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Sample records for hybrid molecular simulations

  1. A hybrid algorithm for parallel molecular dynamics simulations

    Science.gov (United States)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  2. 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.

  3. 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

  4. 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

  5. A conservative and a hybrid early rejection schemes for accelerating Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2014-03-17

    Molecular simulation could provide detailed description of fluid systems when compared to experimental techniques. They can also replace equations of state; however, molecular simulation usually costs considerable computational efforts. Several techniques have been developed to overcome such high computational costs. In this paper, two early rejection schemes, a conservative and a hybrid one, are introduced. In these two methods, undesired configurations generated by the Monte Carlo trials are rejected earlier than it would when using conventional algorithms. The methods are tested for structureless single-component Lennard-Jones particles in both canonical and NVT-Gibbs ensembles. The computational time reduction for both ensembles is observed at a wide range of thermodynamic conditions. Results show that computational time savings are directly proportional to the rejection rate of Monte Carlo trials. The proposed conservative scheme has shown to be successful in saving up to 40% of the computational time in the canonical ensemble and up to 30% in the NVT-Gibbs ensemble when compared to standard algorithms. In addition, it preserves the exact Markov chains produced by the Metropolis scheme. Further enhancement for NVT-Gibbs ensemble is achieved by combining this technique with the bond formation early rejection one. The hybrid method achieves more than 50% saving of the central processing unit (CPU) time.

  6. Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study.

    Science.gov (United States)

    Suresh, Gorle; Priyakumar, U Deva

    2015-09-01

    Modified nucleic acids have found profound applications in nucleic acid based technologies such as antisense and antiviral therapies. Previous studies on chemically modified nucleic acids have suggested that modifications incorporated in furanose sugar especially at 2'-position attribute special properties to nucleic acids when compared to other modifications. 2'-O-methyl modification to deoxyribose sugars of DNA-RNA hybrids is one such modification that increases nucleic acid stability and has become an attractive class of compounds for potential antisense applications. It has been reported that modification of DNA strands with 2'-O-methyl group reverses the thermodynamic stability of DNA-RNA hybrid duplexes. Molecular dynamics simulations have been performed on two hybrid duplexes (DR and RD) which differ from each other and 2'-O-methyl modified counterparts to investigate the effect of 2'-O-methyl modification on their duplex stability. The results obtained suggest that the modification drives the conformations of both the hybrid duplexes towards A-RNA like conformation. The modified hybrid duplexes exhibit significantly contrasting dynamics and hydration patterns compared to respective parent duplexes. In line with the experimental results, the relative binding free energies suggest that the introduced modifications stabilize the less stable DR hybrid, but destabilize the more stable RD duplex. Binding free energy calculations suggest that the increased hydrophobicity is primarily responsible for the reversal of thermodynamic stability of hybrid duplexes. Free energy component analysis further provides insights into the stability of modified duplexes. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. 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.

  8. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study.

    Science.gov (United States)

    Ghobadi, Ahmadreza F; Jayaraman, Arthi

    2016-02-28

    In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.

  9. Molecular dynamics simulations in hybrid particle-continuum schemes: Pitfalls and caveats

    Science.gov (United States)

    Stalter, S.; Yelash, L.; Emamy, N.; Statt, A.; Hanke, M.; Lukáčová-Medvid'ová, M.; Virnau, P.

    2018-03-01

    Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations typically pose a computational bottleneck, which we investigate in detail in this study. We find that it is preferable to simulate many small systems as opposed to a few large systems, and that a choice of a simple isokinetic thermostat is typically sufficient while thermostats such as Lowe-Andersen allow for simulations at elevated viscosity. We discuss suitable choices for time steps and finite-size effects which arise in the limit of very small simulation boxes. We also argue that if colloidal systems are considered as opposed to atomistic systems, the gap between microscopic and macroscopic simulations regarding time and length scales is significantly smaller. We propose a novel reduced-order technique for the coupling to the macroscopic solver, which allows us to approximate a non-linear stress-strain relation efficiently and thus further reduce computational effort of microscopic simulations.

  10. Molecular dynamics simulation of joining process of Ag-Au nanowires and mechanical properties of the hybrid nanojoint

    Directory of Open Access Journals (Sweden)

    Su Ding

    2015-05-01

    Full Text Available The nanojoining process of Ag-Au hybrid nanowires at 800K was comprehensively studied by virtue of molecular dynamics (MD simulation. Three kinds of configurations including end-to-end, T-like and X-like were built in the simulation aiming to understand the nanojoining mechanism. The detailed dynamic evolution of atoms, crystal structure transformation and defects development during the nanojoining processes were performed. The results indicate that there are two stages in the nanojoining process of Ag-Au nanowires which are atom diffusion and new bonds formation. Temperature is a key parameter affecting both stages ascribed to the energy supply and the optimum temperature for Ag-Au nanojoint with diameter of 4.08 nm has been discussed. The mechanical properties of the nanojoint were examined with simulation of tensile test on the end-to-end joint. It was revealed that the nanojoint was strong enough to resist fracture at the joining area.

  11. Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

    Science.gov (United States)

    Bayse, Craig A; Merz, Kenneth M

    2014-08-05

    Understanding the mechanism of prenyltransferases is important to the design of engineered proteins capable of synthesizing derivatives of naturally occurring therapeutic agents. CloQ is a Mg(2+)-independent aromatic prenyltransferase (APTase) that transfers a dimethylallyl group to 4-hydroxyphenylpyruvate in the biosynthetic pathway for clorobiocin. APTases consist of a common ABBA fold that defines a β-barrel containing the reaction cavity. Positively charged basic residues line the inside of the β-barrel of CloQ to activate the pyrophosphate leaving group to replace the function of the Mg(2+) cofactor in other APTases. Classical molecular dynamics simulations of CloQ, its E281G and F68S mutants, and the related NovQ were used to explore the binding of the 4-hydroxyphenylpyruvate (4HPP) and dimethylallyl diphosphate substrates in the reactive cavity and the role of various conserved residues. Hybrid quantum mechanics/molecular mechanics potential of mean force (PMF) calculations show that the effect of the replacement of the Mg(2+) cofactor with basic residues yields a similar activation barrier for prenylation to Mg(2+)-dependent APTases like NphB. The topology of the binding pocket for 4HPP is important for selective prenylation at the ortho position of the ring. Methylation at this position alters the conformation of the substrate for O-prenylation at the phenol group. Further, a two-dimensional PMF scan shows that a "reverse" prenylation product may be a possible target for protein engineering.

