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. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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)

  10. 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

  11. 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...

  12. 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.

  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. 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...

  15. 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)

  16. 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.

  17. 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

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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

  3. 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

  4. 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...

  5. 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%.

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

  11. 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

  12. 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

  13. 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.

  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. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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)

  2. 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

  3. 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).

  4. 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

  5. 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.

  6. 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...

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  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. 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.

  17. 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...

  18. 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

  19. 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.

  20. 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.

  1. 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)

  2. 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.

  3. 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...

  4. 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.

  5. 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

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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)

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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%.

  1. 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 ...

  2. 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.)

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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 ...

  13. Direct Numerical Simulations of Concentration and Temperature Polarization in Direct Contact Membrane Distillation

    Science.gov (United States)

    Lou, Jincheng; Tilton, Nils

    2017-11-01

    Membrane distillation (MD) is a method of desalination with boundary layers that are challenging to simulate. MD is a thermal process in which warm feed and cool distilled water flow on opposite sides of a hydrophobic membrane. The temperature difference causes water to evaporate from the feed, travel through the membrane, and condense in the distillate. Two challenges to MD are temperature and concentration polarization. Temperature polarization represents a reduction in the transmembrane temperature difference due to heat transfer through the membrane. Concentration polarization describes the accumulation of solutes near the membrane. These phenomena reduce filtration and lead to membrane fouling. They are difficult to simulate due to the coupling between the velocity, temperature, and concentration fields on the membrane. Unsteady regimes are particularly challenging because noise at the outlets can pollute the near-membrane flow fields. We present the development of a finite-volume method for the simulation of fluid flow, heat, and mass transport in MD systems. Using the method, we perform a parametric study of the polarization boundary layers, and show that the concentration boundary layer shows self-similar behavior that satisfies power laws for the downstream growth. Funded by the U.S. Bureau of Reclamation.

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. 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.))

  19. 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.))

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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...

  5. On the behavior of water at subfreezing temperatures in a protein crystal: evidence of higher mobility than in bulk water.

    Science.gov (United States)

    Wang, Dongqi; Böckmann, Anja; Dolenc, Jožica; Meier, Beat H; van Gunsteren, Wilfred F

    2013-10-03

    NMR experiments have shown that water molecules in the crystal of the protein Crh are still mobile at temperatures well below 273 K. In order to investigate this water anomaly, a molecular dynamics (MD) simulation study of crystalline Crh was carried out to determine the mobility of water in this crystal. The simulations were carried out at three temperatures, 150, 200, and 291 K. Simulations of bulk water at these temperatures were also done to obtain the properties of the simple point charge (SPC) water model used at these temperatures and to allow a comparison of the properties of water in the Crh crystal with those of bulk water at the same temperatures. According to the simulations, water is immobilized at 150 K both in crystal and in bulk water. As expected, at 291 K it diffuses and rotates more slowly in the protein crystal than in bulk water. However, at 200 K, the translational and rotational mobility of the water molecules is larger in the crystal than in bulk water. The enhancement of water mobility in the crystal at 200 K was further investigated by MD simulations in which the backbone or all protein atoms were positionally restrained, and in which additionally the electrostatic protein-water interactions were removed. Of these changes in the environment of the water molecules, rigidifying the protein backbones slightly enhanced water diffusion, while it slowed down rotation. In contrast, removal of electrostatic protein-water interactions did not change water diffusion but enhanced rotational motion significantly. Further investigations are required to delineate particular features of the protein crystal that induce the anomalous behavior of water at 200 K.

  6. Atomistic simulations of cation hydration in sodium and calcium montmorillonite nanopores

    Science.gov (United States)

    Yang, Guomin; Neretnieks, Ivars; Holmboe, Michael

    2017-08-01

    During the last four decades, numerous studies have been directed to the swelling smectite-rich clays in the context of high-level radioactive waste applications and waste-liners for contaminated sites. The swelling properties of clay mineral particles arise due to hydration of the interlayer cations and the diffuse double layers formed near the negatively charged montmorillonite (MMT) surfaces. To accurately study the cation hydration in the interlayer nanopores of MMT, solvent-solute and solvent-clay surface interactions (i.e., the solvation effects and the shape effects) on the atomic level should be taken into account, in contrast to many recent electric double layer based methodologies using continuum models. Therefore, in this research we employed fully atomistic simulations using classical molecular dynamics (MD) simulations, the software package GROMACS along with the CLAYFF forcefield and the SPC/E water model. We present the ion distributions and the deformation of the hydrated coordination structures, i.e., the hydration shells of Na+ and Ca2+ in the interlayer, respectively, for MMT in the first-layer, the second-layer, the third-layer, the fourth-layer, and the fifth-layer (1W, 2W, 3W, 4W, and 5W) hydrate states. Our MD simulations show that Na+ in Na-MMT nanopores have an affinity to the ditrigonal cavities of the clay layers and form transient inner-sphere complexes at about 3.8 Å from clay midplane at water contents less than the 5W hydration state. However, these phenomena are not observed in Ca-MMT regardless of swelling states. For Na-MMT, each Na+ is coordinated to four water molecules and one oxygen atom of the clay basal-plane in the first hydration shell at the 1W hydration state, and with five to six water molecules in the first hydration shell within a radius of 3.1 Å at all higher water contents. In Ca-MMT, however each Ca2+ is coordinated to approximately seven water molecules in the first hydration shell at the 1W hydration state and

  7. 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.)

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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...

  14. 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

  15. Simulating adsorptive expansion of zeolites: application to biomass-derived solutions in contact with silicalite.

    Science.gov (United States)

    Santander, Julian E; Tsapatsis, Michael; Auerbach, Scott M

    2013-04-16

    We have constructed and applied an algorithm to simulate the behavior of zeolite frameworks during liquid adsorption. We applied this approach to compute the adsorption isotherms of furfural-water and hydroxymethyl furfural (HMF)-water mixtures adsorbing in silicalite zeolite at 300 K for comparison with experimental data. We modeled these adsorption processes under two different statistical mechanical ensembles: the grand canonical (V-Nz-μg-T or GC) ensemble keeping volume fixed, and the P-Nz-μg-T (osmotic) ensemble allowing volume to fluctuate. To optimize accuracy and efficiency, we compared pure Monte Carlo (MC) sampling to hybrid MC-molecular dynamics (MD) simulations. For the external furfural-water and HMF-water phases, we assumed the ideal solution approximation and employed a combination of tabulated data and extended ensemble simulations for computing solvation free energies. We found that MC sampling in the V-Nz-μg-T ensemble (i.e., standard GCMC) does a poor job of reproducing both the Henry's law regime and the saturation loadings of these systems. Hybrid MC-MD sampling of the V-Nz-μg-T ensemble, which includes framework vibrations at fixed total volume, provides better results in the Henry's law region, but this approach still does not reproduce experimental saturation loadings. Pure MC sampling of the osmotic ensemble was found to approach experimental saturation loadings more closely, whereas hybrid MC-MD sampling of the osmotic ensemble quantitatively reproduces such loadings because the MC-MD approach naturally allows for locally anisotropic volume changes wherein some pores expand whereas others contract.

  16. 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.

  17. 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

  18. 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

  19. Bond-Valence Constraints on Liquid Water Structure

    International Nuclear Information System (INIS)

    Bickmore, Barry R.; Rosso, Kevin M.; Brown, I. David; Kerisit, Sebastien N.

    2009-01-01

    The recent controversy about the structure of liquid water pits a new model involving water molecules in relatively stable rings-and-chains structures against the standard model that posits water molecules in distorted tetrahedral coordination. Molecular dynamics (MD) simulations 'both classical and ab initio' almost uniformly support the standard model, but since none of them can yet reproduce all the anomalous properties of water, they leave room for doubt. We argue that it is possible to evaluate these simulations by testing them against their adherence to the bond-valence model, a well known, and quantitatively accurate, empirical summary of the behavior of atoms in the bonded networks of inorganic solids. Here we use the results of ab initio molecular dynamics simulations of ice, water, and several solvated aqueous species to show that the valence sum rule (the first axiom of the bond-valence model,) is followed in both solid and liquid bond networks. We then test MD simulations of water, employing several popular potential models, against this criterion and the experimental O-O radial distribution function. It appears that most of those tested cannot satisfy both criteria well, except TIP4P and TIP5P. If the valence sum rule really can be applied to simulated liquid structures, then it follows that the bonding behaviors of atoms in liquids are in some ways identical to those in solids. We support this interpretation by showing that the simulations produce O-H-O geometries completely consistent with the range of geometries available in solids, and the distributions of instantaneous valence sums reaching the atoms in both the ice and liquid water simulations are essentially identical. Taken together, this is powerful evidence in favor of the standard distorted tetrahedral model of liquid water structure

  20. 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...

  1. A polarizable QM/MM approach to the molecular dynamics of amide groups solvated in water

    Energy Technology Data Exchange (ETDEWEB)

    Schwörer, Magnus; Wichmann, Christoph; Tavan, Paul, E-mail: tavan@physik.uni-muenchen.de [Lehrstuhl für BioMolekulare Optik, Ludwig-Maximilians Universität München, Oettingenstr. 67, 80538 München (Germany)

    2016-03-21

    The infrared (IR) spectra of polypeptides are dominated by the so-called amide bands. Because they originate from the strongly polar and polarizable amide groups (AGs) making up the backbone, their spectral positions sensitively depend on the local electric fields. Aiming at accurate computations of these IR spectra by molecular dynamics (MD) simulations, which derive atomic forces from a hybrid quantum and molecular mechanics (QM/MM) Hamiltonian, here we consider the effects of solvation in bulk liquid water on the amide bands of the AG model compound N-methyl-acetamide (NMA). As QM approach to NMA we choose grid-based density functional theory (DFT). For the surrounding MM water, we develop, largely based on computations, a polarizable molecular mechanics (PMM) model potential called GP6P, which features six Gaussian electrostatic sources (one induced dipole, five static partial charge distributions) and, therefore, avoids spurious distortions of the DFT electron density in hybrid DFT/PMM simulations. Bulk liquid GP6P is shown to have favorable properties at the thermodynamic conditions of the parameterization and beyond. Lennard-Jones (LJ) parameters of the DFT fragment NMA are optimized by comparing radial distribution functions in the surrounding GP6P liquid with reference data obtained from a “first-principles” DFT-MD simulation. Finally, IR spectra of NMA in GP6P water are calculated from extended DFT/PMM-MD trajectories, in which the NMA is treated by three different DFT functionals (BP, BLYP, B3LYP). Method-specific frequency scaling factors are derived from DFT-MD simulations of isolated NMA. The DFT/PMM-MD simulations with GP6P and with the optimized LJ parameters then excellently predict the effects of aqueous solvation and deuteration observed in the IR spectra of NMA. As a result, the methods required to accurately compute such spectra by DFT/PMM-MD also for larger peptides in aqueous solution are now at hand.

  2. 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.

  3. 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.

  4. 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.

  5. Effect of Water Clustering on the Activity of Candida antarctica Lipase B in Organic Medium

    DEFF Research Database (Denmark)

    Banik, Sindrila Dutta; Nordblad, Mathias; Woodley, John M.

    2017-01-01

    The effect of initial water activity of MTBE (methyl tert-butyl ether) medium on CALB (Candida antarctica lipase B) catalyzed esterification reaction is investigated using experimental methods and classical molecular dynamics (MD) simulations. The experimental kinetic studies show that the initial...... reaction rate of CALB-catalyzed esterification reaction between butyric acid and ethanol decreases with increasing initial water activity of the medium. The highest rate of esterification is observed at the lowest water activity studied. MD simulations were performed to gain a molecular insight...... on the effect of initial water activity on the rate of CALB-catalyzed reaction. Our results show that hydration has an insignificant effect on the structure and flexibility of CALB. Rather, it appears that water molecules bind to certain regions ("hot spots") on the CALB surface and form clusters. The size...

  6. Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics.

    Science.gov (United States)

    Medders, Gregory R; Paesani, Francesco

    2015-03-10

    Vibrational spectroscopy is a powerful technique to probe the structure and dynamics of water. However, deriving an unambiguous molecular-level interpretation of the experimental spectral features remains a challenge due to the complexity of the underlying hydrogen-bonding network. In this contribution, we present an integrated theoretical and computational framework (named many-body molecular dynamics or MB-MD) that, by systematically removing uncertainties associated with existing approaches, enables a rigorous modeling of vibrational spectra of water from quantum dynamical simulations. Specifically, we extend approaches used to model the many-body expansion of interaction energies to develop many-body representations of the dipole moment and polarizability of water. The combination of these "first-principles" representations with centroid molecular dynamics simulations enables the simulation of infrared and Raman spectra of liquid water under ambient conditions that, without relying on any ad hoc parameters, are in good agreement with the corresponding experimental results. Importantly, since the many-body energy, dipole, and polarizability surfaces employed in the simulations are derived independently from accurate fits to correlated electronic structure data, MB-MD allows for a systematic analysis of the calculated spectra in terms of both electronic and dynamical contributions. The present analysis suggests that, while MB-MD correctly reproduces both the shifts and the shapes of the main spectroscopic features, an improved description of quantum dynamical effects possibly combined with a dissociable water potential may be necessary for a quantitative representation of the OH stretch band.

  7. Apple (Malus domestica) MdERF2 negatively affects ethylene biosynthesis during fruit ripening by suppressing MdACS1 transcription.

    Science.gov (United States)

    Li, Tong; Jiang, Zhongyu; Zhang, Lichao; Tan, Dongmei; Wei, Yun; Yuan, Hui; Li, Tianlai; Wang, Aide

    2016-12-01

    Ripening in climacteric fruit requires the gaseous phytohormone ethylene. Although ethylene signaling has been well studied, knowledge of the transcriptional regulation of ethylene biosynthesis is still limited. Here we show that an apple (Malus domestica) ethylene response factor, MdERF2, negatively affects ethylene biosynthesis and fruit ripening by suppressing the transcription of MdACS1, a gene that is critical for biosynthesis of ripening-related ethylene. Expression of MdERF2 was suppressed by ethylene during ripening of apple fruit, and we observed that MdERF2 bound to the promoter of MdACS1 and directly suppressed its transcription. Moreover, MdERF2 suppressed the activity of the promoter of MdERF3, a transcription factor that we found to bind to the MdACS1 promoter, thereby increasing MdACS1 transcription. We determined that the MdERF2 and MdERF3 proteins directly interact, and this interaction suppresses the binding of MdERF3 to the MdACS1 promoter. Moreover, apple fruit with transiently downregulated MdERF2 expression showed higher ethylene production and faster ripening. Our results indicate that MdERF2 negatively affects ethylene biosynthesis and fruit ripening in apple by suppressing the transcription of MdACS1 via multiple mechanisms, thereby acting as an antagonist of positive ripening regulators. Our findings offer a deep understanding of the transcriptional regulation of ethylene biosynthesis during climacteric fruit ripening. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  8. 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.

  9. Molecular dynamics simulations of surfactant and nanoparticle self-assembly at liquid-liquid interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Luo Mingxiang; Dai, Lenore L [Department of Chemical Engineering, Texas Tech University, Lubbock, TX 79409 (United States)

    2007-09-19

    We have performed molecular dynamics (MD) simulations to investigate self-assembly at water-trichloroethylene (TCE) interfaces with the emphasis on systems containing modified hydrocarbon nanoparticles (1.2 nm in diameter) and sodium dodecyl sulfate (SDS) surfactants. The nanoparticles and surfactants were first distributed randomly in the water phase. The MD simulations have clearly shown the progress of migration and final equilibrium of the SDS molecules at the water-TCE interfaces with the nanoparticles either at or in the vicinity of the interfaces. One unique feature is the 'attachment' of surfactant molecules to the nanoparticle clusters in the water phase followed by the 'detachment' at the water-TCE interfaces. At low concentrations of surfactants, the surfactants and nanoparticles co-equilibrate at the interfaces. However, the surfactants, at high concentrations, competitively dominate the interfaces and deplete nanoparticles away from the interfaces. The interfacial properties, such as interfacial thickness and interfacial tension, are significantly influenced by the presence of the surfactants, but not the nanoparticles. The order of the surfactants at the interfaces increases with increasing surfactant concentration, but is independent of nanoparticle concentration. Finally, the simulation has shown that surfactants can aggregate along the water-TCE interfaces, with and without the presence of nanoparticles.

  10. 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...

  11. 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.

  12. Separation based adsorption of ethanol-water mixture in azeotropic solution by single-walled carbon, boron-nitride and silicon-carbide nanotubes.

    Science.gov (United States)

    Taheri, Siavash; Lakmehsari, Muhammad Shadman; Soltanabadi, Azim

    2017-08-01

    The separation of the azeotropic ethanol-water mixture (95.57wt% ethanol) over a wide range of pressures (100-100000kPa) was studied on armchair SWCNTs, SWSiCNTs and SWBNNTs with different diameters at 351.30K using GCMC simulations. The GCMC results demonstrated that ethanol and water molecules form a monolayer single-file, chain together in the center of (6,6) SWCNT, while a spiral ring of ethanol and water is formed in the center of (8,8), (10,10) and (12,12) SWCNTs. It was found that in SWCNTs, the adsorption of ethanol reduces the function of pressure, while water adsorption increases its function. Water selectivity rises as a function of pressure. Also, in SWBNNTs, the adsorption of water increases as a function of pressure, while ethanol adsorption is almost constant. However, in the case of SWSiCNTs, ethanol and water adsorptions are very similar to those of SWBNNTs, whereas the adsorptivities of SWSiCNTs are more than those of SWBNNTs. Our findings regarding adsorption and slope of adsorption indicate that higher pressures are favorable for separating water and ethanol by SWCNTs, while SWBNNTs and SWSiCNTs are demonstrate higher ethanol adsorptivities in lower pressures. Also, MD simulations have been performed to study the microscopic structure and diffusion of binary mixtures of water and ethanol within SWCNTs, SWSiCNTs and SWBNNTs. The MD simulations imply that the oxygen atoms are highly well-organized around themselves. Also, the MD results illustrate a similar tendency for oxygen of water (OW) and oxygen of ethanol (OE) to the wall of the nanotubes in all the pressures. In addition, from the MD results, self-diffusion of water and ethanol in all nanotubes were calculated and discussed. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Thermophoretic transport of water nanodroplets confined in carbon nanotubes: the role of friction

    DEFF Research Database (Denmark)

    Oyarzua, Elton; Walther, Jens Honore; Zambrano, Harvey

    The development of efficient nanofluidic devices requires driving mechanisms that provide controlled transport of fluids through nanoconduits. Temperature gradients have been proposed as a mechanism to drive particles, fullerenes and nanodroplets inside carbon nanotubes (CNTs). In this work, molecular...... dynamics (MD) simulations are conducted to study thermophoresis of water nanodroplets inside CNTs. To gain insight into the interplay between the thermophoretic force acting on the droplet and the retarding liquid-solid friction, sets of constrained and unconstrained MD simulations are conducted...

  14. Md-miR156ab and Md-miR395 Target WRKY Transcription Factors to Influence Apple Resistance to Leaf Spot Disease.

    Science.gov (United States)

    Zhang, Qiulei; Li, Yang; Zhang, Yi; Wu, Chuanbao; Wang, Shengnan; Hao, Li; Wang, Shengyuan; Li, Tianzhong

    2017-01-01

    MicroRNAs (miRNAs) are key regulators of gene expression that post-transcriptionally regulate transcription factors involved in plant physiological activities. Little is known about the effects of miRNAs in disease resistance in apple ( Malus × domestica ). We globally profiled miRNAs in the apple cultivar Golden Delicious (GD) infected or not with the apple leaf spot fungus Alternaria alternaria f. sp. mali (ALT1), and identified 58 miRNAs that exhibited more than a 2-fold upregulation upon ALT1 infection. We identified a pair of miRNAs that target protein-coding genes involved in the defense response against fungal pathogens; Md-miR156ab targets a novel WRKY transcription factor, MdWRKYN1, which harbors a TIR and a WRKY domain. Md-miR395 targets another transcription factor, MdWRKY26, which contains two WRKY domains. Real-time PCR analysis showed that Md-miR156ab and Md-miR395 levels increased, while MdWRKYN1 and MdWRKY26 expression decreased in ALT1-inoculated GD leaves; furthermore, the overexpression of Md-miR156ab and Md-miR395 resulted in a significant reduction in MdWRKYN1 and MdWRKY26 expression. To investigate whether these miRNAs and their targets play a crucial role in plant defense, we overexpressed MdWRKYN1 or knocked down Md-miR156ab activity, which in both cases enhanced the disease resistance of the plants by upregulating the expression of the WRKY-regulated pathogenesis-related (PR) protein-encoding genes MdPR3-1, MdPR3-2, MdPR4, MdPR5, MdPR10-1 , and MdPR10-2 . In a similar analysis, we overexpressed MdWRKY26 or suppressed Md-miR395 activity, and found that many PR protein-encoding genes were also regulated by MdWRKY26 . In GD, ALT-induced Md-miR156ab and Md-miR395 suppress MdWRKYN1 and MdWRKY26 expression, thereby decreasing the expression of some PR genes, and resulting in susceptibility to ALT1.

  15. 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.

  16. 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

  17. Molecular dynamics simulation for PBR pebble tracking simulation via a random walk approach using Monte Carlo simulation.

    Science.gov (United States)

    Lee, Kyoung O; Holmes, Thomas W; Calderon, Adan F; Gardner, Robin P

    2012-05-01

    Using a Monte Carlo (MC) simulation, random walks were used for pebble tracking in a two-dimensional geometry in the presence of a biased gravity field. We investigated the effect of viscosity damping in the presence of random Gaussian fluctuations. The particle tracks were generated by Molecular Dynamics (MD) simulation for a Pebble Bed Reactor. The MD simulations were conducted in the interaction of noncohesive Hertz-Mindlin theory where the random walk MC simulation has a correlation with the MD simulation. This treatment can easily be extended to include the generation of transient gamma-ray spectra from a single pebble that contains a radioactive tracer. Then the inverse analysis thereof could be made to determine the uncertainty of the realistic measurement of transient positions of that pebble by any given radiation detection system designed for that purpose. Copyright © 2011 Elsevier Ltd. All rights reserved.

  18. 75 FR 80744 - Airworthiness Directives; McDonnell Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82...

    Science.gov (United States)

    2010-12-23

    ...-1203; Directorate Identifier 2010-NM-168-AD] RIN 2120-AA64 Airworthiness Directives; McDonnell Douglas... amends Sec. 39.13 by adding the following new airworthiness directive (AD): McDonnell Douglas Corporation... Douglas Corporation Model DC-9-81 (MD-81), DC-9-82 (MD-82), DC-9-83 (MD-83), DC-9-87 (MD-87) and MD-88...

  19. Uncommon structure making/breaking behaviour of cholinium taurate in water

    International Nuclear Information System (INIS)

    Gadžurić, Slobodan; Tot, Aleksandar; Armaković, Stevan; Armaković, Sanja; Panić, Jovana; Jović, Branislav; Vraneš, Milan

    2017-01-01

    Highlights: • Structuring of water in cholinium taurate ionic liquids was studied. • Nature of interactions were discussed. • Structure breaking properties were observed below and structure making properties above 300 K. • Molecular dynamics confirmed conclusions derived from experiments. - Abstract: Synthesis, volumetric and transport properties of the new third generation ionic liquid cholinium taurate, [Chol][Tau], are reported. Density, viscosity and electrical conductivity measurements of diluted aqueous solution of [Chol][Tau] were performed, while from the theoretical aspects density functional theory (DFT) calculations and molecular dynamics (MD) simulations have been applied in order to understand the nature of interactions and water structuring in the studied system. DFT approach was used to understand geometry and non-covalent interactions between [Chol] + and [Tau] − ions, while radial distribution functions (RDFs) obtained after MD simulations were applied in order to determine the parts of the ionic liquid that are most responsible for the interaction with water.

  20. Molecular dynamics simulations of the three-layer hydrate of Na-montmorillonite

    International Nuclear Information System (INIS)

    Holmboe, Michael; Bourg, Ian C.

    2012-01-01

    the size of hundreds to tens or hundreds of thousands particles, MD simulations can be used to reveal how dynamic processes on the macro-scale (such as laboratory-scale values of the EA of diffusion), arise from the molecular scale. In order to obtain accurate and realistic transport properties of solutes in clays, such as self-diffusion coefficients, sorption behavior and EA of diffusion, one must probe realistic and physically relevant geochemical systems. Many previous studies using molecular simulation techniques studied relatively small smectite/water systems ( 4 atoms) using 'frozen' smectite clay layers, in order to save computational time, whereas the use of fully flexible clay layers has been advocated by several authors. In this study we present a sensitivity analysis of MD simulations of the three-layer hydrate of Na-montmorillonite. We focus in particular on the self-diffusion coefficients and their temperature-dependence, as well as structural data for the three-layer hydration state, which is expected to be the predominant hydration state in the bentonite barrier in different concepts of geological nuclear waste disposal, such as the Swedish KBS-3 concept. We also present a methodology for calculating the EA of diffusion for solutes in the interlayer nano-pores for temperatures 278 to 353 K, correcting for system size effects inherent to MD simulations as well as viscosity related effects for the SPC/E water model. In brief, our methodology uses the versatile MD code LAMMPS with a rigid SPC/E water model and the CLAYFF force field, which is known to satisfyingly predict structural and thermodynamical properties of smectite interlayer water and exchangeable cations. The CLAYFF force field describes the non-bonded atomic partial charges together with the van der Waals parameters of the clay structural atoms, which in this study is a typical 2:1 Na + -exchanged smectite (Wyoming montmorillonite) containing a negative structural charge of 0.66/unit cell

  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. 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

  3. 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...

  4. 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...

  5. 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

  6. MD and FFM Electron Broadening for Warm and Dense Hydrogen Plasmas

    International Nuclear Information System (INIS)

    Ferri, S.; Calisti, A.; Mosse, C.; Talin, B.; Gonzalez, M. A.; Gigosos, M. A.

    2006-01-01

    Direct integration of the semi-classical evolution equation based on Molecular Dynamics simulations (MD) and the Frequency Fluctuation Model (FFM) have long been used to synthesize spectra accounting for ion dynamics. Cross comparisons of these approaches generally show results in good agreement. Recently, interest in low temperature (Te ∼ 1eV) and high density (Ne ∼ 1018 cm-3) hydrogen plasma spectroscopy has motivated extended applications of FFM. Arising discrepancies were found to originate in electron collision operators suggesting an improper use of impact approximations for warm and dense plasma conditions. In order to clarify this point, new useful cross comparisons between MD and FFM have been carried out for electron broadening

  7. 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.

  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. Preparing MD-PhD students for clinical rotations: navigating the interface between PhD and MD training.

    Science.gov (United States)

    Goldberg, Charles; Insel, Paul A

    2013-06-01

    Many aspects of MD-PhD training are not optimally designed to prepare students for their future roles as translational clinician-scientists. The transition between PhD research efforts and clinical rotations is one hurdle that must be overcome. MD-PhD students have deficits in clinical skills compared with those of their MD-only colleagues at the time of this transition. Reimmersion programs (RPs) targeted to MD-PhD students have the potential to help them navigate this transition.The authors draw on their experience creating and implementing an RP that incorporates multiple types of activities (clinical exam review, objective structured clinical examination, and supervised practice in patient care settings) designed to enhance the participants' skills and readiness for clinical efforts. On the basis of this experience, they note that MD-PhD students' time away from the clinical environment negatively affects their clinical skills, causing them to feel underprepared for clinical rotations. The authors argue that participation in an RP can help students feel more comfortable speaking with and examining patients and decrease their anxiety regarding clinical encounters. The authors propose that RPs can have positive outcomes for improving the transition from PhD to clinical MD training in dual-degree programs. Identifying and addressing this and other transitions need to be considered to improve the educational experience of MD-PhD students.

  10. 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.)

  11. 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.)

  12. 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

  13. 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

  14. 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

  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. 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.

  17. Combined Molecular Dynamics Simulation-Molecular-Thermodynamic Theory Framework for Predicting Surface Tensions.

    Science.gov (United States)

    Sresht, Vishnu; Lewandowski, Eric P; Blankschtein, Daniel; Jusufi, Arben

    2017-08-22

    A molecular modeling approach is presented with a focus on quantitative predictions of the surface tension of aqueous surfactant solutions. The approach combines classical Molecular Dynamics (MD) simulations with a molecular-thermodynamic theory (MTT) [ Y. J. Nikas, S. Puvvada, D. Blankschtein, Langmuir 1992 , 8 , 2680 ]. The MD component is used to calculate thermodynamic and molecular parameters that are needed in the MTT model to determine the surface tension isotherm. The MD/MTT approach provides the important link between the surfactant bulk concentration, the experimental control parameter, and the surfactant surface concentration, the MD control parameter. We demonstrate the capability of the MD/MTT modeling approach on nonionic alkyl polyethylene glycol surfactants at the air-water interface and observe reasonable agreement of the predicted surface tensions and the experimental surface tension data over a wide range of surfactant concentrations below the critical micelle concentration. Our modeling approach can be extended to ionic surfactants and their mixtures with both ionic and nonionic surfactants at liquid-liquid interfaces.

  18. 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.

  19. 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)

  20. Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

    KAUST Repository

    Kadoura, Ahmad

    2016-09-01

    This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method to replace correlations and equations of state in subsurface flow simulators. In order to accelerate MC simulations, a set of early rejection schemes (conservative, hybrid, and non-conservative) in addition to extrapolation methods through reweighting and reconstruction of pre-generated MC Markov chains were developed. Furthermore, an extensive study was conducted to investigate sorption and transport processes of methane, carbon dioxide, water, and their mixtures in the inorganic part of shale using both MC and MD simulations. These simulations covered a wide range of thermodynamic conditions, pore sizes, and fluid compositions shedding light on several interesting findings. For example, the possibility to have more carbon dioxide adsorbed with more preadsorbed water concentrations at relatively large basal spaces. The dissertation is divided into four chapters. The first chapter corresponds to the introductory part where a brief background about molecular simulation and motivations are given. The second chapter is devoted to discuss the theoretical aspects and methodology of the proposed MC speeding up techniques in addition to the corresponding results leading to the successful multi-scale simulation of the compressible single-phase flow scenario. In chapter 3, the results regarding our extensive study on shale gas at laboratory conditions are reported. At the fourth and last chapter, we end the dissertation with few concluding remarks highlighting the key findings and summarizing the future directions.

