocean color field data, an ocean color model suitable for the Zhejiang coastal water was setup and applied in the Hydrolight. A set of 11 remote sensing reflectance spectra above water surface were modeled and calculated. Then, the simulated spectra were compared with the filed measurements. Finally, the spectral shape and characteristics of the remote sensing reflectance spectra were analyzed and discussed.

  3. Simulation of Deposition the Corrosion Waste in a Water Distribution System

    Directory of Open Access Journals (Sweden)

    Peráčková Jana

    2013-04-01

    Full Text Available In water distribution systems can be found particles of rust and other mechanical contaminants. The particles are deposited in locations where the low velocity of water flow. Where a can cause the pitting corrosion. Is a concern in the systems made of galvanized steel pipes. The contribution deals with CFD (Computational Fluid Dynamics simulations of water flow and particles deposition in water distribution system. CFD Simulations were compared with the corrosive deposits in real pipeline. Corrosion is a spontaneous process of destruction of metal material due to electrochemical reactions of metal with the aggressive surrounding. Electrochemical corrosion is caused by the thermodynamic instability of metal and therefore can not be completely suppress, it can only influence the speed of corrosion. The requirement is to keep metal properties during the whole its lifetime. Requested service lifetime the water pipe according to EN 806-2 is 50 years.

  4. Automatic Optimization for Large-Scale Real-Time Coastal Water Simulation

    Directory of Open Access Journals (Sweden)

    Shunli Wang

    2016-01-01

    Full Text Available We introduce an automatic optimization approach for the simulation of large-scale coastal water. To solve the singular problem of water waves obtained with the traditional model, a hybrid deep-shallow-water model is estimated by using an automatic coupling algorithm. It can handle arbitrary water depth and different underwater terrain. As a certain feature of coastal terrain, coastline is detected with the collision detection technology. Then, unnecessary water grid cells are simplified by the automatic simplification algorithm according to the depth. Finally, the model is calculated on Central Processing Unit (CPU and the simulation is implemented on Graphics Processing Unit (GPU. We show the effectiveness of our method with various results which achieve real-time rendering on consumer-level computer.

  5. Investigation on the liquid water droplet instability in a simulated flow channel of PEM fuel cell

    International Nuclear Information System (INIS)

    Ha, Tae Hun; Kim, Bok Yung; Kim, Han Sang; Min, Kyoung Doug

    2008-01-01

    To investigate the characteristics of water droplets on the gas diffusion layer from both top-view and side-view of the flow channel, a rig test apparatus was designed and fabricated with prism attached plate. This experimental device was used to simulate the growth of a single liquid water droplet and its transport process with various air flow velocity and channel height. Not only dry condition but also fully humidified condition was also simulated by using a water absorbing sponge. The detachment height of the water droplet with dry and wet conditions was measured and analyzed. It was found that the droplet tends towards becoming unstable by decreased channel height, increased flow velocity or making a gas diffusion layer (GDL) dryer. Also, peculiar behavior of the water droplet in the channel was presented like attachment to hydrophilic wall or sudden breaking of droplet in case of fully hydrated condition. The simplified force balance model matches with experimental data as well

  6. Hydrogeology and simulation of ground-water flow near the Lantana Landfill, Palm Beach County, Florida

    Science.gov (United States)

    Russell, G.M.; Wexler, E.J.

    1993-01-01

    The Lantana landfill in Palm Beach County has a surface that is 40 to 50 feet above original ground level and consists of about 250 acres of compacted garbage and trash. Parts of the landfill are below the water table. Surface-resistivity measurements and water-quality analyses indicate that leachate-enriched ground water along the eastern perimeter of the landfill has moved about 500 feet eastward toward an adjacent lake. Concentrations of chloride and nutrients within the leachate-enriched ground water were greater than background concentrations. The surficial aquifer system in the area of the landfill consists primarily of sand of moderate permeability, from land surface to a depth of about 68 feet deep, and consists of sand interbedded with sandstone and limestone of high permeability from a depth of about 68 feet to a depth of 200 feet. The potentiometric surface in the landfill is higher than that in adjacent areas to the east, indicating ground-water movement from the landfill toward a lake to the east. Steady-state simulation of ground-water flow was made using a telescoping-grid technique where a model covering a large area is used to determine boundaries and fluxes for a finer scale model. A regional flow model encompassing a 500-square mile area in southeastern Palm Beach County was used to calculate ground-water fluxes in a 126.5-square mile subregional area. Boundary fluxes calculated by the subregional model were then used to calculate boundary fluxes for a local model of the 3.75-square mile area representing the Lantana landfill site and vicinity. Input data required for simulating ground-water flow in the study area were obtained from the regional flow models, thus, effectively coupling the models. Additional simulations were made using the local flow model to predict effects of possible remedial actions on the movement of solutes in the ground-water system. Possible remedial actions simulated included capping the landfill with an impermeable layer

  7. A simulation study of homogeneous ice nucleation in supercooled salty water

    Science.gov (United States)

    Soria, Guiomar D.; Espinosa, Jorge R.; Ramirez, Jorge; Valeriani, Chantal; Vega, Carlos; Sanz, Eduardo

    2018-06-01

    We use computer simulations to investigate the effect of salt on homogeneous ice nucleation. The melting point of the employed solution model was obtained both by direct coexistence simulations and by thermodynamic integration from previous calculations of the water chemical potential. Using a seeding approach, in which we simulate ice seeds embedded in a supercooled aqueous solution, we compute the nucleation rate as a function of temperature for a 1.85 NaCl mol per water kilogram solution at 1 bar. To improve the accuracy and reliability of our calculations, we combine seeding with the direct computation of the ice-solution interfacial free energy at coexistence using the Mold Integration method. We compare the results with previous simulation work on pure water to understand the effect caused by the solute. The model captures the experimental trend that the nucleation rate at a given supercooling decreases when adding salt. Despite the fact that the thermodynamic driving force for ice nucleation is higher for salty water for a given supercooling, the nucleation rate slows down with salt due to a significant increase of the ice-fluid interfacial free energy. The salty water model predicts an ice nucleation rate that is in good agreement with experimental measurements, bringing confidence in the predictive ability of the model. We expect that the combination of state-of-the-art simulation methods here employed to study ice nucleation from solution will be of much use in forthcoming numerical investigations of crystallization in mixtures.

  8. A simulation-optimization model for effective water resources management in the coastal zone

    Science.gov (United States)

    Spanoudaki, Katerina; Kampanis, Nikolaos

    2015-04-01

    Coastal areas are the most densely-populated areas in the world. Consequently water demand is high, posing great pressure on fresh water resources. Climatic change and its direct impacts on meteorological variables (e.g. precipitation) and indirect impact on sea level rise, as well as anthropogenic pressures (e.g. groundwater abstraction), are strong drivers causing groundwater salinisation and subsequently affecting coastal wetlands salinity with adverse effects on the corresponding ecosystems. Coastal zones are a difficult hydrologic environment to represent with a mathematical model due to the large number of contributing hydrologic processes and variable-density flow conditions. Simulation of sea level rise and tidal effects on aquifer salinisation and accurate prediction of interactions between coastal waters, groundwater and neighbouring wetlands requires the use of integrated surface water-groundwater mathematical models. In the past few decades several computer codes have been developed to simulate coupled surface and groundwater flow. However, most integrated surface water-groundwater models are based on the assumption of constant fluid density and therefore their applicability to coastal regions is questionable. Thus, most of the existing codes are not well-suited to represent surface water-groundwater interactions in coastal areas. To this end, the 3D integrated surface water-groundwater model IRENE (Spanoudaki et al., 2009; Spanoudaki, 2010) has been modified in order to simulate surface water-groundwater flow and salinity interactions in the coastal zone. IRENE, in its original form, couples the 3D shallow water equations to the equations describing 3D saturated groundwater flow of constant density. A semi-implicit finite difference scheme is used to solve the surface water flow equations, while a fully implicit finite difference scheme is used for the groundwater equations. Pollution interactions are simulated by coupling the advection

  9. QM/MM-MD simulations of conjugated polyelectrolytes

    DEFF Research Database (Denmark)

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

    2014-01-01

    A methodological development is reported for the study of luminescence properties of conjugated polyelectrolytes, encompassing systems in which dihedral rotational barriers are easily overcome at room temperature. The components of the model include (i) a molecular mechanics (MM) force field desc...

  10. 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

  11. Effect of water phase transition on dynamic ruptures with thermal pressurization: Numerical simulations with changes in physical properties of water

    Science.gov (United States)

    Urata, Yumi; Kuge, Keiko; Kase, Yuko

    2015-02-01

    Phase transitions of pore water have never been considered in dynamic rupture simulations with thermal pressurization (TP), although they may control TP. From numerical simulations of dynamic rupture propagation including TP, in the absence of any water phase transition process, we predict that frictional heating and TP are likely to change liquid pore water into supercritical water for a strike-slip fault under depth-dependent stress. This phase transition causes changes of a few orders of magnitude in viscosity, compressibility, and thermal expansion among physical properties of water, thus affecting the diffusion of pore pressure. Accordingly, we perform numerical simulations of dynamic ruptures with TP, considering physical properties that vary with the pressure and temperature of pore water on a fault. To observe the effects of the phase transition, we assume uniform initial stress and no fault-normal variations in fluid density and viscosity. The results suggest that the varying physical properties decrease the total slip in cases with high stress at depth and small shear zone thickness. When fault-normal variations in fluid density and viscosity are included in the diffusion equation, they activate TP much earlier than the phase transition. As a consequence, the total slip becomes greater than that in the case with constant physical properties, eradicating the phase transition effect. Varying physical properties do not affect the rupture velocity, irrespective of the fault-normal variations. Thus, the phase transition of pore water has little effect on dynamic ruptures. Fault-normal variations in fluid density and viscosity may play a more significant role.

  12. Use of natural user interfaces in water simulations

    Science.gov (United States)

    Donchyts, G.; Baart, F.; van Dam, A.; Jagers, B.

    2013-12-01

    Conventional graphical user interfaces, used to edit input and present results of earth science models, have seen little innovation for the past two decades. In most cases model data is presented and edited using 2D projections even when working with 3D data. The emergence of 3D motion sensing technologies, such as Microsoft Kinect and LEAP Motion, opens new possibilities for user interaction by adding more degrees of freedom compared to a classical way using mouse and keyboard. Here we investigate how interaction with hydrodynamic numerical models can be improved using these new technologies. Our research hypothesis (H1) states that properly designed 3D graphical user interface paired with the 3D motion sensor can significantly reduce the time required to setup and use numerical models. In this work we have used a LEAP motion controller combined with a shallow water flow model engine D-Flow Flexible Mesh. Interacting with numerical model using hands

  13. Steam condensation induced water hammer simulations for different pipelines

    International Nuclear Information System (INIS)

    Barna, I.F.; Ezsol, G.

    2011-01-01

    We investigate steam condensation induced water hammer (CIWH) phenomena and present theoretical results for different kind of pipelines. We analyze the process with the WAHA3 model based on two-phase flow six first-order partial differential equations that present one dimensional, surface averaged mass, momentum and energy balances. A second order accurate high-resolution shock-capturing numerical scheme was applied with different kind of limiters in the numerical calculations. At first, we present calculations for various pipelines in the VVER-440-312 type nuclear reactor. Our recent calculation clearly shows that the six conditions of Griffith are only necessary conditions for CIWH but not sufficient. As second results we performed calculations for various geometries and compare with the theory of Chun. (author)

  14. Simulation of a weather radar display for over-water airborne radar approaches

    Science.gov (United States)

    Clary, G. R.

    1983-01-01

    Airborne radar approach (ARA) concepts are being investigated as a part of NASA's Rotorcraft All-Weather Operations Research Program on advanced guidance and navigation methods. This research is being conducted using both piloted simulations and flight test evaluations. For the piloted simulations, a mathematical model of the airborne radar was developed for over-water ARAs to offshore platforms. This simulated flight scenario requires radar simulation of point targets, such as oil rigs and ships, distributed sea clutter, and transponder beacon replies. Radar theory, weather radar characteristics, and empirical data derived from in-flight radar photographs are combined to model a civil weather/mapping radar typical of those used in offshore rotorcraft operations. The resulting radar simulation is realistic and provides the needed simulation capability for ongoing ARA research.