  12. Recognition of RNA by amide modified backbone nucleic acids: molecular dynamics simulations of DNA-RNA hybrids in aqueous solution.

    Science.gov (United States)

    Nina, Mafalda; Fonné-Pfister, Raymonde; Beaudegnies, Renaud; Chekatt, Habiba; Jung, Pierre M J; Murphy-Kessabi, Fiona; De Mesmaeker, Alain; Wendeborn, Sebastian

    2005-04-27

    Thermodynamic and structural properties of a chemically modified DNA-RNA hybrid in which a phosphodiester linkage is replaced by a neutral amide-3 linkage (3'-CH(2)-CONH-5') were investigated using UV melting experiments, molecular dynamics simulations in explicit water, and continuum solvent models. van't Hoff analysis of the experimental UV melting curves suggests that the significant increase of the thermodynamic stability of a 15-mer DNA-RNA with seven alternated amide-3 modifications (+11 degrees C) is mainly due to an increased binding enthalpy. To further evaluate the origin in the observed affinities differences, the electrostatic contribution to the binding free energy was calculated by solving the Poisson-Boltzmann equation numerically. The nonelectrostatic contribution was estimated as the product of a hydrophobic surface tension coefficient and the surface area that is buried upon double strand formation. Structures were taken from 10 ns molecular dynamics simulations computed in a consistent fashion using explicit solvent, counterions, and the particle-mesh Ewald procedure. The present preliminary thermodynamic study suggests that the favorable binding free energy of the amide-3 DNA single strand to the complementary RNA is equally driven by electrostatic and nonpolar contributions to the binding compared to their natural analogues. In addition, molecular dynamics simulations in explicit water were performed on an amide-3 DNA single strand and the corresponding natural DNA. Results from the conformations cluster analysis of the simulated amide-3 DNA single strand ensembles suggest that the 25% of the population sampled within 10 ns has a pre-organized conformation where the sugar C3' endo pucker is favored at the 3'-flanking nucleotides. These structural and thermodynamic features contribute to the understanding of the observed increased affinities of the amide-3 DNA-RNA hybrids at the microscopic level.

  13. Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

    Science.gov (United States)

    Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

    2018-06-13

    An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

  14. 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.

  15. GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms.

    Science.gov (United States)

    Kobayashi, Chigusa; Jung, Jaewoon; Matsunaga, Yasuhiro; Mori, Takaharu; Ando, Tadashi; Tamura, Koichi; Kamiya, Motoshi; Sugita, Yuji

    2017-09-30

    GENeralized-Ensemble SImulation System (GENESIS) is a software package for molecular dynamics (MD) simulation of biological systems. It is designed to extend limitations in system size and accessible time scale by adopting highly parallelized schemes and enhanced conformational sampling algorithms. In this new version, GENESIS 1.1, new functions and advanced algorithms have been added. The all-atom and coarse-grained potential energy functions used in AMBER and GROMACS packages now become available in addition to CHARMM energy functions. The performance of MD simulations has been greatly improved by further optimization, multiple time-step integration, and hybrid (CPU + GPU) computing. The string method and replica-exchange umbrella sampling with flexible collective variable choice are used for finding the minimum free-energy pathway and obtaining free-energy profiles for conformational changes of a macromolecule. These new features increase the usefulness and power of GENESIS for modeling and simulation in biological research. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  16. 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.

  17. Hybrid Materials for Molecular Sieves

    NARCIS (Netherlands)

    ten Elshof, Johan E.; Klein, Lisa; Aparicio, Mario; Jitianu, Andrei

    2016-01-01

    Hybrid microporous organosilica membranes for molecular separations made by acid-catalyzed solgel synthesis from bridged silsesquioxane precursors have demonstrated good performance in terms of flux and selectivity and remarkable hydrothermal stability in various pervaporation and gas separation

  18. 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

  19. Electric/Hybrid Vehicle Simulation

    Science.gov (United States)

    Slusser, R. A.; Chapman, C. P.; Brennand, J. P.

    1985-01-01

    ELVEC computer program provides vehicle designer with simulation tool for detailed studies of electric and hybrid vehicle performance and cost. ELVEC simulates performance of user-specified electric or hybrid vehicle under user specified driving schedule profile or operating schedule. ELVEC performs vehicle design and life cycle cost analysis.

  20. Molecular dynamics simulations of outer-membrane protease T from E. coli based on a hybrid coarse-grained/atomistic potential

    International Nuclear Information System (INIS)

    Neri, Marilisa; Anselmi, Claudio; Carnevale, Vincenzo; Vargiu, Attilio V; Carloni, Paolo

    2006-01-01

    Outer-membrane proteases T (OmpT) are membrane enzymes used for defense by Gram-negative bacteria. Here we use hybrid molecular mechanics/coarse-grained simulations to investigate the role of large-scale motions of OmpT from Escherichia coli for its function. In this approach, the enzyme active site is treated at the all-atom level, whilst the rest of the protein is described at the coarse-grained level. Our calculations agree well with previously reported all-atom molecular dynamics simulations, suggesting that this approach is well suitable to investigate membrane proteins. In addition, our findings suggest that OmpT large-scale conformational fluctuations might play a role for its biological function, as found for another protease class, the aspartyl proteases

  1. Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory.

    Science.gov (United States)

    Langenbach, K; Heilig, M; Horsch, M; Hasse, H

    2018-03-28

    A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO 2 ). The molecular model of CO 2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

  2. Study of homogeneous bubble nucleation in liquid carbon dioxide by a hybrid approach combining molecular dynamics simulation and density gradient theory

    Science.gov (United States)

    Langenbach, K.; Heilig, M.; Horsch, M.; Hasse, H.