  1. 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

  2. Methodological issues in lipid bilayer simulations

    NARCIS (Netherlands)

    Anezo, C; de Vries, AH; Holtje, HD; Tieleman, DP; Marrink, SJ

    2003-01-01

    Methodological issues in molecular dynamics (MD) simulations, such as the treatment of long-range electrostatic interactions or the type of pressure coupling, have important consequences for the equilibrium properties observed. We report a series of long (up to 150 ns) MD simulations of

  3. 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

  4. 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.

  5. Tutorial: Determination of thermal boundary resistance by molecular dynamics simulations

    Science.gov (United States)

    Liang, Zhi; Hu, Ming

    2018-05-01

    Due to the high surface-to-volume ratio of nanostructured components in microelectronics and other advanced devices, the thermal resistance at material interfaces can strongly affect the overall thermal behavior in these devices. Therefore, the thermal boundary resistance, R, must be taken into account in the thermal analysis of nanoscale structures and devices. This article is a tutorial on the determination of R and the analysis of interfacial thermal transport via molecular dynamics (MD) simulations. In addition to reviewing the commonly used equilibrium and non-equilibrium MD models for the determination of R, we also discuss several MD simulation methods which can be used to understand interfacial thermal transport behavior. To illustrate how these MD models work for various interfaces, we will show several examples of MD simulation results on thermal transport across solid-solid, solid-liquid, and solid-gas interfaces. The advantages and drawbacks of a few other MD models such as approach-to-equilibrium MD and first-principles MD are also discussed.

  6. Studying pressure denaturation of a protein by molecular dynamics simulations.

    Science.gov (United States)

    Sarupria, Sapna; Ghosh, Tuhin; García, Angel E; Garde, Shekhar

    2010-05-15

    Many globular proteins unfold when subjected to several kilobars of hydrostatic pressure. This "unfolding-up-on-squeezing" is counter-intuitive in that one expects mechanical compression of proteins with increasing pressure. Molecular simulations have the potential to provide fundamental understanding of pressure effects on proteins. However, the slow kinetics of unfolding, especially at high pressures, eliminates the possibility of its direct observation by molecular dynamics (MD) simulations. Motivated by experimental results-that pressure denatured states are water-swollen, and theoretical results-that water transfer into hydrophobic contacts becomes favorable with increasing pressure, we employ a water insertion method to generate unfolded states of the protein Staphylococcal Nuclease (Snase). Structural characteristics of these unfolded states-their water-swollen nature, retention of secondary structure, and overall compactness-mimic those observed in experiments. Using conformations of folded and unfolded states, we calculate their partial molar volumes in MD simulations and estimate the pressure-dependent free energy of unfolding. The volume of unfolding of Snase is negative (approximately -60 mL/mol at 1 bar) and is relatively insensitive to pressure, leading to its unfolding in the pressure range of 1500-2000 bars. Interestingly, once the protein is sufficiently water swollen, the partial molar volume of the protein appears to be insensitive to further conformational expansion or unfolding. Specifically, water-swollen structures with relatively low radii of gyration have partial molar volume that are similar to that of significantly more unfolded states. We find that the compressibility change on unfolding is negligible, consistent with experiments. We also analyze hydration shell fluctuations to comment on the hydration contributions to protein compressibility. Our study demonstrates the utility of molecular simulations in estimating volumetric properties

  7. Going beyond clustering in MD trajectory analysis: an application to villin headpiece folding.

    Directory of Open Access Journals (Sweden)

    Aruna Rajan

    2010-04-01

    Full Text Available Recent advances in computing technology have enabled microsecond long all-atom molecular dynamics (MD simulations of biological systems. Methods that can distill the salient features of such large trajectories are now urgently needed. Conventional clustering methods used to analyze MD trajectories suffer from various setbacks, namely (i they are not data driven, (ii they are unstable to noise and changes in cut-off parameters such as cluster radius and cluster number, and (iii they do not reduce the dimensionality of the trajectories, and hence are unsuitable for finding collective coordinates. We advocate the application of principal component analysis (PCA and a non-metric multidimensional scaling (nMDS method to reduce MD trajectories and overcome the drawbacks of clustering. To illustrate the superiority of nMDS over other methods in reducing data and reproducing salient features, we analyze three complete villin headpiece folding trajectories. Our analysis suggests that the folding process of the villin headpiece is structurally heterogeneous.

  8. 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

  9. 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.

  10. The Structural Basis for Lipid and Endotoxin Binding in RP105-MD-1, and Consequences for Regulation of Host Lipopolysaccharide Sensitivity.

    Science.gov (United States)

    Ortiz-Suarez, Maite L; Bond, Peter J

    2016-01-05

    MD-1 is a member of the MD-2-related lipid-recognition (ML) family, and associates with RP105, a cell-surface protein that resembles Toll-like receptor 4 (TLR4). The RP105⋅MD-1 complex has been proposed to play a role in fine-tuning the innate immune response to endotoxin such as bacterial lipopolysaccharide (LPS) via TLR4⋅MD-2, but controversy surrounds its mechanism. We have used atomically detailed simulations to reveal the structural basis for ligand binding and consequent functional dynamics of MD-1 and the RP105 complex. We rationalize reports of endogenous phospholipid binding, by showing that they prevent collapse of the malleable MD-1 fold, before refining crystallographic models and uncovering likely binding modes for LPS analogs. Subsequent binding affinity calculations reveal that endotoxin specificity arises from the entropic cost of expanding the MD-1 cavity to accommodate bulky lipid tails, and support the role of MD-1 as a "sink" that sequesters endotoxin from TLR4 and stabilizes RP105/TLR4 interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. 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.

  12. 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...

  13. Molecular simulations of beta-amyloid protein near hydrated lipids (PECASE).

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Aidan Patrick; Han, Kunwoo (Texas A& M University, College Station, TX); Ford, David M. (Texas A& M University, College Station, TX)

    2005-12-01

    We performed molecular dynamics simulations of beta-amyloid (A{beta}) protein and A{beta} fragment(31-42) in bulk water and near hydrated lipids to study the mechanism of neurotoxicity associated with the aggregation of the protein. We constructed full atomistic models using Cerius2 and ran simulations using LAMMPS. MD simulations with different conformations and positions of the protein fragment were performed. Thermodynamic properties were compared with previous literature and the results were analyzed. Longer simulations and data analyses based on the free energy profiles along the distance between the protein and the interface are ongoing.

  14. Evaporation of tiny water aggregation on solid surfaces with different wetting properties.

    Science.gov (United States)

    Wang, Shen; Tu, Yusong; Wan, Rongzheng; Fang, Haiping

    2012-11-29

    The evaporation of a tiny amount of water on the solid surface with different wettabilities has been studied by molecular dynamics simulations. From nonequilibrium MD simulations, we found that, as the surface changed from hydrophobic to hydrophilic, the evaporation speed did not show a monotonic decrease as intuitively expected, but increased first, and then decreased after it reached a maximum value. The analysis of the simulation trajectory and calculation of the surface water interaction illustrate that the competition between the number of water molecules on the water-gas surface from where the water molecules can evaporate and the potential barrier to prevent those water molecules from evaporating results in the unexpected behavior of the evaporation. This finding is helpful in understanding the evaporation on biological surfaces, designing artificial surfaces of ultrafast water evaporating, or preserving water in soil.

  15. MdMYB9 and MdMYB11 are involved in the regulation of the JA-induced biosynthesis of anthocyanin and proanthocyanidin in apples.

    Science.gov (United States)

    An, Xiu-Hong; Tian, Yi; Chen, Ke-Qin; Liu, Xiao-Juan; Liu, Dan-Dan; Xie, Xing-Bin; Cheng, Cun-Gang; Cong, Pei-Hua; Hao, Yu-Jin

    2015-04-01

    Anthocyanin and proanthocyanidin (PA) are important secondary metabolites and beneficial to human health. Their biosynthesis is induced by jasmonate (JA) treatment and regulated by MYB transcription factors (TFs). However, which and how MYB TFs regulate this process is largely unknown in apple. In this study, MdMYB9 and MdMYB11 which were induced by methyl jasmonate (MeJA) were functionally characterized. Overexpression of MdMYB9 or MdMYB11 promoted not only anthocyanin but also PA accumulation in apple calluses, and the accumulation was further enhanced by MeJA. Subsequently, yeast two-hybrid, pull-down and bimolecular fluorescence complementation assays showed that both MYB proteins interact with MdbHLH3. Moreover, Jasmonate ZIM-domain (MdJAZ) proteins interact with MdbHLH3. Furthermore, chromatin immunoprecipitation-quantitative PCR and yeast one-hybrid assays demonstrated that both MdMYB9 and MdMYB11 bind to the promoters of ANS, ANR and LAR, whereas MdbHLH3 is recruited to the promoters of MdMYB9 and MdMYB11 and regulates their transcription. In addition, transient expression assays indicated that overexpression of MdJAZ2 inhibits the recruitment of MdbHLH3 to the promoters of MdMYB9 and MdMYB11. Our findings provide new insight into the mechanism of how MeJA regulates anthocyanin and PA accumulation in apple. © The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  16. 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 ...

  17. Molecular dynamics simulation of radiation grafted FEP films as proton exchange membranes: Effects of the side chain length

    DEFF Research Database (Denmark)

    Li, Xue; Zhao, Yang; Li, Weiwei

    2017-01-01

    In order to study the microstructure of the prepared potential proton exchange membrane (PEM), molecular dynamics (MD) simulations were used to lucubrate the transport behavior of water molecules and hydronium ions inside the hydrated sulfonated styrene grafted fluorinated ethylene propylene (FEP...... whereas larger water clusters formed. The results of the mean square displacements (MSDs) show that the proton conductivities of the membranes with the proposed side chain lengths were about three fifths of the experimental data, of which the membrane with side chain length of 7 sulfonic styrene units...... was supposed to exhibit the highest proton conductivity, that is 115.69 mS cm-1. All of the supposed membrane models presented good proton conductivity that could definitely meet the application requirements of the proton exchange membranes. The MD simulations can provide an insight to the chain structure...

  18. Synergistic Applications of MD and NMR for the Study of Biological Systems

    Directory of Open Access Journals (Sweden)

    Olivier Fisette

    2012-01-01

    same time, theoretical and computational approaches gain in reliability and their field of application widens. In this short paper, we discuss recent advances in the areas of solution nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations that were made possible by the combination of both methods, that is, through their synergistic use. We present the main NMR observables and parameters that can be computed from simulations, and how they are used in a variety of complementary applications, including dynamics studies, model-free analysis, force field validation, and structural studies.

  19. 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...

  20. 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...

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. A molecular dynamics simulation code ISIS

    International Nuclear Information System (INIS)

    Kambayashi, Shaw

    1992-06-01

    Computer simulation based on the molecular dynamics (MD) method has become an important tool complementary to experiments and theoretical calculations in a wide range of scientific fields such as physics, chemistry, biology, and so on. In the MD method, the Newtonian equations-of-motion of classical particles are integrated numerically to reproduce a phase-space trajectory of the system. In the 1980's, several new techniques have been developed for simulation at constant-temperature and/or constant-pressure in convenient to compare result of computer simulation with experimental results. We first summarize the MD method for both microcanonical and canonical simulations. Then, we present and overview of a newly developed ISIS (Isokinetic Simulation of Soft-spheres) code and its performance on various computers including vector processors. The ISIS code has a capability to make a MD simulation under constant-temperature condition by using the isokinetic constraint method. The equations-of-motion is integrated by a very accurate fifth-order finite differential algorithm. The bookkeeping method is also utilized to reduce the computational time. Furthermore, the ISIS code is well adopted for vector processing: Speedup ratio ranged from 16 to 24 times is obtained on a VP2600/10 vector processor. (author)

  6. Molecular dynamics simulations and applications in computational toxicology and nanotoxicology.

    Science.gov (United States)

    Selvaraj, Chandrabose; Sakkiah, Sugunadevi; Tong, Weida; Hong, Huixiao

    2018-02-01

    Nanotoxicology studies toxicity of nanomaterials and has been widely applied in biomedical researches to explore toxicity of various biological systems. Investigating biological systems through in vivo and in vitro methods is expensive and time taking. Therefore, computational toxicology, a multi-discipline field that utilizes computational power and algorithms to examine toxicology of biological systems, has gained attractions to scientists. Molecular dynamics (MD) simulations of biomolecules such as proteins and DNA are popular for understanding of interactions between biological systems and chemicals in computational toxicology. In this paper, we review MD simulation methods, protocol for running MD simulations and their applications in studies of toxicity and nanotechnology. We also briefly summarize some popular software tools for execution of MD simulations. Published by Elsevier Ltd.

  7. The effects of charge, polymerization, and cluster size on the diffusivity of dissolved Si species in pore water

    Science.gov (United States)

    Yokoyama, Tadashi; Sakuma, Hiroshi

    2018-03-01

    Silicon (Si) is the most abundant cation in crustal rocks. The charge and degree of polymerization of dissolved Si significantly change depending on solution pH and Si concentration. We used molecular dynamics (MD) simulations to predict the self-diffusion coefficients of dissolved Si, DSi, for 15 monomeric and polymeric species at ambient temperature. The results showed that DSi decreased with increasing negative charge and increasing degree of polymerization. The relationship between DSi and charge (Z) can be expressed by DSi/10-6 = 2.0 + 9.8e0.47Z, and that between DSi and number of polymerization (NSi) by DSi/10-6 = 9.7/NSi0.56. The results also revealed that multiple Si molecules assembled into a cluster and D decreased as the cluster size increased. Experiments to evaluate the diffusivity of Si in pore water revealed that the diffusion coefficient decreased with increasing Si concentration, a result consistent with the MD simulations. Simulation results can now be used to quantitatively assess water-rock interactions and water-concrete reactions over a wide range of environmentally relevant conditions.

  8. Low-mass molecular dynamics simulation: A simple and generic technique to enhance configurational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Yuan-Ping, E-mail: pang@mayo.edu

    2014-09-26

    Highlights: • Reducing atomic masses by 10-fold vastly improves sampling in MD simulations. • CLN025 folded in 4 of 10 × 0.5-μs MD simulations when masses were reduced by 10-fold. • CLN025 folded as early as 96.2 ns in 1 of the 4 simulations that captured folding. • CLN025 did not fold in 10 × 0.5-μs MD simulations when standard masses were used. • Low-mass MD simulation is a simple and generic sampling enhancement technique. - Abstract: CLN025 is one of the smallest fast-folding proteins. Until now it has not been reported that CLN025 can autonomously fold to its native conformation in a classical, all-atom, and isothermal–isobaric molecular dynamics (MD) simulation. This article reports the autonomous and repeated folding of CLN025 from a fully extended backbone conformation to its native conformation in explicit solvent in multiple 500-ns MD simulations at 277 K and 1 atm with the first folding event occurring as early as 66.1 ns. These simulations were accomplished by using AMBER forcefield derivatives with atomic masses reduced by 10-fold on Apple Mac Pros. By contrast, no folding event was observed when the simulations were repeated using the original AMBER forcefields of FF12SB and FF14SB. The results demonstrate that low-mass MD simulation is a simple and generic technique to enhance configurational sampling. This technique may propel autonomous folding of a wide range of miniature proteins in classical, all-atom, and isothermal–isobaric MD simulations performed on commodity computers—an important step forward in quantitative biology.

  9. 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...

  10. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  11. 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.

  12. Oxide/water interfaces: how the surface chemistry modifies interfacial water properties

    International Nuclear Information System (INIS)

    Gaigeot, Marie-Pierre; Sprik, Michiel; Sulpizi, Marialore

    2012-01-01

    The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, ‘ice-like’ and ‘liquid-like’ features in these spectra are interpreted as the result of hydrogen bonds of different strengths between surface silanols/aluminols and water. (paper)

  13. Cosurfactants lower surface tension of the diglyceride/water interface : A molecular dynamics study

    NARCIS (Netherlands)

    vanBuuren, AR; Tieleman, DP; deVlieg, J; Berendsen, HJC

    1996-01-01

    We performed molecular dynamics (MD) simulations of bulk 1,2-dilauroyl-sn-glycerol (DLG) systems in contact with a water layer. In the DLG oil phase cosurfactants were placed with increasing concentration: 1-monolauroyl-sn-glycerol (1MG), 2-monolauroylglycerol (2MG), and dodecanoic acid (FA, fatty

  14. Annual International Meeting on Medical Simulation (5th); Simulating Change Together, Held at the Radisson Miami Florida, on January 13-16, 2005

    Science.gov (United States)

    2005-02-01

    Challenging Superiors in the Healthcare Environment: The Two-Challenge Center for Medical Simulation Rule IMMS Singh Shashank Trauma and Awareness Pen...Rochester * Dallas Rochester MN Rochester NY Dallas TX SMartin Eason MD JD Marc Horowitz MD - Swati Argarwal, MD ETSU University of NM Stanford...Murphy, MD Simluation-based training allows educators in medicine to finally Swati Argarwal, MD address the needs of the adult learner. This high

  15. 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

  16. The small ubiquitin-like modifier E3 ligase MdSIZ1 promotes anthocyanin accumulation by sumoylating MdMYB1 under low-temperature conditions in apple.

    Science.gov (United States)

    Zhou, Li-Jie; Li, Yuan-Yuan; Zhang, Rui-Fen; Zhang, Chun-Ling; Xie, Xing-Bin; Zhao, Cheng; Hao, Yu-Jin

    2017-10-01

    MdMYB1 acts as a crucial component of the MYB-bHLH-WD40 complex to regulate anthocyanin biosynthesis in red-skinned apples (Malus domestica), but little is known about its post-translational regulation. Here, a small ubiquitin-like modifier E3 ligase MdSIZ1 was screened out as an MdMYB1-interacting protein with a yeast two-hybridization approach. The interaction between MdSIZ1 and MdMYB1 was further verified with pull-down and CoIP assays. Furthermore, it was found that MdSIZ1 directly sumoylated MdMYB1 proteins in vivo and in vitro, especially under moderately low temperature (17 °C) conditions, and that this sumoylation was required for MdMYB1 protein stability. Moreover, the transcription level of MdSIZ1 gene was remarkably induced by low temperature and phosphorus deficiency, and MdSIZ1 overexpression exerted a large positive influence on anthocyanin accumulation and red fruit coloration, suggesting its important role in the regulation of anthocyanin biosynthesis under stress conditions. Our findings reveal an important role for a small ubiquitin-like modifier modification of MYB transcription factors in regulation of anthocyanin biosynthesis in plants. © 2017 John Wiley & Sons Ltd.

  17. Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

    Science.gov (United States)

    Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

    2017-10-12

    Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

  18. MdCOP1 Ubiquitin E3 Ligases Interact with MdMYB1 to Regulate Light-Induced Anthocyanin Biosynthesis and Red Fruit Coloration in Apple1[W][OA

    Science.gov (United States)

    Li, Yuan-Yuan; Mao, Ke; Zhao, Cheng; Zhao, Xian-Yan; Zhang, Hua-Lei; Shu, Huai-Rui; Hao, Yu-Jin

    2012-01-01

    MdMYB1 is a crucial regulator of light-induced anthocyanin biosynthesis and fruit coloration in apple (Malus domestica). In this study, it was found that MdMYB1 protein accumulated in the light but degraded via a ubiquitin-dependent pathway in the dark. Subsequently, the MdCOP1-1 and MdCOP1-2 genes were isolated from apple fruit peel and were functionally characterized in the Arabidopsis (Arabidopsis thaliana) cop1-4 mutant. Yeast (Saccharomyces cerevisiae) two-hybrid, bimolecular fluorescence complementation, and coimmunoprecipitation assays showed that MdMYB1 interacts with the MdCOP1 proteins. Furthermore, in vitro and in vivo experiments indicated that MdCOP1s are necessary for the ubiquitination and degradation of MdMYB1 protein in the dark and are therefore involved in the light-controlled stability of the MdMYB1 protein. Finally, a viral vector-based transformation approach demonstrated that MdCOP1s negatively regulate the peel coloration of apple fruits by modulating the degradation of the MdMYB1 protein. Our findings provide new insight into the mechanism by which light controls anthocyanin accumulation and red fruit coloration in apple and even other plant species. PMID:22855936

  19. Lipid peroxidation and water penetration in lipid bilayers

    DEFF Research Database (Denmark)

    Conte, Elena; Megli, Francesco Maria; Khandelia, Himanshu

    2012-01-01

    to the hydroperoxide groups to interact with the nitroxide at the methyl-terminal, confirming that the H-bonds experimentally observed are due to increased water penetration in the bilayer. The EPR and MD data on model membranes demonstrate that cell membrane damage by oxidative stress cause alteration of water......(zz) parameters revealed that OHPLPC, but mostly HpPLPC, induced a measurable increase in polarity and H-bonding propensity in the central region of the bilayer. Molecular dynamics simulation performed on 16-DSA in the PLPC-HpPLPC bilayer revealed that water molecules are statistically favored with respect...

  20. Modeling complex and multi-component food systems in molecular dynamics simulations on the example of chocolate conching.

    Science.gov (United States)

    Greiner, Maximilian; Sonnleitner, Bettina; Mailänder, Markus; Briesen, Heiko

    2014-02-01

    Additional benefits of foods are an increasing factor in the consumer's purchase. To produce foods with the properties the consumer demands, understanding the micro- and nanostructure is becoming more important in food research today. We present molecular dynamics (MD) simulations as a tool to study complex and multi-component food systems on the example of chocolate conching. The process of conching is chosen because of the interesting challenges it provides: the components (fats, emulsifiers and carbohydrates) contain diverse functional groups, are naturally fluctuating in their chemical composition, and have a high number of internal degrees of freedom. Further, slow diffusion in the non-aqueous medium is expected. All of these challenges are typical to food systems in general. Simulation results show the suitability of present force fields to correctly model the liquid and crystal density of cocoa butter and sucrose, respectively. Amphiphilic properties of emulsifiers are observed by micelle formation in water. For non-aqueous media, pulling simulations reveal high energy barriers for motion in the viscous cocoa butter. The work for detachment of an emulsifier from the sucrose crystal is calculated and matched with detachment of the head and tail groups separately. Hydrogen bonding is shown to be the dominant interaction between the emulsifier and the crystal surface. Thus, MD simulations are suited to model the interaction between the emulsifier and sugar crystal interface in non-aqueous media, revealing detailed information about the structuring and interactions on a molecular level. With interaction parameters being available for a wide variety of chemical groups, MD simulations are a valuable tool to understand complex and multi-component food systems in general. MD simulations provide a substantial benefit to researchers to verify their hypothesis in dynamic simulations with an atomistic resolution. Rapid rise of computational resources successively

  1. Development of a quantum chemical molecular dynamics tribochemical simulator and its application to tribochemical reaction dynamics of lubricant additives

    International Nuclear Information System (INIS)

    Onodera, T; Tsuboi, H; Hatakeyama, N; Endou, A; Miyamoto, A; Miura, R; Takaba, H; Suzuki, A; Kubo, M

    2010-01-01

    Tribology at the atomistic and molecular levels has been theoretically studied by a classical molecular dynamics (MD) method. However, this method inherently cannot simulate the tribochemical reaction dynamics because it does not consider the electrons in nature. Although the first-principles based MD method has recently been used for understanding the chemical reaction dynamics of several molecules in the tribology field, the method cannot simulate the tribochemical reaction dynamics of a large complex system including solid surfaces and interfaces due to its huge computation costs. On the other hand, we have developed a quantum chemical MD tribochemical simulator on the basis of a hybrid tight-binding quantum chemical/classical MD method. In the simulator, the central part of the chemical reaction dynamics is calculated by the tight-binding quantum chemical MD method, and the remaining part is calculated by the classical MD method. Therefore, the developed tribochemical simulator realizes the study on tribochemical reaction dynamics of a large complex system, which cannot be treated by using the conventional classical MD or the first-principles MD methods. In this paper, we review our developed quantum chemical MD tribochemical simulator and its application to the tribochemical reaction dynamics of a few lubricant additives

  2. 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

  3. 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

  4. A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums

    Science.gov (United States)

    Ion, Bogdan F.; Bushnell, Eric A. C.; De Luna, Phil; Gauld, James W.

    2012-01-01

    Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2 + Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2 + intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. PMID:23202934

  5. A Molecular Dynamics (MD and Quantum Mechanics/Molecular Mechanics (QM/MM Study on Ornithine Cyclodeaminase (OCD: A Tale of Two Iminiums

    Directory of Open Access Journals (Sweden)

    James W. Gauld

    2012-10-01

    Full Text Available Ornithine cyclodeaminase (OCD is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD and a hybrid quantum mechanics/molecular mechanics (QM/MM method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline.

  6. The AINTEGUMENTA genes, MdANT1 and MdANT2, are associated with the regulation of cell production during fruit growth in apple (Malus × domestica Borkh.).

    Science.gov (United States)

    Dash, Madhumita; Malladi, Anish

    2012-06-25

    Fruit growth in apple (Malus × domestica Borkh.) is mediated by cell production and expansion. Genes involved in regulating these processes and thereby fruit growth, are not well characterized. We hypothesized that the apple homolog(s) of AINTEGUMENTA (ANT), an APETALA2-repeat containing transcription factor, regulates cell production during fruit growth in apple. Two ANT genes, MdANT1 and MdANT2, were isolated from apple and their expression was studied during multiple stages of fruit development. MdANT1 and MdANT2 expression was high during early fruit growth coincident with the period of cell production, rapidly declined during exit from cell production, and remained low during the rest of fruit development. The effects of increase in carbohydrate availability during fruit growth were characterized. Increase in carbohydrate availability enhanced fruit growth largely through an increase in cell production. Expression of MdANT1 and MdANT2 increased sharply by up to around 5-fold in response to an increase in carbohydrate availability. Expression of the ANT genes was compared across two apple genotypes, 'Gala' and 'Golden Delicious Smoothee' (GS), which differ in the extent of fruit growth, largely due to differences in cell production. In comparison to 'Gala', the larger fruit-size genotype, GS, displayed higher levels and a longer duration of MdANT1 and MdANT2 expression. Expression of the ANTs and cell cycle genes in the fruit core and cortex tissues isolated using laser capture microdissection was studied. During early fruit growth, expression of the MdANTs was higher within the cortex, the tissue that constitutes the majority of the fruit. Additionally, MdANT1 and MdANT2 expression was positively correlated with that of A- and B-type CYCLINS, B-type CYCLIN-DEPENDENT-KINASES (CDKBs) and MdDEL1. Multiple lines of evidence from this study suggest that MdANT1 and MdANT2 regulate cell production during fruit growth in apple. ANTs may coordinate the expression of

  7. Property Analysis of Exfoliated Graphite Nanoplatelets Modified Asphalt Model Using Molecular Dynamics (MD Method

    Directory of Open Access Journals (Sweden)

    Hui Yao

    2017-01-01

    Full Text Available This Molecular Dynamics (MD simulation paper presents a physical property comparison study between exfoliated graphite nanoplatelets (xGNP modified and control asphalt models, including density, glass transition temperature, viscosity and thermal conductivity. The three-component control asphalt model consists of asphaltenes, aromatics, and saturates based on previous references. The xGNP asphalt model was built by incorporating an xGNP and control asphalt model and controlling mass ratios to represent the laboratory prepared samples. The Amber Cornell Extension Force Field (ACEFF was used with assigned molecular electro-static potential (ESP charge from NWChem analysis. After optimization and ensemble relaxation, the properties of the control and xGNP modified asphalt models were computed and analyzed using the MD method. The MD simulated results have a similar trend as the test results. The property analysis showed that: (1 the density of the xGNP modified model is higher than that of the control model; (2 the glass transition temperature of the xGNP modified model is closer to the laboratory data of the Strategic Highway Research Program (SHRP asphalt binders than that of the control model; (3 the viscosities of the xGNP modified model at different temperatures are higher than those of the control model, and it coincides with the trend in the laboratory data; (4 the thermal conductivities of the xGNP modified asphalt model are higher than those of the control asphalt model at different temperatures, and it is consistent with the trend in the laboratory data.

  8. Theoretical analysis of the domain-swapped dimerization of cytochrome c: An MD and 3D-RISM approach

    Science.gov (United States)

    Yoshida, Norio; Higashi, Masahiro; Motoki, Hideyoshi; Hirota, Shun

    2018-01-01

    The structural stability of a cytochrome c domain-swapped dimer compared with that of the monomer was investigated by molecular dynamics (MD) simulations and by three-dimensional reference interaction site model (3D-RISM) theory. The structural fluctuation and structural energy of cytochrome c were treated by MD simulations, and the solvation thermodynamics was treated by 3D-RISM theory. The domain-swapped dimer state is slightly less stable than the monomer state, which is consistent with experimental observations; the total free energy difference is calculated as 25 kcal mol-1. The conformational change and translational/rotational entropy change contribute to the destabilization of the dimer, whereas the hydration and vibrational entropy contribute to the stabilization. Further analyses on the residues located at the hinge loop for swapping were conducted, and the results reveal details at the molecular level of the structural and interaction changes upon dimerization.

  9. Note: Recombination of H+ and OH− ions along water wires

    International Nuclear Information System (INIS)

    Lee, Song Hi; Rasaiah, Jayendran C.

    2013-01-01

    Transport and recombination of hydrogen and hydroxide ions along a hydrogen-bonded water wire are studied by molecular dynamics simulation using a dissociating model for water. The results are compared with a recent CP-MD study of neutralization in bulk water [A. Hassanali, M. K. Prakrash, H. Eshet, and M. Parrinello, Proc. Natl. Acad. Sci. U.S.A. 108, 20410 (2011)]. The translocation of H + and OH − along the wire is faster than in the bulk water, followed by compression of the water wire when two water molecules separate the transported ions. Neutralization occurs with the concerted transfer of three protons as in the bulk water, followed by energy dissipation along the water chain

  10. Effect of Water Clustering on the Activity of Candida antarctica Lipase B in Organic Medium

    Directory of Open Access Journals (Sweden)

    Sindrila Dutta Banik

    2017-07-01

    Full Text Available The effect of initial water activity of MTBE (methyl tert-butyl ether medium on CALB (Candida antarctica lipase B catalyzed esterification reaction is investigated using experimental methods and classical molecular dynamics (MD simulations. The experimental kinetic studies show that the initial reaction rate of CALB-catalyzed esterification reaction between butyric acid and ethanol decreases with increasing initial water activity of the medium. The highest rate of esterification is observed at the lowest water activity studied. MD simulations were performed to gain a molecular insight on the effect of initial water activity on the rate of CALB-catalyzed reaction. Our results show that hydration has an insignificant effect on the structure and flexibility of CALB. Rather, it appears that water molecules bind to certain regions (“hot spots” on the CALB surface and form clusters. The size of the water clusters at these hot spot regions gradually increase and expand with increasing water activity. Consequently, the surface area of CALB covered by the water molecules also increases. Specifically, our results indicate that a particular water cluster located close to the active site partially cover the binding pocket of substrate at high water activity. As a consequence, the effective concentration of substrate at the catalytic site decreases. Therefore, the reaction rate slows down with increasing water activity, which correlates well with the observed decrease in the experimentally determined initial reaction rate.