  15. Test Plan for the Boiling Water Reactor Dry Cask Simulator

    Energy Technology Data Exchange (ETDEWEB)

    Durbin, Samuel [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lindgren, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-11-01

    The thermal performance of commercial nuclear spent fuel dry storage casks are evaluated through detailed numerical analysis . These modeling efforts are completed by the vendor to demonstrate performance and regulatory compliance. The calculations are then independently verified by the Nuclear Regulatory Commission (NRC). Carefully measured data sets generated from testing of full sized casks or smaller cask analogs are widely recognized as vital for validating these models. Recent advances in dry storage cask designs have significantly increased the maximum thermal load allowed in a cask in part by increasing the efficiency of internal conduction pathways and by increasing the internal convection through greater canister helium pressure. These same vertical, canistered cask systems rely on ventilation between the canister and the overpack to convect heat away from the canister to the environment for both above and below-ground configurations. While several testing programs have been previously conducted, these earlier validation attempts did not capture the effects of elevated helium pressures or accurately portray the external convection of above-ground and below-ground canistered dry cask systems. The purpose of the investigation described in this report is to produce a data set that can be used to test the validity of the assumptions associated with the calculations presently used to determine steady-state cladding temperatures in modern vertical, canistered dry cask systems. The BWR cask simulator (BCS) has been designed in detail for both the above-ground and below-ground venting configurations. The pressure vessel representing the canister has been designed, fabricated, and pressure tested for a maximum allowable pressure (MAWP) rating of 24 bar at 400 deg C. An existing electrically heated but otherwise prototypic BWR Incoloy-clad test assembly is being deployed inside of a representative storage basket and cylindrical pressure vessel that represents the

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-01

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

  17. 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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. Simulation of Deep Water Renewal in Crater Lake, Oregon, USA under Current and Future Climate Conditions

    Science.gov (United States)

    Piccolroaz, S.; Wood, T. M.; Wherry, S.; Girdner, S.

    2015-12-01

    We applied a 1-dimensional lake model developed to simulate deep mixing related to thermobaric instabilities in temperate lakes to Crater Lake, a 590-m deep caldera lake in Oregon's Cascade Range known for its stunning deep blue color and extremely clear water, in order to determine the frequency of deep water renewal in future climate conditions. The lake model was calibrated with 6 years of water temperature profiles, and then simulated 10 years of validation data with an RMSE ranging from 0.81°C at 50 m depth to 0.04°C at 350-460 m depth. The simulated time series of heat content in the deep lake accurately captured extreme years characterized by weak and strong deep water renewal. The lake model uses wind speed and lake surface temperature (LST) as boundary conditions. LST projections under six climate scenarios from the CMIP5 intermodel comparison project (2 representative concentration pathways X 3 general circulation models) were evaluated with air2water, a simple lumped model that only requires daily values of downscaled air temperature. air2water was calibrated with data from 1993-2011, resulting in a RMSE between simulated and observed daily LST values of 0.68°C. All future climate scenarios project increased water temperature throughout the water column and a substantive reduction in the frequency of deepwater renewal events. The least extreme scenario (CNRM-CM5, RCP4.5) projects the frequency of deepwater renewal events to decrease from about 1 in 2 years in the present to about 1 in 3 years by 2100. The most extreme scenario (HadGEM2-ES, RCP8.5) projects the frequency of deepwater renewal events to be less than 1 in 7 years by 2100 and lake surface temperatures never cooling to less than 4°C after 2050. In all RCP4.5 simulations the temperature of the entire water column is greater than 4°C for increasing periods of time. In the RCP8.5 simulations, the temperature of the entire water column is greater than 4°C year round by the year 2060 (HadGEM2

  19. MD simulations and QM/MM calculations show that single-site mutations of cytochrome P450BM3 alter the active site’s complexity and the chemoselectivity of oxidation without changing the active species† †Electronic supplementary information (ESI) available: The RMS deviation of the protein during 100 ns (and 200 ns) of simulation and the total QM/MM and ZPE energies, as well as the Cartesian coordinates of all of the computed species. See DOI: 10.1039/c7sc01932g

    Science.gov (United States)

    Dubey, Kshatresh Dutta; Wang, Binju; Vajpai, Manu

    2017-01-01

    It is a long-standing mechanistic consensus that the mutation of the proton-shuttle mediator Threonine (T) in Cytochrome P450 enzymes severs the water channel and thereby quenches the formation of the active species: the high-valent iron(iv)-oxo porphyrin π-cation radical species, compound I (Cpd I). Using MD simulations and hybrid QM/MM calculations of P450BM3 we demonstrate that this is not the case. Thus, while the original water channel is disrupted in the T268A mutant of the enzyme, a new channel is formed that generates Cpd I. With this new understanding, we address the puzzling regiochemical and kinetic-isotope effect (KIE) results (Volz et al., J. Am. Chem. Soc., 2002, 124, 9724–9725) on the sulfoxidation and N-dealkylation of dimethyl-(4-methylsulfanyl-phenyl)-amine by wild type (WT) P450BM3 and its T268A vs. F87A mutants. We show that the observed variable ratio of S/Me oxidation for these enzymes, vis-à-vis the constant KIE, originates from Cpd I being the sole oxidant. Thus, while the conserved KIE probes the conserved nature of the transition state, the variable regiochemical S/Me ratio reflects the active-site reorganization in the mutants: the shifted location of the new water channel in T268A tightens the binding of the S-end by Cpd I and increases the S/Me ratio, whereas the absence of π-interaction with the S-end in F87A creates a looser binding that lowers the S/Me ratio. Our results match the experimental findings. As such, this study sheds light on puzzling experimental results, and may shift a central paradigm in P450 research. The broader implication on enzymatic research is that a single-site mutation is not a localised alteration but one that may lead to a profound change in the active site, sufficiently so as to change the chemoselectivity of catalyzed reactions. PMID:29568477

  20. Startup transient simulation for natural circulation boiling water reactors in PUMA facility

    International Nuclear Information System (INIS)

    Kuran, S.; Xu, Y.; Sun, X.; Cheng, L.; Yoon, H.J.; Revankar, S.T.; Ishii, M.; Wang, W.

    2006-01-01

    In view of the importance of instabilities that may occur at low-pressure and -flow conditions during the startup of natural circulation boiling water reactors, startup simulation experiments were performed in the Purdue University Multi-Dimensional Integral Test Assembly (PUMA) facility. The simulations used pressure scaling and followed the startup procedure of a typical natural circulation boiling water reactor. Two simulation experiments were performed for the reactor dome pressures ranging from 55 kPa to 1 MPa, where the instabilities may occur. The experimental results show the signature of condensation-induced oscillations during the single-phase-to-two-phase natural circulation transition. The results also suggest that a rational startup procedure is needed to overcome the startup instabilities in natural circulation boiling water reactor designs

  1. Simulation and analysis on thermodynamic performance of surface water source heat pump system

    Institute of Scientific and Technical Information of China (English)

    Nan Lv; Qing Zhang; Zhenqian Chen; Dongsheng Wu

    2017-01-01

    This work established a thermodynamic performance model of a heat pump system containing a heat pump unit model, an air conditioning cooling and heating load calculation model, a heat exchanger model and a water pump performance model based on mass and energy balances. The thermodynamic performance of a surface water source heat pump air conditioning system was simulated and verified by comparing the simulation results to an actual engineering project. In addition, the effects of the surface water temperature, heat exchanger structure and surface water pipeline transportation system on the thermodynamic performance of the heat pump air conditioning system were analyzed. Under the simulated conditions in this paper with a cooling load of 3400 kW, the results showed that a 1 ℃ decrease in the surface water temperature leads to a 2.3 percent increase in the coefficient of performance; furthermore, an additional 100 m of length for the closed-loop surface water heat exchanger tube leads to a 0.08 percent increase in the coefficient of performance. To decrease the system energy consumption, the optimal working point should be specified according to the surface water transportation length.

  2. Numerical simulation of severe water ingress accidents in a modular high temperature gas cooled reactor

    International Nuclear Information System (INIS)

    Zhang Zuoyi; Scherer, W.

    1996-01-01

    This report analyzes reverse water ingress accidents in the SIEMENS 200 MW Modular Pebble-Bed High Temperature Gas Cooled Reactor (HTR-MODULE) under the assumption of no active safety protection systems in order to find the safety margins of the current HTR-MODULE design and to realize a catastrophe-free nuclear technology. A water, steam and helium multi-phase cavity model is developed and implemented in the DSNP simulation system. The DSNP system is then used to simulate the primary and secondary circuit of a HTR-MODULE power plant. Comparisons of the model with experiments and with TINTE calculations serve as validation of the simulation. The analysis of the primary circuit tries to answer the question how fast the water enters the reactor core. It was found that the maximum H 2 O concentration increase in the reactor core is smaller than 0.3 kg/(m 3 s). The liquid water vaporization in the steam generator and H 2 O transport from the steam generator to the reactor core reduce the ingress velocity of the H 2 O into the reactor core. In order to answer the question how much water enters the primary circuit, the full cavitation of the feed water pumps is analyzed. It is found that if the secondary circuit is depressurized enough, the feed water pumps will be inherently stopped by the full cavitation. This limits the water to be pumped from the deaerator to the steam generator. A comprehensive simulation of the MODUL-HTR power plant then shows that the H 2 O inventory in the primary circuit can be limited to about 3000 kg. The nuclear reactivity increase caused by the water ingress leads to a fast power excursion, which, however, is inherently counterbalanced by negative feedback effects. Concerning the integrity of the fuel elements, the safety relevant temperature limit of 1600 C was not reached in any case. (orig.) [de

  3. 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 o...... in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.......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...

  4. Ab initio molecular dynamics simulation of liquid water by quantum Monte Carlo

    International Nuclear Information System (INIS)

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

    2015-01-01

    Although liquid water is ubiquitous in chemical reactions at roots of life and climate on the earth, the prediction of its properties by high-level ab initio molecular dynamics simulations still represents a formidable task for quantum chemistry. In this article, we present a room temperature simulation of liquid water based on the potential energy surface obtained by a many-body wave function through quantum Monte Carlo (QMC) methods. The simulated properties are in good agreement with recent neutron scattering and X-ray experiments, particularly concerning the position of the oxygen-oxygen peak in the radial distribution function, at variance of previous density functional theory attempts. Given the excellent performances of QMC on large scale supercomputers, this work opens new perspectives for predictive and reliable ab initio simulations of complex chemical systems

  5. Simulation of Water Environmental Capacity and Pollution Load Reduction Using QUAL2K for Water Environmental Management

    Science.gov (United States)

    Zhang, Ruibin; Qian, Xin; Yuan, Xingcheng; Ye, Rui; Xia, Bisheng; Wang, Yulei

    2012-01-01

    In recent years, water quality degradation associated with rapid socio-economic development in the Taihu Lake Basin, China, has attracted increasing attention from both the public and the Chinese government. The primary sources of pollution in Taihu Lake are its inflow rivers and their tributaries. Effective water environmental management strategies need to be implemented in these rivers to improve the water quality of Taihu Lake, and to ensure sustainable development in the region. The aim of this study was to provide a basis for water environmental management decision-making. In this study, the QUAL2K model for river and stream water quality was applied to predict the water quality and environmental capacity of the Hongqi River, which is a polluted tributary in the Taihu Lake Basin. The model parameters were calibrated by trial and error until the simulated results agreed well with the observed data. The calibrated QUAL2K model was used to calculate the water environmental capacity of the Hongqi River, and the water environmental capacities of CODCr NH3-N, TN, and TP were 17.51 t, 1.52 t, 2.74 t and 0.37 t, respectively. The results showed that the NH3-N, TN, and TP pollution loads of the studied river need to be reduced by 50.96%, 44.11%, and 22.92%, respectively to satisfy the water quality objectives. Thus, additional water pollution control measures are needed to control and reduce the pollution loads in the Hongqi River watershed. The method applied in this study should provide a basis for water environmental management decision-making. PMID:23222206

  6. Simulation of water environmental capacity and pollution load reduction using QUAL2K for water environmental management.

    Science.gov (United States)

    Zhang, Ruibin; Qian, Xin; Yuan, Xingcheng; Ye, Rui; Xia, Bisheng; Wang, Yulei

    2012-12-07

    In recent years, water quality degradation associated with rapid socio-economic development in the Taihu Lake Basin, China, has attracted increasing attention from both the public and the Chinese government. The primary sources of pollution in Taihu Lake are its inflow rivers and their tributaries. Effective water environmental management strategies need to be implemented in these rivers to improve the water quality of Taihu Lake, and to ensure sustainable development in the region. The aim of this study was to provide a basis for water environmental management decision-making. In this study, the QUAL2K model for river and stream water quality was applied to predict the water quality and environmental capacity of the Hongqi River, which is a polluted tributary in the Taihu Lake Basin. The model parameters were calibrated by trial and error until the simulated results agreed well with the observed data. The calibrated QUAL2K model was used to calculate the water environmental capacity of the Hongqi River, and the water environmental capacities of COD(Cr) NH(3)-N, TN, and TP were 17.51 t, 1.52 t, 2.74 t and 0.37 t, respectively. The results showed that the NH(3)-N, TN, and TP pollution loads of the studied river need to be reduced by 50.96%, 44.11%, and 22.92%, respectively to satisfy the water quality objectives. Thus, additional water pollution control measures are needed to control and reduce the pollution loads in the Hongqi River watershed. The method applied in this study should provide a basis for water environmental management decision-making.