    2018-03-01

    A new method for predicting homogeneous bubble nucleation rates of pure compounds from vapor-liquid equilibrium (VLE) data is presented. It combines molecular dynamics simulation on the one side with density gradient theory using an equation of state (EOS) on the other. The new method is applied here to predict bubble nucleation rates in metastable liquid carbon dioxide (CO2). The molecular model of CO2 is taken from previous work of our group. PC-SAFT is used as an EOS. The consistency between the molecular model and the EOS is achieved by adjusting the PC-SAFT parameters to VLE data obtained from the molecular model. The influence parameter of density gradient theory is fitted to the surface tension of the molecular model. Massively parallel molecular dynamics simulations are performed close to the spinodal to compute bubble nucleation rates. From these simulations, the kinetic prefactor of the hybrid nucleation theory is estimated, whereas the nucleation barrier is calculated from density gradient theory. This enables the extrapolation of molecular simulation data to the whole metastable range including technically relevant densities. The results are tested against available experimental data and found to be in good agreement. The new method does not suffer from typical deficiencies of classical nucleation theory concerning the thermodynamic barrier at the spinodal and the bubble size dependence of surface tension, which is typically neglected in classical nucleation theory. In addition, the density in the center of critical bubbles and their surface tension is determined as a function of their radius. The usual linear Tolman correction to the capillarity approximation is found to be invalid.

  3. Electric-hybrid-vehicle simulation

    Science.gov (United States)

    Pasma, D. C.

    The simulation of electric hybrid vehicles is to be performed using experimental data to model propulsion system components. The performance of an existing ac propulsion system will be used as the baseline for comparative purposes. Hybrid components to be evaluated include electrically and mechanically driven flywheels, and an elastomeric regenerative braking system.

  4. Photochemical reactions in biological systems: probing the effect of the environment by means of hybrid quantum chemistry/molecular mechanics simulations.

    Science.gov (United States)

    Boggio-Pasqua, Martial; Burmeister, Carl F; Robb, Michael A; Groenhof, Gerrit

    2012-06-14

    Organisms have evolved a wide variety of mechanisms to utilize and respond to light. In many cases, the biological response is mediated by structural changes that follow photon absorption in a protein complex. The initial step in such cases is normally the photoisomerization of a highly conjugated prosthetic group. To understand better the factors controlling the isomerization, we perform atomistic molecular dynamics simulations. In this perspective article we briefly review the key theoretical concepts of photochemical reactions and present a practical simulation scheme for simulating photochemical reactions in biomolecular systems. In our scheme, a multi-configurational quantum mechanical description is used to model the electronic rearrangement for those parts of the system that are involved in the photon absorption. For the remainder, typically consisting of the apo-protein and the solvent, a simple force field model is used. The interactions in the systems are thus computed within a hybrid quantum/classical framework. Forces are calculated on-the-fly, and a diabatic surface hopping procedure is used to model the excited-state decay. To demonstrate how this method is used we review our studies on photoactivation of the photoactive yellow protein, a bacterial photoreceptor. We will show what information can be obtained from the simulations, and, by comparing to recent experimental findings, what the limitations of our simulations are.

  5. Hybrid Simulation of Composite Structures

    DEFF Research Database (Denmark)

    Høgh, Jacob Herold

    experiment. The technique has primarily been used within earthquake engineering but many other fields of engineering have utilized the method with benefit. However, these previous efforts have focused on structures with a simple boundary between the numerical and physical substructure i.e. few degrees...... the transfer system and the control and monitoring techniques in the shared boundary is therefore a key issue in this type of hybrid simulation. During the research, hybrid simulation platforms have been programmed capable of running on different time scales with advanced control and monitoring techniques...

  6. Active Site Dynamics in Substrate Hydrolysis Catalyzed by DapE Enzyme and Its Mutants from Hybrid QM/MM-Molecular Dynamics Simulation.

    Science.gov (United States)

    Dutta, Debodyuti; Mishra, Sabyashachi

    2017-07-27

    The mechanism of the catalytic hydrolysis of N-succinyl diaminopimelic acid (SDAP) by the microbial enzyme DapE in its wild-type (wt) form as well as three of its mutants (E134D, H67A, and H349A) is investigated employing a hybrid quantum mechanics/molecular mechanics (QM/MM) method coupled with molecular dynamics (MD) simulations, wherein the time evolution of the atoms of the QM and MM regions are obtained from the forces acting on the individual atoms. The free-energy profiles along the reaction coordinates of this multistep hydrolysis reaction process are explored using a combination of equilibrium and nonequilibrium (umbrella sampling) QM/MM-MD simulation techniques. In the enzyme-substrate complexes of wt-DapE and the E134D mutant, nucleophilic attack is found to be the rate-determining step involving a barrier of 15.3 and 21.5 kcal/mol, respectively, which satisfactorily explains the free energy of activation obtained from kinetic experiments in wt-DapE-SDAP (15.2 kcal/mol) and the 3 orders of magnitude decrease in the catalytic activity due to E134D mutation. The catalysis is found to be quenched in the H67A and H349A mutants of DapE due to conformational rearrangement in the active site induced by the absence of the active site His residues that prohibits activation of the catalytic water molecule.

  7. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp; Tchipev, Nikola

    2012-01-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm

  8. Deriving simulators for hybrid Chi models

    NARCIS (Netherlands)

    Beek, van D.A.; Man, K.L.; Reniers, M.A.; Rooda, J.E.; Schiffelers, R.R.H.

    2006-01-01

    The hybrid Chi language is formalism for modeling, simulation and verification of hybrid systems. The formal semantics of hybrid Chi allows the definition of provably correct implementations for simulation, verification and realtime control. This paper discusses the principles of deriving an

  9. Molecular dynamics simulations

    International Nuclear Information System (INIS)

    Alder, B.J.