  11. 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…

  12. 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.

  13. Simulated tempering distributed replica sampling: A practical guide to enhanced conformational sampling

    Energy Technology Data Exchange (ETDEWEB)

    Rauscher, Sarah; Pomes, Regis, E-mail: pomes@sickkids.ca

    2010-11-01

    Simulated tempering distributed replica sampling (STDR) is a generalized-ensemble method designed specifically for simulations of large molecular systems on shared and heterogeneous computing platforms [Rauscher, Neale and Pomes (2009) J. Chem. Theor. Comput. 5, 2640]. The STDR algorithm consists of an alternation of two steps: (1) a short molecular dynamics (MD) simulation; and (2) a stochastic temperature jump. Repeating these steps thousands of times results in a random walk in temperature, which allows the system to overcome energetic barriers, thereby enhancing conformational sampling. The aim of the present paper is to provide a practical guide to applying STDR to complex biomolecular systems. We discuss the details of our STDR implementation, which is a highly-parallel algorithm designed to maximize computational efficiency while simultaneously minimizing network communication and data storage requirements. Using a 35-residue disordered peptide in explicit water as a test system, we characterize the efficiency of the STDR algorithm with respect to both diffusion in temperature space and statistical convergence of structural properties. Importantly, we show that STDR provides a dramatic enhancement of conformational sampling compared to a canonical MD simulation.

  14. Ectopically expressing MdPIP1;3, an aquaporin gene, increased fruit size and enhanced drought tolerance of transgenic tomatoes.

    Science.gov (United States)

    Wang, Lin; Li, Qing-Tian; Lei, Qiong; Feng, Chao; Zheng, Xiaodong; Zhou, Fangfang; Li, Lingzi; Liu, Xuan; Wang, Zhi; Kong, Jin

    2017-12-19

    Water deficit severely reduces apple growth and production, is detrimental to fruit quality and size. This problem is exacerbated as global warming is implicated in producing more severe drought stress. Thus water-efficiency has becomes the major target for apple breeding. A desired apple tree can absorb and transport water efficiently, which not only confers improved drought tolerance, but also guarantees fruit size for higher income returns. Aquaporins, as water channels, control water transportation across membranes and can regulate water flow by changing their amount and activity. The exploration of molecular mechanism of water efficiency and the gene wealth will pave a way for molecular breeding of drought tolerant apple tree. In the current study, we screened out a drought inducible aquaporin gene MdPIP1;3, which specifically enhanced its expression during fruit expansion in 'Fuji' apple (Malus domestica Borkh. cv. Red Fuji). It localized on plasma membranes and belonged to PIP1 subfamily. The tolerance to drought stress enhanced in transgenic tomato plants ectopically expressing MdPIP1;3, showing that the rate of losing water in isolated transgenic leaves was slower than wild type, and stomata of transgenic plants closed sensitively to respond to drought compared with wild type. Besides, length and diameter of transgenic tomato fruits increased faster than wild type, and in final, fruit sizes and fresh weights of transgenic tomatoes were bigger than wild type. Specially, in cell levels, fruit cell size from transgenic tomatoes was larger than wild type, showing that cell number per mm 2 in transgenic fruits was less than wild type. Altogether, ectopically expressing MdPIP1;3 enhanced drought tolerance of transgenic tomatoes partially via reduced water loss controlled by stomata closure in leaves. In addition, the transgenic tomato fruits are larger and heavier with larger cells via more efficient water transportation across membranes. Our research will

  15. Mixed quantum/classical approach to OH-stretch inelastic incoherent neutron scattering spectroscopy for ambient and supercooled liquid water and ice Ih

    Energy Technology Data Exchange (ETDEWEB)

    Shi, L.; Skinner, J. L. [Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706 (United States)

    2015-07-07

    OH-stretch inelastic incoherent neutron scattering (IINS) has been measured to determine the vibrational density of states (VDOS) in the OH-stretch region for liquid water, supercooled water, and ice Ih, providing complementary information to IR and Raman spectroscopies about hydrogen bonding in these phases. In this work, we extend the combined electronic-structure/molecular-dynamics (ES/MD) method, originally developed by Skinner and co-workers to simulate OH-stretch IR and Raman spectra, to the calculation of IINS spectra with small k values. The agreement between theory and experiment in the limit k → 0 is reasonable, further validating the reliability of the ES/MD method in simulating OH-stretch spectroscopy in condensed phases. The connections and differences between IINS and IR spectra are analyzed to illustrate the advantages of IINS over IR in estimating the OH-stretch VDOS.

  16. Mixed quantum/classical approach to OH-stretch inelastic incoherent neutron scattering spectroscopy for ambient and supercooled liquid water and ice Ih

    International Nuclear Information System (INIS)

    Shi, L.; Skinner, J. L.

    2015-01-01

    OH-stretch inelastic incoherent neutron scattering (IINS) has been measured to determine the vibrational density of states (VDOS) in the OH-stretch region for liquid water, supercooled water, and ice Ih, providing complementary information to IR and Raman spectroscopies about hydrogen bonding in these phases. In this work, we extend the combined electronic-structure/molecular-dynamics (ES/MD) method, originally developed by Skinner and co-workers to simulate OH-stretch IR and Raman spectra, to the calculation of IINS spectra with small k values. The agreement between theory and experiment in the limit k → 0 is reasonable, further validating the reliability of the ES/MD method in simulating OH-stretch spectroscopy in condensed phases. The connections and differences between IINS and IR spectra are analyzed to illustrate the advantages of IINS over IR in estimating the OH-stretch VDOS

  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. 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. 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.

  20. Apple MdACS6 Regulates Ethylene Biosynthesis During Fruit Development Involving Ethylene-Responsive Factor.

    Science.gov (United States)

    Li, Tong; Tan, Dongmei; Liu, Zhi; Jiang, Zhongyu; Wei, Yun; Zhang, Lichao; Li, Xinyue; Yuan, Hui; Wang, Aide

    2015-10-01

    Ethylene biosynthesis in plants involves different 1-aminocyclopropane-1-carboxylic acid synthase (ACS) genes. The regulation of each ACS gene during fruit development is unclear. Here, we characterized another apple (Malus×domestica) ACS gene, MdACS6. The transcript of MdACS6 was observed not only in fruits but also in other tissues. During fruit development, MdACS6 was initiated at a much earlier stage, whereas MdACS3a and MdACS1 began to be expressed at 35 d before harvest and immediateley after harvest, respectively. Moreover, the enzyme activity of MdACS6 was significantly lower than that of MdACS3a and MdACS1, accounting for the low ethylene biosynthesis in young fruits. Overexpression of MdACS6 (MdACS6-OE) by transient assay in apple showed enhanced ethylene production, and MdACS3a was induced in MdACS6-OE fruits but not in control fruits. In MdACS6 apple fruits silenced by the virus-induced gene silencing (VIGS) system (MdACS6-AN), neither ethylene production nor MdACS3a transcript was detectable. In order to explore the mechanism through which MdACS3a was induced in MdACS6-OE fruits, we investigated the expression of apple ethylene-responsive factor (ERF) genes. The results showed that the expression of MdERF2 was induced in MdACS6-OE fruits and inhibited in MdACS6-AN fruits. Yeast one-hybrid assay showed that MdERF2 protein could bind to the promoter of MdACS3a. Moreover, down-regulation of MdERF2 in apple flesh callus led to a decrease of MdACS3a expression, demonstrating the regulation of MdERF2 on MdACS3a. The mechanism through which MdACS6 regulates the action of MdACS3a was discussed. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  1. Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.

    Directory of Open Access Journals (Sweden)

    Kecheng Yang

    Full Text Available Sampling enrichment toward a target state, an analogue of the improvement of sampling efficiency (SE, is critical in both the refinement of protein structures and the generation of near-native structure ensembles for the exploration of structure-function relationships. We developed a hybrid molecular dynamics (MD-Monte Carlo (MC approach to enrich the sampling toward the target structures. In this approach, the higher SE is achieved by perturbing the conventional MD simulations with a MC structure-acceptance judgment, which is based on the coincidence degree of small angle x-ray scattering (SAXS intensity profiles between the simulation structures and the target structure. We found that the hybrid simulations could significantly improve SE by making the top-ranked models much closer to the target structures both in the secondary and tertiary structures. Specifically, for the 20 mono-residue peptides, when the initial structures had the root-mean-squared deviation (RMSD from the target structure smaller than 7 Å, the hybrid MD-MC simulations afforded, on average, 0.83 Å and 1.73 Å in RMSD closer to the target than the parallel MD simulations at 310K and 370K, respectively. Meanwhile, the average SE values are also increased by 13.2% and 15.7%. The enrichment of sampling becomes more significant when the target states are gradually detectable in the MD-MC simulations in comparison with the parallel MD simulations, and provide >200% improvement in SE. We also performed a test of the hybrid MD-MC approach in the real protein system, the results showed that the SE for 3 out of 5 real proteins are improved. Overall, this work presents an efficient way of utilizing solution SAXS to improve protein structure prediction and refinement, as well as the generation of near native structures for function annotation.

  2. Characterization of the thermal expansion properties of graphene using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Zahabul Islam, M; Mahboob, Monon; Robert Lowe, L; Stephen Bechtel, E

    2013-01-01

    In the present study, the temperature-dependent coefficient of thermal expansion (CTE) of a graphene sheet (GS) is determined using molecular dynamics (MD) simulations. Our simulations show that the CTE of a GS (i) varies non-linearly with temperature, (ii) is negative over a temperature range of 0–500 K and (iii) differs by no more than 9% in the armchair and zigzag directions. We find good agreement between our MD results and recent experimental data. The present study also investigates the effect of missing atoms (vacancy defects) on the CTE of a GS. In our MD simulations of a 4.9 nm × 4.9 nm GS, we find that the presence of two vacant atoms (about 1.56% by volume) increases the negative CTE by as much as 40%. Correlations between the CTE and the number of missing atoms have been developed based on MD simulation results for a perfect GS and a GS with 1.56% defects by volume. Predictions of the CTE of a defective GS from the correlations compare favourably with MD simulations at 3.13% defects by volume. (paper)

  3. 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

  4. A conceptual demonstration of freeze desalination-membrane distillation (FD-MD) hybrid desalination process utilizing liquefied natural gas (LNG) cold energy.

    Science.gov (United States)

    Wang, Peng; Chung, Tai-Shung

    2012-09-01

    The severe global water scarcity and record-high fossil oil price have greatly stimulated the research interests on new desalination technologies which can be driven by renewable energy or waste energy. In this study, a hybrid desalination process comprising freeze desalination and membrane distillation (FD-MD) processes was developed and explored in an attempt to utilize the waste cold energy released from re-gasification of liquefied natural gas (LNG). The concept of this technology was demonstrated using indirect-contact freeze desalination (ICFD) and direct-contact membrane distillation (DCMD) configurations. By optimizing the ICFD operation parameters, namely, the usage of nucleate seeds, operation duration and feed concentration, high quality drinkable water with a low salinity ∼0.144 g/L was produced in the ICFD process. At the same time, using the optimized hollow fiber module length and packing density in the DCMD process, ultra pure water with a low salinity of 0.062 g/L was attained at a condition of high energy efficiency (EE). Overall, by combining FD and MD processes and adopting the optimized operation parameters, the hybrid FD-MD system has been successfully demonstrated. A high total water recovery of 71.5% was achieved, and the water quality obtained met the standard for drinkable water. In addition, with results from specific energy calculation, it was proven that the hybrid process is an energy-saving process and utilization of LNG cold energy could greatly reduce the total energy consumption. Copyright © 2012 Elsevier Ltd. All rights reserved.

  5. Simulation study of transfer characteristics for spacer-filled membrane distillation desalination modules

    International Nuclear Information System (INIS)

    Chang, Hsuan; Hsu, Jian-An; Chang, Cheng-Liang; Ho, Chii-Dong; Cheng, Tung-Wen

    2017-01-01

    Highlights: • A 3D CFD model takes in transmembrane heat and mass transfer developed. • DCMD modules using spacer-filled and empty channels for desalination simulated. • Fluid flow, heat transfer and mass transfer profiles revealed. • Correlations of friction factor and Nusselt number developed. - Abstract: Membrane distillation (MD) is an emerging and promising membrane separation process, which can directly utilize renewable thermal energy or low-grade waste heat, for applications in water or wastewater treatment and food industry. However, a major drawback of MD process is its low energy efficiency. Spacer is the most suggested and studied eddy promoter to enhance the heat and mass transfer, which further improves both the separation and the energy utilization performance, of MD processes. This paper presents the results of a 3D computational fluid dynamics (CFD) simulation of DCMD (direct contact membrane distillation) modules using channels with and without spacers for desalination application. The model employs permeable wall boundary condition to take into account the transmembrane heat and mass transfer and simulates the entire module length. The simulation reveals similar fluctuating distributions of temperature polarization coefficient, transmembrane heat and mass fluxes as well as the shear stress on the membrane surface along the entire module length. Correlations have been developed for friction factor and average Nusselt number. These correlations are useful for the analysis and design of DCMD modules. The extent of heat transfer enhancement by spacers depends on the geometry of spacers and the Reynolds number of fluid.

  6. 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.

  7. Computer simulation of sputtering: A review

    International Nuclear Information System (INIS)

    Robinson, M.T.; Hou, M.

    1992-08-01

    In 1986, H. H. Andersen reviewed attempts to understand sputtering by computer simulation and identified several areas where further research was needed: potential energy functions for molecular dynamics (MD) modelling; the role of inelastic effects on sputtering, especially near the target surface; the modelling of surface binding in models based on the binary collision approximation (BCA); aspects of cluster emission in MD models; and angular distributions of sputtered particles. To these may be added kinetic energy distributions of sputtered particles and the relationships between MD and BCA models, as well as the development of intermediate models. Many of these topics are discussed. Recent advances in BCA modelling include the explicit evaluation of the time in strict BCA codes and the development of intermediate codes able to simulate certain many-particle problems realistically. Developments in MD modelling include the wide-spread use of many-body potentials in sputtering calculations, inclusion of realistic electron excitation and electron-phonon interactions, and several studies of cluster ion impacts on solid surfaces

  8. 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.

  9. 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.

  10. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application

    Directory of Open Access Journals (Sweden)

    Lauren Boldon

    2015-02-01

    Full Text Available In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS experiments, molecular dynamics (MD simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics’ equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  11. Review of the fundamental theories behind small angle X-ray scattering, molecular dynamics simulations, and relevant integrated application.

    Science.gov (United States)

    Boldon, Lauren; Laliberte, Fallon; Liu, Li

    2015-01-01

    In this paper, the fundamental concepts and equations necessary for performing small angle X-ray scattering (SAXS) experiments, molecular dynamics (MD) simulations, and MD-SAXS analyses were reviewed. Furthermore, several key biological and non-biological applications for SAXS, MD, and MD-SAXS are presented in this review; however, this article does not cover all possible applications. SAXS is an experimental technique used for the analysis of a wide variety of biological and non-biological structures. SAXS utilizes spherical averaging to produce one- or two-dimensional intensity profiles, from which structural data may be extracted. MD simulation is a computer simulation technique that is used to model complex biological and non-biological systems at the atomic level. MD simulations apply classical Newtonian mechanics' equations of motion to perform force calculations and to predict the theoretical physical properties of the system. This review presents several applications that highlight the ability of both SAXS and MD to study protein folding and function in addition to non-biological applications, such as the study of mechanical, electrical, and structural properties of non-biological nanoparticles. Lastly, the potential benefits of combining SAXS and MD simulations for the study of both biological and non-biological systems are demonstrated through the presentation of several examples that combine the two techniques.

  12. 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

  13. 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.

  14. 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

  15. A 3-D Approach for Teaching and Learning about Surface Water Systems through Computational Thinking, Data Visualization and Physical Models

    Science.gov (United States)

    Caplan, B.; Morrison, A.; Moore, J. C.; Berkowitz, A. R.

    2017-12-01

    Understanding water is central to understanding environmental challenges. Scientists use `big data' and computational models to develop knowledge about the structure and function of complex systems, and to make predictions about changes in climate, weather, hydrology, and ecology. Large environmental systems-related data sets and simulation models are difficult for high school teachers and students to access and make sense of. Comp Hydro, a collaboration across four states and multiple school districts, integrates computational thinking and data-related science practices into water systems instruction to enhance development of scientific model-based reasoning, through curriculum, assessment and teacher professional development. Comp Hydro addresses the need for 1) teaching materials for using data and physical models of hydrological phenomena, 2) building teachers' and students' comfort or familiarity with data analysis and modeling, and 3) infusing the computational knowledge and practices necessary to model and visualize hydrologic processes into instruction. Comp Hydro teams in Baltimore, MD and Fort Collins, CO are integrating teaching about surface water systems into high school courses focusing on flooding (MD) and surface water reservoirs (CO). This interactive session will highlight the successes and challenges of our physical and simulation models in helping teachers and students develop proficiency with computational thinking about surface water. We also will share insights from comparing teacher-led vs. project-led development of curriculum and our simulations.

  16. MD290: Q4 IP6 Quench Level

    CERN Document Server

    Bednarek, Mateusz Jakub; Lechner, Anton; CERN. Geneva. ATS Department

    2016-01-01

    The detailed program proposed for the LHC Machine Development concerning a quench induced by fast losses on the MQY.4L6 quadrupole is presented. The merit of the MD, the necessary modifications of the machine protection systems are presented together with a preliminary analysis of the MD results.

  17. Chosen-Prefix Collisions for MD5 and Applications

    NARCIS (Netherlands)

    M.M.J. Stevens (Marc); A.K. Lenstra (Arjen); B. de Weger (Benne)

    2012-01-01

    textabstractWe present a novel, automated way to find differential paths for MD5. Its main application is in the construction of \\emph{chosen-prefix collisions}. We have shown how, at an approximate expected cost of $2^{39}$ calls to the MD5 compression function, for any two chosen

  18. Competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion by acetonitrile and water

    Science.gov (United States)

    Chaban, Vitaly

    2014-10-01

    Competitive solvation of an ion by two or more solvents is one of the key phenomena determining the identity of our world. Solvation in polar solvents frequently originates from non-additive non-covalent interactions. Pre-parametrized potentials poorly capture these interactions, unless the force field derivation is repeated for every new system. Development cost increases drastically as new chemical species are supplied. This work represents an alternative simulation approach, PM7-MD, by coupling the latest semiempirical parametrization, PM7, with equation-of-motion propagation scheme and temperature coupling. Using a competitive solvation of (bis)(trifluoromethanesulfonyl)imide anion in acetonitrile and water, the work demonstrates efficiency and robustness of PM7-MD.

  19. Assessing the allelotypic effect of two aminocyclopropane carboxylic acid synthase-encoding genes MdACS1 and MdACS3a on fruit ethylene production and softening in Malus

    Science.gov (United States)

    Dougherty, Laura; Zhu, Yuandi; Xu, Kenong

    2016-01-01

    Phytohormone ethylene largely determines apple fruit shelf life and storability. Previous studies demonstrated that MdACS1 and MdACS3a, which encode 1-aminocyclopropane-1-carboxylic acid synthases (ACS), are crucial in apple fruit ethylene production. MdACS1 is well-known to be intimately involved in the climacteric ethylene burst in fruit ripening, while MdACS3a has been regarded a main regulator for ethylene production transition from system 1 (during fruit development) to system 2 (during fruit ripening). However, MdACS3a was also shown to have limited roles in initiating the ripening process lately. To better assess their roles, fruit ethylene production and softening were evaluated at five time points during a 20-day post-harvest period in 97 Malus accessions and in 34 progeny from 2 controlled crosses. Allelotyping was accomplished using an existing marker (ACS1) for MdACS1 and two markers (CAPS866 and CAPS870) developed here to specifically detect the two null alleles (ACS3a-G289V and Mdacs3a) of MdACS3a. In total, 952 Malus accessions were allelotyped with the three markers. The major findings included: The effect of MdACS1 was significant on fruit ethylene production and softening while that of MdACS3a was less detectable; allele MdACS1–2 was significantly associated with low ethylene and slow softening; under the same background of the MdACS1 allelotypes, null allele Mdacs3a (not ACS3a-G289V) could confer a significant delay of ethylene peak; alleles MdACS1–2 and Mdacs3a (excluding ACS3a-G289V) were highly enriched in M. domestica and M. hybrid when compared with those in M. sieversii. These findings are of practical implications in developing apples of low and delayed ethylene profiles by utilizing the beneficial alleles MdACS1-2 and Mdacs3a. PMID:27231553

  20. 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 ...

  1. Modeling ramp compression experiments using large-scale molecular dynamics simulation.

    Energy Technology Data Exchange (ETDEWEB)

    Mattsson, Thomas Kjell Rene; Desjarlais, Michael Paul; Grest, Gary Stephen; Templeton, Jeremy Alan; Thompson, Aidan Patrick; Jones, Reese E.; Zimmerman, Jonathan A.; Baskes, Michael I. (University of California, San Diego); Winey, J. Michael (Washington State University); Gupta, Yogendra Mohan (Washington State University); Lane, J. Matthew D.; Ditmire, Todd (University of Texas at Austin); Quevedo, Hernan J. (University of Texas at Austin)

    2011-10-01

    Molecular dynamics simulation (MD) is an invaluable tool for studying problems sensitive to atomscale physics such as structural transitions, discontinuous interfaces, non-equilibrium dynamics, and elastic-plastic deformation. In order to apply this method to modeling of ramp-compression experiments, several challenges must be overcome: accuracy of interatomic potentials, length- and time-scales, and extraction of continuum quantities. We have completed a 3 year LDRD project with the goal of developing molecular dynamics simulation capabilities for modeling the response of materials to ramp compression. The techniques we have developed fall in to three categories (i) molecular dynamics methods (ii) interatomic potentials (iii) calculation of continuum variables. Highlights include the development of an accurate interatomic potential describing shock-melting of Beryllium, a scaling technique for modeling slow ramp compression experiments using fast ramp MD simulations, and a technique for extracting plastic strain from MD simulations. All of these methods have been implemented in Sandia's LAMMPS MD code, ensuring their widespread availability to dynamic materials research at Sandia and elsewhere.

  2. Swiss national MD-PhD-program: an outcome analysis.

    Science.gov (United States)

    Kuehnle, Katrin; Winkler, David T; Meier-Abt, Peter J

    2009-09-19

    This study aims at a first evaluation of the outcome of the Swiss national MD-PhD program during the last 16 years. One hundred and twenty six former and current students in the Swiss national MD-PhD program were surveyed via a Web-based questionnaire in September 2007. Twenty-four questions assessed information regarding participant demographics, information on the PhD thesis and publication activity, current positions and research activity, as well as participant's opinions, attitudes and career goals. Eighty questionnaires were received from 126 MD-PhD students and graduates (63.5% response rate). The responders consisted of present students (36%), former graduates (56%), and dropouts (8%). The percentage of women in the program was 23%, and the average duration of the program was 4.2 +/- 1.4 years. Research interests were predominantly in the fields of neuroscience, immunology, molecular biology and cancer research. A considerable portion of the MD-PhD graduates had an excellent publication record stemming from their PhD research work, and 89% were planning to continue a research-orientated career. Over 50% of those MD-PhD graduates completing their thesis before 2002 had already reached an assistant or full professor position at the time of the survey. Nearly all participants considered the MD-PhD training helpful to their career and high quality standards were assigned to the acquired practical and intellectual skills. However, criticism was expressed concerning the general mentoring and the career related mentoring. Moreover, general mentoring and career related mentoring were significantly less well perceived in research groups employing more than seven PhD students at the same time. The MD-PhD students and graduates surveyed were satisfied with their education and most of them continued a research-orientated career. Regarding the overall positive evaluation, this study supports the view that MD-PhD graduates are well qualified for a successful career in

  3. 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 ...

  4. 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.

  5. 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

  6. 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

  7. Towards realistic molecular dynamics simulations of grain boundary mobility

    International Nuclear Information System (INIS)

    Zhou, J.; Mohles, V.

    2011-01-01

    In order to investigate grain boundary migration by molecular dynamics (MD) simulations a new approach involving a crystal orientation-dependent driving force has been developed by imposing an appropriate driving force on grain boundary atoms and enlarging the effective range of driving force. The new approach has been validated by the work of the driving force associated with the motion of grain boundaries. With the new approach the relation between boundary migration velocity and driving force is found to be nonlinear, as was expected from rate theory for large driving forces applied in MD simulations. By evaluating grain boundary mobility nonlinearly for a set of symmetrical tilt boundaries in aluminum at high temperature, high-angle grain boundaries were shown to move much faster than low-angle grain boundaries. This agrees well with experimental findings for recrystallization and grain growth. In comparison with the available data the simulated mobility of a 38.21 o Σ7 boundary was found to be significantly lower than other MD simulation results and comparable with the experimental values. Furthermore, the average volume involved during atomic jumps for boundary migration is determined in MD simulations for the first time. The large magnitude of the volume indicates that grain boundary migration is accomplished by the correlated motion of atom groups.

  8. Modeling CO2-Water-Mineral Wettability and Mineralization for Carbon Geosequestration.

    Science.gov (United States)

    Liang, Yunfeng; Tsuji, Shinya; Jia, Jihui; Tsuji, Takeshi; Matsuoka, Toshifumi

    2017-07-18

    Carbon dioxide (CO 2 ) capture and storage (CCS) is an important climate change mitigation option along with improved energy efficiency, renewable energy, and nuclear energy. CO 2 geosequestration, that is, to store CO 2 under the subsurface of Earth, is feasible because the world's sedimentary basins have high capacity and are often located in the same region of the world as emission sources. How CO 2 interacts with the connate water and minerals is the focus of this Account. There are four trapping mechanisms that keep CO 2 in the pores of subsurface rocks: (1) structural trapping, (2) residual trapping, (3) dissolution trapping, and (4) mineral trapping. The first two are dominated by capillary action, where wettability controls CO 2 and water two-phase flow in porous media. We review state-of-the-art studies on CO 2 /water/mineral wettability, which was found to depend on pressure and temperature conditions, salt concentration in aqueous solutions, mineral surface chemistry, and geometry. We then review some recent advances in mineral trapping. First, we show that it is possible to reproduce the CO 2 /water/mineral wettability at a wide range of pressures using molecular dynamics (MD) simulations. As the pressure increases, CO 2 gas transforms into a supercritical fluid or liquid at ∼7.4 MPa depending on the environmental temperature. This transition leads to a substantial decrease of the interfacial tension between CO 2 and reservoir brine (or pure water). However, the wettability of CO 2 /water/rock systems depends on the type of rock surface. Recently, we investigated the contact angle of CO 2 /water/silica systems with two different silica surfaces using MD simulations. We found that contact angle increased with pressure for the hydrophobic (siloxane) surface while it was almost constant for the hydrophilic (silanol) surface, in excellent agreement with experimental observations. Furthermore, we found that the CO 2 thin films at the CO 2 -hydrophilic

  9. Equations of states for an ionic liquid under high pressure: A molecular dynamics simulation study

    International Nuclear Information System (INIS)

    Ribeiro, Mauro C.C.; Pádua, Agílio A.H.; Gomes, Margarida F.C.

    2014-01-01

    Highlights: • We compare different equation of states, EoS, for an ionic liquid under high pressure. • Molecular dynamics, MD, simulations have been used to evaluate the best EoS. • MD simulations show that a group contribution model can be extrapolated to P ∼ 1.0 GPa. • A perturbed hard-sphere EoS also fits the densities calculated by MD simulations. - Abstract: The high-pressure dependence of density given by empirical equation of states (EoS) for the ionic liquid 1-butyl-3-methylimidazolium trifluoromethanesulfonate (or triflate), [C 4 C 1 im][TfO], is compared with results obtained by molecular dynamics (MD) simulations. Two EoS proposed for [C 4 C 1 im][TfO] in the pressure range of tens of MPa, which give very different densities when extrapolated to pressures beyond the original experiments, are compared with a group contribution model (GCM). The MD simulations provide support that one of the empirical EoS and the GCM is valid in the pressure range of hundreds of MPa. As an alternative to these EoS that are based on modified Tait equations, it is shown that a perturbed hard-sphere EoS based on the Carnahan–Starling–van der Waals equation also fits the densities calculated by MD simulations of [C 4 C 1 im][TfO] up to ∼1.0 GPa

  10. 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

  11. 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...

  12. 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

  13. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-21

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  14. Efficient hybrid non-equilibrium molecular dynamics - Monte Carlo simulations with symmetric momentum reversal

    Science.gov (United States)

    Chen, Yunjie; Roux, Benoît

    2014-09-01

    Hybrid schemes combining the strength of molecular dynamics (MD) and Metropolis Monte Carlo (MC) offer a promising avenue to improve the sampling efficiency of computer simulations of complex systems. A number of recently proposed hybrid methods consider new configurations generated by driving the system via a non-equilibrium MD (neMD) trajectory, which are subsequently treated as putative candidates for Metropolis MC acceptance or rejection. To obey microscopic detailed balance, it is necessary to alter the momentum of the system at the beginning and/or the end of the neMD trajectory. This strict rule then guarantees that the random walk in configurational space generated by such hybrid neMD-MC algorithm will yield the proper equilibrium Boltzmann distribution. While a number of different constructs are possible, the most commonly used prescription has been to simply reverse the momenta of all the particles at the end of the neMD trajectory ("one-end momentum reversal"). Surprisingly, it is shown here that the choice of momentum reversal prescription can have a considerable effect on the rate of convergence of the hybrid neMD-MC algorithm, with the simple one-end momentum reversal encountering particularly acute problems. In these neMD-MC simulations, different regions of configurational space end up being essentially isolated from one another due to a very small transition rate between regions. In the worst-case scenario, it is almost as if the configurational space does not constitute a single communicating class that can be sampled efficiently by the algorithm, and extremely long neMD-MC simulations are needed to obtain proper equilibrium probability distributions. To address this issue, a novel momentum reversal prescription, symmetrized with respect to both the beginning and the end of the neMD trajectory ("symmetric two-ends momentum reversal"), is introduced. Illustrative simulations demonstrate that the hybrid neMD-MC algorithm robustly yields a correct

  15. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations.