  7. Simulation of Water Environmental Capacity and Pollution Load Reduction Using QUAL2K for Water Environmental Management

    Directory of Open Access Journals (Sweden)

    Yulei Wang

    2012-12-01

    Full Text Available In recent years, water quality degradation associated with rapid socio-economic development in the Taihu Lake Basin, China, has attracted increasing attention from both the public and the Chinese government. The primary sources of pollution in Taihu Lake are its inflow rivers and their tributaries. Effective water environmental management strategies need to be implemented in these rivers to improve the water quality of Taihu Lake, and to ensure sustainable development in the region. The aim of this study was to provide a basis for water environmental management decision-making. In this study, the QUAL2K model for river and stream water quality was applied to predict the water quality and environmental capacity of the Hongqi River, which is a polluted tributary in the Taihu Lake Basin. The model parameters were calibrated by trial and error until the simulated results agreed well with the observed data. The calibrated QUAL2K model was used to calculate the water environmental capacity of the Hongqi River, and the water environmental capacities of CODCr NH3-N, TN, and TP were 17.51 t, 1.52 t, 2.74 t and 0.37 t, respectively. The results showed that the NH3-N, TN, and TP pollution loads of the studied river need to be reduced by 50.96%, 44.11%, and 22.92%, respectively to satisfy the water quality objectives. Thus, additional water pollution control measures are needed to control and reduce the pollution loads in the Hongqi River watershed. The method applied in this study should provide a basis for water environmental management decision-making.

  8. Shallow boron dopant on silicon An MD study

    International Nuclear Information System (INIS)

    Perez-Martin, A. Mari Carmen; Jimenez-Rodriguez, Jose J.; Jimenez-Saez, Jose Carlos

    2004-01-01

    Low energy boron bombardment of silicon has been simulated at room temperature by molecular dynamics (MD). Tersoff potential T3 was used in the simulation smoothly linked up with the universal potential. The boron-silicon (B-Si) interaction was simulated according to Tersoff potential for SiC but modified to account for the B-Si interaction. The algorithm can distinguish a B from a Si neighbour. Si-c, with (2 x 1) surface reconstruction, was bombarded with boron at 200 and 500 eV. These energies were initially chosen as good representative values of the low energy range. Reliable results require of a reasonable good statistic so that 1000-impact points were chosen uniformly distributed over a representative area of a 2 x 1 surface. The distribution of mean projected range for B is given. All kinds of point defect were looked for in a Si damaged target after bombardment. Energetically stable substitutional and interstitial configurations are presented and the relative appearances of the different types of interstitials, for both Si and B, are given. It is also determined the mean length of the distance to the first neighbours of defects

  9. Separation of ethanol and water by extractive distillation with salt and solvent as entrainer: process simulation

    OpenAIRE

    Gil, I. D.; Uyazán, A. M.; Aguilar, J. L.; Rodríguez, G.; Caicedo, L. A.

    2008-01-01

    The aim of this work is to simulate and analyze an extractive distillation process for azeotropic ethanol dehydration with ethylene glycol and calcium chloride mixture as entrainer. The work was developed with Aspen Plus® simulator version 11.1. Calculation of the activity coefficients employed to describe vapor liquid equilibrium of ethanol - water - ethylene glycol - calcium chloride system was done with the NRTL-E equation and they were validated with experimental data. The dehydration pro...

  10. Dynamically adaptive Lattice Boltzmann simulation of shallow water flows with the Peano framework

    KAUST Repository

    Neumann, Philipp

    2015-09-01

    © 2014 Elsevier Inc. All rights reserved. We present a dynamically adaptive Lattice Boltzmann (LB) implementation for solving the shallow water equations (SWEs). Our implementation extends an existing LB component of the Peano framework. We revise the modular design with respect to the incorporation of new simulation aspects and LB models. The basic SWE-LB implementation is validated in different breaking dam scenarios. We further provide a numerical study on stability of the MRT collision operator used in our simulations.

  11. Modeling and simulation of water flow on containment walls with inhomogeneous contact angle distribution

    International Nuclear Information System (INIS)

    Amend, Katharina; Klein, Markus

    2017-01-01

    The paper presents a three-dimensional numerical simulation for water running down inclined surfaces using OpenFOAM. This research project aims at developing a CFD model to describe the run down behavior of liquids and the resulting wash down of fission products on surfaces in the reactor containment. An empirical contact angle model with wetted history is introduced as well as a filtered randomized initial contact angle field. Simulation results are in good agreement with the experiments. Experimental Investigation on Passive.

  12. Modeling and simulation of water flow on containment walls with inhomogeneous contact angle distribution

    Energy Technology Data Exchange (ETDEWEB)

    Amend, Katharina; Klein, Markus [Univ. der Bundeswehr Muenchen, Neubiberg (Germany). Inst. for Numerical Methods in Aerospace Engineering

    2017-07-15

    The paper presents a three-dimensional numerical simulation for water running down inclined surfaces using OpenFOAM. This research project aims at developing a CFD model to describe the run down behavior of liquids and the resulting wash down of fission products on surfaces in the reactor containment. An empirical contact angle model with wetted history is introduced as well as a filtered randomized initial contact angle field. Simulation results are in good agreement with the experiments. Experimental Investigation on Passive.

  13. About Body Water

    Science.gov (United States)

    ... Video) Thyroid Disease Additional Content Medical News About Body Water By James L. Lewis, III, MD, Attending ... here for the Professional Version Water Balance About Body Water Dehydration Overhydration Water accounts for about one ...

  14. Simultaneous ion and neutral evaporation in aqueous nanodrops: experiment, theory, and molecular dynamics simulations.

    Science.gov (United States)

    Higashi, Hidenori; Tokumi, Takuya; Hogan, Christopher J; Suda, Hiroshi; Seto, Takafumi; Otani, Yoshio

    2015-06-28

    We use a combination of tandem ion mobility spectrometry (IMS-IMS, with differential mobility analyzers), molecular dynamics (MD) simulations, and analytical models to examine both neutral solvent (H2O) and ion (solvated Na(+)) evaporation from aqueous sodium chloride nanodrops. For experiments, nanodrops were produced via electrospray ionization (ESI) of an aqueous sodium chloride solution. Two nanodrops were examined in MD simulations: a 2500 water molecule nanodrop with 68 Na(+) and 60 Cl(-) ions (an initial net charge of z = +8), and (2) a 1000 water molecule nanodrop with 65 Na(+) and 60 Cl(-) ions (an initial net charge of z = +5). Specifically, we used MD simulations to examine the validity of a model for the neutral evaporation rate incorporating both the Kelvin (surface curvature) and Thomson (electrostatic) influences, while both MD simulations and experimental measurements were compared to predictions of the ion evaporation rate equation of Labowsky et al. [Anal. Chim. Acta, 2000, 406, 105-118]. Within a single fit parameter, we find excellent agreement between simulated and modeled neutral evaporation rates for nanodrops with solute volume fractions below 0.30. Similarly, MD simulation inferred ion evaporation rates are in excellent agreement with predictions based on the Labowsky et al. equation. Measurements of the sizes and charge states of ESI generated NaCl clusters suggest that the charge states of these clusters are governed by ion evaporation, however, ion evaporation appears to have occurred with lower activation energies in experiments than was anticipated based on analytical calculations as well as MD simulations. Several possible reasons for this discrepancy are discussed.

  15. Preliminary Computational Fluid Dynamics (CFD) Simulation of EIIB Push Barge in Shallow Water

    Science.gov (United States)

    Beneš, Petr; Kollárik, Róbert

    2011-12-01

    This study presents preliminary CFD simulation of EIIb push barge in inland conditions using CFD software Ansys Fluent. The RANSE (Reynolds Averaged Navier-Stokes Equation) methods are used for the viscosity solution of turbulent flow around the ship hull. Different RANSE methods are used for the comparison of their results in ship resistance calculations, for selecting the appropriate and removing inappropriate methods. This study further familiarizes on the creation of geometrical model which considers exact water depth to vessel draft ratio in shallow water conditions, grid generation, setting mathematical model in Fluent and evaluation of the simulations results.

  16. The simulation of stationary and non-stationary regime operation of heavy water production facilities

    International Nuclear Information System (INIS)

    Peculea, M.; Beca, T.; Constantinescu, D.M.; Dumitrescu, M.; Dimulescu, A.; Isbasescu, G.; Stefanescu, I.; Mihai, M.; Dogaru, C.; Marinescu, M.; Olariu, S.; Constantin, T.; Necula, A.

    1995-01-01

    This paper refers to testing procedures of the production capacity of heavy water production pilot, industrial scale plants and of heavy water reconcentration facilities. Simulation codes taking into account the mass and heat transfers inside the exchange columns were developed. These codes provided valuable insight about the isotope build-up of the installation which allowed estimating the time of reaching the stationary regime. Also transient regimes following perturbations in the operating parameters (i.e. temperature, pressure, fluid rates) of the installation were simulated and an optimal rate of routine inspections and adjustments was thus established

  17. Simulation of a two phase boiling flow in Poseidon geometry with Astrid steam-water software

    International Nuclear Information System (INIS)

    Larrauri, D.

    1997-01-01

    After different validation test runs in tube an annular geometries, the simulation of a subcooled boiling flow in a rod bundle geometry has been achieved with ASTRID Steam-Water software. The experiment we have simulated is the Poseidon experiment. It is a three heating tube geometry. The thermohydraulic conditions of the simulated flow are closed to the DNB conditions. The simulation results are analysed and compared against the available measurements of liquid and wall temperatures. ASTRID Steam-Water behaviour in such a geometry brings satisfaction. The wall and the liquid temperatures are well predicted in the different parts of the flow. The void fraction reaches 40 % in the vicinity of the heating rods. Besides, the evolution of the different calculated variables shows that a three-dimensional simulation gives capital information for the analyse of the physical phenomena involved in this kind of flow. The good results obtained in Poseidon geometry lead us to think about simulating and analyzing rod bundle flows with ASTRID Steam-Water code. (author)

  18. Isobaric-isothermal Monte Carlo simulations from first principles: Application to liquid water at ambient conditions

    Energy Technology Data Exchange (ETDEWEB)

    McGrath, M; Siepmann, J I; Kuo, I W; Mundy, C J; VandeVondele, J; Hutter, J; Mohamed, F; Krack, M

    2004-12-02

    A series of first principles Monte Carlo simulations in the isobaric-isothermal ensemble were carried out for liquid water at ambient conditions (T = 298 K and p = 1 atm). The Becke-Lee-Yang-Parr (BLYP) exchange and correlation energy functionals and norm-conserving Goedecker-Teter-Hutter (GTH) pseudopotentials were employed with the CP2K simulation package to examine systems consisting of 64 water molecules. The fluctuations in the system volume encountered in simulations in the isobaric-isothermal ensemble requires a reconsideration of the suitability of the typical charge density cutoff and the regular grid generation method previously used for the computation of the electrostatic energy in first principles simulations in the microcanonical or canonical ensembles. In particular, it is noted that a much higher cutoff is needed and that the most computationally efficient method of creating grids can result in poor simulations. Analysis of the simulation trajectories using a very large charge density cutoff at 1200 Ry and four different grid generation methods point to a substantially underestimated liquid density of about 0.85 g/cm{sup 3} resulting in a somewhat understructured liquid (with a value of about 2.7 for the height of the first peak in the oxygen/oxygen radial distribution function) for BLYP-GTH water at ambient conditions.

  19. North American water availability under stress and duress: building understanding from simulations, observations and data products

    Science.gov (United States)

    Maxwell, R. M.; Condon, L. E.; Atchley, A. L.; Hector, B.

    2017-12-01

    Quantifying the available freshwater for human use and ecological function depends on fluxes and stores that are hard to observe. Evapotranspiration (ET) is the largest terrestrial flux of water behind precipitation but is observed with low spatial density. Likewise, groundwater is the largest freshwater store, yet is equally uncertain. The ability to upscale observations of these variables is an additional complication; point measurements are made at scales orders of magnitude smaller than remote sensing data products. Integrated hydrologic models that simulate continental extents at fine spatial resolution are now becoming an additional tool to constrain fluxes and address interconnections. For example, recent work has shown connections between water table depth and transpiration partitioning, and demonstrated the ability to reconcile point observations and large-scale inferences. Here we explore the dynamics of large hydrologic systems experiencing change and stress across continental North America using integrated model simulations, observations and data products. Simulations of aquifer depletion due to pervasive groundwater pumping diagnose both stream depletion and changes in ET. Simulations of systematic increases in temperature are used to understand the relationship between snowpack dynamics, surface and groundwater flow, ET and a changing climate. Remotely sensed products including the GRACE estimates of total storage change are downscaled using model simulations to better understand human impacts to the hydrologic cycle. These example applications motivate a path forward to better use simulations to understand water availability.