    1985-07-01

    The molecular dynamics computer simulation discovery of the slow decay of the velocity autocorrelation function in fluids is briefly reviewed in order to contrast that long time tail with those observed for the stress autocorrelation function in fluids and the velocity autocorrelation function in the Lorentz gas. For a non-localized particle in the Lorentz gas it is made plausible that even if it behaved quantum mechanically its long time tail would be the same as the classical one. The generalization of Fick's law for diffusion for the Lorentz gas, necessary to avoid divergences due to the slow decay of correlations, is presented. For fluids, that generalization has not yet been established, but the region of validity of generalized hydrodynamics is discussed. 20 refs., 5 figs

  10. Hybrid2 - The hybrid power system simulation model

    Energy Technology Data Exchange (ETDEWEB)

    Baring-Gould, E.I.; Green, H.J.; Dijk, V.A.P. van [National Renewable Energy Lab., Golden, CO (United States); Manwell, J.F. [Univ. of Massachusetts, Amherst, MA (United States)

    1996-12-31

    There is a large-scale need and desire for energy in remote communities, especially in the developing world; however the lack of a user friendly, flexible performance prediction model for hybrid power systems incorporating renewables hindered the analysis of hybrids as options to conventional solutions. A user friendly model was needed with the versatility to simulate the many system locations, widely varying hardware configurations, and differing control options for potential hybrid power systems. To meet these ends, researchers from the National Renewable Energy Laboratory (NREL) and the University of Massachusetts (UMass) developed the Hybrid2 software. This paper provides an overview of the capabilities, features, and functionality of the Hybrid2 code, discusses its validation and future plans. Model availability and technical support provided to Hybrid2 users are also discussed. 12 refs., 3 figs., 4 tabs.

  11. Multitarget Molecular Hybrids of Cinnamic Acids

    Directory of Open Access Journals (Sweden)

    Aikaterini Peperidou

    2014-12-01

    Full Text Available In an attempt to synthesize potential new multitarget agents, 11 novel hybrids incorporating cinnamic acids and paracetamol, 4-/7-hydroxycoumarin, benzocaine, p-aminophenol and m-aminophenol were synthesized. Three hybrids—2e, 2a, 2g—and 3b were found to be multifunctional agents. The hybrid 2e derived from the phenoxyphenyl cinnamic acid and m-acetamidophenol showed the highest lipoxygenase (LOX inhibition and analgesic activity (IC50 = 0.34 μΜ and 98.1%, whereas the hybrid 3b of bromobenzyloxycinnamic acid and hymechromone exhibited simultaneously good LOX inhibitory activity (IC50 = 50 μΜ and the highest anti-proteolytic activity (IC50= 5 μΜ. The hybrid 2a of phenyloxyphenyl acid with paracetamol showed a high analgesic activity (91% and appears to be a promising agent for treating peripheral nerve injuries. Hybrid 2g which has an ester and an amide bond presents an interesting combination of anti-LOX and anti-proteolytic activity. The esters were found very potent and especially those derived from paracetamol and m-acetamidophenol. The amides follow. Based on 2D-structure–activity relationships it was observed that both steric and electronic parameters play major roles in the activity of these compounds. Molecular docking studies point to the fact that allosteric interactions might govern the LOX-inhibitor binding.

  12. 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.

  13. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  14. Hybrid CMOS/Molecular Integrated Circuits

    Science.gov (United States)

    Stan, M. R.; Rose, G. S.; Ziegler, M. M.

    CMOS silicon technologies are likely to run out of steam in the next 10-15 years despite revolutionary advances in the past few decades. Molecular and other nanoscale technologies show significant promise but it is unlikely that they will completely replace CMOS, at least in the near term. This chapter explores opportunities for using CMOS and nanotechnology to enhance and complement each other in hybrid circuits. As an example of such a hybrid CMOS/nano system, a nanoscale programmable logic array (PLA) based on majority logic is described along with its supplemental CMOS circuitry. It is believed that such systems will be able to sustain the historical advances in the semiconductor industry while addressing manufacturability, yield, power, cost, and performance challenges.

  15. Simulation of Hybrid Solar Dryer

    International Nuclear Information System (INIS)

    Yunus, Y M; Al-Kayiem, H H

    2013-01-01

    The efficient performance of a solar dryer is mainly depending on the good distribution of the thermal and flow field inside the dryer body. This paper presents simulation results of a solar dryer with a biomass burner as backup heater. The flow and thermal fields were simulated by CFD tools under different operational modes. GAMBIT software was used for the model and grid generation while FLUENT software was used to simulate the velocity and temperature distribution inside the dryer body. The CFD simulation procedure was validated by comparing the simulation results with experimental measurement. The simulation results show acceptable agreement with the experimental measurements. The simulations have shown high temperature spot with very low velocity underneath the solar absorber and this is an indication for the poor design. Many other observations have been visualized from the temperature and flow distribution which cannot be captured by experimental measurements.

  16. Hybrid simulation models of production networks

    CERN Document Server

    Kouikoglou, Vassilis S

    2001-01-01

    This book is concerned with a most important area of industrial production, that of analysis and optimization of production lines and networks using discrete-event models and simulation. The book introduces a novel approach that combines analytic models and discrete-event simulation. Unlike conventional piece-by-piece simulation, this method observes a reduced number of events between which the evolution of the system is tracked analytically. Using this hybrid approach, several models are developed for the analysis of production lines and networks. The hybrid approach combines speed and accuracy for exceptional analysis of most practical situations. A number of optimization problems, involving buffer design, workforce planning, and production control, are solved through the use of hybrid models.

  17. Assessment of Molecular Modeling & Simulation

    Energy Technology Data Exchange (ETDEWEB)

    None

    2002-01-03

    This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materials modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.

  18. Understanding molecular simulation: from algorithms to applications

    NARCIS (Netherlands)

    Frenkel, D.; Smit, B.