    Science.gov (United States)

    Dixit, Surjit B; Mezei, Mihaly; Beveridge, David L

    2012-07-01

    Detailed analyses of the sequence-dependent solvation and ion atmosphere of DNA are presented based on molecular dynamics (MD) simulations on all the 136 unique tetranucleotide steps obtained by the ABC consortium using the AMBER suite of programs. Significant sequence effects on solvation and ion localization were observed in these simulations. The results were compared to essentially all known experimental data on the subject. Proximity analysis was employed to highlight the sequence dependent differences in solvation and ion localization properties in the grooves of DNA. Comparison of the MD-calculated DNA structure with canonical A- and B-forms supports the idea that the G/C-rich sequences are closer to canonical A- than B-form structures, while the reverse is true for the poly A sequences, with the exception of the alternating ATAT sequence. Analysis of hydration density maps reveals that the flexibility of solute molecule has a significant effect on the nature of observed hydration. Energetic analysis of solute-solvent interactions based on proximity analysis of solvent reveals that the GC or CG base pairs interact more strongly with water molecules in the minor groove of DNA that the AT or TA base pairs, while the interactions of the AT or TA pairs in the major groove are stronger than those of the GC or CG pairs. Computation of solvent-accessible surface area of the nucleotide units in the simulated trajectories reveals that the similarity with results derived from analysis of a database of crystallographic structures is excellent. The MD trajectories tend to follow Manning's counterion condensation theory, presenting a region of condensed counterions within a radius of about 17 A from the DNA surface independent of sequence. The GC and CG pairs tend to associate with cations in the major groove of the DNA structure to a greater extent than the AT and TA pairs. Cation association is more frequent in the minor groove of AT than the GC pairs. In general, the

  16. Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

    Science.gov (United States)

    Rajendiran, Nivedita; Durrant, Jacob D

    2018-05-05

    Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Hanhui [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Collaborative Innovation Center of Advanced Aero-Engine, Hangzhou 310027 (China); Liu, Ningning [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Ku, Xiaoke, E-mail: xiaokeku@zju.edu.cn [School of Aeronautics and Astronautics, Zhejiang University, Hangzhou 310027 (China); Fan, Jianren [State Key Laboratory of Clean Energy Utilization, Zhejiang University, Hangzhou 310027 (China)

    2017-05-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  18. A novel energy conversion based method for velocity correction in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Jin, Hanhui; Liu, Ningning; Ku, Xiaoke; Fan, Jianren

    2017-01-01

    Molecular dynamics (MD) simulation has become an important tool for studying micro- or nano-scale dynamics and the statistical properties of fluids and solids. In MD simulations, there are mainly two approaches: equilibrium and non-equilibrium molecular dynamics (EMD and NEMD). In this paper, a new energy conversion based correction (ECBC) method for MD is developed. Unlike the traditional systematic correction based on macroscopic parameters, the ECBC method is developed strictly based on the physical interaction processes between the pair of molecules or atoms. The developed ECBC method can apply to EMD and NEMD directly. While using MD with this method, the difference between the EMD and NEMD is eliminated, and no macroscopic parameters such as external imposed potentials or coefficients are needed. With this method, many limits of using MD are lifted. The application scope of MD is greatly extended.

  19. Total water production capacity inversion phenomenon in multi-stage direct contact membrane distillation: A theoretical study

    KAUST Repository

    Lee, Jung Gil

    2017-09-09

    The low thermal efficiency and low water production are among the major challenges that prevent membrane distillation (MD) process from being commercialized. In an effort to design an efficient multi-stage direct contact MD (DCMD) unit through mathematical simulation, a new phenomenon that we refer to as total water production capacity inversion (WPI) has been detected. It is represented by a decrease in the total water production beyond a number of stages or a certain module length. WPI phenomenon, which was confirmed by using two different mathematical models validated experimentally, was found to take place due to the decrease in water vapor flux across the membrane as well as the increase in heat loss by conduction as the membrane length increases. Therefore, WPI should be considered as a critical MD design-criterion, especially for large scale units. Investigations conducted for a simulated multi-stage DCMD process showed that inlet feed and permeate temperatures difference, feed and permeate flow rates, and feed salinity have different effects on WPI. The number of stages (or module length at constant width) that leads to a maximum water production has been determined for different operating parameters. Decreasing inlet feed and permeate temperatures difference, or inlet feed and permeate flow rates and increasing inlet feed temperature at constant temperature difference or inlet feed salinity cause the WPI to take place at lower number of stages. Even though the feed salinity affects negligibly the mean permeate flux, it was clearly shown that it can affect WPI. The results presented herein unveil a hidden phenomenon that is likely to occur during process scale-up procedures and should be considered by process engineers for a proper choice of system design and operating conditions.

  20. 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.

  1. Structure of Cu64.5Zr35.5 metallic glass by reverse Monte Carlo simulations

    International Nuclear Information System (INIS)

    Fang, X. W.; Huang, Li; Wang, C. Z.; Ho, K. M.; Ding, Z. J.

    2014-01-01

    Reverse Monte Carlo simulations (RMC) have been widely used to generate three dimensional (3D) atomistic models for glass systems. To examine the reliability of the method for metallic glass, we use RMC to predict the atomic configurations of a “known” structure from molecular dynamics (MD) simulations, and then compare the structure obtained from the RMC with the target structure from MD. We show that when the structure factors and partial pair correlation functions from the MD simulations are used as inputs for RMC simulations, the 3D atomistic structure of the glass obtained from the RMC gives the short- and medium-range order in good agreement with those from the target structure by the MD simulation. These results suggest that 3D atomistic structure model of the metallic glass alloys can be reasonably well reproduced by RMC method with a proper choice of input constraints

  2. Reducing phosphorus loss in tile water with managed drainage in a claypan soil.

    Science.gov (United States)

    Nash, Patrick R; Nelson, Kelly A; Motavalli, Peter P; Nathan, Manjula; Dudenhoeffer, Chris

    2015-03-01

    Installing subsurface tile drain systems in poorly drained claypan soils to improve corn ( L.) yields could potentially increase environmental phosphorus (P) loss through the tile drainage system. The objectives of the study were to quantify the average concentration and loss of ortho-P in tile drain water from a claypan soil and to determine whether managed subsurface drainage (MD) could reduce ortho-P loss in tile water compared with free subsurface drainage (FD). Flow-weighted ortho-P concentration in the tile water was significantly lower with MD (0.09 mg L) compared with that of FD (0.15 mg L). Ortho-P loss in the tile water of this study was reduced with MD (36 g ha) by 80% compared with FD (180 g ha). Contrary to previous research, reduced ortho-P loss observed over the 4-yr study was not solely due to the reduced amount of water drained annually (63%) with MD compared with FD. During the spring period, when flow was similar between MD and FD, the concentration of ortho-P in the tile water generally was lower with MD compared with FD, which resulted in significantly less ortho-P loss with MD. We speculate that MD's ability to conserve water during the dry summer months increased corn's uptake of water and P, which reduced the amount of P available for leaching loss in the subsequent springs. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  3. Layering of confined water between two graphene sheets and its liquid–liquid transition

    International Nuclear Information System (INIS)

    Zhou Xuyan; Duan Yunrui; Wang Long; Liu Sida; Li Tao; Li Yifan; Li Hui

    2017-01-01

    Molecular dynamics (MD) simulations are performed to explore the layering structure and liquid–liquid transition of liquid water confined between two graphene sheets with a varied distance at different pressures. Both the size of nanoslit and pressure could cause the layering and liquid–liquid transition of the confined water. With increase of pressure and the nanoslit’s size, the confined water could have a more obvious layering. In addition, the neighboring water molecules firstly form chain structure, then will transform into square structure, and finally become triangle with increase of pressure. These results throw light on layering and liquid–liquid transition of water confined between two graphene sheets. (paper)

  4. Structure of the floating water bridge and water in an electric field.

    Science.gov (United States)

    Skinner, Lawrie B; Benmore, Chris J; Shyam, Badri; Weber, J K R; Parise, John B

    2012-10-09

    The floating water bridge phenomenon is a freestanding rope-shaped connection of pure liquid water, formed under the influence of a high potential difference (approximately 15 kV). Several recent spectroscopic, optical, and neutron scattering studies have suggested that the origin of the bridge is associated with the formation of anisotropic chains of water molecules in the liquid. In this work, high energy X-ray diffraction experiments have been performed on a series of floating water bridges as a function of applied voltage, bridge length, and position within the bridge. The two-dimensional X-ray scattering data showed no direction-dependence, indicating that the bulk water molecules do not exhibit any significant preferred orientation along the electric field. The only structural changes observed were those due to heating, and these effects were found to be the same as for bulk water. These X-ray scattering measurements are supported by molecular dynamics (MD) simulations which were performed under electric fields of 10(6) V/m and 10(9) V/m. Directional structure factor calculations were made from these simulations parallel and perpendicular to the E-field. The 10(6) V/m model showed no significant directional-dependence (anisotropy) in the structure factors. The 10(9) V/m model however, contained molecules aligned by the E-field, and had significant structural anisotropy.

  5. The ABCs of molecular dynamics simulations on B-DNA, circa 2012

    Indian Academy of Sciences (India)

    2012-06-25

    Jun 25, 2012 ... Introduction ... methods and applications of MD simulations to nucleic acids. ... access to high-performance computing, all-atom MD on DNA ... Specifically, the focus in this article is (a) ... of MD on DNA using AMBER came with the development ..... python-based tool for managing this task on widely.

  6. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Huiding Xie

    2015-11-01

    Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  7. 76 FR 5686 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

    Science.gov (United States)

    2011-02-02

    ... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to.... The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke City MD, has a vertical clearance in...

  8. 76 FR 48898 - Robert Leigh Kale, M.D., Decision and Order

    Science.gov (United States)

    2011-08-09

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration Robert Leigh Kale, M.D., Decision and Order... Enforcement Administration, issued an Order to Show Cause to Robert Leigh Kale, M.D. (Registrant), of Fort... Certificate of Registration, BK9514375, issued to Robert Leigh Kale, M.D., be, and it hereby is, revoked. I...

  9. 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.

  10. 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

  11. Infrared microspectroscopy of live cells in microfluidic devices (MD-IRMS): toward a powerful label-free cell-based assay.

    Science.gov (United States)

    Vaccari, L; Birarda, G; Businaro, L; Pacor, S; Grenci, G

    2012-06-05

    Until nowadays most infrared microspectroscopy (IRMS) experiments on biological specimens (i.e., tissues or cells) have been routinely carried out on fixed or dried samples in order to circumvent water absorption problems. In this paper, we demonstrate the possibility to widen the range of in-vitro IRMS experiments to vibrational analysis of live cellular samples, thanks to the development of novel biocompatible IR-visible transparent microfluidic devices (MD). In order to highlight the biological relevance of IRMS in MD (MD-IRMS), we performed a systematic exploration of the biochemical alterations induced by different fixation protocols, ethanol 70% and formaldehyde solution 4%, as well as air-drying on U937 leukemic monocytes by comparing their IR vibrational features with the live U937 counterpart. Both fixation and air-drying procedures affected lipid composition and order as well as protein structure at a different extent while they both induced structural alterations in nucleic acids. Therefore, only IRMS of live cells can provide reliable information on both DNA and RNA structure and on their cellular dynamic. In summary, we show that MD-IRMS of live cells is feasible, reliable, and biologically relevant to be recognized as a label-free cell-based assay.

  12. 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.

  13. Millennial-Scale Planktic Foraminifer Faunal Variability in the East China Sea during the Past 40000 Years (IMAGES MD012404 from the Okinawa Trough

    Directory of Open Access Journals (Sweden)

    Yuan-Pin Chang

    2008-01-01

    Full Text Available High resolution planktic foraminifer fauna assemblage data are used to reconstruct the millennial-scale sea surface temperature (SST variability of the past 40000 years at an IMAGES core site (MD012404 in the Okinawa Trough in the East China Sea (ECS. The fauna assemblages in core MD012404 are dominated by five species - Globigerinoides ruber, Globigerina bulloides, Neogloboquadrina dutertrei, Pulleniatina obliquiloculata, and Globigerinita glutinata, which account for > 70% in relative abundance. Our Q-mode factor analysis decomposed the fauna abundance data into three factors, which indicate cold water mass, warm water mass, and possibly coastal water flow with low salinity in the ECS. The MD012404 fauna data show abrupt changes at ~16 kya, suggesting a return to a warmer climate or warm water intrusion of the Kuroshio into the Okinawa Trough since the Last Glacial Maximum (LGM. SST estimates based on the fauna assemblages of planktic foraminifers indicate a LGM cooling of 1 - 2°C. Amaximum cooling by 3 - 4°C is observed in episodic, millennial-scale events in the glacial stages of the record. The SST record displays variability that closely tracks the structure of oxygen isotopes of stalagmites from Hulu Cave and ice cores from GISP 2 Dansgaard/Oeschger cycles and Heinrich events. Low salinity in the ECS is inferred based on MD012404 fauna SST and planktic foraminifer oxygen isotope records for the cold millennial-scale intervals, pointing to the Intertropical Convergence Zone (ITCZ and/or East Asian monsoon as important factors driving SST and salinity in the subtropical western Pacific, both on orbital and suborbital time scales.

  14. Hybrid method coupling molecular dynamics and Monte Carlo simulations to study the properties of gases in microchannels and nanochannels

    NARCIS (Netherlands)

    Nedea, S.V.; Frijns, A.J.H.; Steenhoven, van A.A.; Markvoort, Albert. J.; Hilbers, P.A.J.

    2005-01-01

    We combine molecular dynamics (MD) and Monte Carlo (MC) simulations to study the properties of gas molecules confined between two hard walls of a microchannel or nanochannel. The coupling between MD and MC simulations is introduced by performing MD near the boundaries for accuracy and MC in the bulk

  15. 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

  16. Advanced, Energy-Efficient Hybrid Membrane System for Industrial Water Reuse

    Energy Technology Data Exchange (ETDEWEB)

    Toy, Lora [RTI International, Research Triangle Park, NC (United States); Choi, Young Chul [RTI International, Research Triangle Park, NC (United States); Hendren, Zachary [RTI International, Research Triangle Park, NC (United States); Kim, Gyu Dong [RTI International, Research Triangle Park, NC (United States)

    2017-03-31

    In the U.S. manufacturing sector, current industrial water use practices are energy-intensive and utilize and discharge high volumes of waters, rendering them not sustainable especially in light of the growing scarcity of suitable water supplies. To help address this problem, the goal of this project was to develop an advanced, cost-effective, hybrid membrane-based water treatment system that can improve the energy efficiency of industrial wastewater treatment while allowing at least 50% water reuse efficiency. This hybrid process would combine emerging Forward Osmosis (FO) and Membrane Distillation (MD) technology components into an integrated FO-MD system that can beneficially utilize low-grade waste heat (i.e., T < 450 °F) in industrial facilities to produce distilled-quality product water for reuse. In this project, laboratory-, bench-, and pilot-scale experiments on the hybrid FO-MD system were conducted for industrial wastewater treatment. It was demonstrated at laboratory, bench, and pilot scales that FO-MD membrane technology can concentrate brine to very high total dissolved solids (TDS) levels (>200,000 ppm) that are at least 2.5 times higher than the TDS level to which RO can achieve. In laboratory testing, currently available FO and MD membranes were tested to select for high-performing membranes with high salt rejection and high water flux. Multiple FO membrane/draw-salt solution combinations that gave high water flux with higher than 98% salt rejection were also identified. Reverse draw-salt fluxes were observed to be much lower for divalent salts than for monovalent salts. MD membranes were identified that had 99.9+% salt rejection and water flux as high as 50-90 L/(m2·h) for flat-sheet membranes and >20 L/(m2·h) for hollow fibers. In bench-scale testing, a single unit of commercially available FO and MD membrane modules were evaluated for continuous, integrated operation. Using the laboratory- and bench-scale test data

  17. 76 FR 20032 - Thomas E. Mitchell, M.D.; Dismissal of Proceeding

    Science.gov (United States)

    2011-04-11

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 10-7] Thomas E. Mitchell, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Thomas E. Mitchell, M.D....100(b) and 0.104, I hereby order that the Order to Show Cause issued to Thomas E. Mitchell, M.D., be...

  18. Computer Simulation Studies of Trishomocubane Heptapeptide of ...

    African Journals Online (AJOL)

    As part of an extension on the cage peptide chemistry, the present work involves an assessment of the conformational profile of trishomocubane heptapeptide of the type Ac-Ala3-Tris-Ala3-NHMe using molecular dynamics (MD) simulations. All MD protocols were explored within the framework of a molecular mechanics ...

  19. Structural and energetic properties of La3+ in water/DMSO mixtures

    Science.gov (United States)

    Montagna, Maria; Spezia, Riccardo; Bodo, Enrico

    2017-11-01

    By using molecular dynamics based on a custom polarizable force field, we have studied the solvation of La3+ in an equimolar mixture of dimethylsulfoxide (DMSO) with water. An extended structural analysis has been performed to provide a complete picture of the physical properties at the basis of the interaction of La3+ with both solvents. Through our simulations we found that, very likely, the first solvation shell in the mixture is not unlike the one found in pure water or pure DMSO and contains 9 solvent molecules. We have also found that the solvation is preferentially due to DMSO molecules with the water initially present in first shell quickly leaving to the bulk. The dehydration process of the first shell has been analyzed by both plain MD simulations and a constrained dynamics approach; the free energy profiles for the extraction of water from first shell have also been computed.

  20. 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

  1. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    Science.gov (United States)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  2. 77 FR 7182 - Scott W. Houghton, M.D.; Decision and Order

    Science.gov (United States)

    2012-02-10

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 12-09] Scott W. Houghton, M.D... CFR 0.100(b), I order that DEA Certificate of Registration BH8796077, issued to Scott W. Houghton, M.D., be, and it hereby is, revoked. I further order that any pending application of Scott W. Houghton, M.D...

  3. Computer Simulations of Lipid Bilayers and Proteins

    DEFF Research Database (Denmark)

    Sonne, Jacob

    2006-01-01

    The importance of computer simulations in lipid bilayer research has become more prominent for the last couple of decades and as computers get even faster, simulations will play an increasingly important part of understanding the processes that take place in and across cell membranes. This thesis...... entitled Computer simulations of lipid bilayers and proteins describes two molecular dynamics (MD) simulation studies of pure lipid bilayers as well as a study of a transmembrane protein embedded in a lipid bilayer matrix. Below follows a brief overview of the thesis. Chapter 1. This chapter is a short...... in the succeeding chapters is presented. Details on system setups, simulation parameters and other technicalities can be found in the relevant chapters. Chapter 3, DPPC lipid parameters: The quality of MD simulations is intimately dependent on the empirical potential energy function and its parameters, i...

  4. Trends in MD/PhD Graduates Entering Psychiatry: Assessing the Physician-Scientist Pipeline.

    Science.gov (United States)

    Arbuckle, Melissa R; Luo, Sean X; Pincus, Harold Alan; Gordon, Joshua A; Chung, Joyce Y; Chavez, Mark; Oquendo, Maria A

    2018-06-01

    The goal of this study was to identify trends in MD/PhD graduates entering psychiatry, to compare these trends with other specialties, and to review strategies for enhancing the physician-scientist pipeline. Data on 226,588 medical students graduating from Liaison Committee on Medical Education accredited programs between 1999 and 2012 (6626 MD/PhDs) were used to evaluate the number, percentage, and proportion of MD/PhDs entering psychiatry in comparison with other specialties (neurology, neurosurgery, internal medicine, family medicine, and radiation oncology). Linear regression and multiple linear regression determined whether these values increased over time and varied by sex. Over 14 years, an average of 18 MD/PhDs (range 13-29) enrolled in psychiatry each year. The number of MD/PhDs going into psychiatry significantly increased, although these gains were modest (less than one additional MD/PhD per year). The proportion of students entering psychiatry who were MD/PhDs varied between 2.9 and 5.9 per 100 residents, with no significant change over time. There was also no change in the percentage of MD/PhDs entering psychiatry from among all MD/PhD graduates. The rate of increase in the number of MD/PhDs going into psychiatry did not differ significantly from other specialties except for family medicine, which is decreasing. The rate of MD/PhDs going into psychiatry was higher for women, suggesting closure of the sex gap in 17 years. Despite the increase in the number of MD/PhDs entering psychiatry, these numbers remain low. Expanding the cohort of physician-scientists dedicated to translational research in psychiatry will require a multipronged approach.

  5. Characterization of an Autophagy-related Gene MdATG8i from apple

    Directory of Open Access Journals (Sweden)

    Ping eWang

    2016-05-01

    Full Text Available Nutrient deficiencies restrict apple (Malus sp. tree growth and productivity in Northwest China. The process of autophagy, a conserved degradation pathway in eukaryotic cells, has important roles in nutrient-recycling and helps improve plant performance during periods of nutrient-starvation. Little is known about the functioning of autophagy-related genes (ATGs in apple. In this study, one of the ATG8 gene family members MdATG8i was isolated from M. domestica. MdATG8i has conserved putative tubulin binding sites and ATG7 interaction domains. A 1865-bp promoter region cloned from apple genome DNA was predicated to have cis-regulatory elements responsive to light, environmental stresses and hormones. MdATG8i transcriptions were induced in response to leaf senescence, nitrogen depletion, and oxidative stress. At cellular level, MdATG8i protein was expressed in the nucleus and cytoplasm of onion epidermal cells. Yeast two-hybrid tests showed that MdATG8i could interact with MdATG7a and MdATG7b. In Arabidopsis, its heterologous expression was associated with enhanced vegetative growth, leaf senescence, and tolerance to nitrogen- and carbon-starvation. MdATG8i-overexpressing ‘Orin’ apple callus lines also displayed improved tolerance to nutrient-limited conditions. Our results demonstrate that MdATG8i protein could function in autophagy in a conserved way, as a positive regulator in the response to nutrient-starvation.

  6. [MD PhD programs: Providing basic science education for ophthalmologists].

    Science.gov (United States)

    Spaniol, K; Geerling, G

    2015-06-01

    Enrollment in MD PhD programs offers the opportunity of a basic science education for medical students and doctors. These programs originated in the USA where structured programs have been offered for many years, but now German universities also run MD PhD programs. The MD PhD programs provided by German universities were investigated regarding entrance requirements, structure and financing modalities. An internet and telephone-based search was carried out. Out of 34 German universities 22 offered MD PhD programs. At 15 of the 22 universities a successfully completed course of studies in medicine was required for enrollment, 7 programs admitted medical students in training and 7 programs required a medical doctoral thesis, which had to be completed with at least a grade of magna cum laude in 3 cases. Financing required scholarships in many cases. Several German universities currently offer MD PhD programs; however, these differ considerably regarding entrance requirements, structure and financing. A detailed analysis investigating the success rates of these programs (e.g. successful completion and career paths of graduates) would be of benefit.

  7. Molecular dynamics simulations study of nano bubble attachment at hydrophobic surfaces

    Energy Technology Data Exchange (ETDEWEB)

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

    2018-01-01

    Bubble attachment phenomena are examined using Molecular Dynamics Simulations (MDS) for the first time. The simulation involves a nitrogen nano bubble containing 906 nitrogen molecules in a water phase with 74,000 water molecules at molybdenite surfaces. During a simulation period of 1 ns, film rupture and displacement occurs. The attached nanobubble at the hydrophobic molybdenite face surface results in a contact angle of about 90º. This spontaneous attachment is due to a “water exclusion zone” at the molybdenite face surface and can be explained by a van der Waals (vdW) attractive force, as discussed in the literature. In contrast, the film is stable at the hydrophilic quartz (001) surface and the bubble does not attach. Contact angles determined from MD simulations are reported, and these results agree well with experimental and MDS sessile drop results. In this way, film stability and bubble attachment are described with respect to interfacial water structure for surfaces of different polarity. Interfacial water molecules at the hydrophobic molybdenite face surface have relatively weak interactions with the surface when compared to the hydrophilic quartz (001) surface, as revealed by the presence of a 3 Å “water exclusion zone” at the molybdenite/water interface. The molybdenite armchair-edge and zigzag-edge surfaces show a comparably slow process for film rupture and displacement when compared to the molybdenite face surface, which is consistent with their relatively weak hydrophobic character.

  8. 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

  9. 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.

  10. 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.

  11. Characterization of the conformational space of a triple-stranded beta-sheet forming peptide with molecular dynamics simulations

    NARCIS (Netherlands)

    Soto, P; Colombo, G

    2004-01-01

    Molecular dynamics (MD) simulations have been performed on a series of mutants of the 20 amino acid peptide Betanova in order to critically assess the ability of MD simulations to reproduce the folding and stability of small beta-sheet-forming peptides on currently accessible timescales. Simulations

  12. Deviation from equilibrium conditions in molecular dynamic simulations of homogeneous nucleation.

    Science.gov (United States)

    Halonen, Roope; Zapadinsky, Evgeni; Vehkamäki, Hanna

    2018-04-28

    We present a comparison between Monte Carlo (MC) results for homogeneous vapour-liquid nucleation of Lennard-Jones clusters and previously published values from molecular dynamics (MD) simulations. Both the MC and MD methods sample real cluster configuration distributions. In the MD simulations, the extent of the temperature fluctuation is usually controlled with an artificial thermostat rather than with more realistic carrier gas. In this study, not only a primarily velocity scaling thermostat is considered, but also Nosé-Hoover, Berendsen, and stochastic Langevin thermostat methods are covered. The nucleation rates based on a kinetic scheme and the canonical MC calculation serve as a point of reference since they by definition describe an equilibrated system. The studied temperature range is from T = 0.3 to 0.65 ϵ/k. The kinetic scheme reproduces well the isothermal nucleation rates obtained by Wedekind et al. [J. Chem. Phys. 127, 064501 (2007)] using MD simulations with carrier gas. The nucleation rates obtained by artificially thermostatted MD simulations are consistently lower than the reference nucleation rates based on MC calculations. The discrepancy increases up to several orders of magnitude when the density of the nucleating vapour decreases. At low temperatures, the difference to the MC-based reference nucleation rates in some cases exceeds the maximal nonisothermal effect predicted by classical theory of Feder et al. [Adv. Phys. 15, 111 (1966)].

  13. Effect of hydrophobic groups on the adsorption conformation of modified polycarboxylate superplasticizer investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Hongxia [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Wang, Yanwei, E-mail: wangyanwei@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Yang, Yong; Shu, Xin; Yan, Han [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China); Ran, Qianping, E-mail: qpran@cnjsjk.cn [State Key Laboratory of High Performance Civil Engineering Materials, Nanjing 210008, Jiangsu (China); Jiangsu Sobute New Materials Co. Ltd., Nanjing 211103, Jiangsu (China)

    2017-06-15

    Highlights: • Adsorption conformation of comb-like PCE was studied by all-atom MD simulations. • A comparison is made between vacuum-based and solution-based simulations. • Effects of hydrophobic modifications on adsorption properties are elucidated. - Abstract: All-atom molecular dynamics (MD) simulations were used to study the adsorption conformations of hydrophobically-modified comb-shaped polycarboxylate ether-based (PCE) superplasticizer molecules on a model surface of dicalcium silicate (C{sub 2}S) in vacuum and in an explicit solution, respectively. Three different hydrophobic modifying groups, namely, the ethyl group, the n-butyl group and the phenyl group, decorated to the backbone, were examined. Comparing the hydrophobically-modified PCEs to the unmodified one, differences were found in the binding energy, the adsorption conformation and the water density at the interface. The interaction between PCE molecules and C{sub 2}S was weakened in a solution with explicit solvents than that obtained from vacuum-based simulations. The presence of hydrophobic groups lowered the polymer-surface binding energy, decreased the radius of gyration (Rg) of the adsorbed polymer, increased the peak position in the heavy-atom density profiles in the direction perpendicular to the surface, and also caused the adsorbed conformations to be more globular in shape. The parallel and perpendicular components (relative to the surface plane) of the geometric sizes of the adsorbed polymers were calculated, and the results showed that the presence of hydrophobically modifying groups decreased the in-plane radius while increased the adsorption layer thickness compared to the unmodified control. The presence of PCEs perturbed the dense water layer above the C{sub 2}S surface and lowered the water density. Perturbations to the interfacial water density were found to correlate nicely with the adsorbed conformations of PCEs.

  14. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Science.gov (United States)

    Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

    2012-01-01

    The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. Why should biochemistry students be introduced to molecular dynamics simulations--and how can we introduce them?

    Science.gov (United States)

    Elmore, Donald E

    2016-01-01

    Molecular dynamics (MD) simulations play an increasingly important role in many aspects of biochemical research but are often not part of the biochemistry curricula at the undergraduate level. This article discusses the pedagogical value of exposing students to MD simulations and provides information to help instructors consider what software and hardware resources are necessary to successfully introduce these simulations into their courses. In addition, a brief review of the MD-based activities in this issue and other sources are provided. © 2016 The International Union of Biochemistry and Molecular Biology.

  1. 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.

  2. 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)

  3. Molecular dynamics simulation of three plastic additives' diffusion in polyethylene terephthalate.

    Science.gov (United States)

    Li, Bo; Wang, Zhi-Wei; Lin, Qin-Bao; Hu, Chang-Ying

    2017-06-01

    Accurate diffusion coefficient data of additives in a polymer are of paramount importance for estimating the migration of the additives over time. This paper shows how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2,6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K. The diffusion coefficient was calculated through the Einstein relationship connecting the data of mean-square displacement at different times. Comparison of the diffusion coefficients simulated by the MD simulation technique, predicted by the Piringer model and experiments, showed that, except for a few samples, the MD-simulated values were in agreement with the experimental values within one order of magnitude. Furthermore, the diffusion process for additives is discussed in detail, and four factors - the interaction energy between additive molecules and PET, fractional free volume, molecular shape and size, and self-diffusion of the polymer - are proposed to illustrate the microscopic diffusion mechanism. The movement trajectories of additives in PET cell models suggested that the additive molecules oscillate slowly rather than hopping for a long time. Occasionally, when a sufficiently large hole was created adjacently, the molecule could undergo spatial motion by jumping into the free-volume hole and consequently start a continuous oscillation and hop. The results indicate that MD simulation is a useful approach for predicting the microstructure and diffusion coefficient of plastic additives, and help to estimate the migration level of additives from PET packaging.

  4. 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)

  5. 3MdB: the Mexican Million Models database

    Science.gov (United States)

    Morisset, C.; Delgado-Inglada, G.

    2014-10-01

    The 3MdB is an original effort to construct a large multipurpose database of photoionization models. This is a more modern version of a previous attempt based on Cloudy3D and IDL tools. It is accessed by MySQL requests. The models are obtained using the well known and widely used Cloudy photoionization code (Ferland et al, 2013). The database is aimed to host grids of models with different references to identify each project and to facilitate the extraction of the desired data. We present here a description of the way the database is managed and some of the projects that use 3MdB. Anybody can ask for a grid to be run and stored in 3MdB, to increase the visibility of the grid and the potential side applications of it.