  20. Enhancement of a parsimonious water balance model to simulate surface hydrology in a glacierized watershed

    Science.gov (United States)

    Valentin, Melissa M.; Viger, Roland J.; Van Beusekom, Ashley E.; Hay, Lauren E.; Hogue, Terri S.; Foks, Nathan Leon

    2018-01-01

    The U.S. Geological Survey monthly water balance model (MWBM) was enhanced with the capability to simulate glaciers in order to make it more suitable for simulating cold region hydrology. The new model, MWBMglacier, is demonstrated in the heavily glacierized and ecologically important Copper River watershed in Southcentral Alaska. Simulated water budget components compared well to satellite‐based observations and ground measurements of streamflow, evapotranspiration, snow extent, and total water storage, with differences ranging from 0.2% to 7% of the precipitation flux. Nash Sutcliffe efficiency for simulated and observed streamflow was greater than 0.8 for six of eight stream gages. Snow extent matched satellite‐based observations with Nash Sutcliffe efficiency values of greater than 0.89 in the four Copper River ecoregions represented. During the simulation period 1949 to 2009, glacier ice melt contributed 25% of total runoff, ranging from 12% to 45% in different tributaries, and glacierized area was reduced by 6%. Statistically significant (p < 0.05) decreasing and increasing trends in annual glacier mass balance occurred during the multidecade cool and warm phases of the Pacific Decadal Oscillation, respectively, reinforcing the link between climate perturbations and glacier mass balance change. The simulations of glaciers and total runoff for a large, remote region of Alaska provide useful data to evaluate hydrologic, cryospheric, ecologic, and climatic trends. MWBM glacier is a valuable tool to understand when, and to what extent, streamflow may increase or decrease as glaciers respond to a changing climate.

  1. Field Test Design Simulations of Pore-Water Extraction for the SX Tank Farm

    Energy Technology Data Exchange (ETDEWEB)

    Truex, Michael J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Oostrom, Martinus [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2013-09-01

    A proof of principle test of pore water extraction is being performed by Washington River Protection Solutions for the U.S. Department of Energy, Office of River Protection. This test is being conducted to meet the requirements of Hanford Federal Facility Agreement and Consent Order (HFFACO) (Ecology et al. 1989) Milestone M 045-20, and is described in RPP-PLAN-53808, 200 West Area Tank Farms Interim Measures Investigation Work Plan. To support design of this test, numerical simulations were conducted to help define equipment and operational parameters. The modeling effort builds from information collected in laboratory studies and from field characterization information collected at the test site near the Hanford Site 241-SX Tank Farm. Numerical simulations were used to evaluate pore-water extraction performance as a function of the test site properties and for the type of extraction well configuration that can be constructed using the direct-push installation technique. Output of simulations included rates of water and soil-gas production as a function of operational conditions for use in supporting field equipment design. The simulations also investigated the impact of subsurface heterogeneities in sediment properties and moisture distribution on pore-water extraction performance. Phenomena near the extraction well were also investigated because of their importance for pore-water extraction performance.

  2. Integrated hydraulic and organophosphate pesticide injection simulations for enhancing event detection in water distribution systems.

    Science.gov (United States)

    Schwartz, Rafi; Lahav, Ori; Ostfeld, Avi

    2014-10-15

    As a complementary step towards solving the general event detection problem of water distribution systems, injection of the organophosphate pesticides, chlorpyrifos (CP) and parathion (PA), were simulated at various locations within example networks and hydraulic parameters were calculated over 24-h duration. The uniqueness of this study is that the chemical reactions and byproducts of the contaminants' oxidation were also simulated, as well as other indicative water quality parameters such as alkalinity, acidity, pH and the total concentration of free chlorine species. The information on the change in water quality parameters induced by the contaminant injection may facilitate on-line detection of an actual event involving this specific substance and pave the way to development of a generic methodology for detecting events involving introduction of pesticides into water distribution systems. Simulation of the contaminant injection was performed at several nodes within two different networks. For each injection, concentrations of the relevant contaminants' mother and daughter species, free chlorine species and water quality parameters, were simulated at nodes downstream of the injection location. The results indicate that injection of these substances can be detected at certain conditions by a very rapid drop in Cl2, functioning as the indicative parameter, as well as a drop in alkalinity concentration and a small decrease in pH, both functioning as supporting parameters, whose usage may reduce false positive alarms. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Simulating the effects of ground-water withdrawals on streamflow in a precipitation-runoff model

    Science.gov (United States)

    Zarriello, Philip J.; Barlow, P.M.; Duda, P.B.

    2004-01-01

    Precipitation-runoff models are used to assess the effects of water use and management alternatives on streamflow. Often, ground-water withdrawals are a major water-use component that affect streamflow, but the ability of surface-water models to simulate ground-water withdrawals is limited. As part of a Hydrologic Simulation Program-FORTRAN (HSPF) precipitation-runoff model developed to analyze the effect of ground-water and surface-water withdrawals on streamflow in the Ipswich River in northeastern Massachusetts, an analytical technique (STRMDEPL) was developed for calculating the effects of pumped wells on streamflow. STRMDEPL is a FORTRAN program based on two analytical solutions that solve equations for ground-water flow to a well completed in a semi-infinite, homogeneous, and isotropic aquifer in direct hydraulic connection to a fully penetrating stream. One analytical method calculates unimpeded flow at the stream-aquifer boundary and the other method calculates the resistance to flow caused by semipervious streambed and streambank material. The principle of superposition is used with these analytical equations to calculate time-varying streamflow depletions due to daily pumping. The HSPF model can readily incorporate streamflow depletions caused by a well or surface-water withdrawal, or by multiple wells or surface-water withdrawals, or both, as a combined time-varying outflow demand from affected channel reaches. These demands are stored as a time series in the Watershed Data Management (WDM) file. This time-series data is read into the model as an external source used to specify flow from the first outflow gate in the reach where these withdrawals are located. Although the STRMDEPL program can be run independently of the HSPF model, an extension was developed to run this program within GenScn, a scenario generator and graphical user interface developed for use with the HSPF model. This extension requires that actual pumping rates for each well be stored

  4. MD-11 PCA - First Landing at Edwards

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 approaches the first landing ever of a transport aircraft under engine power only on Aug. 29, 1995, at NASA's Dryden Flight Research Center, Edwards, California. The milestone flight, flown by NASA research pilot and former astronaut Gordon Fullerton, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when it normal control surfaces are disabled. The Propulsion-Controlled Aircraft (PCA) system uses standard autopilot controls already present in the cockpit, together with the new programming in the aircraft's flight control computers. The PCA concept is simple--for pitch control, the program increases thrust to climb and reduces thrust to descend. To turn right, the autopilot increases the left engine thrust while decreasing the right engine thrust. The initial Propulsion-Controlled Aircraft studies by NASA were carried out at Dryden with a modified twin-engine F-15 research aircraft.

  5. MD-11 PCA - Research flight team egress

    Science.gov (United States)

    1995-01-01

    This McDonnell Douglas MD-11 has parked on the flightline at NASA's Dryden Flight Research Center, Edwards, California, following its completion of the first and second landings ever performed by a transport aircraft under engine power only (on Aug. 29, 1995). The milestone flight, with NASA research pilot and former astronaut Gordon Fullerton at the controls, was part of a NASA project to develop a computer-assisted engine control system that enables a pilot to land a plane safely when its normal control surfaces are disabled. Coming down the steps from the aircraft are Gordon Fullerton (in front), followed by Bill Burcham, Propulsion Controlled Aircraft (PCA) project engineer at Dryden; NASA Dryden controls engineer John Burken; John Feather of McDonnell Douglas; and Drew Pappas, McDonnell Douglas' project manager for PCA.

  6. Simulation of ground-water flow and land subsidence in the Antelope Valley ground-water basin, California

    Science.gov (United States)

    Leighton, David A.; Phillips, Steven P.

    2003-01-01

    ground-water development have eliminated the natural sources of discharge, and pumping for agricultural and urban uses have become the primary source of discharge from the ground-water system. Infiltration of return flows from agricultural irrigation has become an important source of recharge to the aquifer system. The ground-water flow model of the basin was discretized horizontally into a grid of 43 rows and 60 columns of square cells 1 mile on a side, and vertically into three layers representing the upper, middle, and lower aquifers. Faults that were thought to act as horizontal-flow barriers were simulated in the model. The model was calibrated to simulate steady-state conditions, represented by 1915 water levels and transient-state conditions during 1915-95 using water-level and subsidence data. Initial estimates of the aquifer-system properties and stresses were obtained from a previously published numerical model of the Antelope Valley ground-water basin; estimates also were obtained from recently collected hydrologic data and from results of simulations of ground-water flow and land subsidence models of the Edwards Air Force Base area. Some of these initial estimates were modified during model calibration. Ground-water pumpage for agriculture was estimated on the basis of irrigated crop acreage and crop consumptive-use data. Pumpage for public supply, which is metered, was compiled and entered into a database used for this study. Estimated annual pumpage peaked at 395,000 acre-feet (acre-ft) in 1952 and then declined because of declining agricultural production. Recharge from irrigation-return flows was estimated to be 30 percent of agricultural pumpage; the irrigation-return flows were simulated as recharge to the regional water table 10 years following application at land surface. The annual quantity of natural recharge initially was based on estimates from previous studies. During model calibration, natural recharge was reduced from the initial

  7. Rainfall simulation experiments and Water Drop Penetration Time measurements shed light on the impact of water repellency on soils under organic farming management in Eastern Spain

    Science.gov (United States)

    Cerdà, Artemi; González, Óscar; León, Javier; Jordán, Antonio

    2015-04-01

    ., Geißler, C., Gómez, J.A., Gómez-Macpherson, H., Kuhn, N.J., Lázaro, R., León, F.J., Martínez-Mena, M., Martínez-Murillo, J.F., Marzen, M., Mingorance, M.D., Ortigosa, L., Peters, P., Regüés, D., Ruiz-Sinoga, J.D., Scholten, T., Seeger, M., Solé-Benet, A., Wengel, R., Wirtz, S. 2013. European small portable rainfall simulators: a comparison of rainfall characteristics. Catena, 110, 100-112. Doi: 10.1016/j.catena.2013.05.013 Iserloh, T., Ries, J.B., Cerdà, A., Echeverría, M.T., Fister, W., Geißler, C., Kuhn, N.J., León, F.J., Peters, P., Schindewolf, M., Schmidt, J., Scholten, T., Seeger, M. (2012): Comparative measurements with seven rainfall simulators on uniform bare fallow land. Zeitschrift für Geomorphologie, 57, 193-201. DOI: 10.1127/0372-8854/2012/S-00118. Jiménez-Morillo, N. T., González-Pérez, J. A., Jordán, A., Zavala, L. M., Rosa, J. M., Jiménez-González, M. A., & González-Vila, F. J. (2014). Organic matter fractions controlling soil water repellency in Sandy soils from the Doñana National Park (Southwestern Spain). Land Degradation & Development.| DOI: 10.1002/ldr.2314 Jordán, A., García-Moreno, J., Gordillo-Rivero, Á. J., Zavala, L. M., Cerdà, A. 2014. Organic carbon, water repellency and soil stability to slaking under different crops and managements: a case study at aggregate and intra-aggregate scales. SOIL Discussions, 1(1), 295-325. Jordán, A., Zavala, L. M., Mataix-Solera, J., Doerr, S. H. 2013. Soil water repellency: origin, assessment and geomorphological consequences. Catena, 108, 1-5. Jordán, A., Zavala, L. M., Mataix-Solera, J., Nava, A. L., & Alanís, N. 2011. Effect of fire severity on water repellency and aggregate stability on Mexican volcanic soils. Catena, 84(3), 136-147. Jouquet, P., Janeau, J. L., Pisano, A., Sy, H. T., Orange, D., Minh, L. T. N., Valentin, C. 2012. Influence of earthworms and termites on runoff and erosion in a tropical steep slope fallow in Vietnam: A rainfall simulation experiment. Applied

  8. Pickering NGS emergency water supply system emergency start flow simulation and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Davidge, E.; Misra, A. [Ontario Power Generation Inc., Nuclear Safety Analysis & Technology Department, Toronto, Ontario (Canada)

    2012-07-01

    A proposed modification to the OPG Pickering Nuclear Generation Station Emergency Water Supply (EWS) system was analyzed using the Industry Standard Toolset code GOTHIC to determine the acceptability of the proposed system configuration during pump start-up. The new configuration of the system included a vertical dead-ended pipe, initially filled with air. The simulation demonstrated that no significant water hammer effects were predicted and tests performed with the new configuration confirmed the analysis results. (author)

  9. How should we build a generic open-source water management simulator?

    Science.gov (United States)

    Khadem, M.; Meier, P.; Rheinheimer, D. E.; Padula, S.; Matrosov, E.; Selby, P. D.; Knox, S.; Harou, J. J.

    2014-12-01

    Increasing water needs for agriculture, industry and cities mean effective and flexible water resource system management tools will remain in high demand. Currently many regions or countries use simulators that have been adapted over time to their unique system properties and water management rules and realities. Most regions operate with a preferred short-list of water management and planning decision support systems. Is there scope for a simulator, shared within the water management community, that could be adapted to different contexts, integrate community contributions, and connect to generic data and model management software? What role could open-source play in such a project? How could a genericuser-interface and data/model management software sustainably be attached to this model or suite of models? Finally, how could such a system effectively leverage existing model formulations, modeling technologies and software? These questions are addressed by the initial work presented here. We introduce a generic water resource simulation formulation that enables and integrates both rule-based and optimization driven technologies. We suggest how it could be linked to other sub-models allowing for detailed agent-based simulation of water management behaviours. An early formulation is applied as an example to the Thames water resource system in the UK. The model uses centralised optimisation to calculate allocations but allows for rule-based operations as well in an effort to represent observed behaviours and rules with fidelity. The model is linked through import/export commands to a generic network model platform named Hydra. Benefits and limitations of the approach are discussed and planned work and potential use cases are outlined.