    2002-01-01

    Second and revised edition Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the "recipes" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique

  19. TRNSYS HYBRID wind diesel PV simulator

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, P.J.A.; Mitchell, J.W.; Klein, S.A.; Beckman, W.A.; Blair, N.J. [Univ. of Wisconsin, Madison, WI (United States)

    1996-12-31

    The Solar Energy Laboratory (SEL) has developed a wind diesel PV hybrid systems simulator, UW-HYBRID 1.0, an application of the TRNSYS 14.2 time-series simulation environment. An AC/DC bus links up to five diesels and wind turbine models, along with PV modules, a battery bank, and an AC/DC converter. Multiple units can be selected. PV system simulations include solar angle and peak power tracking options. Weather data are Typical Meteorological Year data, parametrically generated synthesized data, or external data files. PV performance simulations rely on long-standing SEL-developed algorithms. Loads data are read as scalable time series. Diesel simulations include estimated fuel-use and waste heat output, and are dispatched using a least-cost of fuel strategy. Wind system simulations include varying air density, wind shear and wake effects. Time step duration is user-selectable. UW-HYBRID 1.0 runs in Windows{reg_sign}, with TRNSED providing a customizable user interface. 12 refs., 6 figs.

  20. Recent progress of hybrid simulation for energetic particles and MHD

    International Nuclear Information System (INIS)

    Todo, Y.

    2013-01-01

    Several hybrid simulation models have been constructed to study the evolution of Alfven eigenmodes destabilized by energetic particles. Recent hybrid simulation results of energetic particle driven instabilities are presented in this paper. (J.P.N.)

  1. Biological Applications of Hybrid Quantum Mechanics/Molecular Mechanics Calculation

    Directory of Open Access Journals (Sweden)

    Jiyoung Kang

    2012-01-01

    Full Text Available Since in most cases biological macromolecular systems including solvent water molecules are remarkably large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Accordingly, QM calculations that are jointed with MM calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. A UNIX-shell-based interface program connecting the quantum mechanics (QMs and molecular mechanics (MMs calculation engines, GAMESS and AMBER, was developed in our lab. The system was applied to a metalloenzyme, azurin, and PU.1-DNA complex; thereby, the significance of the environmental effects on the electronic structures of the site of interest was elucidated. Subsequently, hybrid QM/MM molecular dynamics (MD simulation using the calculation system was employed for investigation of mechanisms of hydrolysis (editing reaction in leucyl-tRNA synthetase complexed with the misaminoacylated tRNALeu, and a novel mechanism of the enzymatic reaction was revealed. Thus, our interface program can play a critical role as a powerful tool for state-of-the-art sophisticated hybrid ab initio QM/MM MD simulations of large systems, such as biological macromolecules.

  2. Key parameters analysis of hybrid HEMP simulator

    International Nuclear Information System (INIS)

    Mao Congguang; Zhou Hui

    2009-01-01

    According to the new standards on the high-altitude electromagnetic pulse (HEMP) developed by International Electrotechnical Commission (IEC), the target parameter requirements of the key structure of the hybrid HEMP simulator are decomposed. Firstly, the influences of the different excitation sources and biconical structures to the key parameters of the radiated electric field wave shape are investigated and analyzed. Then based on the influence curves the target parameter requirements of the pulse generator are proposed. Finally the appropriate parameters of the biconical structure and the excitation sources are chosen, and the computational result of the electric field in free space is presented. The results are of great value for the design of the hybrid HEMP simulator. (authors)

  3. Hybrid Method Simulation of Slender Marine Structures

    DEFF Research Database (Denmark)

    Christiansen, Niels Hørbye

    This present thesis consists of an extended summary and five appended papers concerning various aspects of the implementation of a hybrid method which combines classical simulation methods and artificial neural networks. The thesis covers three main topics. Common for all these topics...... only recognize patterns similar to those comprised in the data used to train the network. Fatigue life evaluation of marine structures often considers simulations of more than a hundred different sea states. Hence, in order for this method to be useful, the training data must be arranged so...... that a single neural network can cover all relevant sea states. The applicability and performance of the present hybrid method is demonstrated on a numerical model of a mooring line attached to a floating offshore platform. The second part of the thesis demonstrates how sequential neural networks can be used...

  4. HTTR plant dynamic simulation using a hybrid computer

    International Nuclear Information System (INIS)

    Shimazaki, Junya; Suzuki, Katsuo; Nabeshima, Kunihiko; Watanabe, Koichi; Shinohara, Yoshikuni; Nakagawa, Shigeaki.

    1990-01-01

    A plant dynamic simulation of High-Temperature Engineering Test Reactor has been made using a new-type hybrid computer. This report describes a dynamic simulation model of HTTR, a hybrid simulation method for SIMSTAR and some results obtained from dynamics analysis of HTTR simulation. It concludes that the hybrid plant simulation is useful for on-line simulation on account of its capability of computation at high speed, compared with that of all digital computer simulation. With sufficient accuracy, 40 times faster computation than real time was reached only by changing an analog time scale for HTTR simulation. (author)

  5. Hybridization and molecular geometry: A number game | Ojha ...

    African Journals Online (AJOL)

    Present article emphasize the new pedagogy to learn the hybridization and molecular geometry. It is always a challenge for the students to remember the hybridization and geometry of the molecule correctly. This topic has several importance in subjective and objective type questions and answers since in most of the ...

  6. Control of DNA hybridization by photoswitchable molecular glue.

    Science.gov (United States)

    Dohno, Chikara; Nakatani, Kazuhiko

    2011-12-01

    Hybridization of DNA is one of the most intriguing events in molecular recognition and is essential for living matter to inherit life beyond generations. In addition to the function of DNA as genetic material, DNA hybridization is a key to control the function of DNA-based materials in nanoscience. Since the hybridization of two single stranded DNAs is a thermodynamically favorable process, dissociation of the once formed DNA duplex is normally unattainable under isothermal conditions. As the progress of DNA-based nanoscience, methodology to control the DNA hybridization process has become increasingly important. Besides many reports using the chemically modified DNA for the regulation of hybridization, we focused our attention on the use of a small ligand as the molecular glue for the DNA. In 2001, we reported the first designed molecule that strongly and specifically bound to the mismatched base pairs in double stranded DNA. Further studies on the mismatch binding molecules provided us a key discovery of a novel mode of the binding of a mismatch binding ligand that induced the base flipping. With these findings we proposed the concept of molecular glue for DNA for the unidirectional control of DNA hybridization and, eventually photoswitchable molecular glue for DNA, which enabled the bidirectional control of hybridization under photoirradiation. In this tutorial review, we describe in detail how we integrated the mismatch binding ligand into photoswitchable molecular glue for DNA, and the application and perspective in DNA-based nanoscience.