  6. 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.

  7. Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

    International Nuclear Information System (INIS)

    Kobayashi, Kazuya; Liang, Yunfeng; Matsuoka, Toshifumi; Sakka, Tetsuo

    2014-01-01

    The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules

  8. Predicting Flory-Huggins χ from Simulations

    Science.gov (United States)

    Zhang, Wenlin; Gomez, Enrique D.; Milner, Scott T.

    2017-07-01

    We introduce a method, based on a novel thermodynamic integration scheme, to extract the Flory-Huggins χ parameter as small as 10-3k T for polymer blends from molecular dynamics (MD) simulations. We obtain χ for the archetypical coarse-grained model of nonpolar polymer blends: flexible bead-spring chains with different Lennard-Jones interactions between A and B monomers. Using these χ values and a lattice version of self-consistent field theory (SCFT), we predict the shape of planar interfaces for phase-separated binary blends. Our SCFT results agree with MD simulations, validating both the predicted χ values and our thermodynamic integration method. Combined with atomistic simulations, our method can be applied to predict χ for new polymers from their chemical structures.

  9. Multi-Device to Multi-Device (MD2MD Content-Centric Networking Based on Multi-RAT Device

    Directory of Open Access Journals (Sweden)

    Cheolhoon Kim

    2017-11-01

    Full Text Available This paper proposes a method whereby a device can transmit and receive information using a beacon, and also describes application scenarios for the proposed method. In a multi-device to multi-device (MD2MD content-centric networking (CCN environment, the main issue involves searching for and connecting to nearby devices. However, if a device can’t find another device that satisfies its requirements, the connection is delayed due to the repetition of processes. It is possible to rapidly connect to a device without repetition through the selection of the optimal device using the proposed method. Consequently, the proposed method and scenarios are advantageous in that they enable efficient content identification and delivery in a content-centric Internet of Things (IoT environment, in which multiple mobile devices coexist.

  10. Picking a Fight with Water, and Water Lost ... an Electron

    Science.gov (United States)

    Herr, Jonathan D.

    The global need for energy is increasing, as is the importance of producing energy by green and renewable methodologies. This document outlines a research program dedicated to investigating a possible source for this form of energy generation and storage: solar fuels. The photon-induced splitting of water into molecular hydrogen and oxygen is currently hindered by large overpotentials from the oxidation half-reaction of water-splitting. This study concentrated on fundamental models of water-spitting chemistry, using a physical and computational chemistry analysis. The oxidation was first explored via ab initio electronic structure calculations of bare cationic water clusters, comprised of 2 to 21 molecules, in order to determine key electronic interactions that facilitate oxidation. Deeper understanding of these interactions could serve as guides for the development of viable water oxidation catalysts (WOC) designed to reduce overpotentials. The cationic water cluster study was followed by an investigation into hydrated copper (I) clusters, which acted as precursor models for real WOCs. Analyzing how the copper ion perturbed the properties of water clusters led to important electronic considerations for the development of WOCs, such as copper-water interactions that go beyond simple electrostatics. The importance of diagnostic thermodynamic properties, as well as anharmonic characteristics being persistent throughout oxidized water clusters, necessitated the use of quantum and classical molecular dynamics (MD) routines. Therefore, two new methods for accelerating computationally demanding classical and quantum MD methods were developed to increase their accessibility. The first method utilized a new form of electronic extrapolation - a linear prediction routine incorporating a Burg minimization - to decrease the iterations required for solving the electronic equations throughout the dynamics. The second method utilized a multiple-timestepping description of the

  11. Dynamics of water bound to crystalline cellulose

    Energy Technology Data Exchange (ETDEWEB)

    O’Neill, Hugh; Pingali, Sai Venkatesh; Petridis, Loukas; He, Junhong; Mamontov, Eugene; Hong, Liang; Urban, Volker; Evans, Barbara; Langan, Paul; Smith, Jeremy C.; Davison, Brian H.

    2017-09-19

    Interactions of water with cellulose are of both fundamental and technological importance. Here, we characterize the properties of water associated with cellulose using deuterium labeling, neutron scattering and molecular dynamics simulation. Quasi-elastic neutron scattering provided quantitative details about the dynamical relaxation processes that occur and was supported by structural characterization using small-angle neutron scattering and X-ray diffraction. We can unambiguously detect two populations of water associated with cellulose. The first is “non-freezing bound” water that gradually becomes mobile with increasing temperature and can be related to surface water. The second population is consistent with confined water that abruptly becomes mobile at ~260 K, and can be attributed to water that accumulates in the narrow spaces between the microfibrils. Quantitative analysis of the QENS data showed that, at 250 K, the water diffusion coefficient was 0.85 ± 0.04 × 10-10 m2sec-1 and increased to 1.77 ± 0.09 × 10-10 m2sec-1 at 265 K. MD simulations are in excellent agreement with the experiments and support the interpretation that water associated with cellulose exists in two dynamical populations. Our results provide clarity to previous work investigating the states of bound water and provide a new approach for probing water interactions with lignocellulose materials.

  12. Apple F-box Protein MdMAX2 Regulates Plant Photomorphogenesis and Stress Response

    Directory of Open Access Journals (Sweden)

    Jian-Ping An

    2016-11-01

    Full Text Available MAX2 (MORE AXILLARY GROWTH2 is involved in diverse physiological processes, including photomorphogenesis, the abiotic stress response, as well as karrikin and strigolactone signaling-mediated shoot branching. In this study, MdMAX2, an F-box protein that is a homolog of Arabidopsis MAX2, was identified and characterized. Overexpression of MdMAX2 in apple calli enhanced the accumulation of anthocyanin. Ectopic expression of MdMAX2 in Arabidopsis exhibited photomorphogenesis phenotypes, including increased anthocyanin content and decreased hypocotyl length. Further study indicated that MdMAX2 might promote plant photomorphogenesis by affecting the auxin signaling as well as other plant hormones. Transcripts of MdMAX2 were noticeably up-regulated in response to NaCl and Mannitol treatments. Moreover, compared with the wild type, the MdMAX2-overexpressing apple calli and Arabidopsis exhibited increased tolerance to salt and drought stresses. Taken together, these results suggest that MdMAX2 plays a positive regulatory role in plant photomorphogenesis and stress response.

  13. 75 FR 30296 - Special Local Regulation for Marine Event; Maryland Swim for Life, Chester River, Chestertown, MD

    Science.gov (United States)

    2010-06-01

    ... safety of life on navigable waters during the event. DATES: This rule is effective from 5:30 a.m. to 2:30...-AA08 Special Local Regulation for Marine Event; Maryland Swim for Life, Chester River, Chestertown, MD AGENCY: Coast Guard, DHS. ACTION: Temporary final rule. SUMMARY: The Coast Guard is temporarily changing...

  14. 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)

  15. Molecular dynamics study of room temperature ionic liquids with water at mica surface

    Directory of Open Access Journals (Sweden)

    Huanhuan Zhang

    2018-04-01

    Full Text Available Water in room temperature ionic liquids (RTILs could impose significant effects on their interfacial properties at a charged surface. Although the interfaces between RTILs and mica surfaces exhibit rich microstructure, the influence of water content on such interfaces is little understood, in particular, considering the fact that RTILs are always associated with water due to their hygroscopicity. In this work, we studied how different types of RTILs and different amounts of water molecules affect the RTIL-mica interfaces, especially the water distribution at mica surfaces, using molecular dynamics (MD simulation. MD results showed that (1 there is more water and a thicker water layer adsorbed on the mica surface as the water content increases, and correspondingly the average location of K+ ions is farther from mica surface; (2 more water accumulated at the interface with the hydrophobic [Emim][TFSI] than in case of the hydrophilic [Emim][BF4] due to the respective RTIL hydrophobicity and ion size. A similar trend was also observed in the hydrogen bonds formed between water molecules. Moreover, the 2D number density map of adsorbed water revealed that the high-density areas of water seem to be related to K+ ions and silicon/aluminum atoms on mica surface. These results are of great importance to understand the effects of hydrophobicity/hydrophicility of RTIL and water on the interfacial microstructure at electrified surfaces. Keywords: Room temperature ionic liquids, Hydrophobicity/hydrophicility, Water content, Electrical double layer, Mica surface

  16. Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

    Science.gov (United States)

    Peter, Emanuel K.

    2017-12-01

    In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

  17. Correlating TEM images of damage in irradiated materials to molecular dynamics simulations

    International Nuclear Information System (INIS)

    Schaeublin, R.; Caturla, M.-J.; Wall, M.; Felter, T.; Fluss, M.; Wirth, B.D.; Diaz de la Rubia, T.; Victoria, M.

    2002-01-01

    TEM image simulations are used to couple the results from molecular dynamics (MD) simulations to experimental TEM images. In particular we apply this methodology to the study of defects produced during irradiation. MD simulations have shown that irradiation of FCC metals results in a population of vacancies and interstitials forming clusters. The limitation of these simulations is the short time scales available, on the order of 100 s of picoseconds. Extrapolation of the results from these short times to the time scales of the laboratory has been difficult. We address this problem by two methods: we perform TEM image simulations of MD simulations of cascades with an improved technique, to relate defects produced at short time scales with those observed experimentally at much longer time scales. On the other hand we perform in situ TEM experiments of Au irradiated at liquid-nitrogen temperatures, and study the evolution of the produced damage as the temperature is increased to room temperature. We find that some of the defects observed in the MD simulations at short time scales using the TEM image simulation technique have features that resemble those observed in laboratory TEM images of irradiated samples. In situ TEM shows that stacking fault tetrahedra are present at the lowest temperatures and are stable during annealing up to room temperature, while other defect clusters migrate one dimensionally above -100 deg. C. Results are presented here

  18. Multinuclear NMR of CaSiO(3) glass: simulation from first-principles.

    Science.gov (United States)

    Pedone, Alfonso; Charpentier, Thibault; Menziani, Maria Cristina

    2010-06-21

    An integrated computational method which couples classical molecular dynamics simulations with density functional theory calculations is used to simulate the solid-state NMR spectra of amorphous CaSiO(3). Two CaSiO(3) glass models are obtained by shell-model molecular dynamics simulations, successively relaxed at the GGA-PBE level of theory. The calculation of the NMR parameters (chemical shielding and quadrupolar parameters), which are then used to simulate solid-state 1D and 2D-NMR spectra of silicon-29, oxygen-17 and calcium-43, is achieved by the gauge including projector augmented-wave (GIPAW) and the projector augmented-wave (PAW) methods. It is shown that the limitations due to the finite size of the MD models can be overcome using a Kernel Estimation Density (KDE) approach to simulate the spectra since it better accounts for the disorder effects on the NMR parameter distribution. KDE allows reconstructing a smoothed NMR parameter distribution from the MD/GIPAW data. Simulated NMR spectra calculated with the present approach are found to be in excellent agreement with the experimental data. This further validates the CaSiO(3) structural model obtained by MD simulations allowing the inference of relationships between structural data and NMR response. The methods used to simulate 1D and 2D-NMR spectra from MD GIPAW data have been integrated in a package (called fpNMR) freely available on request.

  19. Waiting time distribution in M/D/1 queueing systems

    DEFF Research Database (Denmark)

    Iversen, Villy Bæk; Staalhagen, Lars

    1999-01-01

    The well-known formula for the waiting time distribution of M/D/1 queueing systems is numerically unsuitable when the load is close to 1.0 and/or the results for a large waiting time are required. An algorithm for any load and waiting time is presented, based on the state probabilities of M/D/1...

  20. 75 FR 49992 - Peter W.S. Grigg, M.D.; Revocation of Registration

    Science.gov (United States)

    2010-08-16

    ... DEPARTMENT OF JUSTICE Drug Enforcement Administration Peter W.S. Grigg, M.D.; Revocation of... Order to Show Cause and Immediate Suspension of Registration to Peter W.S. Grigg, M.D. (Respondent), of... Registration, BG2107856, issued to Peter W.S. Grigg, M.D., be, and it hereby is, revoked. This Order is...

  1. Mass and heat transfer between evaporation and condensation surfaces: Atomistic simulation and solution of Boltzmann kinetic equation.

    Science.gov (United States)

    Zhakhovsky, Vasily V; Kryukov, Alexei P; Levashov, Vladimir Yu; Shishkova, Irina N; Anisimov, Sergey I

    2018-04-16

    Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard-Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data. The collision cross-section is also adjusted to provide a thermal flux in vapor identical to that in MD. Our MD simulations of evaporation toward a nonreflective absorbing boundary show that the velocity distribution function (VDF) of evaporated atoms has the nearly semi-Maxwellian shape because the binding energy of atoms evaporated from the interphase layer between bulk phase and vapor is much smaller than the cohesive energy in the condensed phase. Indeed, the calculated temperature and density profiles within the interphase layer indicate that the averaged kinetic energy of atoms remains near-constant with decreasing density almost until the interphase edge. Using consistent BKE and MD methods, the profiles of gas density, mass velocity, and temperatures together with VDFs in a gap of many mean free paths between the evaporation and condensation surfaces are obtained and compared. We demonstrate that the best fit of BKE results with MD simulations can be achieved with the evaporation and condensation coefficients both close to unity.

  2. 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....

  3. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Borg, Matthew K., E-mail: matthew.borg@strath.ac.uk [Department of Mechanical and Aerospace Engineering, University of Strathclyde, Glasgow G1 1XJ (United Kingdom); Lockerby, Duncan A., E-mail: duncan.lockerby@warwick.ac.uk [School of Engineering, University of Warwick, Coventry CV4 7AL (United Kingdom); Reese, Jason M., E-mail: jason.reese@ed.ac.uk [School of Engineering, University of Edinburgh, Edinburgh EH9 3JL (United Kingdom)

    2014-02-21

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C{sub 60} Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors.

  4. The FADE mass-stat: A technique for inserting or deleting particles in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Borg, Matthew K.; Lockerby, Duncan A.; Reese, Jason M.

    2014-01-01

    The emergence of new applications of molecular dynamics (MD) simulation calls for the development of mass-statting procedures that insert or delete particles on-the-fly. In this paper we present a new mass-stat which we term FADE, because it gradually “fades-in” (inserts) or “fades-out” (deletes) molecules over a short relaxation period within a MD simulation. FADE applies a time-weighted relaxation to the intermolecular pair forces between the inserting/deleting molecule and any neighbouring molecules. The weighting function we propose in this paper is a piece-wise polynomial that can be described entirely by two parameters: the relaxation time scale and the order of the polynomial. FADE inherently conserves overall system momentum independent of the form of the weighting function. We demonstrate various simulations of insertions of atomic argon, polyatomic TIP4P water, polymer strands, and C 60 Buckminsterfullerene molecules. We propose FADE parameters and a maximum density variation per insertion-instance that restricts spurious potential energy changes entering the system within desired tolerances. We also demonstrate in this paper that FADE compares very well to an existing insertion algorithm called USHER, in terms of accuracy, insertion rate (in dense fluids), and computational efficiency. The USHER algorithm is applicable to monatomic and water molecules only, but we demonstrate that FADE can be generally applied to various forms and sizes of molecules, such as polymeric molecules of long aspect ratio, and spherical carbon fullerenes with hollow interiors

  5. Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Karp, Jerome M.; Erylimaz, Ertan; Cowburn, David, E-mail: cowburn@cowburnlab.org, E-mail: David.cowburn@einstein.yu.edu [Albert Einstein College of Medicine of Yeshiva University, Department of Biochemistry (United States)

    2015-01-15

    There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

  6. All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies.

    Science.gov (United States)

    Prior, C; Danilāne, L; Oganesyan, V S

    2018-05-16

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of electron paramagnetic resonance (EPR) spectra of spin labelled DNA. Models for two structurally different DNA spin probes with either the rigid or flexible position of the nitroxide group in the base pair, employed in experimental studies previously, have been developed. By the application of the combined MD-EPR simulation methodology we aimed at the following. Firstly, to provide a test bed against a sensitive spectroscopic technique for the recently developed improved version of the parmbsc1 force field for MD modelling of DNA. The predicted EPR spectra show good agreement with the experimental ones available from the literature, thus confirming the accuracy of the currently employed DNA force fields. Secondly, to provide a quantitative interpretation of the motional contributions into the dynamics of spin probes in both duplex and single-strand DNA fragments and to analyse their perturbing effects on the local DNA structure. Finally, a combination of MD and EPR allowed us to test the validity of the application of the Model-Free (M-F) approach coupled with the partial averaging of magnetic tensors to the simulation of EPR spectra of DNA systems by comparing the resultant EPR spectra with those simulated directly from MD trajectories. The advantage of the M-F based EPR simulation approach over the direct propagation techniques is that it requires motional and order parameters that can be calculated from shorter MD trajectories. The reported MD-EPR methodology is transferable to the prediction and interpretation of EPR spectra of higher order DNA structures with novel types of spin labels.

  7. 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

  8. A molecular dynamics approach for predicting the glass transition temperature and plasticization effect in amorphous pharmaceuticals.

    Science.gov (United States)

    Gupta, Jasmine; Nunes, Cletus; Jonnalagadda, Sriramakamal

    2013-11-04

    The objectives of this study were as follows: (i) To develop an in silico technique, based on molecular dynamics (MD) simulations, to predict glass transition temperatures (Tg) of amorphous pharmaceuticals. (ii) To computationally study the effect of plasticizer on Tg. (iii) To investigate the intermolecular interactions using radial distribution function (RDF). Amorphous sucrose and water were selected as the model compound and plasticizer, respectively. MD simulations were performed using COMPASS force field and isothermal-isobaric ensembles. The specific volumes of amorphous cells were computed in the temperature range of 440-265 K. The characteristic "kink" observed in volume-temperature curves, in conjunction with regression analysis, defined the Tg. The MD computed Tg values were 367 K, 352 K and 343 K for amorphous sucrose containing 0%, 3% and 5% w/w water, respectively. The MD technique thus effectively simulated the plasticization effect of water; and the corresponding Tg values were in reasonable agreement with theoretical models and literature reports. The RDF measurements revealed strong hydrogen bond interactions between sucrose hydroxyl oxygens and water oxygen. Steric effects led to weak interactions between sucrose acetal oxygens and water oxygen. MD is thus a powerful predictive tool for probing temperature and water effects on the stability of amorphous systems during drug development.

  9. 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

  10. 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.

  11. MD Anderson's Population Health Approaches to Cancer Prevention.

    Science.gov (United States)

    Foxhall, Lewis; Moreno, Mark; Hawk, Ernest

    2018-02-01

    Texas's size and unique population demographics present challenges to addressing the state's cancer burden. The University of Texas MD Anderson Cancer Center is one of 69 National Cancer Institute-designated cancer centers across the United States. While these centers traditionally have focused on research, education and training, and providing research-driven patient care, they are in a unique position to collaboratively advance population health through cancer control. Unlike the traditional academic model of a three-legged stool representing research, education, and patient care, MD Anderson's mission includes a fourth leg that incorporates population health approaches. MD Anderson has leveraged state- and national-level data and freely available resources to develop population-health priorities and a set of evidence-based actions across policy, public and professional education, and community-based clinical service domains to address these priorities. Population health approaches complement dissemination and implementation research and treatment, and will be increasingly needed to address the growing cancer burden in Texas and the nation.

  12. 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.

  13. Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation.

    Science.gov (United States)

    Rayevsky, A V; Sharifi, M; Tukalo, M A

    2017-09-01

    Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA Leu was modeled wherever tRNA's acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS's editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA Leu and isoleucyl-tRNA Leu . In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Hydration of Caffeine at High Temperature by Neutron Scattering and Simulation Studies.

    Science.gov (United States)

    Tavagnacco, L; Brady, J W; Bruni, F; Callear, S; Ricci, M A; Saboungi, M L; Cesàro, A

    2015-10-22

    The solvation of caffeine in water is examined with neutron diffraction experiments at 353 K. The experimental data, obtained by taking advantage of isotopic H/D substitution in water, were analyzed by empirical potential structure refinement (EPSR) in order to extract partial structure factors and site-site radial distribution functions. In parallel, molecular dynamics (MD) simulations were carried out to interpret the data and gain insight into the intermolecular interactions in the solutions and the solvation process. The results obtained with the two approaches evidence differences in the individual radial distribution functions, although both confirm the presence of caffeine stacks at this temperature. The two approaches point to different accessibility of water to the caffeine sites due to different stacking configurations.

  15. 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.

  16. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    . Molecular dynamics (MD) simulation provides a complementary approach to the study of protein dynamics on similar time scales. Comparisons between NMR spectroscopy and MD simulations can be used to interpret experimental results and to improve the quality of simulation-related force fields and integration......A molecular-level understanding of the function of a protein requires knowledge of both its structural and dynamic properties. NMR spectroscopy allows the measurement of generalized order parameters that provide an atomistic description of picosecond and nanosecond fluctuations in protein structure...... methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...

  17. 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

  18. 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

  19. 76 FR 17673 - Bienvenido Tan, M.D.; Denial of Application

    Science.gov (United States)

    2011-03-30

    ... (alprazolam) to help him sleep. Id. at 64. R.E. opted to buy the drugs from Respondent's dispensary and... DEPARTMENT OF JUSTICE Drug Enforcement Administration [Docket No. 09-12] Bienvenido Tan, M.D... Control, Drug Enforcement Administration, issued an Order to Show Cause to Bienvenido Tan, M.D...

  20. 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.

  1. 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)

  2. Stochastic annealing simulations of defect interactions among subcascades

    Energy Technology Data Exchange (ETDEWEB)

    Heinisch, H.L. [Pacific Northwest National Lab., Richland, WA (United States); Singh, B.N.

    1997-04-01

    The effects of the subcascade structure of high energy cascades on the temperature dependencies of annihilation, clustering and free defect production are investigated. The subcascade structure is simulated by closely spaced groups of lower energy MD cascades. The simulation results illustrate the strong influence of the defect configuration existing in the primary damage state on subsequent intracascade evolution. Other significant factors affecting the evolution of the defect distribution are the large differences in mobility and stability of vacancy and interstitial defects and the rapid one-dimensional diffusion of small, glissile interstitial loops produced directly in cascades. Annealing simulations are also performed on high-energy, subcascade-producing cascades generated with the binary collision approximation and calibrated to MD results.

  3. A study on the plasticity of soda-lime silica glass via molecular dynamics simulations

    Science.gov (United States)

    Urata, Shingo; Sato, Yosuke

    2017-11-01

    Molecular dynamics (MD) simulations were applied to construct a plasticity model, which enables one to simulate deformations of soda-lime silica glass (SLSG) by using continuum methods. To model the plasticity, stress induced by uniaxial and a variety of biaxial deformations was measured by MD simulations. We found that the surfaces of yield and maximum stresses, which are evaluated from the equivalent stress-strain curves, are reasonably represented by the Mohr-Coulomb ellipsoid. Comparing a finite element model using the constructed plasticity model to a large scale atomistic model on a nanoindentation simulation of SLSG reveals that the empirical method is accurate enough to evaluate the SLSG mechanical responses. Furthermore, the effect of ion-exchange on the SLSG plasticity was examined by using MD simulations. As a result, it was demonstrated that the effects of the initial compressive stress on the yield and maximum stresses are anisotropic contrary to our expectations.

  4. Molecular dynamics simulation of melting of finite and infinite size silicene

    OpenAIRE

    Min, Tjun Kit; Yoon, Tiem Leong; Lim, Thong Leng

    2017-01-01

    We report the melting temperature of free-standing silicene by carrying out molecular dynamics (MD) simulation experiments using optimzed Stillinger-Weber (SW) potential by Zhang {\\it et al.}. The melting scenario of a free-standing silicene is well captured visually in our MD simulations. The data are systematically analyzed using a few qualitatively different indicators, including caloric curve, radial distribution function and a numerical indicator known as `global similarity index'. The o...

  5. 77 FR 5201 - Drawbridge Operation Regulation; Bear Creek, Dundalk, MD

    Science.gov (United States)

    2012-02-02

    ...-AA09 Drawbridge Operation Regulation; Bear Creek, Dundalk, MD AGENCY: Coast Guard, DHS. ACTION: Notice... operation of the Baltimore County highway bridge at Wise Avenue across Bear Creek, mile 3.4, between Dundalk... Avenue across Bear Creek, mile 3.4 between Dundalk and Sparrows Point, MD. This change would require the...

  6. 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...

  7. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  8. Molecular dynamics simulations suggest ligand's binding to nicotinamidase/pyrazinamidase.

    Directory of Open Access Journals (Sweden)

    Ji-Long Zhang

    Full Text Available The research on the binding process of ligand to pyrazinamidase (PncA is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA's activity. In the present study, molecular dynamics (MD simulation methods were performed to investigate the unbinding process of nicotinamide (NAM from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF based on the steered molecular dynamics (SMD simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM's unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand's binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs.

  9. 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.

  10. 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

  11. 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

  12. GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.

    Science.gov (United States)

    Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji

    2015-07-01

    GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.

  13. 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.

  14. Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

    Science.gov (United States)

    Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

    2018-01-09

    We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

  15. Pengaruh Brand Ambassador Terhadap Minat Beli Konsumen MD Clinic By Lazeta

    Directory of Open Access Journals (Sweden)

    Nurvita Septya Ningrum

    2016-10-01

    Full Text Available This research at MD Clinic by Lazeta which is in the beauty services that offer health care and facial, under of PT. Medina Global Care. MD Cilinic by Lazeta use the brand ambassador of introducing their products. The selection of brand ambassador motivated by positive image brought by the celebrities. Brand ambassadors chosen by the company as a symbol or a marker to represent the wishes and needs of prospective customers. MD Clinic by Lazeta choose Syahnaz as a brand ambassador for their products which is expected to to represent the product of MD Clinic by Lazeta, so the message can be understood by the consumer, who eventually would to lead the purchase intention. The purpose of this research was to investigate the influence of brand ambassadors on consumer purchase intention MD Clinic by Lazeta, Study on Business Administration Students year in 2103 Telkom University. Researchers used quantitative research methods. This research is population research, because all population is being respondent in this research. Populations of this research are 137 respondents. Collecting data in this research is conducted by using questionnaire distributed to all respondents, which all Students on Business Administration Telkom University who knows the MD Clinic by Lazeta. Data were analyzed using simple regression analysis and descriptive analysis.The results showed that the Brand Ambassador impact of consumer purchase intention on MD Clinic by Lazeta at the Students on Business Administration Telkom University years in 2013. Based on the calculation of the coefficient of determination (R2 can be seen the influence of brand ambassador variable (X on purchase intention (Y is 42.9%. While the remaining 57.1% is influenced by other factors which not examined in this research such as, pricing, marketing strategy and others.

  16. De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

    Energy Technology Data Exchange (ETDEWEB)

    Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H

    2006-09-04

    We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM/MD

  17. 77 FR 29692 - Segun M. Rasaki, M.D.; Decision and Order

    Science.gov (United States)

    2012-05-18

    ... CFR 1316.67. Dated: May 4, 2012. Michele M. Leonhart, Administrator. Paul E. Soeffing, Esq., for the... reinstatement.'' Stuart A. Bergman, M.D., 70 Fed. Reg. 33,193 (DEA 2005); Roger A. Rodriguez, M.D., 70 Fed. Reg...

  18. 77 FR 35021 - Kwan Bo Jin, M.D.; Decision and Order

    Science.gov (United States)

    2012-06-12

    ...] DEA registration is not appropriate.'' Anibal P. Herrera, M.D., 61 FR 65,075, 65,078 (DEA 1996); see... ``there were serious questions as to the integrity of the registrant.'' Anibal P. Herrera, M.D., 61 FR 65...

  19. Molecular Cloning and Expression Analysis of a Hexokinase Gene, MdHXK1 in Apple

    Directory of Open Access Journals (Sweden)

    Jin Zhao

    2016-03-01

    Full Text Available A hexokinase gene named MdHXK1 (MDP0000309677 was cloned from ‘Gala’ apple (Malus × domestica Borkh.. Sequence analysis showed that the MdHXK1 gene was 1 497 bp long and encoded 499 amino acids. The predicted molecular mass of this protein was 54.05 kD, and the pI was 5.76. A phylogenetic tree indicated apple MdHXK1 exhibited the highest sequence similarity to Pyrus bretschneideri PbHXK1. Analysis of the functional domain showed that the MdHXK1 protein included two conserved kinase domains. The prediction of subcellular localization suggested that the MdHXK1 protein was mainly localized in the cytoplasm. There was an indication that MdHXK1 existed as one copy in the apple genome by Southern blotting. Silico analysis suggested that the promoter sequence contained several typical cis-acting elements, including defense, sugar signaling and phytohormone responsive elements. Quantitative real-time PCR analysis demonstrated that the MdHXK1 gene was mainly expressed in stem and flower tissues. During the development of apple fruits, the expression of the MdHXK1 gene initially increased and then decreased. The changes on Glc phosphorylation relative activity and glucose concentration showed the same trend. In addition, the expression of this gene was induced by salt stress, low temperature, and abscisic acid (ABA. Finally, we obtained and purified the fused MdHXK1 protein by recombinant prokaryotic expression. Studies have demonstrated that MdHXK1 may participate in sugar metabolism in apple fruits. Enzyme encoded by MdHXK1 is a key factor in the mediation of sugar accumulation. Recently, researchers on hexokinase at home and abroad mainly focused on model plants, such as Arabidopsis, tobacco and rice, but orchard fruit like apple were underresearched. Our research established the foundation for the further study of the functions of MdHXK1.

  20. 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.

  1. A pilot study of MD (psychiatry) theses-based research.

    Science.gov (United States)

    Srivastava, Shrikant; Agarwal, Vivek; Subramanyam, Alka; Srivastava, Mona; Sathyanarayana Rao, T S; Rao, G Prasad; Khurana, Hitesh; Singh, Archana

    2018-01-01

    Undertaking a research project is mandatory for MD Psychiatry trainees. The present study was undertaken to assess the type of research activity being undertaken as part of MD Psychiatry dissertation, and its contribution to national and international literature. Three medical colleges supplied the data about the topic, names of the supervisor and the candidate, collaboration, funding accrued, and publication details of MD-based research carried out between years 2000 and 2010 inclusive; 95 records were collected for the final analysis. The details of the publications provided were cross-checked on the internet, which would have taken care of missed publications as well. Most studies were single-point assessment clinical studies. Only 2 studies had been funded, 11 had collaboration with other departments within the same institute, and 5 had inter-institute collaborations. Majority of the studies were not published. Only 30 were published as full paper and 9 as abstracts. Of these 30 full publications, only 3 were published in journals having JCI impact factor values (1.4, 1.3, and 1.4, respectively). The main finding of this pilot study was that MD-based research has low contribution to the national and international literature, and those articles which are published are in low impact journals. Suggestions for modifying this state of affairs are discussed.