  10. An Efficient Hybrid DSMC/MD Algorithm for Accurate Modeling of Micro Gas Flows

    KAUST Repository

    Liang, Tengfei

    2013-01-01

    Aiming at simulating micro gas flows with accurate boundary conditions, an efficient hybrid algorithmis developed by combining themolecular dynamics (MD) method with the direct simulationMonte Carlo (DSMC)method. The efficiency comes from the fact that theMD method is applied only within the gas-wall interaction layer, characterized by the cut-off distance of the gas-solid interaction potential, to resolve accurately the gas-wall interaction process, while the DSMC method is employed in the remaining portion of the flow field to efficiently simulate rarefied gas transport outside the gas-wall interaction layer. A unique feature about the present scheme is that the coupling between the two methods is realized by matching the molecular velocity distribution function at the DSMC/MD interface, hence there is no need for one-toone mapping between a MD gas molecule and a DSMC simulation particle. Further improvement in efficiency is achieved by taking advantage of gas rarefaction inside the gas-wall interaction layer and by employing the "smart-wall model" proposed by Barisik et al. The developed hybrid algorithm is validated on two classical benchmarks namely 1-D Fourier thermal problem and Couette shear flow problem. Both the accuracy and efficiency of the hybrid algorithm are discussed. As an application, the hybrid algorithm is employed to simulate thermal transpiration coefficient in the free-molecule regime for a system with atomically smooth surface. Result is utilized to validate the coefficients calculated from the pure DSMC simulation with Maxwell and Cercignani-Lampis gas-wall interaction models. ©c 2014 Global-Science Press.

  11. Extraction of Water from Martian Regolith Simulant via Open Reactor Concept

    Science.gov (United States)

    Trunek, Andrew J.; Linne, Diane L.; Kleinhenz, Julie E.; Bauman, Steven W.

    2018-01-01

    To demonstrate proof of concept water extraction from simulated Martian regolith, an open reactor design is presented along with experimental results. The open reactor concept avoids sealing surfaces and complex moving parts. In an abrasive environment like the Martian surface, those reactor elements would be difficult to maintain and present a high probability of failure. A general lunar geotechnical simulant was modified by adding borax decahydrate (Na2B4O7·10H2O) (BDH) to mimic the 3 percent water content of hydrated salts in near surface soils on Mars. A rotating bucket wheel excavated the regolith from a source bin and deposited the material onto an inclined copper tray, which was fitted with heaters and a simple vibration system. The combination of vibration, tilt angle and heat was used to separate and expose as much regolith surface area as possible to liberate the water contained in the hydrated minerals, thereby increasing the efficiency of the system. The experiment was conducted in a vacuum system capable of maintaining a Martian like atmosphere. Evolved water vapor was directed to a condensing system using the ambient atmosphere as a sweep gas. The water vapor was condensed and measured. Processed simulant was captured in a collection bin and weighed in real time. The efficiency of the system was determined by comparing pre- and post-processing soil mass along with the volume of water captured.

  12. Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations

    Science.gov (United States)

    Yuhara, Daisuke; Brumby, Paul E.; Wu, David T.; Sum, Amadeu K.; Yasuoka, Kenji

    2018-05-01

    To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

  13. Analysis of three-phase equilibrium conditions for methane hydrate by isometric-isothermal molecular dynamics simulations.

    Science.gov (United States)

    Yuhara, Daisuke; Brumby, Paul E; Wu, David T; Sum, Amadeu K; Yasuoka, Kenji

    2018-05-14

    To develop prediction methods of three-phase equilibrium (coexistence) conditions of methane hydrate by molecular simulations, we examined the use of NVT (isometric-isothermal) molecular dynamics (MD) simulations. NVT MD simulations of coexisting solid hydrate, liquid water, and vapor methane phases were performed at four different temperatures, namely, 285, 290, 295, and 300 K. NVT simulations do not require complex pressure control schemes in multi-phase systems, and the growth or dissociation of the hydrate phase can lead to significant pressure changes in the approach toward equilibrium conditions. We found that the calculated equilibrium pressures tended to be higher than those reported by previous NPT (isobaric-isothermal) simulation studies using the same water model. The deviations of equilibrium conditions from previous simulation studies are mainly attributable to the employed calculation methods of pressure and Lennard-Jones interactions. We monitored the pressure in the methane phase, far from the interfaces with other phases, and confirmed that it was higher than the total pressure of the system calculated by previous studies. This fact clearly highlights the difficulties associated with the pressure calculation and control for multi-phase systems. The treatment of Lennard-Jones interactions without tail corrections in MD simulations also contributes to the overestimation of equilibrium pressure. Although improvements are still required to obtain accurate equilibrium conditions, NVT MD simulations exhibit potential for the prediction of equilibrium conditions of multi-phase systems.

  14. [Simulation of water and carbon fluxes in harvard forest area based on data assimilation method].

    Science.gov (United States)

    Zhang, Ting-Long; Sun, Rui; Zhang, Rong-Hua; Zhang, Lei

    2013-10-01

    Model simulation and in situ observation are the two most important means in studying the water and carbon cycles of terrestrial ecosystems, but have their own advantages and shortcomings. To combine these two means would help to reflect the dynamic changes of ecosystem water and carbon fluxes more accurately. Data assimilation provides an effective way to integrate the model simulation and in situ observation. Based on the observation data from the Harvard Forest Environmental Monitoring Site (EMS), and by using ensemble Kalman Filter algorithm, this paper assimilated the field measured LAI and remote sensing LAI into the Biome-BGC model to simulate the water and carbon fluxes in Harvard forest area. As compared with the original model simulated without data assimilation, the improved Biome-BGC model with the assimilation of the field measured LAI in 1998, 1999, and 2006 increased the coefficient of determination R2 between model simulation and flux observation for the net ecosystem exchange (NEE) and evapotranspiration by 8.4% and 10.6%, decreased the sum of absolute error (SAE) and root mean square error (RMSE) of NEE by 17.7% and 21.2%, and decreased the SAE and RMSE of the evapotranspiration by 26. 8% and 28.3%, respectively. After assimilated the MODIS LAI products of 2000-2004 into the improved Biome-BGC model, the R2 between simulated and observed results of NEE and evapotranspiration was increased by 7.8% and 4.7%, the SAE and RMSE of NEE were decreased by 21.9% and 26.3%, and the SAE and RMSE of evapotranspiration were decreased by 24.5% and 25.5%, respectively. It was suggested that the simulation accuracy of ecosystem water and carbon fluxes could be effectively improved if the field measured LAI or remote sensing LAI was integrated into the model.

  15. Simulating the Current Water Cycle with the NASA Ames Mars Global Climate Model

    Science.gov (United States)

    Kahre, M. A.; Haberle, R. M.; Hollingsworth, J. L.; Brecht, A. S.; Urata, R. A.; Montmessin, F.

    2017-12-01

    The water cycle is a critical component of the current Mars climate system, and it is now widely recognized that water ice clouds significantly affect the nature of the simulated water cycle. Two processes are key to implementing clouds in a Mars global climate model (GCM): the microphysical processes of formation and dissipation, and their radiative effects on atmospheric heating/cooling rates. Together, these processes alter the thermal structure, change the atmospheric dynamics, and regulate inter-hemispheric transport. We have made considerable progress using the NASA Ames Mars GCM to simulate the current-day water cycle with radiatively active clouds. Cloud fields from our baseline simulation are in generally good agreement with observations. The predicted seasonal extent and peak IR optical depths are consistent MGS/TES observations. Additionally, the thermal response to the clouds in the aphelion cloud belt (ACB) is generally consistent with observations and other climate model predictions. Notably, there is a distinct gap in the predicted clouds over the North Residual Cap (NRC) during local summer, but the clouds reappear in this simulation over the NRC earlier than the observations indicate. Polar clouds are predicted near the seasonal CO2 ice caps, but the column thicknesses of these clouds are generally too thick compared to observations. Our baseline simulation is dry compared to MGS/TES-observed water vapor abundances, particularly in the tropics and subtropics. These areas of disagreement appear to be a consistent with other current water cycle GCMs. Future avenues of investigation will target improving our understanding of what controls the vertical extent of clouds and the apparent seasonal evolution of cloud particle sizes within the ACB.

  16. Molecular simulation of the water-triolein-oleic acid mixture: Local structure and thermodynamic properties

    Science.gov (United States)

    Couallier, E.; Riaublanc, A.; David Briand, E.; Rousseau, B.

    2018-05-01

    An artificial oil-in-water emulsion analogous to those found in bioresources or food matrices is simulated and studied experimentally. It is composed of one of the major natural free fatty acids (the oleic acid, OA) and the corresponding triacylglyceride (trioleic glyceride, or triolein, GTO). Because of the large time and length scales involved, the molecular simulations are done with the Martini force field, a coarse-grained model. This allowed us to study the water-OA-GTO system at different compositions with more than 20 000 molecules and up to 2 μs. Interfacial tension was measured using the pendant drop method and compared with molecular simulation results. We observe very good agreement at high OA concentrations and deviations up to 15% at low OA concentrations. The water solubility in the lipid phase is in fair agreement with experiments, between 0.03 and 0.32 mol/l, rising with the OA content. The area occupied by OA and GTO at the interface between water and the pure product fitted with experimental data (AOA = 36.6 Å2 and AGTO = 152.1 Å2). The consistency between simulation and experimental results allowed a structural analysis of the interface. A bilayer structure of the lipids at the water/oil interface is proposed, containing preferentially oleic acid but also triolein. Through all these results, the usefulness of coarse-grained simulation for the description of water-oil interfacial organization is demonstrated. This method will be used later to bring local information on the organization of target compounds, necessary in biomass fractionation processes or food additive formulations, for example.

  17. Hydrogeology, simulated ground-water flow, and ground-water quality, Wright-Patterson Air Force Base, Ohio

    Science.gov (United States)

    Dumouchelle, D.H.; Schalk, C.W.; Rowe, G.L.; De Roche, J.T.

    1993-01-01

    Ground water is the primary source of water in the Wright-Patterson Air Force Base area. The aquifer consists of glacial sands and gravels that fill a buried bedrock-valley system. Consolidated rocks in the area consist of poorly permeable Ordovician shale of the Richmondian stage, in the upland areas, the Brassfield Limestone of Silurian age. The valleys are filled with glacial sediments of Wisconsinan age consisting of clay-rich tills and coarse-grained outwash deposits. Estimates of hydraulic conductivity of the shales based on results of displacement/recovery tests range from 0.0016 to 12 feet per day; estimates for the glacial sediments range from less than 1 foot per day to more than 1,000 feet per day. Ground water flow from the uplands towards the valleys and the major rivers in the region, the Great Miami and the Mad Rivers. Hydraulic-head data indicate that ground water flows between the bedrock and unconsolidated deposits. Data from a gain/loss study of the Mad River System and hydrographs from nearby wells reveal that the reach of the river next to Wright-Patterson Air Force Base is a ground-water discharge area. A steady-state, three-dimensional ground-water-flow model was developed to simulate ground-water flow in the region. The model contains three layers and encompasses about 100 square miles centered on Wright-Patterson Air Force Base. Ground water enters the modeled area primarily by river leakage and underflow at the model boundary. Ground water exits the modeled area primarily by flow through the valleys at the model boundaries and through production wells. A model sensitivity analysis involving systematic changes in values of hydrologic parameters in the model indicates that the model is most sensitive to decreases in riverbed conductance and vertical conductance between the upper two layers. The analysis also indicates that the contribution of water to the buried-valley aquifer from the bedrock that forms the valley walls is about 2 to 4

  18. Development of capacitive sensor for automatically measuring tumbler water level with FEA simulation.

    Science.gov (United States)

    Wei, Qun; Kim, Mi-Jung; Lee, Jong-Ha

    2018-01-01

    Drinking water has several advantages that have already been established, such as improving blood circulation, reducing acid in the stomach, etc. However, due to people not noticing the amount of water they consume every time they drink, most people drink less water than the recommended daily allowance. In this paper, a capacitive sensor for developing an automatic tumbler to measure water level is proposed. Different than in previous studies, the proposed capacitive sensor was separated into two sets: the main sensor for measuring the water level in the tumbler, and the reference sensor for measuring the incremental level unit. In order to confirm the feasibility of the proposed idea, and to optimize the shape of the sensor, a 3D model of the capacitive sensor with the tumbler was designed and subjected to Finite Element Analysis (FEA) simulation. According to the simulation results, the electrodes were made of copper and assembled in a tumbler manufactured by a 3D printer. The tumbler was filled with water and was subjected to experiments in order to assess the sensor's performance. The comparison of experimental results to the simulation results shows that the measured capacitance value of the capacitive sensor changed linearly as the water level varied. This proves that the proposed sensor can accurately measure the water level in the tumbler. Additionally, by use of the curve fitting method, a compensation algorithm was found to match the actual level with the measured level. The experimental results proved that the proposed capacitive sensor is able to measure the actual water level in the tumbler accurately. A digital control part with micro-processor will be designed and fixed on the bottom of the tumbler for developing a smart tumbler.