  7. Scalable Simulation of Electromagnetic Hybrid Codes

    International Nuclear Information System (INIS)

    Perumalla, Kalyan S.; Fujimoto, Richard; Karimabadi, Dr. Homa

    2006-01-01

    New discrete-event formulations of physics simulation models are emerging that can outperform models based on traditional time-stepped techniques. Detailed simulation of the Earth's magnetosphere, for example, requires execution of sub-models that are at widely differing timescales. In contrast to time-stepped simulation which requires tightly coupled updates to entire system state at regular time intervals, the new discrete event simulation (DES) approaches help evolve the states of sub-models on relatively independent timescales. However, parallel execution of DES-based models raises challenges with respect to their scalability and performance. One of the key challenges is to improve the computation granularity to offset synchronization and communication overheads within and across processors. Our previous work was limited in scalability and runtime performance due to the parallelization challenges. Here we report on optimizations we performed on DES-based plasma simulation models to improve parallel performance. The net result is the capability to simulate hybrid particle-in-cell (PIC) models with over 2 billion ion particles using 512 processors on supercomputing platforms

  8. Odd-flavor Simulations by the Hybrid Monte Carlo

    CERN Document Server

    Takaishi, Tetsuya; Takaishi, Tetsuya; De Forcrand, Philippe

    2001-01-01

    The standard hybrid Monte Carlo algorithm is known to simulate even flavors QCD only. Simulations of odd flavors QCD, however, can be also performed in the framework of the hybrid Monte Carlo algorithm where the inverse of the fermion matrix is approximated by a polynomial. In this exploratory study we perform three flavors QCD simulations. We make a comparison of the hybrid Monte Carlo algorithm and the R-algorithm which also simulates odd flavors systems but has step-size errors. We find that results from our hybrid Monte Carlo algorithm are in agreement with those from the R-algorithm obtained at very small step-size.

  9. Understanding molecular simulation from algorithms to applications

    CERN Document Server

    Frenkel, Daan

    2001-01-01

    Understanding Molecular Simulation: From Algorithms to Applications explains the physics behind the ""recipes"" of molecular simulation for materials science. Computer simulators are continuously confronted with questions concerning the choice of a particular technique for a given application. A wide variety of tools exist, so the choice of technique requires a good understanding of the basic principles. More importantly, such understanding may greatly improve the efficiency of a simulation program. The implementation of simulation methods is illustrated in pseudocodes and their practic

  10. HYBRIDIZATION AND MOLECULAR GEOMETRY: A NUMBER GAME

    African Journals Online (AJOL)

    Temechegn

    This article is not emphasizing the theory behind the hybridization, but only on how to ... The new orbitals have the same total electron capacity .... the quantum mechanics and from a theory of paramagnetic susceptibility to the structure.

  11. Multiscale Hy3S: Hybrid stochastic simulation for supercomputers

    Directory of Open Access Journals (Sweden)

    Kaznessis Yiannis N

    2006-02-01

    Full Text Available Abstract Background Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce a more accurate picture of single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations and transitions between stable states. However, the computational cost of the original stochastic simulation algorithm can be high, motivating the use of hybrid stochastic methods. Hybrid stochastic methods partition the system into multiple subsets and describe each subset as a different representation, such as a jump Markov, Poisson, continuous Markov, or deterministic process. By applying valid approximations and self-consistently merging disparate descriptions, a method can be considerably faster, while retaining accuracy. In this paper, we describe Hy3S, a collection of multiscale simulation programs. Results Building on our previous work on developing novel hybrid stochastic algorithms, we have created the Hy3S software package to enable scientists and engineers to both study and design extremely large well-mixed biological systems with many thousands of reactions and chemical species. We have added adaptive stochastic numerical integrators to permit the robust simulation of dynamically stiff biological systems. In addition, Hy3S has many useful features, including embarrassingly parallelized simulations with MPI; special discrete events, such as transcriptional and translation elongation and cell division; mid-simulation perturbations in both the number of molecules of species and reaction kinetic parameters; combinatorial variation of both initial conditions and kinetic parameters to enable sensitivity analysis; use of NetCDF optimized binary format to quickly read and write large datasets; and a simple graphical user interface, written in Matlab, to help users

  12. Accelerating Climate Simulations Through Hybrid Computing

    Science.gov (United States)

    Zhou, Shujia; Sinno, Scott; Cruz, Carlos; Purcell, Mark

    2009-01-01

    Unconventional multi-core processors (e.g., IBM Cell B/E and NYIDIDA GPU) have emerged as accelerators in climate simulation. However, climate models typically run on parallel computers with conventional processors (e.g., Intel and AMD) using MPI. Connecting accelerators to this architecture efficiently and easily becomes a critical issue. When using MPI for connection, we identified two challenges: (1) identical MPI implementation is required in both systems, and; (2) existing MPI code must be modified to accommodate the accelerators. In response, we have extended and deployed IBM Dynamic Application Virtualization (DAV) in a hybrid computing prototype system (one blade with two Intel quad-core processors, two IBM QS22 Cell blades, connected with Infiniband), allowing for seamlessly offloading compute-intensive functions to remote, heterogeneous accelerators in a scalable, load-balanced manner. Currently, a climate solar radiation model running with multiple MPI processes has been offloaded to multiple Cell blades with approx.10% network overhead.