  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. 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. MD 2485: Active halo control using narrowband and colored noise excitations

    CERN Document Server

    Garcia Morales, Hector; Kotzian, Gerd; Maclean, Ewen Hamish; Redaelli, Stefano; Valuch, Daniel; Wagner, Joschka; CERN. Geneva. ATS Department

    2018-01-01

    This MD note summarizes the actions carried out during the MD 2485 on Active halo control using narrowband and colored noise excitations. The goal of the MD was to repeat some promising cases already tested in the past and introduce a new excitation type based on applying a colored noise. Although we were able to repeat some cases using a narrowband excitation, due to a problem with the waveform generator, the colored noise excitation could not be accomplished as expected. In any case, we provide some results that may be useful for future MDs.

  6. 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.

  7. Dynamic Simulation of a Trigeneration Scheme for Domestic Purposes Based on Hybrid Techniques

    Directory of Open Access Journals (Sweden)

    Luis Acevedo

    2016-11-01

    Full Text Available In this paper, the design of a system providing electricity by coupling photovoltaic/thermal (PVT collectors and a wind turbine (WT, sanitary hot water (SHW coming from the PVT and evacuated tube collectors (ETCs and fresh water (FW produced in two seawater desalting facilities (membrane distillation, MD, and reverse osmosis, RO, has been carefully analyzed by means of a dynamic model developed in TRNSYS®. This analysis is compulsory to operate a lab-scale pilot plant that is being erected at Zaragoza, Spain. A new model-type has been included in TRNSYS® in order to include the MD unit in the scheme. A sensitivity analysis of some free-design variables, such that the ETC surface, PVT and ETC tilt, water storage tank, batteries capacities, and mass flow rates delivered to the SHW service and/or feeding the MD unit has been performed in order to propose the definite design of the scheme. The proposed base case was able to produce up to 15,311 L per year in the MD system and cover an electric energy demand of 1890 kWh. Coverage of SHW, water (including RO and MD and power is respectively 99.3%, 100% and 70%. However, daily and yearly assessment of FW, SHW and power produced with the optimized design gave a better coverage of water and energy demands for a typical single family home. The improved and definite design was able to increase its MD production in 35% and the electric energy in 7% compared with base case.

  8. Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169

    Science.gov (United States)

    Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

    2018-01-01

    Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3–6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0–4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications. PMID:29293588

  9. Rhodotorula taiwanensis MD1149 produces hypoacetylated PEFA compounds with increased surface activity compared to Rhodotorula babjevae MD1169.

    Science.gov (United States)

    Lyman, Mathew; Rubinfeld, Bonnee; Leif, Roald; Mulcahy, Heather; Dugan, Lawrence; Souza, Brian

    2018-01-01

    Biosurfactants have several desirable characteristics in the industrial sector: detergency, antimicrobial effects, skin hydration, and emulsibility. Several yeast glycolipids are currently being utilized in these capacities: sophorolipids, ustilagic acid, and mannosylerythritol lipids (MELs). An emerging class of glycolipids, termed polyol esters of fatty acids (PEFA), have recently been reported for Rhodotorula babjevae, a basidiomycetous yeast species that secretes hyperacetylated congeners of PEFA (typically with 3-6 acetylation modifications). While screening Rhodotorula species for surfactant production, we identified a new environmental isolate identified as Rhodotorula taiwanensis MD1149 that dropped the surface tension of the liquid medium, indicating that it produced a potent biosurfactant. Acid depolymerization of the purified biosurfactants, followed by gas chromatography-mass spectrometry (GC-MS) analysis revealed that the biosurfactants were composed of PEFA compounds composed mainly of mannitol and arabitol esters of 3-hydroxy fatty acid, 3-methoxy fatty acid, and fatty acids with a single double bond; chain lengths were mainly C16 and C18. Liquid chromatography-mass spectrometry (LC-MS) confirmed the predicted accurate mass of these compounds. Interestingly, PEFA compounds produced by Rhodotorula taiwanensis MD1149 were more surface active due to their hypoacetylation profile (0-4 acetylation modifications) compared to Rhodotorula babjevae MD1169. These disparate surface active properties, based on acetylation, change the hydrophilic-lipophilic balance (HLB) of these compounds, and their potential utility within industrial applications.

  10. Innovative Treatment Technologies for Natural Waters and Wastewaters

    Energy Technology Data Exchange (ETDEWEB)

    Childress, Amy E.

    2011-07-01

    The research described in this report focused on the development of novel membrane contactor processes (in particular, forward osmosis (FO), pressure retarded osmosis (PRO), and membrane distillation (MD)) in low energy desalination and wastewater treatment applications and in renewable energy generation. FO and MD are recently gaining national and international attention as viable, economic alternatives for removal of both established and emerging contaminants from natural and process waters; PRO is gaining worldwide attention as a viable source of renewable energy. The interrelationship of energy and water are at the core of this study. Energy and water are inextricably bound; energy usage and production must be considered when evaluating any water treatment process for practical application. Both FO and MD offer the potential for substantial energy and resource savings over conventional treatment processes and PRO offers the potential for renewable energy or energy offsets in desalination. Combination of these novel technologies with each other, with existing technologies (e.g., reverse osmosis (RO)), and with existing renewable energy sources (e.g., salinity gradient solar ponds) may enable much less expensive water production and also potable water production in remote or distributed locations. Two inter-related projects were carried out in this investigation. One focused on membrane bioreactors for wastewater treatment and PRO for renewable energy generation; the other focused on MD driven by a salinity gradient solar pond.

  11. 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.

  12. 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.

  13. 78 FR 47412 - Tyson D. Quy, M.D.; Decision and Order

    Science.gov (United States)

    2013-08-05

    ... Green, Jr., M.D., 59 FR 51,453 (DEA 1994); David E. Trawick, D.D.S., 53 FR 5,326 (DEA 1988). Here, the...) (ten years); Norman Alpert, M.D., 58 FR 67,420, 67,421 (DEA 1993) (seven years). Here, the conditions...

  14. Validating clustering of molecular dynamics simulations using polymer models

    Directory of Open Access Journals (Sweden)

    Phillips Joshua L

    2011-11-01

    Full Text Available Abstract Background Molecular dynamics (MD simulation is a powerful technique for sampling the meta-stable and transitional conformations of proteins and other biomolecules. Computational data clustering has emerged as a useful, automated technique for extracting conformational states from MD simulation data. Despite extensive application, relatively little work has been done to determine if the clustering algorithms are actually extracting useful information. A primary goal of this paper therefore is to provide such an understanding through a detailed analysis of data clustering applied to a series of increasingly complex biopolymer models. Results We develop a novel series of models using basic polymer theory that have intuitive, clearly-defined dynamics and exhibit the essential properties that we are seeking to identify in MD simulations of real biomolecules. We then apply spectral clustering, an algorithm particularly well-suited for clustering polymer structures, to our models and MD simulations of several intrinsically disordered proteins. Clustering results for the polymer models provide clear evidence that the meta-stable and transitional conformations are detected by the algorithm. The results for the polymer models also help guide the analysis of the disordered protein simulations by comparing and contrasting the statistical properties of the extracted clusters. Conclusions We have developed a framework for validating the performance and utility of clustering algorithms for studying molecular biopolymer simulations that utilizes several analytic and dynamic polymer models which exhibit well-behaved dynamics including: meta-stable states, transition states, helical structures, and stochastic dynamics. We show that spectral clustering is robust to anomalies introduced by structural alignment and that different structural classes of intrinsically disordered proteins can be reliably discriminated from the clustering results. To our

  15. Structural and dynamical properties of the porins OmpF and OmpC: insights from molecular simulations

    International Nuclear Information System (INIS)

    Kumar, Amit; Hajjar, Eric; Ruggerone, Paolo; Ceccarelli, Matteo

    2010-01-01

    In this paper we investigate the structural and dynamical properties of the two major porins (OmpF and OmpC) in Escherichia coli, using molecular dynamics (MD) simulations. In particular we characterized the atomic fluctuations, correlated motions, temperature dependence, solvent-accessible cross-sectional area and water dynamics in the key regions of the two channels. Our in-depth analysis allows us to highlight the importance of both the key conserved and substituted residues between OmpF and OmpC. The latter is characterized by a narrower and longer constriction region with respect to OmpF. OmpC also showed a higher stability upon increasing temperature. We then present the results of transport properties by using accelerated MD simulations to probe the diffusion of norfloxacin (a fluoroquinolone antibiotic) through the two porins OmpF/OmpC. Our study constitutes a step forward towards understanding the structure-function relationship of the two porins' channels. This will benefit the research of antibacterials with improved permeation properties and nanopores that aim to use these porins as sensing systems.

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

    International Nuclear Information System (INIS)

    Khomami, Bamin; Cui, Shengting; De Almeida, Valmor F.

    2013-01-01

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

  17. Functional Characterization of the Apple RING E3 Ligase MdMIEL1 in Transgenic Arabidopsis

    Directory of Open Access Journals (Sweden)

    Jianping AN

    2017-03-01

    Full Text Available E3 ubiquitin ligases are involved in various physiological processes, and they play pivotal roles in growth and development. In this study, we identified a previously unknown gene in the apple fruit (Malus × domestica and named it MdMIEL1. The MdMIEL1 gene encoded a protein that contained a zinc-finger domain at its N-terminus and a RING-finger motif at its C-terminus. To investigate MdMIEL1 functions, we generated transgenic Arabidopsis lines expressing the MdMIEL1 gene under the control of the Cauliflower mosaic virus 35S promoter. Interestingly, ectopic expression of MdMIEL1 in Arabidopsis produced multiple phenotypes, including early germination, early flowering and a lateral root number increase relative to wild-type plants. Further analysis indicated that MdMIEL1 regulated lateral root initiation by increasing auxin accumulation in the roots. In a word, these results suggest that, MdMIEL1 as a novel RING-finger ubiquitin ligase influences plant growth and development, and highlight that MdMIEL1 regulates lateral root growth.

  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. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  20. Simulation of Ground-Water Flow and Effects of Ground-Water Irrigation on Base Flow in the Elkhorn and Loup River Basins, Nebraska

    Science.gov (United States)

    Peterson, Steven M.; Stanton, Jennifer S.; Saunders, Amanda T.; Bradley, Jesse R.

    2008-01-01

    Irrigated agriculture is vital to the livelihood of communities in the Elkhorn and Loup River Basins in Nebraska, and ground water is used to irrigate most of the cropland. Concerns about the sustainability of ground-water and surface-water resources have prompted State and regional agencies to evaluate the cumulative effects of ground-water irrigation in this area. To facilitate understanding of the effects of ground-water irrigation, a numerical computer model was developed to simulate ground-water flow and assess the effects of ground-water irrigation (including ground-water withdrawals, hereinafter referred to as pumpage, and enhanced recharge) on stream base flow. The study area covers approximately 30,800 square miles, and includes the Elkhorn River Basin upstream from Norfolk, Nebraska, and the Loup River Basin upstream from Columbus, Nebraska. The water-table aquifer consists of Quaternary-age sands and gravels and Tertiary-age silts, sands, and gravels. The simulation was constructed using one layer with 2-mile by 2-mile cell size. Simulations were constructed to represent the ground-water system before 1940 and from 1940 through 2005, and to simulate hypothetical conditions from 2006 through 2045 or 2055. The first simulation represents steady-state conditions of the system before anthropogenic effects, and then simulates the effects of early surface-water development activities and recharge of water leaking from canals during 1895 to 1940. The first simulation ends at 1940 because before that time, very little pumpage for irrigation occurred, but after that time it became increasingly commonplace. The pre-1940 simulation was calibrated against measured water levels and estimated long-term base flow, and the 1940 through 2005 simulation was calibrated against measured water-level changes and estimated long-term base flow. The calibrated 1940 through 2005 simulation was used as the basis for analyzing hypothetical scenarios to evaluate the effects of

  1. Transport of water molecules through noncylindrical pores in multilayer nanoporous graphene.

    Science.gov (United States)

    Shahbabaei, Majid; Kim, Daejoong

    2017-08-09

    In this study, molecular dynamics (MD) simulations are used to examine the water transport properties through asymmetric hourglass-shaped pores in multilayer nanoporous graphene with a constant interlayer separation of 6 Å. The properties of the tested asymmetric hourglass-shaped pores [with the models having long cone (l 1 , -P) and short cone (l 2 , +P) entrances] are compared to a symmetric pore model. The study findings indicate that the water occupancy increases across the asymmetric pore (l 1 , -P) compared to (l 2 , +P), because of the length effect. The asymmetric pore, (l 1 , -P), yields higher flux compared to (l 2 , +P) and even the symmetric model, which can be attributed to the increase in the hydrogen bonds. In addition, the single-file water molecules across the narrowest pore diameter inside the (l 2 , +P) pore exhibit higher viscosity compared to those in the (l 1 , -P) pore because of the increase in the water layering effect. Moreover, it is found that the permeability inside the multilayer hourglass-shaped pore depends on the length of the flow path of the water molecules before approaching the layer with the smallest pore diameter. The probability of dipole orientation exhibits wider distribution inside the (l 1 , -P) system compared to (l 2 , +P), implying an enhanced formation of hydrogen bonding of water molecules. This results in the fast flow of water molecules. The MD trajectory shows that the dipole orientation across the single-layer graphene has frequently flipped compared to the dipole orientation across the pores in multilayer graphene, which is maintained during the whole simulation time (although the dipole orientation has flipped for a few picoseconds at the beginning of the simulation). This can be attributed to the energy barrier induced by the individual layer. The diffusion coefficient of water molecules inside the (l 2 , +P) system increases with pressure difference, however, it decreases inside the (l 1 , -P) system because

  2. Molecular dynamics modeling and simulation of void growth in two dimensions

    Science.gov (United States)

    Chang, H.-J.; Segurado, J.; Rodríguez de la Fuente, O.; Pabón, B. M.; LLorca, J.

    2013-10-01

    The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids.

  3. Molecular dynamics modeling and simulation of void growth in two dimensions

    International Nuclear Information System (INIS)

    Chang, H-J; Segurado, J; LLorca, J; Rodríguez de la Fuente, O; Pabón, B M

    2013-01-01

    The mechanisms of growth of a circular void by plastic deformation were studied by means of molecular dynamics in two dimensions (2D). While previous molecular dynamics (MD) simulations in three dimensions (3D) have been limited to small voids (up to ≈10 nm in radius), this strategy allows us to study the behavior of voids of up to 100 nm in radius. MD simulations showed that plastic deformation was triggered by the nucleation of dislocations at the atomic steps of the void surface in the whole range of void sizes studied. The yield stress, defined as stress necessary to nucleate stable dislocations, decreased with temperature, but the void growth rate was not very sensitive to this parameter. Simulations under uniaxial tension, uniaxial deformation and biaxial deformation showed that the void growth rate increased very rapidly with multiaxiality but it did not depend on the initial void radius. These results were compared with previous 3D MD and 2D dislocation dynamics simulations to establish a map of mechanisms and size effects for plastic void growth in crystalline solids. (paper)

  4. Molecular Dynamics Simulations Suggest Ligand’s Binding to Nicotinamidase/Pyrazinamidase

    Science.gov (United States)

    Zhang, Ji-Long; Zheng, Qing-Chuan; Li, Zheng-Qiang; Zhang, Hong-Xing

    2012-01-01

    The research on the binding process of ligand to pyrazinamidase (PncA) is crucial for elucidating the inherent relationship between resistance of Mycobacterium tuberculosis and PncA’s activity. In the present study, molecular dynamics (MD) simulation methods were performed to investigate the unbinding process of nicotinamide (NAM) from two PncA enzymes, which is the reverse of the corresponding binding process. The calculated potential of mean force (PMF) based on the steered molecular dynamics (SMD) simulations sheds light on an optimal binding/unbinding pathway of the ligand. The comparative analyses between two PncAs clearly exhibit the consistency of the binding/unbinding pathway in the two enzymes, implying the universality of the pathway in all kinds of PncAs. Several important residues dominating the pathway were also determined by the calculation of interaction energies. The structural change of the proteins induced by NAM’s unbinding or binding shows the great extent interior motion in some homologous region adjacent to the active sites of the two PncAs. The structure comparison substantiates that this region should be very important for the ligand’s binding in all PncAs. Additionally, MD simulations also show that the coordination position of the ligand is displaced by one water molecule in the unliganded enzymes. These results could provide the more penetrating understanding of drug resistance of M. tuberculosis and be helpful for the development of new antituberculosis drugs. PMID:22761821

  5. Crystal twinning of human MD-2 recognizing endotoxin cores of lipopolysaccharide

    International Nuclear Information System (INIS)

    Ohto, Umeharu; Satow, Yoshinori

    2008-01-01

    Twinned crystals of humaan MD-2 are transformed into single crystals with cryoprotectant optimization. Twinning of crystals causes overlapping of two or more reciprocal lattice points, and hence structure amplitudes for a single crystalline domain are hardly obtained from X-ray diffraction intensities. MD-2 protein forms a stable complex with Toll-like receptor 4 and recognizes bacterial lipopolysaccharide (LPS). Excessive immune responses activated by LPS cause septic shocks. Saccharide-trimmed human MD-2 crystallizes in the tetragonal form with apparent Laue symmetry of 4/mmm, and diffraction intensities from these crystals indicate crystal twinning. The crystal consists of two different domains, A and B. The c A axis of domain A coincides with the c B axis of domain B with a smaller lattice, and the a A axis corresponds to the (a B + b B ) axis. This twinning severely imposes difficulty in structure determination. Through optimization of cryoprotectant, domain A was thoroughly transformed into domain B. The crystal containing only domain B is in space group P4 1 2 1 2 with one MD-2 molecule in the asymmetric unit. The structure of this form of MD-2 as well as its complex with antiendotoxic lipid IVa was successfully determined using the multiple isomorphous replacement method

  6. 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.

  7. Alpha-gamma decay studies of 253No and its daughter products 253Md, 249Fm

    International Nuclear Information System (INIS)

    Hessberger, F.P.; Antalic, S.; Kalaninova, Z.; Saro, S.; Venhart, M.; Ackermann, D.; Heinz, S.; Kindler, B.; Kojouharov, I.; Kuusiniemi, P.; Lommel, B.; Mann, R.; Sulignano, B.; Hofmann, S.; Streicher, B.; Leino, M.; Nishio, K.

    2012-01-01

    Nuclear structure and decay of the isotope 253 No and its decay products 249 Fm and 253 Md were investigated by means of α - γ spectroscopy. Besides the established strong γ transitions from the 9/2 - [734] Nilsson level in 249 Fm, populated predominantly by the α decay of 253 No, into the ground-state (gs) rotational band, a couple of weaker γ lines (58.3, 129.2, 209.3 and 669.5keV) were observed and placed into the 249 Fm level scheme. The transition from the 7/2 - level in 249 Es, populated by the α decay of 253 Md, into the 9/2 + member of the gs rotational band, so far established for other odd-mass Es isotopes, was observed clearly. GEANT4 simulations were performed to investigate the influence of energy summing between α particles and conversion electrons (CE) on the shape of the α spectra at different implantation energies, leading to evidence for a weak α decay branch of 253 No into the gs of 249 Fm or the ground-state rotational band, respectively. (orig.)

  8. Center of excellence for mobile sensor data-to-knowledge (MD2K).

    Science.gov (United States)

    Kumar, Santosh; Abowd, Gregory D; Abraham, William T; al'Absi, Mustafa; Beck, J Gayle; Chau, Duen Horng; Condie, Tyson; Conroy, David E; Ertin, Emre; Estrin, Deborah; Ganesan, Deepak; Lam, Cho; Marlin, Benjamin; Marsh, Clay B; Murphy, Susan A; Nahum-Shani, Inbal; Patrick, Kevin; Rehg, James M; Sharmin, Moushumi; Shetty, Vivek; Sim, Ida; Spring, Bonnie; Srivastava, Mani; Wetter, David W

    2015-11-01

    Mobile sensor data-to-knowledge (MD2K) was chosen as one of 11 Big Data Centers of Excellence by the National Institutes of Health, as part of its Big Data-to-Knowledge initiative. MD2K is developing innovative tools to streamline the collection, integration, management, visualization, analysis, and interpretation of health data generated by mobile and wearable sensors. The goal of the big data solutions being developed by MD2K is to reliably quantify physical, biological, behavioral, social, and environmental factors that contribute to health and disease risk. The research conducted by MD2K is targeted at improving health through early detection of adverse health events and by facilitating prevention. MD2K will make its tools, software, and training materials widely available and will also organize workshops and seminars to encourage their use by researchers and clinicians. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  9. Dynamic Stabilization of Metal Oxide–Water Interfaces

    Energy Technology Data Exchange (ETDEWEB)

    McBriarty, Martin E.; von Rudorff, Guido Falk; Stubbs, Joanne; Eng, Peter; Blumberger, Jochen; Rosso, Kevin M.

    2017-02-08

    Metal oxide growth, dissolution, and redox reactivity depend on the structure and dynamics at the interface with aqueous solution. We present the most definitive analysis to date of the hydrated naturally abundant r-cut (11$\\bar{0}$2) termination of the iron oxide hematite (α-Fe2O3). In situ synchrotron X-ray scattering analysis reveals a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Large-scale hybrid-functional density functional theory-based molecular dynamics (DFT-MD) simulations show how this structure is dynamically stabilized by picosecond exchange between aquo groups and adsorbed water, even under nominally dry conditions. Surface pKa prediction based on bond valence analysis suggests that water exchange may influence the proton transfer reactions associated with acid/base reactivity at the interface. Our findings rectify inconsistencies between existing models and may be extended to resolving more complex electrochemical phenomena at metal oxide-water interfaces.

  10. MdHB1 down-regulation activates anthocyanin biosynthesis in the white-fleshed apple cultivar 'Granny Smith'.

    Science.gov (United States)

    Jiang, Yonghua; Liu, Cuihua; Yan, Dan; Wen, Xiaohong; Liu, Yanli; Wang, Haojie; Dai, Jieyu; Zhang, Yujie; Liu, Yanfei; Zhou, Bin; Ren, Xiaolin

    2017-02-01

    Coloration in apple (Malus×domestica) flesh is mainly caused by the accumulation of anthocyanin. Anthocyanin is biosynthesized through the flavonoid pathway and regulated by MYB, bHLH, and WD40 transcription factors (TFs). Here, we report that the HD-Zip I TF MdHB1 was also involved in the regulation of anthocyanin accumulation. MdHB1 silencing caused the accumulation of anthocyanin in 'Granny Smith' flesh, whereas its overexpression reduced the flesh content of anthocyanin in 'Ballerina' (red-fleshed apple). Moreover, flowers of transgenic tobacco (Nicotiana tabacum 'NC89') overexpressing MdHB1 showed a remarkable reduction in pigmentation. Transient promoter activation assays and yeast one-hybrid results indicated that MdHB1 indirectly inhibited expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and UDP-glucose:flavonoid 3-O-glycosyltransferase (UFGT). Yeast two-hybrid and bimolecular fluorescence complementation determined that MdHB1 acted as a homodimer and could interact with MYB, bHLH, and WD40 in the cytoplasm, consistent with its cytoplasmic localization by green fluorescent protein fluorescence observations. Together, these results suggest that MdHB1 constrains MdMYB10, MdbHLH3, and MdTTG1 to the cytoplasm, and then represses the transcription of MdDFR and MdUFGT indirectly. When MdHB1 is silenced, these TFs are released to activate the expression of MdDFR and MdUFGT and also anthocyanin biosynthesis, resulting in red flesh in 'Granny Smith'. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  11. 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.

  12. Membrane distillation for wastewater reverse osmosis concentrate treatment with water reuse potential

    KAUST Repository

    Naidu, Gayathri; Jeong, Sanghyun; Choi, Youngkwon; Vigneswaran, Saravanamuthu

    2016-01-01

    Membrane distillation (MD) was evaluated as a treatment option of wastewater reverse osmosis concentrate (WWROC) discharged from wastewater reclamation plants (WRPs). A direct contact MD (DCMD), at obtaining 85% water recovery of WWROC showed only 13–15% flux decline and produced good quality permeate (10–15 µS/cm, 99% ion rejection) at moderate feed temperature of 55 °C. Prevalent calcium carbonate (CaCO3) deposition on the MD membrane occurred in treating WWROC at elevated concentrations. The combination of low salinity and loose CaCO3 adhesion on the membrane did not significantly contribute to DCMD flux decline. Meanwhile, high organic content in WWROC (58–60 mg/L) resulted in a significant membrane hydrophobicity reduction (70% lower water contact angle than virgin membrane) attributed to low molecular weight organic adhesion onto the MD membrane. Granular activated carbon (GAC) pretreatment helped in reducing organic contents of WWROC by 46–50%, and adsorbed a range of hydrophobic and hydrophilic micropollutants. This ensured high quality water production by MD (micropollutants-free) and enhanced its reuse potential. The MD concentrated WWROC was suitable for selective ion precipitation, promising a near zero liquid discharge in WRPs.

  13. Membrane distillation for wastewater reverse osmosis concentrate treatment with water reuse potential

    KAUST Repository

    Naidu, Gayathri

    2016-11-29

    Membrane distillation (MD) was evaluated as a treatment option of wastewater reverse osmosis concentrate (WWROC) discharged from wastewater reclamation plants (WRPs). A direct contact MD (DCMD), at obtaining 85% water recovery of WWROC showed only 13–15% flux decline and produced good quality permeate (10–15 µS/cm, 99% ion rejection) at moderate feed temperature of 55 °C. Prevalent calcium carbonate (CaCO3) deposition on the MD membrane occurred in treating WWROC at elevated concentrations. The combination of low salinity and loose CaCO3 adhesion on the membrane did not significantly contribute to DCMD flux decline. Meanwhile, high organic content in WWROC (58–60 mg/L) resulted in a significant membrane hydrophobicity reduction (70% lower water contact angle than virgin membrane) attributed to low molecular weight organic adhesion onto the MD membrane. Granular activated carbon (GAC) pretreatment helped in reducing organic contents of WWROC by 46–50%, and adsorbed a range of hydrophobic and hydrophilic micropollutants. This ensured high quality water production by MD (micropollutants-free) and enhanced its reuse potential. The MD concentrated WWROC was suitable for selective ion precipitation, promising a near zero liquid discharge in WRPs.

  14. 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.

  15. Functional and structural insights revealed by molecular dynamics simulations of an essential RNA editing ligase in Trypanosoma brucei.

    Directory of Open Access Journals (Sweden)

    Rommie E Amaro

    2007-11-01

    Full Text Available RNA editing ligase 1 (TbREL1 is required for the survival of both the insect and bloodstream forms of Trypanosoma brucei, the parasite responsible for the devastating tropical disease African sleeping sickness. The type of RNA editing that TbREL1 is involved in is unique to the trypanosomes, and no close human homolog is known to exist. In addition, the high-resolution crystal structure revealed several unique features of the active site, making this enzyme a promising target for structure-based drug design. In this work, two 20 ns atomistic molecular dynamics (MD simulations are employed to investigate the dynamics of TbREL1, both with and without the ATP substrate present. The flexibility of the active site, dynamics of conserved residues and crystallized water molecules, and the interactions between TbREL1 and the ATP substrate are investigated and discussed in the context of TbREL1's function. Differences in local and global motion upon ATP binding suggest that two peripheral loops, unique to the trypanosomes, may be involved in interdomain signaling events. Notably, a significant structural rearrangement of the enzyme's active site occurs during the apo simulations, opening an additional cavity adjacent to the ATP binding site that could be exploited in the development of effective inhibitors directed against this protozoan parasite. Finally, ensemble averaged electrostatics calculations over the MD simulations reveal a novel putative RNA binding site, a discovery that has previously eluded scientists. Ultimately, we use the insights gained through the MD simulations to make several predictions and recommendations, which we anticipate will help direct future experimental studies and structure-based drug discovery efforts against this vital enzyme.

  16. 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.

  17. 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...

  18. Fluids density functional theory and initializing molecular dynamics simulations of block copolymers

    Science.gov (United States)

    Brown, Jonathan R.; Seo, Youngmi; Maula, Tiara Ann D.; Hall, Lisa M.

    2016-03-01

    Classical, fluids density functional theory (fDFT), which can predict the equilibrium density profiles of polymeric systems, and coarse-grained molecular dynamics (MD) simulations, which are often used to show both structure and dynamics of soft materials, can be implemented using very similar bead-based polymer models. We aim to use fDFT and MD in tandem to examine the same system from these two points of view and take advantage of the different features of each methodology. Additionally, the density profiles resulting from fDFT calculations can be used to initialize the MD simulations in a close to equilibrated structure, speeding up the simulations. Here, we show how this method can be applied to study microphase separated states of both typical diblock and tapered diblock copolymers in which there is a region with a gradient in composition placed between the pure blocks. Both methods, applied at constant pressure, predict a decrease in total density as segregation strength or the length of the tapered region is increased. The predictions for the density profiles from fDFT and MD are similar across materials with a wide range of interfacial widths.

  19. 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.

  20. Stability of nanocrystalline Ni-based alloys: coupling Monte Carlo and molecular dynamics simulations

    Science.gov (United States)

    Waseda, O.; Goldenstein, H.; Silva, G. F. B. Lenz e.; Neiva, A.; Chantrenne, P.; Morthomas, J.; Perez, M.; Becquart, C. S.; Veiga, R. G. A.

    2017-10-01

    The thermal stability of nanocrystalline Ni due to small additions of Mo or W (up to 1 at%) was investigated in computer simulations by means of a combined Monte Carlo (MC)/molecular dynamics (MD) two-steps approach. In the first step, energy-biased on-lattice MC revealed segregation of the alloying elements to grain boundaries. However, the condition for the thermodynamic stability of these nanocrystalline Ni alloys (zero grain boundary energy) was not fulfilled. Subsequently, MD simulations were carried out for up to 0.5 μs at 1000 K. At this temperature, grain growth was hindered for minimum global concentrations of 0.5 at% W and 0.7 at% Mo, thus preserving most of the nanocrystalline structure. This is in clear contrast to a pure Ni model system, for which the transformation into a monocrystal was observed in MD simulations within 0.2 μs at the same temperature. These results suggest that grain boundary segregation of low-soluble alloying elements in low-alloyed systems can produce high-temperature metastable nanocrystalline materials. MD simulations carried out at 1200 K for 1 at% Mo/W showed significant grain boundary migration accompanied by some degree of solute diffusion, thus providing additional evidence that solute drag mostly contributed to the nanostructure stability observed at lower temperature.