  19. Simulation of water-energy fluxes through small-scale reservoir systems under limited data availability

    Science.gov (United States)

    Papoulakos, Konstantinos; Pollakis, Giorgos; Moustakis, Yiannis; Markopoulos, Apostolis; Iliopoulou, Theano; Dimitriadis, Panayiotis; Koutsoyiannis, Demetris; Efstratiadis, Andreas

    2017-04-01

    Small islands are regarded as promising areas for developing hybrid water-energy systems that combine multiple sources of renewable energy with pumped-storage facilities. Essential element of such systems is the water storage component (reservoir), which implements both flow and energy regulations. Apparently, the representation of the overall water-energy management problem requires the simulation of the operation of the reservoir system, which in turn requires a faithful estimation of water inflows and demands of water and energy. Yet, in small-scale reservoir systems, this task in far from straightforward, since both the availability and accuracy of associated information is generally very poor. For, in contrast to large-scale reservoir systems, for which it is quite easy to find systematic and reliable hydrological data, in the case of small systems such data may be minor or even totally missing. The stochastic approach is the unique means to account for input data uncertainties within the combined water-energy management problem. Using as example the Livadi reservoir, which is the pumped storage component of the small Aegean island of Astypalaia, Greece, we provide a simulation framework, comprising: (a) a stochastic model for generating synthetic rainfall and temperature time series; (b) a stochastic rainfall-runoff model, whose parameters cannot be inferred through calibration and, thus, they are represented as correlated random variables; (c) a stochastic model for estimating water supply and irrigation demands, based on simulated temperature and soil moisture, and (d) a daily operation model of the reservoir system, providing stochastic forecasts of water and energy outflows. Acknowledgement: This research is conducted within the frame of the undergraduate course "Stochastic Methods in Water Resources" of the National Technical University of Athens (NTUA). The School of Civil Engineering of NTUA provided moral support for the participation of the students

  20. Stable water isotope and surface heat flux simulation using ISOLSM: Evaluation against in-situ measurements

    KAUST Repository

    Cai, Mick Y.; Wang, Lixin; Parkes, Stephen; Strauss, Josiah; McCabe, Matthew; Evans, Jason P.; Griffiths, Alan D.

    2015-01-01

    The stable isotopes of water are useful tracers of water sources and hydrological processes. Stable water isotope-enabled land surface modeling is a relatively new approach for characterizing the hydrological cycle, providing spatial and temporal variability for a number of hydrological processes. At the land surface, the integration of stable water isotopes with other meteorological measurements can assist in constraining surface heat flux estimates and discriminate between evaporation (E) and transpiration (T). However, research in this area has traditionally been limited by a lack of continuous in-situ isotopic observations. Here, the National Centre for Atmospheric Research stable isotope-enabled Land Surface Model (ISOLSM) is used to simulate the water and energy fluxes and stable water isotope variations. The model was run for a period of one month with meteorological data collected from a coastal sub-tropical site near Sydney, Australia. The modeled energy fluxes (latent heat and sensible heat) agreed reasonably well with eddy covariance observations, indicating that ISOLSM has the capacity to reproduce observed flux behavior. Comparison of modeled isotopic compositions of evapotranspiration (ET) against in-situ Fourier Transform Infrared spectroscopy (FTIR) measured bulk water vapor isotopic data (10. m above the ground), however, showed differences in magnitude and temporal patterns. The disparity is due to a small contribution from local ET fluxes to atmospheric boundary layer water vapor (~1% based on calculations using ideal gas law) relative to that advected from the ocean for this particular site. Using ISOLSM simulation, the ET was partitioned into E and T with 70% being T. We also identified that soil water from different soil layers affected T and E differently based on the simulated soil isotopic patterns, which reflects the internal working of ISOLSM. These results highlighted the capacity of using the isotope-enabled models to discriminate

  1. Stable water isotope and surface heat flux simulation using ISOLSM: Evaluation against in-situ measurements

    KAUST Repository

    Cai, Mick Y.

    2015-04-01

    The stable isotopes of water are useful tracers of water sources and hydrological processes. Stable water isotope-enabled land surface modeling is a relatively new approach for characterizing the hydrological cycle, providing spatial and temporal variability for a number of hydrological processes. At the land surface, the integration of stable water isotopes with other meteorological measurements can assist in constraining surface heat flux estimates and discriminate between evaporation (E) and transpiration (T). However, research in this area has traditionally been limited by a lack of continuous in-situ isotopic observations. Here, the National Centre for Atmospheric Research stable isotope-enabled Land Surface Model (ISOLSM) is used to simulate the water and energy fluxes and stable water isotope variations. The model was run for a period of one month with meteorological data collected from a coastal sub-tropical site near Sydney, Australia. The modeled energy fluxes (latent heat and sensible heat) agreed reasonably well with eddy covariance observations, indicating that ISOLSM has the capacity to reproduce observed flux behavior. Comparison of modeled isotopic compositions of evapotranspiration (ET) against in-situ Fourier Transform Infrared spectroscopy (FTIR) measured bulk water vapor isotopic data (10. m above the ground), however, showed differences in magnitude and temporal patterns. The disparity is due to a small contribution from local ET fluxes to atmospheric boundary layer water vapor (~1% based on calculations using ideal gas law) relative to that advected from the ocean for this particular site. Using ISOLSM simulation, the ET was partitioned into E and T with 70% being T. We also identified that soil water from different soil layers affected T and E differently based on the simulated soil isotopic patterns, which reflects the internal working of ISOLSM. These results highlighted the capacity of using the isotope-enabled models to discriminate

  2. Adaptive resolution simulation of supramolecular water : The concurrent making, breaking, and remaking of water bundles

    NARCIS (Netherlands)

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

    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

  3. Numerical simulation of the impact of water-air fronts on radionuclides plumes in heterogeneous media

    International Nuclear Information System (INIS)

    Aquino, J.; Francisco, A.S.; Pereira, F.; Amaral Souto, H.P.

    2004-01-01

    The goal of this paper is to investigate the interaction of water-air fronts with radionuclide plumes in unsaturated heterogeneous porous media. This problem is modeled by a system of equations that describes both the water-air flow and the radionuclide transport. The water-air problem is solved numerically by a mixed finite element combined with a non-oscillatory central difference scheme. For the radionuclide transport equation we use the Modified Method of Characteristics (MMOC). We present the results of numerical simulations for heterogeneous permeability fields taking into account sorption effects. (author)

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

    Directory of Open Access Journals (Sweden)

    Jun Liu

    2015-11-01

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

  5. General and Localized corrosion of Austenitic and Borated Stainless Steels in Simulated Concentrated Ground Waters

    International Nuclear Information System (INIS)

    Fix, D.; Estill, J.; Wong, L.; Rebak, R.

    2004-01-01

    Boron containing stainless steels are used in the nuclear industry for applications such as spent fuel storage, control rods and shielding. It was of interest to compare the corrosion resistance of three borated stainless steels with standard austenitic alloy materials such as type 304 and 316 stainless steels. Tests were conducted in three simulated concentrated ground waters at 90 C. Results show that the borated stainless were less resistant to corrosion than the witness austenitic materials. An acidic concentrated ground water was more aggressive than an alkaline concentrated ground water

  6. Simulation study of a hydrostat design for detecting underground leakage of water supply using neutron backscattering

    International Nuclear Information System (INIS)

    Kurosawa, Tadahiro; Nakamura, Takashi; Suzuki, Takashi; Okano, Yasuhiro; Chisaka, Haruo

    1998-01-01

    We have embarked upon the development of a new detection method for underground water leakage using a neutron backscattering system. We have estimated the performance capabilities of such a system using Monte Carlo simulation. It is indicated that a leak which results in 40% water content in the surrounding soils could be detected at depths of up to 40 cm from the surface to the center of the source of leakage. This new detection system could be useful as a hydrostat of underground water supply in noisy areas such as Tokyo, in place of presently-used hydrostats which are based on detection of changes in sound

  7. Protein kinase A (PKA) phosphorylation of Na+/K+-ATPase opens intracellular C-terminal water pathway leading to third Na+-binding site in molecular dynamics simulations

    DEFF Research Database (Denmark)

    Poulsen, Hanne; Nissen, Poul; Mouritsen, Ole G.

    2012-01-01

    -atom Molecular Dynamics (MD) simulations to investigate the structural consequences of phosphorylating the Na+/K+- ATPase (NKA) residue S936, which is the best characterized phosphorylation site in NKA, targeted in vivo by Protein Kinase A (PKA) (1-3). The MD simulations suggest that S936 phosphorylation opens......Phosphorylation is one of the major mechanisms for posttranscriptional modification of proteins. The addition of a compact, negatively charged moiety to a protein can significantly change its function and localization by affecting its structure and interaction network. We have used all...... a C-terminal hydrated pathway leading to D926, a transmembrane residue proposed to form part of the third sodium ion-binding site (4). Simulations of a S936E mutant form, for which only subtle effects are observed when expressed in Xenopus oocytes and studied with electrophysiology, does not mimic...

  8. Reassessment of Ground-Water Recharge and Simulated Ground-Water Availability for the Hawi Area of North Kohala, Hawaii

    Science.gov (United States)

    Oki, Delwyn S.

    2002-01-01

    An estimate of ground-water availability in the Hawi area of north Kohala, Hawaii, is needed to determine whether ground-water resources are adequate to meet future demand within the area and other areas to the south. For the Hawi area, estimated average annual recharge from infiltration of rainfall, fog drip, and irrigation is 37.5 million gallons per day from a daily water budget. Low and high annual recharge estimates for the Hawi area that incorporate estimated uncertainty are 19.9 and 55.4 million gallons per day, respectively. The recharge estimates from this study are lower than the recharge of 68.4 million gallons per day previously estimated from a monthly water budget. Three ground-water models, using the low, intermediate, and high recharge estimates (19.9, 37.5, and 55.4 million gallons per day, respectively), were developed for the Hawi area to simulate ground-water levels and discharges for the 1990?s. To assess potential ground-water availability, the numerical ground-water flow models were used to simulate the response of the freshwater-lens system to withdrawals at rates in excess of the average 1990?s withdrawal rates. Because of uncertainty in the recharge estimate, estimates of ground-water availability also are uncertain. Results from numerical simulations indicate that for appropriate well sites, depths, and withdrawal rates (1) for the low recharge estimate (19.9 million gallons per day) it may be possible to develop an additional 10 million gallons per day of fresh ground water from the Hawi area and maintain a freshwater-lens thickness of 160 feet near the withdrawal sites, (2) for the intermediate recharge estimate (37.5 million gallons per day) it may be possible to develop an additional 15 million gallons per day of fresh ground water from the Hawi area and maintain a freshwater-lens thickness of 190 feet near the withdrawal sites, and (3) for the high recharge estimate (55.4 million gallons per day) it may be possible to develop at

  9. Simulating streamflow and water table depth with a coupled hydrological model

    Directory of Open Access Journals (Sweden)

    Alphonce Chenjerayi Guzha

    2010-09-01

    Full Text Available A coupled model integrating MODFLOW and TOPNET with the models interacting through the exchange of recharge and baseflow and river-aquifer interactions was developed and applied to the Big Darby Watershed in Ohio, USA. Calibration and validation results show that there is generally good agreement between measured streamflow and simulated results from the coupled model. At two gauging stations, average goodness of fit (R2, percent bias (PB, and Nash Sutcliffe efficiency (ENS values of 0.83, 11.15%, and 0.83, respectively, were obtained for simulation of streamflow during calibration, and values of 0.84, 8.75%, and 0.85, respectively, were obtained for validation. The simulated water table depths yielded average R2 values of 0.77 and 0.76 for calibration and validation, respectively. The good match between measured and simulated streamflows and water table depths demonstrates that the model is capable of adequately simulating streamflows and water table depths in the watershed and also capturing the influence of spatial and temporal variation in recharge.