  13. Hybrid numerical methods for multiscale simulations of subsurface biogeochemical processes

    International Nuclear Information System (INIS)

    Scheibe, T D; Tartakovsky, A M; Tartakovsky, D M; Redden, G D; Meakin, P

    2007-01-01

    Many subsurface flow and transport problems of importance today involve coupled non-linear flow, transport, and reaction in media exhibiting complex heterogeneity. In particular, problems involving biological mediation of reactions fall into this class of problems. Recent experimental research has revealed important details about the physical, chemical, and biological mechanisms involved in these processes at a variety of scales ranging from molecular to laboratory scales. However, it has not been practical or possible to translate detailed knowledge at small scales into reliable predictions of field-scale phenomena important for environmental management applications. A large assortment of numerical simulation tools have been developed, each with its own characteristic scale. Important examples include 1. molecular simulations (e.g., molecular dynamics); 2. simulation of microbial processes at the cell level (e.g., cellular automata or particle individual-based models); 3. pore-scale simulations (e.g., lattice-Boltzmann, pore network models, and discrete particle methods such as smoothed particle hydrodynamics); and 4. macroscopic continuum-scale simulations (e.g., traditional partial differential equations solved by finite difference or finite element methods). While many problems can be effectively addressed by one of these models at a single scale, some problems may require explicit integration of models across multiple scales. We are developing a hybrid multi-scale subsurface reactive transport modeling framework that integrates models with diverse representations of physics, chemistry and biology at different scales (sub-pore, pore and continuum). The modeling framework is being designed to take advantage of advanced computational technologies including parallel code components using the Common Component Architecture, parallel solvers, gridding, data and workflow management, and visualization. This paper describes the specific methods/codes being used at each

  14. Molecular simulations and visualization: introduction and overview.

    Science.gov (United States)

    Hirst, Jonathan D; Glowacki, David R; Baaden, Marc

    2014-01-01

    Here we provide an introduction and overview of current progress in the field of molecular simulation and visualization, touching on the following topics: (1) virtual and augmented reality for immersive molecular simulations; (2) advanced visualization and visual analytic techniques; (3) new developments in high performance computing; and (4) applications and model building.

  15. Numerical Study on Couette Flow in Nanostructured Channel using Molecular-continuum Hybrid Method

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Youngjin; Jeong, Myunggeun; Ha, Man Yeong [Pusan Nat’l Univ., Busan (Korea, Republic of)

    2017-06-15

    A molecular-continuum hybrid method was developed to simulate microscale and nanoscale fluids where continuum fluidic cannot be used to predict Couette flow. Molecular dynamics simulation is used near the solid surface where the flow cannot be predicted by continuum fluidic, and Navier-Stokes equations are used in the other regions. Numerical simulation of Couette flow was performed using the hybrid method to investigate the effect of solid-liquid interaction and surface roughness in a nanochannel. It was found that the solid-liquid interaction and surface roughness influence the boundary condition. When the surface energy is low, slippage occurs near the solid surface, and the magnitude of slippage decreases with increase in surface energy. When the surface energy is high, a locking boundary condition is formed. The roughness disturbs slippage near the solid surface and promotes the locking boundary condition.

  16. Optimized molecular reconstruction procedure combining hybrid reverse Monte Carlo and molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Bousige, Colin; Boţan, Alexandru; Coasne, Benoît, E-mail: coasne@mit.edu [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Ulm, Franz-Josef [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); Pellenq, Roland J.-M. [Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); UMI 3466 CNRS-MIT, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139 (United States); CINaM, CNRS/Aix Marseille Université, Campus de Luminy, 13288 Marseille Cedex 09 (France)

    2015-03-21

    We report an efficient atom-scale reconstruction method that consists of combining the Hybrid Reverse Monte Carlo algorithm (HRMC) with Molecular Dynamics (MD) in the framework of a simulated annealing technique. In the spirit of the experimentally constrained molecular relaxation technique [Biswas et al., Phys. Rev. B 69, 195207 (2004)], this modified procedure offers a refined strategy in the field of reconstruction techniques, with special interest for heterogeneous and disordered solids such as amorphous porous materials. While the HRMC method generates physical structures, thanks to the use of energy penalties, the combination with MD makes the method at least one order of magnitude faster than HRMC simulations to obtain structures of similar quality. Furthermore, in order to ensure the transferability of this technique, we provide rational arguments to select the various input parameters such as the relative weight ω of the energy penalty with respect to the structure optimization. By applying the method to disordered porous carbons, we show that adsorption properties provide data to test the global texture of the reconstructed sample but are only weakly sensitive to the presence of defects. In contrast, the vibrational properties such as the phonon density of states are found to be very sensitive to the local structure of the sample.

  17. 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

  18. Simulation and Analysis of the Hybrid Operating Mode in ITER

    International Nuclear Information System (INIS)

    Kessel, C.E.; Budny, R.V.; Indireshkumar, K.

    2005-01-01

    The hybrid operating mode in ITER is examined with 0D systems analysis, 1.5D discharge scenario simulations using TSC and TRANSP, and the ideal MHD stability is discussed. The hybrid mode has the potential to provide very long pulses and significant neutron fluence if the physics regime can be produced in ITER. This paper reports progress in establishing the physics basis and engineering limitation for the hybrid mode in ITER

  19. HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks

    Directory of Open Access Journals (Sweden)

    Luca Marchetti

    2017-01-01

    Full Text Available HSimulator is a multithread simulator for mass-action biochemical reaction systems placed in a well-mixed environment. HSimulator provides optimized implementation of a set of widespread state-of-the-art stochastic, deterministic, and hybrid simulation strategies including the first publicly available implementation of the Hybrid Rejection-based Stochastic Simulation Algorithm (HRSSA. HRSSA, the fastest hybrid algorithm to date, allows for an efficient simulation of the models while ensuring the exact simulation of a subset of the reaction network modeling slow reactions. Benchmarks show that HSimulator is often considerably faster than the other considered simulators. The software, running on Java v6.0 or higher, offers a simulation GUI for modeling and visually exploring biological processes and a Javadoc-documented Java library to support the development of custom applications. HSimulator is released under the COSBI Shared Source license agreement (COSBI-SSLA.