  1. Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach

    Science.gov (United States)

    Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I.; Wang, Cai-Zhuang; Ho, Kai-Ming

    2018-02-01

    The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B 2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

  2. Overcoming the Time Limitation in Molecular Dynamics Simulation of Crystal Nucleation: A Persistent-Embryo Approach.

    Science.gov (United States)

    Sun, Yang; Song, Huajing; Zhang, Feng; Yang, Lin; Ye, Zhuo; Mendelev, Mikhail I; Wang, Cai-Zhuang; Ho, Kai-Ming

    2018-02-23

    The crystal nucleation from liquid in most cases is too rare to be accessed within the limited time scales of the conventional molecular dynamics (MD) simulation. Here, we developed a "persistent embryo" method to facilitate crystal nucleation in MD simulations by preventing small crystal embryos from melting using external spring forces. We applied this method to the pure Ni case for a moderate undercooling where no nucleation can be observed in the conventional MD simulation, and obtained nucleation rate in good agreement with the experimental data. Moreover, the method is applied to simulate an even more sluggish event: the nucleation of the B2 phase in a strong glass-forming Cu-Zr alloy. The nucleation rate was found to be 8 orders of magnitude smaller than Ni at the same undercooling, which well explains the good glass formability of the alloy. Thus, our work opens a new avenue to study solidification under realistic experimental conditions via atomistic computer simulation.

  3. Expansion shock waves in the implosion process from a time-reversible molecular-dynamics simulation of a dual explosion process

    International Nuclear Information System (INIS)

    Komatsu, Nobuyoshi; Abe, Takashi

    2007-01-01

    Why does not an expansion shock wave exist in a gaseous medium in nature? The reason has been widely believed to be the irreversibility in nature, while an obvious demonstration for this belief has not been accomplished yet. In order to resolve the question from a microscopic viewpoint, an implosion process dual to an explosion process was investigated by means of the molecular-dynamics method (MD). To this aim, we employed a ''bit-reversible algorithm (Bit MD)'' that was completely time-reversible in a microscopic viewpoint and was free from any round-off error. Here we show that, through a dual implosion simulation (i.e., a time-reversible simulation of the explosion), a kind of expansion shock wave is successfully formed in the Bit MD simulation. Furthermore, we show that when the controlled noise is intentionally added to the Bit MD, the expansion shock wave disappears dramatically and turns into an isentropic expansion wave, even if the noise is extremely small. Since the controlled noise gives rise to the irreversibility in the Bit MD simulation, it can be concluded that the irreversibility in the system prohibits the expansion shock wave from appearing in the system

  4. 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

  5. Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

    International Nuclear Information System (INIS)

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

    2015-01-01

    Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties

  6. The hydration enthalpies of Md3+ and Lr3+

    International Nuclear Information System (INIS)

    Bruechle, W.; Schaedel, M.; Scherer, U.W.; Kratz, J.V.

    1987-10-01

    Lawrencium (3-min 260 Lr) and lighter actinides were produced in the bombardement of a 249 Bk target with 18 O ions and loaded onto a cation exchange column in 0.05 M α-hydroxy-isobutyrate solution at pH = 4.85 together with the radioactive lanthanide tracers 166 Ho, 171 Er, and 171 Tm. In elutions with 0.12 M α-hydroxy-isobutyrate solution (pH = 4.85) trivalent Lr was eluted exactly together with the Er tracer and Md close to Ho. Lr elutes much later than expected based on the known elution positions of the lighter actinides and the expected analogy to the elution positions of the homologous lanthanides. From the measured elution positions, ionic radii were calculated for Lr 3+ and Md 3+ . Semiempirical models allow the calculation of the heat of hydration from the ionic radii, resulting in ΔH hyd ≅ - 3654 kJ/mol for Md 3+ and ΔH hyd ≅ - 3689 kJ/mol for Lr 3+ . (orig.)

  7. Molecular Simulation towards Efficient and Representative Subsurface Reservoirs Modeling

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-01-01

    This dissertation focuses on the application of Monte Carlo (MC) molecular simulation and Molecular Dynamics (MD) in modeling thermodynamics and flow of subsurface reservoir fluids. At first, MC molecular simulation is proposed as a promising method

  8. Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

    Science.gov (United States)

    Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

    2012-10-01

    Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

  9. 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.

  10. Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation.

    Directory of Open Access Journals (Sweden)

    Kei Moritsugu

    Full Text Available Molecular dynamics (MD simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a "Motion Tree", to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory.

  11. Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

    International Nuclear Information System (INIS)

    Ko, Soon Heum; Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel; Jha, Shantenu

    2014-01-01

    Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

  12. 76 FR 81826 - Drawbridge Operation Regulation; Pocomoke River, Pocomoke City, MD

    Science.gov (United States)

    2011-12-29

    ... Operation Regulation; Pocomoke River, Pocomoke City, MD AGENCY: Coast Guard, DHS. ACTION: Notice of... River, mile 15.6, at Pocomoke City, MD. The deviation restricts the operation of the draw span to... five hours advance notice is given. The Route 675 Bridge across Pocomoke River, mile 15.6 at Pocomoke...

  13. Proteomics and SSH analyses of ALA-promoted fruit coloration and evidence for the involvement of a MADS-box gene, MdMADS1

    Directory of Open Access Journals (Sweden)

    Xinxin Feng

    2016-11-01

    Full Text Available Skin color is a key quality attribute of fruits and how to improve fruit coloration has long been a major concern. 5-Aminolevulinic acid (ALA, a natural plant growth regulator, can significantly increase anthocyanin accumulation in fruit skin and therefore effectively improve coloration of many fruits, including apple. However, the molecular mechanism how ALA stimulates anthocyanin accumulation in fruit skin remains unknown. Here, we investigated the impact of ALA on apple skin at the protein and mRNA levels. A total of 85 differentially expressed proteins in apple skins between ALA and water treatment (control were identified by complementary gel-based and gel-freeseparation techniques. Most of these differentially expressed proteins were up-regulated by ALA. Function analysis suggested that 87.06% of the ALA-responsive proteins were associated with fruit ripening. To further screen ALA-responsive regulators, we constructed a subtracted cDNA library (tester: ALA treatment; driver: control and obtained 104 differentially expressed unigenes, of which 38 unigenes were indicators for the fruit ripening-related gene. The differentially changed proteins and transcripts did not correspond well at an individual level, but showed similar regulated direction in function at the pathway level. Among the identified fruit ripening-related genes, the expression of MdMADS1, a developmental transcription regulator of fruit ripening, was positively correlated with expression of anthocyanin biosynthetic genes (MdCHS, MdDFR, MdLDOX and MdUFGT in apple skin under ALA treatment. Moreover, overexpression of MdMADS1 enhanced anthocyanin content in transformed apple calli, which was further enhanced by ALA. The anthocyanin content in MdMADS1-silenced calli was less than that in the control with ALA treatment, but higher than that without ALA treatment. These results indicated that MdMADS1 is involved in ALA-induced anthocyanin accumulation. In addition, anthocyanin

  14. Scalable Atomistic Simulation Algorithms for Materials Research

    Directory of Open Access Journals (Sweden)

    Aiichiro Nakano

    2002-01-01

    Full Text Available A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD simulations and quantum-mechanical (QM calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-quality programs also feature wavelet-based computational-space decomposition for adaptive load balancing, spacefilling-curve-based adaptive data compression with user-defined error bound for scalable I/O, and octree-based fast visibility culling for immersive and interactive visualization of massive simulation data.

  15. 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.

  16. The molecular mechanism underlying anthocyanin metabolism in apple using the MdMYB16 and MdbHLH33 genes.

    Science.gov (United States)

    Xu, Haifeng; Wang, Nan; Liu, Jingxuan; Qu, Changzhi; Wang, Yicheng; Jiang, Shenghui; Lu, Ninglin; Wang, Deyun; Zhang, Zongying; Chen, Xuesen

    2017-05-01

    MdMYB16 forms homodimers and directly inhibits anthocyanin synthesis via its C-terminal EAR repressor. It weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis when overexpressing MdbHLH33 in callus overexpressing MdMYB16. MdMYB16 could interact with MdbHLH33. Anthocyanins are strong antioxidants that play a key role in the prevention of cardiovascular disease, cancer, and diabetes. The germplasm of Malus sieversii f. neidzwetzkyana is important for the study of anthocyanin metabolism. To date, only limited studies have examined the negative regulatory mechanisms underlying anthocyanin synthesis in apple. Here, we analyzed the relationship between anthocyanin levels and MdMYB16 expression in mature Red Crisp 1-5 apple (M. domestica) fruit, generated an evolutionary tree, and identified an EAR suppression sequence and a bHLH binding motif of the MdMYB16 protein using protein sequence analyses. Overexpression of MdMYB16 or MdMYB16 without bHLH binding sequence (LBSMdMYB16) in red-fleshed callus inhibited MdUFGT and MdANS expression and anthocyanin synthesis. However, overexpression of MdMYB16 without the EAR sequence (LESMdMYB16) in red-fleshed callus had no inhibitory effect on anthocyanin. The yeast one-hybrid assay showed that MdMYB16 and LESMdMYB16 interacted the promoters of MdANS and MdUFGT, respectively. Yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays showed that MdMYB16 formed homodimers and interacted with MdbHLH33, however, the LBSMdMYB16 could not interact with MdbHLH33. We overexpressed MdbHLH33 in callus overexpressing MdMYB16 and found that it weakened the inhibitory effect of MdMYB16 on anthocyanin synthesis. Together, these results suggested that MdMYB16 and MdbHLH33 may be important part of the regulatory network controlling the anthocyanin biosynthetic pathway.

  17. Temperature dependence of creep compliance of highly cross-linked epoxy: A molecular simulation study

    International Nuclear Information System (INIS)

    Khabaz, Fardin; Khare, Ketan S.; Khare, Rajesh

    2014-01-01

    We have used molecular dynamics (MD) simulations to study the effect of temperature on the creep compliance of neat cross-linked epoxy. Experimental studies of mechanical behavior of cross-linked epoxy in literature commonly report creep compliance values, whereas molecular simulations of these systems have primarily focused on the Young’s modulus. In this work, in order to obtain a more direct comparison between experiments and simulations, atomistically detailed models of the cross-linked epoxy are used to study their creep compliance as a function of temperature using MD simulations. The creep tests are performed by applying a constant tensile stress and monitoring the resulting strain in the system. Our results show that simulated values of creep compliance increase with an increase in both time and temperature. We believe that such calculations of the creep compliance, along with the use of time temperature superposition, hold great promise in connecting the molecular insight obtained from molecular simulation at small length- and time-scales with the experimental behavior of such materials. To the best of our knowledge, this work is the first reported effort that investigates the creep compliance behavior of cross-linked epoxy using MD simulations

  18. Evaporation of nanoscale water on a uniformly complete wetting surface at different temperatures.

    Science.gov (United States)

    Guo, Yuwei; Wan, Rongzheng

    2018-05-03

    The evaporation of nanoscale water films on surfaces affects many processes in nature and industry. Using molecular dynamics (MD) simulations, we show the evaporation of a nanoscale water film on a uniformly complete wetting surface at different temperatures. With the increase in temperature, the growth of the water evaporation rate becomes slow. Analyses show that the hydrogen bond (H-bond) lifetimes and orientational autocorrelation times of the outermost water film decrease slowly with the increase in temperature. Compared to a thicker water film, the H-bond lifetimes and orientational autocorrelation times of a monolayer water film are much slower. This suggests that the lower evaporation rate of the monolayer water film on a uniformly complete wetting surface may be caused by the constriction of the water rotation due to the substrate. This finding may be helpful for controlling nanoscale water evaporation within a certain range of temperatures.

  19. Molecular Dynamics Simulations of Escherichia coli Ammonia Channel AmtB

    DEFF Research Database (Denmark)

    Nygaard, Thomas Pedersen

    2007-01-01

    p°a s°akaldte styrede MD simuleringer, hvor NH3 og NH+4 blev trukket igennem kanalen. Selve mekanismen, som involverer ovenfor nævnte A162 og D160, blev dernæst testet vha. af en special type MD simulering, hvor dele af systemet behandles kvantemekanisk. Den foresl°aede mekanisme kunne dog hverken...

  20. Validity of displacement energy evaluation using molecular statics simulation in Li2O

    International Nuclear Information System (INIS)

    Oda, Takuji; Tanaka, Satoru

    2007-01-01

    Understanding on radiation damage processes in Li-containing oxides has been regarded as an important subject in fusion blanket engineering, because radiation defects significantly affect the tritium behavior and the material property. The displacement energy is a key parameter that determines the number of defects created by radiation, and thus should be evaluated. However, its determination by experiments has not been done, probably due to difficulties arising from insulating property and complicated crystalline structures of Li-containing oxides. Molecular simulation is an alternative method to evaluate the displacement energy. Two techniques have been used; one is molecular dynamics simulation (MD) and the other is molecular statics simulation (MS) with the sudden approximation. MD can provide atomic-scale views of radiation events in the dynamics and has been more widely applied. MS seems to provide less reliable results than MD for lack of the dynamics. Nevertheless, its low computational cost could be attractive for application to ternary Li-containing oxides of complicated structures. In the present work, therefore, we aimed to verify how reliable values MS can provide in comparison with MD. Li2O was chosen to be a test material, because Li2O has the simplest structure among Li-containing oxides, which facilitates verification of MS results. We evaluated threshold displacement energies by MS for a few tens of different irradiation direction, and compared with previous MD results. DL-POLY code was used for MD, while GULP code for MS. In MD, lower threshold energies have been observed for Li than O (20 eV for Li and 50 eV for O on average). This tendency was also realized in MS (15 eV for Li and 40 eV for O), although values were often underestimated by a few tens %. As for dependence of displacement energy on irradiation direction, MS basically gave results different from MD, not only in quantity but also in quality. It was considered that MS is useful to

  1. Hybrid Quantum Mechanics/Molecular Mechanics Solvation Scheme for Computing Free Energies of Reactions at Metal-Water Interfaces.

    Science.gov (United States)

    Faheem, Muhammad; Heyden, Andreas

    2014-08-12

    We report the development of a quantum mechanics/molecular mechanics free energy perturbation (QM/MM-FEP) method for modeling chemical reactions at metal-water interfaces. This novel solvation scheme combines planewave density function theory (DFT), periodic electrostatic embedded cluster method (PEECM) calculations using Gaussian-type orbitals, and classical molecular dynamics (MD) simulations to obtain a free energy description of a complex metal-water system. We derive a potential of mean force (PMF) of the reaction system within the QM/MM framework. A fixed-size, finite ensemble of MM conformations is used to permit precise evaluation of the PMF of QM coordinates and its gradient defined within this ensemble. Local conformations of adsorbed reaction moieties are optimized using sequential MD-sampling and QM-optimization steps. An approximate reaction coordinate is constructed using a number of interpolated states and the free energy difference between adjacent states is calculated using the QM/MM-FEP method. By avoiding on-the-fly QM calculations and by circumventing the challenges associated with statistical averaging during MD sampling, a computational speedup of multiple orders of magnitude is realized. The method is systematically validated against the results of ab initio QM calculations and demonstrated for C-C cleavage in double-dehydrogenated ethylene glycol on a Pt (111) model surface.

  2. 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

  3. 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.

  4. 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.

  5. Long-time atomistic simulations with the Parallel Replica Dynamics method

    Science.gov (United States)

    Perez, Danny

    Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.

  6. An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

    Energy Technology Data Exchange (ETDEWEB)

    Donev, A; Garcia, A L; Alder, B J

    2007-07-30

    A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

  7. Evaluation of melting point of UO2 by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Arima, Tatsumi; Idemitsu, Kazuya; Inagaki, Yaohiro; Tsujita, Yuichi; Kinoshita, Motoyasu; Yakub, Eugene

    2009-01-01

    The melting point of UO 2 has been evaluated by molecular dynamics simulation (MD) in terms of interatomic potential, pressure and Schottky defect concentration. The Born-Mayer-Huggins potentials with or without a Morse potential were explored in the present study. Two-phase simulation whose supercell at the initial state consisted of solid and liquid phases gave the melting point comparable to the experimental data using the potential proposed by Yakub. The heat of fusion was determined by the difference in enthalpy at the melting point. In addition, MD calculations showed that the melting point increased with pressure applied to the system. Thus, the Clausius-Clapeyron equation was verified. Furthermore, MD calculations clarified that an addition of Schottky defects, which generated the local disorder in the UO 2 crystal, lowered the melting point.

  8. 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...

  9. 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.

  10. 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.

  11. Molecular dynamics simulation of amplitude modulation atomic force microscopy

    International Nuclear Information System (INIS)

    Hu, Xiaoli; Martini, Ashlie; Egberts, Philip; Dong, Yalin

    2015-01-01

    Molecular dynamics (MD) simulations were used to model amplitude modulation atomic force microscopy (AM-AFM). In this novel simulation, the model AFM tip responds to both tip–substrate interactions and to a sinusoidal excitation signal. The amplitude and phase shift of the tip oscillation observed in the simulation and their variation with tip–sample distance were found to be consistent with previously reported trends from experiments and theory. These simulation results were also fit to an expression enabling estimation of the energy dissipation, which was found to be smaller than that in a corresponding experiment. The difference was analyzed in terms of the effects of tip size and substrate thickness. Development of this model is the first step toward using MD to gain insight into the atomic-scale phenomena that occur during an AM-AFM measurement. (paper)

  12. 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)

  13. Effective As(III) Removal by A Multi-Charged Hydroacid Complex Draw Solute Facilitated Forward Osmosis-Membrane Distillation (FO-MD) Processes.

    Science.gov (United States)

    Ge, Qingchun; Han, Gang; Chung, Tai-Shung

    2016-03-01

    Effective removal of As(III) from water by an oxalic acid complex with the formula of Na3[Cr(C2O4)3] (Na-Cr-OA) is demonstrated via an forward osmosis-membrane distillation (FO-MD) hybrid system in this study. Na-Cr-OA first proved its superiority as a draw solute with high water fluxes and negligible reverse fluxes in FO, then a systematic investigation of the Na-Cr-OA promoted FO process was conducted to ascertain the factors in As(III) removal. Relatively high water fluxes of 28 LMH under the FO mode and 74 LMH under the pressure retarded osmosis (PRO) mode were achieved when using a 1000 ppm As(III) solution as the feed and 1.0 M Na-Cr-OA as the draw solution at 60 °C. As(III) removal with a water recovery up to 21.6% (FO mode) and 48.3% (PRO mode) were also achieved in 2 h. An outstanding As(III) rejection with 30-3000 μg/L As(III) in the permeate was accomplished when As(III) feed solutions varied from 5 × 10(4) to 1 × 10(6) μg/L, superior to the best FO performance reported for As(III) removal. Incorporating MD into FO not only makes As(III) removal sustainable by reconcentrating the Na-Cr-OA solution simultaneously, but also reduces the As(III) concentration below 10 μg/L in the product water, meeting the WHO standard.

  14. Short- and medium-range order in a Zr73Pt27 glass: Experimental and simulation studies

    International Nuclear Information System (INIS)

    Wang, S.Y.; Wang, C.Z.; Li, M.Z.; Huang, L.; Ott, R.T.; Kramer, M.J.; Sordelet, D.J.; Ho, K.M.

    2008-01-01

    The structure of a Zr 73 Pt 27 metallic glass, which forms a Zr 5 Pt 3 (Mn 5 Si 3 -type) phase having local atomic clusters with distorted icosahedral coordination during the primary crystallization, has been investigated by means of x-ray diffraction and combining ab initio molecular-dynamics (MD) and reverse Monte Carlo (RMC) simulations. The ab initio MD simulation provides an accurate description of short-range structural and chemical ordering in the glass. A three-dimensional atomistic model of 18?000 atoms for the glass structure has been generated by the RMC method utilizing both the structure factor S(k) from x-ray diffraction experiment and the partial pair-correlation functions from ab initio MD simulation. Honeycutt and Andersen index and Voronoi cell analyses, respectively, were used to characterize the short- and medium-range order in the atomistic structure models generated by ab initio MD and RMC simulations. The ab initio results show that an icosahedral type of short-range order is predominant in the glass state. Furthermore, analysis of the atomic model from the constrained RMC simulations reveals that the icosahedral-like clusters are packed in arrangements having higher-order correlations, thus establishing medium-range topological order up to two or three cluster shells.

  15. Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers

    International Nuclear Information System (INIS)

    Vashishta, Priya; Kalia, Rajiv

    2005-01-01

    Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report

  16. MD#2183: Calibration of the IR6 B2 diamond BLMs

    CERN Document Server

    Valette, Matthieu; Lindstrom, Bjorn Hans Filip

    2018-01-01

    In case of an asynchronous beam dump with a fully filled LHC machine, causing ~40 bunches to impact on the movable dump protection absorber (TCDQ), it is expected that all standard ionisation chamber Beam Loss Monitors (IC BLM) around the LHC dumping region in IR6 will be saturated. Diamond Beam Loss Monitors (dBLM) were therefore installed next to the TCDQ downstream of the extraction kickers. These detectors allow resolving losses at a nanosecond timescale and with a dynamic range of several orders of magnitude; thus, allowing to derive the number of nominal bunches impacting the TCDQ. After a first series of calibrations using asynchronous beam dump tests, an experiment was conducted during MD#1182 to demonstrate the possibility of resolving a nominal bunch hitting the TCDQ. During this first MD only the Beam 1 dBLM was calibrated appropriately, a second calibration MD was therefore performed in 2017 for the B2 system. Results from this MD and conclusions regarding dBLM saturation with a top energy nominal...

  17. 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

  18. 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

  19. 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

  20. Vacancy profile in reverse osmosis membranes studied by positron annihilation lifetime measurements and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Shimazu, A; Shintani, T; Hirose, M; Goto, H; Suzuki, R; Kobayashi, Y

    2013-01-01

    The positron annihilation technique using a slow positron beam can be used for the study of the vacancy profiles in typical reverse osmosis (RO) membranes. In this study, the vacancy profile in the polyamide membrane that exhibits a high permselectivity between ions and water was studied using the positron annihilation technique and molecular dynamics simulations. Ortho-positronium (o-Ps) lifetimes in the surface region of the membranes were evaluated by using a slow positron beam. The diffusion behavior of Na + and water in the polyamides was simulated by molecular dynamics (MD) methods using the TSUBAME2 supercomputer at the Tokyo Institute of Technology and discussed with the vacancy profile probed by the o-Ps. The results suggested that the large hydration size of Na + compared to the vacancy size in the polyamides contributes to the increased diffusivity selectivity of water/Na + that is related to the NaCl desalination performance of the membrane. Both the hydration size of the ions and the vacancy size appeared to be significant parameters to discuss the diffusivity selectivity of water/ions in typical polyamide membranes.

  1. Isotope effects in lithium hydride and lithium deuteride crystals by molecular dynamics simulations.

    Science.gov (United States)

    Dammak, Hichem; Antoshchenkova, Ekaterina; Hayoun, Marc; Finocchi, Fabio

    2012-10-31

    Molecular dynamics (MD) simulations have been carried out to study isotope effects in lithium hydride and lithium deuteride crystals. Quantum effects on nuclear motion have been included through a quantum thermal bath (QTB). The interatomic forces were described either within the density functional theory (DFT) in the generalized gradient approximation (GGA) or by the phenomenological approach using the shell model. For both models, the isotopic shift in the lattice parameter can be successfully predicted by QTB-MD simulations. The slope of the experimental isotopic shift in pressure is satisfactorily reproduced by QTB-MD within DFT-GGA, in contrast to both density functional perturbation theory and QTB-MD with the shell model. We have analyzed the reasons for these discrepancies through the vibrational densities of states and the isotopic shifts in bulk modulus. The results illustrate the importance of anharmonic contributions to vibrations and to the isotopic pressure shift between LiH and LiD.

  2. 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.

  3. Hydrogen bond dynamical properties of adsorbed liquid water monolayers with various TiO2 interfaces

    Science.gov (United States)

    English, Niall J.; Kavathekar, Ritwik S.; MacElroy, J. M. D.

    2012-12-01

    Equilibrium classical molecular dynamics (MD) simulations have been performed to investigate the hydrogen-bonding kinetics of water in contact with rutile-(110), rutile-(101), rutile-(100), and anatase-(101) surfaces at room temperature (300 K). It was observed that anatase-(101) exhibits the longest-lived hydrogen bonds in terms of overall persistence, followed closely by rutile-(110). The relaxation times, defined as the integral of the autocorrelation of the hydrogen bond persistence function, were also longer for these two cases, while decay of the autocorrelation function was slower. The increased number and overall persistence of hydrogen bonds in the adsorbed water monolayers at these surfaces, particularly for anatase-(101), may serve to promote possible water photolysis activity thereon.

  4. Effects of deformability and thermal motion of lipid membrane on electroporation: By molecular dynamics simulations

    International Nuclear Information System (INIS)

    Sun, Sheng; Yin, Guangyao; Lee, Yi-Kuen; Wong, Joseph T.Y.; Zhang, Tong-Yi

    2011-01-01

    Research highlights: → MD simulations show that deformability and thermal motion of membrane affect electroporation. → Stiffer membrane inhibits electroporation and makes water penetrate from both sides. → Higher temperature accelerates electroporation. -- Abstract: Effects of mechanical properties and thermal motion of POPE lipid membrane on electroporation were studied by molecular dynamics simulations. Among simulations in which specific atoms of lipids were artificially constrained at their equilibrium positions using a spring with force constant of 2.0 kcal/(mol A 2 ) in the external electric field of 1.4 kcal/(mol A e), only constraint on lateral motions of lipid tails prohibited electroporation while non-tail parts had little effects. When force constant decreased to 0.2 kcal/(mol A 2 ) in the position constraints on lipid tails in the external electric field of 2.0 kcal/(mol A e), water molecules began to enter the membrane. Position constraints of lipid tails allow water to penetrate from both sides of membrane. Thermal motion of lipids can induce initial defects in the hydrophobic core of membrane, which are favorable nucleation sites for electroporation. Simulations at different temperatures revealed that as the temperature increases, the time taken to the initial pore formation will decrease.

  5. Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model-Free Approach.

    Science.gov (United States)

    Prior, Christopher; Oganesyan, Vasily S

    2017-09-21

    We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Molecular simulations of hydrated proton exchange membranes. The structure

    Energy Technology Data Exchange (ETDEWEB)

    Marcharnd, Gabriel [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie; Bordeaux Univ., Talence (France). Dept. of Chemistry; Bopp, Philippe A. [Bordeaux Univ., Talence (France). Dept. of Chemistry; Spohr, Eckhard [Duisburg-Essen Univ., Essen (Germany). Lehrstuhl fuer Theoretische Chemie

    2013-01-15

    The structure of two hydrated proton exchange membranes for fuel cells (PEMFC), Nafion {sup registered} (Dupont) and Hyflon {sup registered} (Solvay), is studied by all-atom molecular dynamics (MD) computer simulations. Since the characteristic times of these systems are long compared to the times for which they can be simulated, several different, but equivalent, initial configurations with a large degree of randomness are generated for different water contents and then equilibrated and simulated in parallel. A more constrained structure, analog to the newest model proposed in the literature based on scattering experiments, is investigated in the same way. One might speculate that a limited degree of entanglement of the polymer chains is a key feature of the structures showing the best agreement with experiment. Nevertheless, the overall conclusion remains that the scattering experiments cannot distinguish between the several, in our view equally plausible, structural models. We thus find that the characteristic features of experimental scattering curves are, after equilibration, fairly well reproduced by all systems prepared with our method. We thus study in more detail some structural details. We attempt to characterize the spatial and size distribution of the water rich domains, which is where the proton diffusion mostly takes place, using several clustering algorithms. (orig.)

  7. The rotation of NO3− as a probe of molecular ion - water interactions

    Directory of Open Access Journals (Sweden)

    Ogden T.

    2013-03-01

    Full Text Available The hydration dynamics of aqueous nitrate, NO3−(aq, is studied by 2D-IR spectroscopy, UV-IR- and UV-UV transient absorption spectroscopy. The experimental results are compared to Car-Parinello molecular dynamics (MD simulations. The 2D-IR measurements and MD simulations of the non-degenerate asymmetric stretch vibrations of nitrate reveal an intermodal energy exchange occurring on a 0.2 ps time scale related to hydrogen bond fluctuations. The transient absorption measurements find that the nitrate ions rotate in 2 ps. The MD simulations indicate that the ion rotation is associated with the formation of new hydrogen bonds. The 2 ps rotation time thus indicates that the hydration shell of aqueous nitrate is rather labile.

  8. Desalination and water recycling by air gap membrane distillation

    NARCIS (Netherlands)

    Meindersma, G.W.; Guijt, C.M.; Haan, de A.B.

    2006-01-01

    Membrane distillation (MD) is an emerging technology for desalination. Membrane distillation differs from other membrane technologies in that the driving force for desalination is the difference in vapour pressure of water across the membrane, rather than total pressure. The membranes for MD are

  9. Desalination and Water Recycling by Air Gap Membrane Distillation

    NARCIS (Netherlands)

    Meindersma, G.W.; Guijt, C.M.; de Haan, A.B.

    2006-01-01

    Membrane distillation (MD) is an emerging technology for desalination. Membrane distillation differs from other membrane technologies in that the driving force for desalination is the difference in vapour pressure of water across the membrane, rather than total pressure. The membranes for MD are

  10. MdATG18a overexpression improves tolerance to nitrogen deficiency and regulates anthocyanin accumulation through increased autophagy in transgenic apple.

    Science.gov (United States)

    Sun, Xun; Jia, Xin; Huo, Liuqing; Che, Runmin; Gong, Xiaoqing; Wang, Ping; Ma, Fengwang

    2018-02-01

    Nitrogen (N) availability is an essential factor for plant growth. Recycling and remobilization of N have strong impacts on crop yield and quality under N deficiency. Autophagy is a critical nutrient-recycling process that facilitates remobilization under starvation. We previously showed that an important AuTophaGy (ATG) protein from apple, MdATG18a, has a positive role in drought tolerance. In this study, we explored its biological role in response to low-N. Overexpression of MdATG18a in both Arabidopsis and apple improved tolerance to N-depletion and caused a greater accumulation of anthocyanin. The increased anthocyanin concentration in transgenic apple was possibly due to up-regulating flavonoid biosynthetic and regulatory genes (MdCHI, MdCHS, MdANS, MdPAL, MdUFGT, and MdMYB1) and higher soluble sugars concentration. MdATG18a overexpression enhanced starch degradation with up-regulating amylase gene (MdAM1) and up-regulated sugar metabolism related genes (MdSS1, MdHXKs, MdFK1, and MdNINVs). Furthermore, MdATG18a functioned in nitrate uptake and assimilation by up-regulating nitrate reductase MdNIA2 and 3 high-affinity nitrate transporters MdNRT2.1/2.4/2.5. MdATG18a overexpression also elevated other important MdATG genes expression and autophagosomes formation under N-depletion, which play key contributions to above changes. Together, these results demonstrate that overexpression of MdATG18a enhances tolerance to N-deficiencies and plays positive roles in anthocyanin biosynthesis through greater autophagic activity. © 2017 John Wiley & Sons Ltd.