  10. The Design and Development of a Simulation to Teach Water Conservation to Primary School Students

    Science.gov (United States)

    Campbell, Lee

    2004-01-01

    Information and Communications Technology (ICT) plays a dominant role in enhancing teaching and learning. Similar advances have been made in the use of multimedia in the classroom. These advances are coupled with newer developmental tools and techniques. This paper examines the design and development of a simulation on water conservation. Science…

  11. MATHEMATICAL MODEL FOR THE SIMULATION OF WATER QUALITY IN RIVERS USING THE VENSIM PLE® SOFTWARE

    Directory of Open Access Journals (Sweden)

    Julio Cesar de S. I. Gonçalves

    2013-06-01

    Full Text Available Mathematical modeling of water quality in rivers is an important tool for the planning and management of water resources. Nevertheless, the available models frequently show structural and functional limitations. With the objective of reducing these drawbacks, a new model has been developed to simulate water quality in rivers under unsteady conditions; this model runs on the Vensim PLE® software and can also be operated for steady-state conditions. The following eighteen water quality variables can be simulated: DO, BODc, organic nitrogen (No, ammonia nitrogen (Na, nitrite (Ni, nitrate (Nn, organic and inorganic phosphorus (Fo and Fi, respectively, inorganic solids (Si, phytoplankton (F, zooplankton (Z, bottom algae (A, detritus (D, total coliforms (TC, alkalinity (Al., total inorganic carbon (TIC, pH, and temperature (T. Methane as well as nitrogen and phosphorus compounds that are present in the aerobic and anaerobic layers of the sediment can also be simulated. Several scenarios were generated for computational simulations produced using the new model by using the QUAL2K program, and, when possible, analytical solutions. The results obtained using the new model strongly supported the results from the QUAL family and analytical solutions.

  12. Primary biodegradation of veterinary antibiotics in aerobic and anaerobic surface water simulation systems

    DEFF Research Database (Denmark)

    Ingerslev, Flemming; Toräng, Lars; Loke, M.-L.

    2001-01-01

    The primary aerobic and anaerobic biodegradability at intermediate concentrations (50-5000 mug/l) of the antibiotics olaquindox (OLA), metronidazole (MET), tylosin (TYL) and oxytetracycline (OTC) was studied in a simple shake flask system simulating the conditions in surface waters. The purpose...

  13. Numerical simulation of runoff from extreme rainfall events in a mountain water catchment

    Directory of Open Access Journals (Sweden)

    J. Burguete

    2002-01-01

    Full Text Available A numerical model for unsteady shallow water flow over initially dry areas is applied to a case study in a small drainage area at the Spanish Ebro River basin. Several flood mitigation measures (reforestation, construction of a small reservoir and channelization are simulated in the model in order to compare different extreme rainfall-runoff scenarios.

  14. Simulation of Water Percolation in a FEBEX Bentonite Block using TOUGH2 Program

    International Nuclear Information System (INIS)

    Bru, A.

    2001-01-01

    We use Tough2 program to simulate the water percolation in a Febex bentonite Block. From obtained results, we conclude that mean field approximation does not describe this process because the heterogeneity of the medium it is not include in mathematical formalism. (Author) 17 refs

  15. A hydrological simulation of the water regime in two playa lakes ...

    Indian Academy of Sciences (India)

    The definition of the surface–groundwater rela- tionship of the two unaltered playa lakes. Ballestera (henceforth 'Ball') and Calderón. (henceforth 'Cald'). • The simulation of an altered water regime caused by an increased anthropogenic GW consumption within the watershed area of Ball playa-lake. 2. The area of research.

  16. Penetration of n-hexadecane and water into wood under conditions simulating catastrophic floods

    Science.gov (United States)

    Ganna Baglayeva; Wayne S. Seames; Charles R. Frihart; Jane O' Dell; Evguenii I. Kozliak

    2017-01-01

    To simulate fuel oil spills occurring during catastrophic floods, short-term absorption of two chemicals, n-hexadecane (representative of semivolatile organic compounds in fuel oil) and water, into southern yellow pine was gravimetrically monitored as a function of time at ambient conditions. Different scenarios were run on the basis of (1) the...

  17. Numerical Simulation of the Effects of Water Surface in Building Environment

    Science.gov (United States)

    Li, Guangyao; Pan, Yuqing; Yang, Li

    2018-03-01

    Water body could affect the thermal environment and airflow field in the building districts, because of its special thermal characteristics, evaporation and flat surface. The thermal influence of water body in Tongji University Jiading Campus front area was evaluated. First, a suitable evaporation model was selected and then was applied to calculate the boundary conditions of the water surface in the Fluent software. Next, the computational fluid dynamics (CFD) simulations were conducted on the models both with and without water, following the CFD practices guidelines. Finally, the outputs of the two simulations were compared with each other. Results showed that the effect of evaporative cooling from water surface strongly depends on the wind direction and temperature decrease was about 2∼5°C. The relative humidity within the enclosing area was affected by both the building arrangement and surrounding water. An increase of about 0.1∼0.2m/s of wind speed induced by the water evaporation was observed in the open space.

  18. Characterization of the glass transition of water predicted by molecular dynamics simulations using nonpolarizable intermolecular potentials.

    Science.gov (United States)

    Kreck, Cara A; Mancera, Ricardo L

    2014-02-20

    Molecular dynamics simulations allow detailed study of the experimentally inaccessible liquid state of supercooled water below its homogeneous nucleation temperature and the characterization of the glass transition. Simple, nonpolarizable intermolecular potentials are commonly used in classical molecular dynamics simulations of water and aqueous systems due to their lower computational cost and their ability to reproduce a wide range of properties. Because the quality of these predictions varies between the potentials, the predicted glass transition of water is likely to be influenced by the choice of potential. We have thus conducted an extensive comparative investigation of various three-, four-, five-, and six-point water potentials in both the NPT and NVT ensembles. The T(g) predicted from NPT simulations is strongly correlated with the temperature of minimum density, whereas the maximum in the heat capacity plot corresponds to the minimum in the thermal expansion coefficient. In the NVT ensemble, these points are instead related to the maximum in the internal pressure and the minimum of its derivative, respectively. A detailed analysis of the hydrogen-bonding properties at the glass transition reveals that the extent of hydrogen-bonds lost upon the melting of the glassy state is related to the height of the heat capacity peak and varies between water potentials.

  19. [Review on HSPF model for simulation of hydrology and water quality processes].

    Science.gov (United States)

    Li, Zhao-fu; Liu, Hong-Yu; Li, Yan

    2012-07-01

    Hydrological Simulation Program-FORTRAN (HSPF), written in FORTRAN, is one ol the best semi-distributed hydrology and water quality models, which was first developed based on the Stanford Watershed Model. Many studies on HSPF model application were conducted. It can represent the contributions of sediment, nutrients, pesticides, conservatives and fecal coliforms from agricultural areas, continuously simulate water quantity and quality processes, as well as the effects of climate change and land use change on water quantity and quality. HSPF consists of three basic application components: PERLND (Pervious Land Segment) IMPLND (Impervious Land Segment), and RCHRES (free-flowing reach or mixed reservoirs). In general, HSPF has extensive application in the modeling of hydrology or water quality processes and the analysis of climate change and land use change. However, it has limited use in China. The main problems with HSPF include: (1) some algorithms and procedures still need to revise, (2) due to the high standard for input data, the accuracy of the model is limited by spatial and attribute data, (3) the model is only applicable for the simulation of well-mixed rivers, reservoirs and one-dimensional water bodies, it must be integrated with other models to solve more complex problems. At present, studies on HSPF model development are still undergoing, such as revision of model platform, extension of model function, method development for model calibration, and analysis of parameter sensitivity. With the accumulation of basic data and imorovement of data sharing, the HSPF model will be applied more extensively in China.

  20. Numerical simulation and structural optimization of the inclined oil/water separator.

    Directory of Open Access Journals (Sweden)

    Liqiong Chen

    Full Text Available Improving the separation efficiency of the inclined oil/water separator, a new type of gravity separation equipment, is of great importance. In order to obtain a comprehensive understanding of the internal flow field of the separation process of oil and water within this separator, a numerical simulation based on Euler multiphase flow analysis and the realizable k-ε two equation turbulence model was executed using Fluent software. The optimal value ranges of the separator's various structural parameters used in the numerical simulation were selected through orthogonal array experiments. A field experiment on the separator was conducted with optimized structural parameters in order to validate the reliability of the numerical simulation results. The research results indicated that the horizontal position of the dispenser, the hole number, and the diameter had significant effects on the oil/water separation efficiency, and that the longitudinal position of the dispenser and the position of the weir plate had insignificant effects on the oil/water separation efficiency. The optimal structural parameters obtained through the orthogonal array experiments resulted in an oil/water separation efficiency of up to 95%, which was 4.996% greater than that realized by the original structural parameters.

  1. Simulation of water movement and isoproturon behaviour in a heavy clay soil using the MACRO model

    Directory of Open Access Journals (Sweden)

    T. J. Besien

    1997-01-01

    Full Text Available In this paper, the dual-porosity MACRO model has been used to investigate methods of reducing leaching of isoproturon from a structured heavy clay soil. The MACRO model was applied to a pesticide leaching data-set generated from a plot scale experiment on a heavy clay soil at the Oxford University Farm, Wytham, England. The field drain was found to be the most important outflow from the plot in terms of pesticide removal. Therefore, this modelling exercise concentrated on simulating field drain flow. With calibration of field-saturated and micropore saturated hydraulic conductivity, the drain flow hydrographs were simulated during extended periods of above average rainfall, with both the hydrograph shape and peak flows agreeing well. Over the whole field season, the observed drain flow water budget was well simulated. However, the first and second drain flow events after pesticide application were not simulated satisfactorily. This is believed to be due to a poor simulation of evapotranspiration during a period of low rainfall around the pesticide application day. Apart from an initial rapid drop in the observed isoproturon soil residue, the model simulated isoproturon residues during the 100 days after pesticide application reasonably well. Finally, the calibrated model was used to show that changes in agricultural practice (deep ploughing, creating fine consolidated seed beds and organic matter applications could potentially reduce pesticide leaching to surface waters by up to 60%.

  2. Modifying a dynamic global vegetation model for simulating large spatial scale land surface water balance

    Science.gov (United States)

    Tang, G.; Bartlein, P. J.

    2012-01-01

    Water balance models of simple structure are easier to grasp and more clearly connect cause and effect than models of complex structure. Such models are essential for studying large spatial scale land surface water balance in the context of climate and land cover change, both natural and anthropogenic. This study aims to (i) develop a large spatial scale water balance model by modifying a dynamic global vegetation model (DGVM), and (ii) test the model's performance in simulating actual evapotranspiration (ET), soil moisture and surface runoff for the coterminous United States (US). Toward these ends, we first introduced development of the "LPJ-Hydrology" (LH) model by incorporating satellite-based land covers into the Lund-Potsdam-Jena (LPJ) DGVM instead of dynamically simulating them. We then ran LH using historical (1982-2006) climate data and satellite-based land covers at 2.5 arc-min grid cells. The simulated ET, soil moisture and surface runoff were compared to existing sets of observed or simulated data for the US. The results indicated that LH captures well the variation of monthly actual ET (R2 = 0.61, p 0.46, p 0.52) with observed values over the years 1982-2006, respectively. The modeled spatial patterns of annual ET and surface runoff are in accordance with previously published data. Compared to its predecessor, LH simulates better monthly stream flow in winter and early spring by incorporating effects of solar radiation on snowmelt. Overall, this study proves the feasibility of incorporating satellite-based land-covers into a DGVM for simulating large spatial scale land surface water balance. LH developed in this study should be a useful tool for studying effects of climate and land cover change on land surface hydrology at large spatial scales.

  3. Simulation of the solidification in a channel of a water-cooled glass flow

    Directory of Open Access Journals (Sweden)

    G. E. Ovando Chacon

    2014-12-01

    Full Text Available A computer simulation study of a laminar steady-state glass flow that exits from a channel cooled with water is reported. The simulations are carried out in a two-dimensional, Cartesian channel with a backward-facing step for three different angles of the step and different glass outflow velocities. We studied the interaction of the fluid dynamics, phase change and thermal behavior of the glass flow due to the heat that transfers to the cooling water through the wall of the channel. The temperature, streamline, phase change and pressure fields are obtained and analyzed for the glass flow. Moreover, the temperature increments of the cooling water are characterized. It is shown that, by reducing the glass outflow velocity, the solidification is enhanced; meanwhile, an increase of the step angle also improves the solidification of the glass flow.

  4. Simulating Mobility of Chemical Contaminants from Unconventional Gas Development for Protection of Water Resources

    Science.gov (United States)

    Kanno, C.; Edlin, D.; Borrillo-Hutter, T.; McCray, J. E.

    2014-12-01

    Potential contamination of ground water and surface water supplies from chemical contaminants in hydraulic fracturing fluids or in natural gas is of high public concern. However, quantitative assessments have rarely been conducted at specific energy-producing locations so that the true risk of contamination can be evaluated. The most likely pathways for contamination are surface spills and faulty well bores that leak production fluids directly into an aquifer. This study conducts fate and transport simulations of the most mobile chemical contaminants, based on reactivity to subsurface soils, degradation potential, and source concentration, to better understand which chemicals are most likely to contaminate water resources, and to provide information to planners who wish to be prepared for accidental releases. The simulations are intended to be most relevant to the Niobrara shale formation.

  5. Bringing Water to a Lesotho Village: A Classroom Simulation. Water in Africa.

    Science.gov (United States)

    Ray, Dany M.