  11. JGromacs: a Java package for analyzing protein simulations.

    Science.gov (United States)

    Münz, Márton; Biggin, Philip C

    2012-01-23

    In this paper, we introduce JGromacs, a Java API (Application Programming Interface) that facilitates the development of cross-platform data analysis applications for Molecular Dynamics (MD) simulations. The API supports parsing and writing file formats applied by GROMACS (GROningen MAchine for Chemical Simulations), one of the most widely used MD simulation packages. JGromacs builds on the strengths of object-oriented programming in Java by providing a multilevel object-oriented representation of simulation data to integrate and interconvert sequence, structure, and dynamics information. The easy-to-learn, easy-to-use, and easy-to-extend framework is intended to simplify and accelerate the implementation and development of complex data analysis algorithms. Furthermore, a basic analysis toolkit is included in the package. The programmer is also provided with simple tools (e.g., XML-based configuration) to create applications with a user interface resembling the command-line interface of GROMACS applications. JGromacs and detailed documentation is freely available from http://sbcb.bioch.ox.ac.uk/jgromacs under a GPLv3 license .

  12. Molecular Dynamics Studies of Overbased Detergents on a Water Surface.

    Science.gov (United States)

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

    2017-07-25

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

  13. STRATEGI PEMASARAN PUBLIC RELATIONS MD ENTERTAINMENT PADA PEMASARAN FILM HABIBIE & AINUN

    OpenAIRE

    Trisna Adi Permana; Lilis Puspitasari

    2015-01-01

    Tujuan penelitian ini adalah untuk mengetahui perencanaan, implementasi serta evaluasi dari strategi Marketing Public Relations yang ditetapkan PR MD Entertainment pada film Habibie & Ainun pada tahun 2012-2013. Metode yang dilakukan adalah metode deskriptif yang bertujuan melukiskan secara sistematis fakta atau karakteristik populasi tertentu atau bidang tertentu secara faktual dan cermat. Hasil penelitian menunjukan PR MD Entertainment telah melakukan tahapan-tahapan atau Teknik...

  14. 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.

  15. 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.

  16. 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.

  17. Dynamics of ligand exchange mechanism at Cu(II) in water: an ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region.

    Science.gov (United States)

    Moin, Syed Tarique; Hofer, Thomas S; Weiss, Alexander K H; Rode, Bernd M

    2013-07-07

    Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment.

  18. Dynamics of ligand exchange mechanism at Cu(II) in water: An ab initio quantum mechanical charge field molecular dynamics study with extended quantum mechanical region

    International Nuclear Information System (INIS)

    Moin, Syed Tarique; Hofer, Thomas S.; Weiss, Alexander K. H.; Rode, Bernd M.

    2013-01-01

    Ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) were successfully applied to Cu(II) embedded in water to elucidate structure and to understand dynamics of ligand exchange mechanism. From the simulation studies, it was found that using an extended large quantum mechanical region including two shells of hydration is required for a better description of the dynamics of exchanging water molecules. The structural features characterized by radial distribution function, angular distribution function and other analytical parameters were consistent with experimental data. The major outcome of this study was the dynamics of exchange mechanism and reactions in the first hydration shell that could not be studied so far. The dynamical data such as mean residence time of the first shell water molecules and other relevant data from the simulations are close to the results determined experimentally. Another major characteristic of hydrated Cu(II) is the Jahn-Teller distortion which was also successfully reproduced, leading to the final conclusion that the dominating aqua complex is a 6-coordinated species. The ab initio QMCF-MD formalism proved again its capabilities of unraveling even ambiguous properties of hydrated species that are far difficult to explore by any conventional quantum mechanics/molecular mechanics (QM/MM) approach or experiment

  19. 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.

  20. 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

  1. InforMD: a new initiative to raise public awareness about breast density.

    Science.gov (United States)

    Hugo, Honor J; Zysk, Aneta; Dasari, Pallave; Britt, Kara; Hopper, John L; Stone, Jennifer; Thompson, Erik W; Ingman, Wendy V

    2018-01-01

    On a mammogram, breast density (also known as mammographic density) is shown as white and bright regions and is associated with reduced sensitivity in cancer detection and increased breast cancer risk. However, many Australian women are unaware of the significance of breast density as it is not routinely reported or discussed. In order to address this lack of knowledge, Australian breast cancer researchers with expertise in mammographic density formed the InforMD alliance (INformation FORum on Mammographic Density) in 2016. The alliance is working to raise awareness of breast density with the goal of improving breast cancer diagnosis and health outcomes for women. The InforMD website (www.InforMD.org.au) was launched in October 2016, coinciding with a major nationwide public awareness campaign by the alliance during breast cancer awareness month. The website contains unbiased, accurate, updated information on breast density. The website also provides summaries of major research articles in layperson language, recent news items related to breast density, links to relevant information for health professionals, events, and feature articles. Members of the public and health professionals can also subscribe for news updates. The interactive online Forum section facilitates discussion between health professionals, scientists and members of the public. To increase online traffic to the website, Facebook (www.facebook.com/BeInforMD) and Twitter (https://twitter.com/BeInforMD_) pages were launched in December 2016. Since its launch, InforMD has generated considerable interest. The public awareness campaign reached over 7 million Australians through a combination of newspaper, TV, radio, and online news. The website has attracted 13,058 unique visitors and 30,353 page views (data as of 19/12/2017). Breast cancer researchers have a significant role to play in disseminating information to the public on breast density. A combination of mainstream and social media, together with

  2. An apple B-box protein, MdCOL11, is involved in UV-B- and temperature-induced anthocyanin biosynthesis.

    Science.gov (United States)

    Bai, Songling; Saito, Takanori; Honda, Chikako; Hatsuyama, Yoshimichi; Ito, Akiko; Moriguchi, Takaya

    2014-11-01

    Our studies showed that an apple B-box protein, MdCOL11, the homolog of AtBBX22, is involved in UV-B- and temperature-induced anthocyanin biosynthesis in apple peel. Anthocyanin is responsible for the red pigmentation in apple peel and a R2R3 MYB gene, MdMYBA/1/10, a homolog of MdMYBA, controls its accumulation. Arabidopsis PAP1 is under the control of a series of upstream factors involved in light signal transduction and photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5) and B-box family (BBX) proteins. In this study, we identified and characterized the homolog of Arabidopsis BBX22 in apple, designated as MdCOL11. Overexpression of MdCOL11 in Arabidopsis enhanced the accumulation of anthocyanin. In apples, MdCOL11 was differentially expressed in all tissues, with the highest expression in petals and the lowest expression in the xylem. Transcripts of MdCOL11 noticeably accumulated at the ripening stage, concomitant with increases in the expressions of anthocyanin biosynthesis-related genes. In an in vitro treatment experiment, MdCOL11 was upregulated in an ultra-violet (UV)-B- and temperature-dependent manner, together with the inductions of anthocyanin biosynthesis-related genes and anthocyanin accumulation in apple peel. Furthermore, a dual-luciferase assay indicated that (1) MdCOL11 regulated the expression of MdMYBA and (2) MdCOL11 was a target of MdHY5. Taken together, our results suggest that MdCOL11 is involved in MdHY5-mediated signal transduction and regulates anthocyanin accumulation in apple peel, which sheds new light on anthocyanin accumulation in apples.

  3. 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...

  4. Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

    Science.gov (United States)

    Putri, A. M.; Sumaryada, T.; Wahyudi, S. T.

    2017-07-01

    Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.

  5. Simulation of Intra- or transboundary surface-water-rights hierarchies using the farm process for MODFLOW-2000

    Science.gov (United States)

    Schmid, W.; Hanson, R.T.

    2007-01-01

    Water-rights driven surface-water allocations for irrigated agriculture can be simulated using the farm process for MODFLOW-2000. This paper describes and develops a model, which simulates routed surface-water deliveries to farms limited by streamflow, equal-appropriation allotments, or a ranked prior-appropriation system. Simulated diversions account for deliveries to all farms along a canal according to their water-rights ranking and for conveyance losses and gains. Simulated minimum streamflow requirements on diversions help guarantee supplies to senior farms located on downstream diverting canals. Prior appropriation can be applied to individual farms or to groups of farms modeled as "virtual farms" representing irrigation districts, irrigated regions in transboundary settings, or natural vegetation habitats. The integrated approach of jointly simulating canal diversions, surface-water deliveries subject to water-rights constraints, and groundwater allocations is verified on numerical experiments based on a realistic, but hypothetical, system of ranked virtual farms. Results are discussed in light of transboundary water appropriation and demonstrate the approach's suitability for simulating effects of water-rights hierarchies represented by international treaties, interstate stream compacts, intrastate water rights, or ecological requirements. ?? 2007 ASCE.

  6. Strategi Pemasaran Public Relations Md Entertainment Pada Pemasaran Film Habibie & Ainun

    OpenAIRE

    Permana, Trisna Adi; Puspitasari, Lilis

    2015-01-01

    Tujuan penelitian ini adalah untuk mengetahui perencanaan, implementasi serta evaluasi dari strategiMarketing Public Relations yang ditetapkan PR MD Entertainment pada film Habibie & Ainun pada tahun2012-2013. Metode yang dilakukan adalah metode deskriptif yang bertujuan melukiskan secara sistematisfakta atau karakteristik populasi tertentu atau bidang tertentu secara faktual dan cermat. Hasil penelitianmenunjukan PR MD Entertainment telah melakukan tahapan-tahapan atau Teknik PR pada film Ha...

  7. Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

    2015-04-24

    Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

  8. 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.

  9. 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.

  10. Effective As(III) Removal by A Multi-Charged Hydroacid Complex Draw Solute Facilitated Forward Osmosis-Membrane Distillation (FO-MD) Processes

    KAUST Repository

    Ge, Qingchun

    2016-01-29

    © 2016 American Chemical Society. Effective removal of As(III) from water by an oxalic acid complex with the formula of Na3[Cr(C2O4)3] (Na-Cr-OA) is demonstrated via an forward osmosis-membrane distillation (FO-MD) hybrid system in this study. Na-Cr-OA first proved its superiority as a draw solute with high water fluxes and negligible reverse fluxes in FO, then a systematic investigation of the Na-Cr-OA promoted FO process was conducted to ascertain the factors in As(III) removal. Relatively high water fluxes of 28 LMH under the FO mode and 74 LMH under the pressure retarded osmosis (PRO) mode were achieved when using a 1000 ppm As(III) solution as the feed and 1.0 M Na-Cr-OA as the draw solution at 60 °C. As(III) removal with a water recovery up to 21.6% (FO mode) and 48.3% (PRO mode) were also achieved in 2 h. An outstanding As(III) rejection with 30-3000 μg/L As(III) in the permeate was accomplished when As(III) feed solutions varied from 5 × 104 to 1 × 106 μg/L, superior to the best FO performance reported for As(III) removal. Incorporating MD into FO not only makes As(III) removal sustainable by reconcentrating the Na-Cr-OA solution simultaneously, but also reduces the As(III) concentration below 10 μg/L in the product water, meeting the WHO standard.

  11. Effective As(III) Removal by A Multi-Charged Hydroacid Complex Draw Solute Facilitated Forward Osmosis-Membrane Distillation (FO-MD) Processes

    KAUST Repository

    Ge, Qingchun; Han, Gang; Chung, Neal Tai-Shung

    2016-01-01

    © 2016 American Chemical Society. Effective removal of As(III) from water by an oxalic acid complex with the formula of Na3[Cr(C2O4)3] (Na-Cr-OA) is demonstrated via an forward osmosis-membrane distillation (FO-MD) hybrid system in this study. Na-Cr-OA first proved its superiority as a draw solute with high water fluxes and negligible reverse fluxes in FO, then a systematic investigation of the Na-Cr-OA promoted FO process was conducted to ascertain the factors in As(III) removal. Relatively high water fluxes of 28 LMH under the FO mode and 74 LMH under the pressure retarded osmosis (PRO) mode were achieved when using a 1000 ppm As(III) solution as the feed and 1.0 M Na-Cr-OA as the draw solution at 60 °C. As(III) removal with a water recovery up to 21.6% (FO mode) and 48.3% (PRO mode) were also achieved in 2 h. An outstanding As(III) rejection with 30-3000 μg/L As(III) in the permeate was accomplished when As(III) feed solutions varied from 5 × 104 to 1 × 106 μg/L, superior to the best FO performance reported for As(III) removal. Incorporating MD into FO not only makes As(III) removal sustainable by reconcentrating the Na-Cr-OA solution simultaneously, but also reduces the As(III) concentration below 10 μg/L in the product water, meeting the WHO standard.

  12. molecular dynamics simulations and quantum chemical calculations

    African Journals Online (AJOL)

    ABSTRACT. The molecular dynamic (MD) simulation and quantum chemical calculations for the adsorption of [2-(2-Henicos-10- .... electronic properties of molecule clusters, surfaces and ... The local reactivity was analyzed by determining the.

  13. 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...

  14. 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.

  15. Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and nanoindentation on ceramics.

    Science.gov (United States)

    Vashishta, Priya; Kalia, Rajiv K; Nakano, Aiichiro

    2006-03-02

    We have developed a first-principles-based hierarchical simulation framework, which seamlessly integrates (1) a quantum mechanical description based on the density functional theory (DFT), (2) multilevel molecular dynamics (MD) simulations based on a reactive force field (ReaxFF) that describes chemical reactions and polarization, a nonreactive force field that employs dynamic atomic charges, and an effective force field (EFF), and (3) an atomistically informed continuum model to reach macroscopic length scales. For scalable hierarchical simulations, we have developed parallel linear-scaling algorithms for (1) DFT calculation based on a divide-and-conquer algorithm on adaptive multigrids, (2) chemically reactive MD based on a fast ReaxFF (F-ReaxFF) algorithm, and (3) EFF-MD based on a space-time multiresolution MD (MRMD) algorithm. On 1920 Intel Itanium2 processors, we have demonstrated 1.4 million atom (0.12 trillion grid points) DFT, 0.56 billion atom F-ReaxFF, and 18.9 billion atom MRMD calculations, with parallel efficiency as high as 0.953. Through the use of these algorithms, multimillion atom MD simulations have been performed to study the oxidation of an aluminum nanoparticle. Structural and dynamic correlations in the oxide region are calculated as well as the evolution of charges, surface oxide thickness, diffusivities of atoms, and local stresses. In the microcanonical ensemble, the oxidizing reaction becomes explosive in both molecular and atomic oxygen environments, due to the enormous energy release associated with Al-O bonding. In the canonical ensemble, an amorphous oxide layer of a thickness of approximately 40 angstroms is formed after 466 ps, in good agreement with experiments. Simulations have been performed to study nanoindentation on crystalline, amorphous, and nanocrystalline silicon nitride and silicon carbide. Simulation on nanocrystalline silicon carbide reveals unusual deformation mechanisms in brittle nanophase materials, due to

  16. 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.

  17. 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

  18. 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

  19. Generation of thermodynamic data for organic liquid mixtures from molecular simulations

    DEFF Research Database (Denmark)

    Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

    2007-01-01

    Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic thermodynamic property models. Two benchmark systems, benzene-methyl acetate at 303.15 K and benzene-ethanol at 298.......15 K, are used. MD simulations are performed in the isobaric-isothermal ensemble (NPT) at the respective temperatures and at a pressure of 1 atm. We use the CHARMM27 force field at different mixing ratios. We sample positions to determine the binary (between the centers-of-mass of molecules of a pair...

  20. Angiotensin II induces kidney inflammatory injury and fibrosis through binding to myeloid differentiation protein-2 (MD2).

    Science.gov (United States)

    Xu, Zheng; Li, Weixin; Han, Jibo; Zou, Chunpeng; Huang, Weijian; Yu, Weihui; Shan, Xiaoou; Lum, Hazel; Li, Xiaokun; Liang, Guang

    2017-03-21

    Growing evidence indicates that angiotensin II (Ang II), a potent biologically active product of RAS, is a key regulator of renal inflammation and fibrosis. In this study, we tested the hypothesis that Ang II induces renal inflammatory injury and fibrosis through interaction with myeloid differentiation protein-2 (MD2), the accessory protein of toll-like receptor 4 (TLR4) of the immune system. Results indicated that in MD2 -/- mice, the Ang II-induced renal fibrosis, inflammation and kidney dysfunction were significantly reduced compared to control Ang II-infused wild-type mice. Similarly, in the presence of small molecule MD2 specific inhibitor L6H21 or siRNA-MD2, the Ang II-induced increases of pro-fibrotic and pro-inflammatory molecules were prevented in tubular NRK-52E cells. MD2 blockade also inhibited activation of NF-κB and ERK. Moreover, MD2 blockade prevented the Ang II-stimulated formation of the MD2/TLR4/MyD88 signaling complex, as well as the increased surface binding of Ang II in NRK-52E cells. In addition, Ang II directly bound recombinant MD2 protein, rather than TLR4 protein. We conclude that MD2 is a significant contributor in the Ang II-induced kidney inflammatory injury in chronic renal diseases. Furthermore, MD2 inhibition could be a new and important therapeutic strategy for preventing progression of chronic renal diseases.

  1. 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.

  2. Image fusion in craniofacial virtual reality modeling based on CT and 3dMD photogrammetry.

    Science.gov (United States)

    Xin, Pengfei; Yu, Hongbo; Cheng, Huanchong; Shen, Shunyao; Shen, Steve G F

    2013-09-01

    The aim of this study was to demonstrate the feasibility of building a craniofacial virtual reality model by image fusion of 3-dimensional (3D) CT models and 3 dMD stereophotogrammetric facial surface. A CT scan and stereophotography were performed. The 3D CT models were reconstructed by Materialise Mimics software, and the stereophotogrammetric facial surface was reconstructed by 3 dMD patient software. All 3D CT models were exported as Stereo Lithography file format, and the 3 dMD model was exported as Virtual Reality Modeling Language file format. Image registration and fusion were performed in Mimics software. Genetic algorithm was used for precise image fusion alignment with minimum error. The 3D CT models and the 3 dMD stereophotogrammetric facial surface were finally merged into a single file and displayed using Deep Exploration software. Errors between the CT soft tissue model and 3 dMD facial surface were also analyzed. Virtual model based on CT-3 dMD image fusion clearly showed the photorealistic face and bone structures. Image registration errors in virtual face are mainly located in bilateral cheeks and eyeballs, and the errors are more than 1.5 mm. However, the image fusion of whole point cloud sets of CT and 3 dMD is acceptable with a minimum error that is less than 1 mm. The ease of use and high reliability of CT-3 dMD image fusion allows the 3D virtual head to be an accurate, realistic, and widespread tool, and has a great benefit to virtual face model.

  3. On the hydration of subnanometric antifouling organosilane adlayers: a molecular dynamics simulation.

    Science.gov (United States)

    Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael

    2015-01-01

    The connection between antifouling and surface hydration is a fascinating but daunting question to answer. Herein, we use molecular dynamics (MD) computer simulations to gain further insight into the role of surface functionalities in the molecular-level structuration of water (surface kosmotropicity)--within and atop subnanometric organosilane adlayers that were shown in previous experimental work to display varied antifouling behavior. Our simulations support the hypothesized intimate link between surface hydration and antifouling, in particular the importance of both internal and interfacial hydrophilicity and kosmotropicity. The antifouling mechanism is also discussed in terms of surface dehydration energy and water dynamicity (lability and mobility), notably the crucial requirement for clustered water molecules to remain tightly bound for extensive periods of time--i.e. exhibit slow exchange dynamics. A substrate effect on surface hydration, which would also participate in endowing antifouling adlayers with hydrogel-like characteristics, is also proposed. In contrast, the role of adlayer flexibility, if any, is assigned a secondary role in these ultrathin structures made of short building blocks. The conclusions from this work are well in line with those previously drawn in the literature. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. 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

  5. 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.

  6. Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations.

    Science.gov (United States)

    Anfinrud, Philip

    2006-03-01

    Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. In collaboration with Friedrich Schotte and Gerhard Hummer, NIH.

  7. 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.

  8. Molecular Insight into Human Lysozyme and Its Ability to Form Amyloid Fibrils in High Concentrations of Sodium Dodecyl Sulfate: A View from Molecular Dynamics Simulations.

    Directory of Open Access Journals (Sweden)

    Majid Jafari

    Full Text Available Changes in the tertiary structure of proteins and the resultant fibrillary aggregation could result in fatal heredity diseases, such as lysozyme systemic amyloidosis. Human lysozyme is a globular protein with antimicrobial properties with tendencies to fibrillate and hence is known as a fibril-forming protein. Therefore, its behavior under different ambient conditions is of great importance. In this study, we conducted two 500000 ps molecular dynamics (MD simulations of human lysozyme in sodium dodecyl sulfate (SDS at two ambient temperatures. To achieve comparative results, we also performed two 500000 ps human lysozyme MD simulations in pure water as controls. The aim of this study was to provide further molecular insight into all interactions in the lysozyme-SDS complexes and to provide a perspective on the ability of human lysozyme to form amyloid fibrils in the presence of SDS surfactant molecules. SDS, which is an anionic detergent, contains a hydrophobic tail with 12 carbon atoms and a negatively charged head group. The SDS surfactant is known to be a stabilizer for helical structures above the critical micelle concentration (CMC [1]. During the 500000 ps MD simulations, the helical structures were maintained by the SDS surfactant above its CMC at 300 K, while at 370 K, human lysozyme lost most of its helices and gained β-sheets. Therefore, we suggest that future studies investigate the β-amyloid formation of human lysozyme at SDS concentrations above the CMC and at high temperatures.

  9. Conformational analysis of oligosaccharides and polysaccharides using molecular dynamics simulations.

    Science.gov (United States)

    Frank, Martin

    2015-01-01

    Complex carbohydrates usually have a large number of rotatable bonds and consequently a large number of theoretically possible conformations can be generated (combinatorial explosion). The application of systematic search methods for conformational analysis of carbohydrates is therefore limited to disaccharides and trisaccharides in a routine analysis. An alternative approach is to use Monte-Carlo methods or (high-temperature) molecular dynamics (MD) simulations to explore the conformational space of complex carbohydrates. This chapter describes how to use MD simulation data to perform a conformational analysis (conformational maps, hydrogen bonds) of oligosaccharides and how to build realistic 3D structures of large polysaccharides using Conformational Analysis Tools (CAT).

  10. 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.

  11. Water flow prediction for Membranes using 3D simulations with detailed morphology

    KAUST Repository

    Shi, Meixia

    2015-04-01

    The membrane morphology significantly influences membrane performance. For osmotically driven membrane processes, the morphology strongly affects the internal concentration polarization. Different membrane morphologies were generated by simulation and their influence on membrane performance was studied, using a 3D model. The simulation results were experimentally validated for two classical phase-inversion membrane morphologies: sponge- and finger-like structures. Membrane porosity and scanning electron microscopy image information were used as model input. The permeance results from the simulation fit well the experimentally measured permeances. Water permeances were predicted for different kinds of finger-like cavity membranes with different finger-like cavity lengths and various finger-like cavity sets, as well as for membranes with cylindrical cavities. The results provide realistic information on how to increase water permeance, and also illustrate that membrane’s complete morphology is important for the accurate water permeance evaluation. Evaluations only based on porosity might be misleading, and the new 3D simulation approach gives a more realistic representation.

  12. Water flow prediction for Membranes using 3D simulations with detailed morphology

    KAUST Repository

    Shi, Meixia; Printsypar, Galina; Iliev, Oleg; Calo, Victor M.; Amy, Gary L.; Nunes, Suzana Pereira

    2015-01-01

    The membrane morphology significantly influences membrane performance. For osmotically driven membrane processes, the morphology strongly affects the internal concentration polarization. Different membrane morphologies were generated by simulation and their influence on membrane performance was studied, using a 3D model. The simulation results were experimentally validated for two classical phase-inversion membrane morphologies: sponge- and finger-like structures. Membrane porosity and scanning electron microscopy image information were used as model input. The permeance results from the simulation fit well the experimentally measured permeances. Water permeances were predicted for different kinds of finger-like cavity membranes with different finger-like cavity lengths and various finger-like cavity sets, as well as for membranes with cylindrical cavities. The results provide realistic information on how to increase water permeance, and also illustrate that membrane’s complete morphology is important for the accurate water permeance evaluation. Evaluations only based on porosity might be misleading, and the new 3D simulation approach gives a more realistic representation.

  13. Enhanced performance of PVDF nanocomposite membrane by nanofiber coating: A membrane for sustainable desalination through MD.

    Science.gov (United States)

    Efome, Johnson E; Rana, Dipak; Matsuura, Takeshi; Lan, Christopher Q

    2016-02-01

    Membrane distillation (MD) is a promising separation technique capable of being used in the desalination of marine and brackish water. Poly(vinylidene fluoride) (PVDF) flat sheet nano-composite membranes were surface modified by coating with electro-spun PVDF nano-fibres to increase the surface hydrophobicity. For this purpose, the nano-composite membrane containing 7 wt.% superhydrophobic SiO2 nano-particles, which showed the highest flux in our previous work, was first subjected to pore size augmentation by increasing the concentration of the pore forming agent (Di-ionized water). Then, the prepared flat sheet membranes were subjected to nanofibres coating by electro-spinning. The uncoated and coated composite fabricated membranes were characterized using contact angle, liquid entry pressure of water, and scanning electron microscopy. The membranes were further tested for 6 h desalination by direct contact membrane distillation (DCMD) and vacuum membrane distillation (VMD), with a 3.5 wt.% synthetic NaClaq as the feed. In DCMD the feed liquid and permeate side temperature were maintained at 27.5 °C and 15 °C, respectively. For VMD, the feed liquid temperature was 27 °C and a vacuum of 94.8 kPa was applied on the permeate side. The maximum permeate flux achieved was 3.2 kg/m(2).h for VMD and 6.5 kg/m(2).h for DCMD. The salt rejection obtained was higher than 99.98%. The coated membranes showed a more stable flux than the uncoated membranes indicating that the double layered membranes have great potential in solving the pore wetting problem in MD. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Diffusion in Liquids : Equilibrium Molecular Simulations and Predictive Engineering Models

    NARCIS (Netherlands)

    Liu, X.

    2013-01-01

    The aim of this thesis is to study multicomponent diffusion in liquids using Molecular Dynamics (MD) simulations. Diffusion plays an important role in mass transport processes. In binary systems, mass transfer processes have been studied extensively using both experiments and molecular simulations.

  15. MDGRAPE-4: a special-purpose computer system for molecular dynamics simulations.

    Science.gov (United States)

    Ohmura, Itta; Morimoto, Gentaro; Ohno, Yousuke; Hasegawa, Aki; Taiji, Makoto

    2014-08-06

    We are developing the MDGRAPE-4, a special-purpose computer system for molecular dynamics (MD) simulations. MDGRAPE-4 is designed to achieve strong scalability for protein MD simulations through the integration of general-purpose cores, dedicated pipelines, memory banks and network interfaces (NIFs) to create a system on chip (SoC). Each SoC has 64 dedicated pipelines that are used for non-bonded force calculations and run at 0.8 GHz. Additionally, it has 65 Tensilica Xtensa LX cores with single-precision floating-point units that are used for other calculations and run at 0.6 GHz. At peak performance levels, each SoC can evaluate 51.2 G interactions per second. It also has 1.8 MB of embedded shared memory banks and six network units with a peak bandwidth of 7.2 GB s(-1) for the three-dimensional torus network. The system consists of 512 (8×8×8) SoCs in total, which are mounted on 64 node modules with eight SoCs. The optical transmitters/receivers are used for internode communication. The expected maximum power consumption is 50 kW. While MDGRAPE-4 software has still been improved, we plan to run MD simulations on MDGRAPE-4 in 2014. The MDGRAPE-4 system will enable long-time molecular dynamics simulations of small systems. It is also useful for multiscale molecular simulations where the particle simulation parts often become bottlenecks.

  16. 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.

  17. 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)

  18. Basic research of developed the evaluation model of buffer material

    International Nuclear Information System (INIS)

    Kawamura, K.; Ichikawa, Y.; Suzuki, S.; Shibata, M.; Sato, H.; Ueno, K.

    2003-07-01

    For the better understanding of mass transport property of the buffer material of the high-level radioactive waste disposal, the unified method of molecular dynamics simulations (MD) and homogenization analysis (HA) method and model were developed. Interaction of atoms and multi-body potential model which needed in MD calculation was improved. Na-smectite surface and water molecule system were calculated by MD, the structure of water molecule, viscosity of water nearby the Na-smectite surface and distribution of diffusion coefficient of which were estimated. According to the results of the MD calculation, first water layer adjacent to Na-smectite surface was structured, and about 1nm thick diffuse layer was observed in which viscosity of water in higher than ordinary water. Structure modeling for Na-smectite including edge was also discussed. The HA analysis needs the results of the micro-scale properties from MD calculation and the microstructure of the field, i.e. microstructure of buffer material. Microstructure of compacted Na-smectite were studied by Scanning Electron Microscope (SEM), Transmission Electron Microscope (TEM) and X-ray diffraction (XRD). On the basis of the simplified observation results, the equation was formulated that the external pore size was expressed as a function of the number of clay layers and dry density. Using MD simulation results and pore structure model, diffusion coefficient of water molecule in compacted Na-smectite were calculated by the unified MD/HA analysis method. For this analysis Multi-scale HA method which can handle for porous media consists of various scale particles was developed. Calculated diffusion coefficient of water was in agreement with the results of diffusion experiment of triturated water (HTO). Regarding solute diffusion through compacted bentonite, experimental results are accumulated and discussed. Modelling frameworks for diffusion and sorption of ion were also developed. (author)

  19. An Insight into the Environmental Effects of the Pocket of the Active Site of the Enzyme. Ab initio ONIOM-Molecular Dynamics (MD) Study on Cytosine Deaminase

    International Nuclear Information System (INIS)

    Matsubara, Toshiaki; Dupuis, Michel; Aida, Misako

    2008-01-01

    We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases. TM and MA were partly supported by grants from the Ministry of Education, Culture, Sports, Science and Technology of Japan.MD was supported by the Division of Chemical Sciences, Office of Basic Energy Sciences, and by the Office of Biological and Environmental Research of the U.S. Department of Energy DOE. Battelle operates Pacific Northwest National Laboratory for DOE

  20. 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