    The Water in Africa Project was realized over a 2-year period by a team of Peace Corps volunteers, World Wise Schools (WWS) classroom teachers, and WWS staff members. As part of an expanded, detailed design, resources were collected from over 90 volunteers serving in African countries, photos and stories were prepared, and standards-based learning…

  6. A flexible hydrological warning system in Denmark for real-time surface water and groundwater simulations

    Science.gov (United States)

    He, Xin; Stisen, Simon; Wiese, Marianne B.; Jørgen Henriksen, Hans

    2015-04-01

    In Denmark, increasing focus on extreme weather events has created considerable demand for short term forecasts and early warnings in relation to groundwater and surface water flooding. The Geological Survey of Denmark and Greenland (GEUS) has setup, calibrated and applied a nationwide water resources model, the DK-Model, primarily for simulating groundwater and surface water flows and groundwater levels during the past 20 years. So far, the DK-model has only been used in offline historical and future scenario simulations. Therefore, challenges arise in operating such a model for online forecasts and early warnings, which requires access to continuously updated observed climate input data and forecast data of precipitation, temperature and global radiation for the next 48 hours or longer. GEUS has a close collaboration with the Danish Meteorological Institute in order to test and enable this data input for the DK model. Due to the comprehensive physical descriptions of the DK-Model, the simulation results can potentially be any component of the hydrological cycle within the models domain. Therefore, it is important to identify which results need to be updated and saved in the real-time mode, since it is not computationally economical to save every result considering the heavy load of data. GEUS have worked closely with the end-users and interest groups such as water planners and emergency managers from the municipalities, water supply and waste water companies, consulting companies and farmer organizations, in order to understand their possible needs for real time simulation and monitoring of the nationwide water cycle. This participatory process has been supported by a web based questionnaire survey, and a workshop that connected the model developers and the users. For qualifying the stakeholder engagement, GEUS has selected a representative catchment area (Skjern River) for testing and demonstrating a prototype of the web based hydrological warning system at the

  7. Molecular Dynamics Simulations with Quantum Mechanics/Molecular Mechanics and Adaptive Neural Networks.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2018-03-13

    Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in a complex environment but also very time-consuming. The computational cost of QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive idea. Recently, we reported a neural network (NN) method as QM/MM-NN to predict the potential energy difference between semiempirical and ab initio QM/MM approaches. The high-level results can be obtained using neural network based on semiempirical QM/MM MD simulations, but the lack of direct MD samplings at the ab initio QM/MM level is still a deficiency that limits the applications of QM/MM-NN. In the present paper, we developed a dynamic scheme of QM/MM-NN for direct MD simulations on the NN-predicted potential energy surface to approximate ab initio QM/MM MD. Since some configurations excluded from the database for NN training were encountered during simulations, which may cause some difficulties on MD samplings, an adaptive procedure inspired by the selection scheme reported by Behler [ Behler Int. J. Quantum Chem. 2015 , 115 , 1032 ; Behler Angew. Chem., Int. Ed. 2017 , 56 , 12828 ] was employed with some adaptions to update NN and carry out MD iteratively. We further applied the adaptive QM/MM-NN MD method to the free energy calculation and transition path optimization on chemical reactions in water. The results at the ab initio QM/MM level can be well reproduced using this method after 2-4 iteration cycles. The saving in computational cost is about 2 orders of magnitude. It demonstrates that the QM/MM-NN with direct MD simulations has great potentials not only for the calculation of thermodynamic properties but also for the characterization of

  8. Simulation of Farmers’ Response to Irrigation Water Pricing and Rationing Policies (Case Study: Zabol City

    Directory of Open Access Journals (Sweden)

    abouzar parhizkari

    2014-10-01

    Full Text Available Considering that agricultural sector is the largest consumer of water, presenting integrated management for water resources and formulating effective policies to increase water productivity in this sector is essential. Therefore, using economic modeling , this study simulated the farmers’ responses to irrigation water pricing and rationing policies in Zabol city. To achieve the study purpose, the State Wide Agricultural Production Model and Positive Mathematical Programming were applied. The required data for the years 2010-2011 was collected by completing questionnaires and collecting data sets from the relevant agencies of Zabol city in personal attendance. The results showed that imposing irrigation water pricing and rationing policies in Zabol city leads to a reduction in the total cultivated area by 9/54 and 5/14 percent and a reduction in the water consumption by 6/23 and 7/01 percent, compared to the base year. Ultimately, irrigation water rationing policy, considering frugality of 18/9 million m3 of water, as the appropriate solution for the sustainability of water resources of Zabol city was proposed.

  9. Guide to the Revised Ground-Water Flow and Heat Transport Simulator: HYDROTHERM - Version 3

    Science.gov (United States)

    Kipp, Kenneth L.; Hsieh, Paul A.; Charlton, Scott R.

    2008-01-01

    The HYDROTHERM computer program simulates multi-phase ground-water flow and associated thermal energy transport in three dimensions. It can handle high fluid pressures, up to 1 ? 109 pascals (104 atmospheres), and high temperatures, up to 1,200 degrees Celsius. This report documents the release of Version 3, which includes various additions, modifications, and corrections that have been made to the original simulator. Primary changes to the simulator include: (1) the ability to simulate unconfined ground-water flow, (2) a precipitation-recharge boundary condition, (3) a seepage-surface boundary condition at the land surface, (4) the removal of the limitation that a specified-pressure boundary also have a specified temperature, (5) a new iterative solver for the linear equations based on a generalized minimum-residual method, (6) the ability to use time- or depth-dependent functions for permeability, (7) the conversion of the program code to Fortran 90 to employ dynamic allocation of arrays, and (8) the incorporation of a graphical user interface (GUI) for input and output. The graphical user interface has been developed for defining a simulation, running the HYDROTHERM simulator interactively, and displaying the results. The combination of the graphical user interface and the HYDROTHERM simulator forms the HYDROTHERM INTERACTIVE (HTI) program. HTI can be used for two-dimensional simulations only. New features in Version 3 of the HYDROTHERM simulator have been verified using four test problems. Three problems come from the published literature and one problem was simulated by another partially saturated flow and thermal transport simulator. The test problems include: transient partially saturated vertical infiltration, transient one-dimensional horizontal infiltration, two-dimensional steady-state drainage with a seepage surface, and two-dimensional drainage with coupled heat transport. An example application to a hypothetical stratovolcano system with unconfined

  10. Analysis of air-to-water heat pump in cold climate: comparison between experiment and simulation

    Directory of Open Access Journals (Sweden)

    Karolis Januševičius

    2015-10-01

    Full Text Available Heat pump systems are promising technologies for current and future buildings and this research presents the performance of air source heat pump (ASHP system. The system was monitored, analysed and simulated using TRNSYS software. The experimental data were used to calibrate the simulation model of ASHP. The specific climate conditions are evaluated in the model. It was noticed for the heating mode that the coefficient of performance (COP varied from 1.98 to 3.05 as the outdoor temperature changed from –7.0 ºC to +5.0 ºC, respectively. TRNSYS simulations were also performed to predict seasonal performance factor of the ASHP for Vilnius city. It was identified that seasonal performance prediction could be approximately 15% lower if frost formation effects are not included to air-water heat pump simulation model.

  11. The comparison of solar water heating system operation parameters calculated using traditional method and dynamic simulations

    Directory of Open Access Journals (Sweden)

    Sornek Krzysztof

    2016-01-01

    Full Text Available The proper design of renewable energy based systems is really important to provide their efficient and safe operation. The aim of this paper is to compare the results obtained during traditional static calculations, with the results of dynamic simulations. For this reason, simulations of solar water heating (SWH system, designed for a typical residential building, were conducted in the TRNSYS (Transient System Simulation Tool. Carried out calculations allowed to determine the heat generation in the discussed system as well as to estimate the efficiency of considered installation. Obtained results were compared with the results from other available tool based on the static calculations. It may be concluded, that using dynamic simulations at the designing stage of renewable energy based systems may help to avoid many exploitation problems (including low efficiency, overheating etc. and allows to provide safe exploitation of such installations.

  12. Numerical simulation of water flow through the bottom en piece of a nuclear fuel assembly

    International Nuclear Information System (INIS)

    Navarro, Moyses A.; Santos, Andre A. Campagnole dos

    2007-01-01

    The water flow through the bottom nozzle of a nuclear fuel assembly was simulated using a commercial CFD code, CFX 10.0. Previously, simulations with a perforated plate similar to the bottom nozzle plate were performed to define the appropriate mesh refinement and turbulence model (κ-ε or SST). Subsequently, the numerical simulation was performed with the optimized mesh using the turbulence model (κ-ε in a standard bottom nozzle with some geometric simplifications. The numerical results were compared with experimental results to determine the pressure drop through the bottom nozzle in the Reynolds range from ∼10500 to ∼95000. The agreement between the numerical simulations and experimental results may be considered satisfactory. The study indicated that the CFD codes can play an important role in the development of pieces with complex geometries, optimizing the planning of the experiments and aiding in the experimental analysis. (author)

  13. Orbit Feedback Operation with RCBX (MD 1209)

    CERN Document Server

    Wenninger, Jorg; Nisbet, David; Ponce, Laurette; Louro Alves, Diogo Miguel; CERN. Geneva. ATS Department

    2017-01-01

    The LHC Orbit Feedback (OFB) is able to drive any orbit corrector circuit (COD) to steer the LHC orbit. But during the first feedback tests in 2010, all attempts to use the common triplet orbit correctors (MCBX) failed because the QPS system installed to protect those magnets triggered power aborts as soon as the OFB steered the beam with those CODs. The reason was most likely the violation of the RCBX circuit acceleration limits. For this reason the MCBX orbit correctors were never driven by the OFB in regular operation. Although the performance of the OFB is generally excellent, the quality of the beam steering around IRs could be improved if the OFB could correct the orbit with the MCBX to counteract locally triplet quadrupole movements. The aim of this MD was to make a new attempt to use the MCBX in the OFB. The test was successful at injection (no circuit trip) and failed during the ramp (QPS power abort). The PC voltages and QPS Ures signals revealed the presence of voltage spikes with a period of 10~s...

  14. The millennium water vapour drop in chemistry–climate model simulations

    Directory of Open Access Journals (Sweden)

    S. Brinkop

    2016-07-01

    Full Text Available This study investigates the abrupt and severe water vapour decline in the stratosphere beginning in the year 2000 (the "millennium water vapour drop" and other similarly strong stratospheric water vapour reductions by means of various simulations with the state-of-the-art Chemistry-Climate Model (CCM EMAC (ECHAM/MESSy Atmospheric Chemistry Model. The model simulations differ with respect to the prescribed sea surface temperatures (SSTs and whether nudging is applied or not. The CCM EMAC is able to most closely reproduce the signature and pattern of the water vapour drop in agreement with those derived from satellite observations if the model is nudged. Model results confirm that this extraordinary water vapour decline is particularly obvious in the tropical lower stratosphere and is related to a large decrease in cold point temperature. The drop signal propagates under dilution to the higher stratosphere and to the poles via the Brewer–Dobson circulation (BDC. We found that the driving forces for this significant decline in water vapour mixing ratios are tropical sea surface temperature (SST changes due to a coincidence with a preceding strong El Niño–Southern Oscillation event (1997/1998 followed by a strong La Niña event (1999/2000 and supported by the change of the westerly to the easterly phase of the equatorial stratospheric quasi-biennial oscillation (QBO in 2000. Correct (observed SSTs are important for triggering the strong decline in water vapour. There are indications that, at least partly, SSTs contribute to the long period of low water vapour values from 2001 to 2006. For this period, the specific dynamical state of the atmosphere (overall atmospheric large-scale wind and temperature distribution is important as well, as it causes the observed persistent low cold point temperatures. These are induced by a period of increased upwelling, which, however, has no corresponding pronounced signature in SSTs anomalies in the tropics

  15. Virtual synthesis of crystals using ab initio MD: Case study on LiFePO4

    Science.gov (United States)

    Mishra, S. B.; Nanda, B. R. K.

    2017-05-01

    Molecular dynamics simulation technique is fairly successful in studying the structural aspects and dynamics of fluids. Here we study the ability of ab initio molecular dynamics (ab initio MD) to carry out virtual experiments to synthesize new crystalline materials and to predict their structures. For this purpose the olivine phosphate LiFePO4 (LFPO) is used as an example. As transition metal oxides in general are stabilized with layered geometry, we carried out ab initio MD simulations over a hypothetical layered configuration consisting of alternate LiPO2 and FeO2 layers. With intermittent steps of electron minimization, the resulted equilibrium lattice consist of PO4 tetrahedra and distorted Fe-O complexes similar to the one observed in the experimental lattice.

  16. Computational simulation of water transport in PEM fuel cells using an improved membrane model

    International Nuclear Information System (INIS)

    Cao, J.; Djilali, N.

    2000-01-01

    Computational models and simulation tools can provide valuable insight and guidance for design, performance optimization, and cost reduction of fuel cells. In proton-exchange membrane fuel cells it is particularly i