  20. Hybrid and Electric Advanced Vehicle Systems Simulation

    Science.gov (United States)

    Beach, R. F.; Hammond, R. A.; Mcgehee, R. K.

    1985-01-01

    Predefined components connected to represent wide variety of propulsion systems. Hybrid and Electric Advanced Vehicle System (HEAVY) computer program is flexible tool for evaluating performance and cost of electric and hybrid vehicle propulsion systems. Allows designer to quickly, conveniently, and economically predict performance of proposed drive train.

  1. 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.

  2. Real-time hybrid simulation using the convolution integral method

    International Nuclear Information System (INIS)

    Kim, Sung Jig; Christenson, Richard E; Wojtkiewicz, Steven F; Johnson, Erik A

    2011-01-01

    This paper proposes a real-time hybrid simulation method that will allow complex systems to be tested within the hybrid test framework by employing the convolution integral (CI) method. The proposed CI method is potentially transformative for real-time hybrid simulation. The CI method can allow real-time hybrid simulation to be conducted regardless of the size and complexity of the numerical model and for numerical stability to be ensured in the presence of high frequency responses in the simulation. This paper presents the general theory behind the proposed CI method and provides experimental verification of the proposed method by comparing the CI method to the current integration time-stepping (ITS) method. Real-time hybrid simulation is conducted in the Advanced Hazard Mitigation Laboratory at the University of Connecticut. A seismically excited two-story shear frame building with a magneto-rheological (MR) fluid damper is selected as the test structure to experimentally validate the proposed method. The building structure is numerically modeled and simulated, while the MR damper is physically tested. Real-time hybrid simulation using the proposed CI method is shown to provide accurate results

  3. Fluctuation Solution Theory Properties from Molecular Simulation

    DEFF Research Database (Denmark)

    Abildskov, Jens; Wedberg, R.; O’Connell, John P.

    2013-01-01

    The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

  4. 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.)

  5. 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.)

  6. Molecular Simulation of Adsorption in Microporous Materials

    OpenAIRE

    Yiannourakou M.; Ungerer P.; Leblanc B.; Rozanska X.; Saxe P.; Vidal-Gilbert S.; Gouth F.; Montel F.

    2013-01-01

    The development of industrial software, the decreasing cost of computing time, and the availability of well-tested forcefields make molecular simulation increasingly attractive for chemical engineers. We present here several applications of Monte-Carlo simulation techniques, applied to the adsorption of fluids in microporous solids such as zeolites and model carbons (pores < 2 nm). Adsorption was computed in the Grand Canonical ensemble ...

  7. 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.

  8. Caged molecular beacons: controlling nucleic acid hybridization with light.

    Science.gov (United States)

    Wang, Chunming; Zhu, Zhi; Song, Yanling; Lin, Hui; Yang, Chaoyong James; Tan, Weihong

    2011-05-28

    We have constructed a novel class of light-activatable caged molecular beacons (cMBs) that are caged by locking two stems with a photo-labile biomolecular interaction or covalent bond. With the cMBs, the nucleic acid hybridization process can be easily controlled with light, which offers the possibility for a high spatiotemporal resolution study of intracellular mRNAs. © The Royal Society of Chemistry 2011

  9. Plasma environment of Titan: a 3-D hybrid simulation study

    Directory of Open Access Journals (Sweden)

    S. Simon

    2006-05-01

    Full Text Available Titan possesses a dense atmosphere, consisting mainly of molecular nitrogen. Titan's orbit is located within the Saturnian magnetosphere most of the time, where the corotating plasma flow is super-Alfvénic, yet subsonic and submagnetosonic. Since Titan does not possess a significant intrinsic magnetic field, the incident plasma interacts directly with the atmosphere and ionosphere. Due to the characteristic length scales of the interaction region being comparable to the ion gyroradii in the vicinity of Titan, magnetohydrodynamic models can only offer a rough description of Titan's interaction with the corotating magnetospheric plasma flow. For this reason, Titan's plasma environment has been studied by using a 3-D hybrid simulation code, treating the electrons as a massless, charge-neutralizing fluid, whereas a completely kinetic approach is used to cover ion dynamics. The calculations are performed on a curvilinear simulation grid which is adapted to the spherical geometry of the obstacle. In the model, Titan's dayside ionosphere is mainly generated by solar UV radiation; hence, the local ion production rate depends on the solar zenith angle. Because the Titan interaction features the possibility of having the densest ionosphere located on a face not aligned with the ram flow of the magnetospheric plasma, a variety of different scenarios can be studied. The simulations show the formation of a strong magnetic draping pattern and an extended pick-up region, being highly asymmetric with respect to the direction of the convective electric field. In general, the mechanism giving rise to these structures exhibits similarities to the interaction of the ionospheres of Mars and Venus with the supersonic solar wind. The simulation results are in agreement with data from recent Cassini flybys.

  10. Plasma environment of Titan: a 3-D hybrid simulation study

    Directory of Open Access Journals (Sweden)

    S. Simon

    2006-05-01

    Full Text Available Titan possesses a dense atmosphere, consisting mainly of molecular nitrogen. Titan's orbit is located within the Saturnian magnetosphere most of the time, where the corotating plasma flow is super-Alfvénic, yet subsonic and submagnetosonic. Since Titan does not possess a significant intrinsic magnetic field, the incident plasma interacts directly with the atmosphere and ionosphere. Due to the characteristic length scales of the interaction region being comparable to the ion gyroradii in the vicinity of Titan, magnetohydrodynamic models can only offer a rough description of Titan's interaction with the corotating magnetospheric plasma flow. For this reason, Titan's plasma environment has been studied by using a 3-D hybrid simulation code, treating the electrons as a massless, charge-neutralizing fluid, whereas a completely kinetic approach is used to cover ion dynamics. The calculations are performed on a curvilinear simulation grid which is adapted to the spherical geometry of the obstacle. In the model, Titan's dayside ionosphere is mainly generated by solar UV radiation; hence, the local ion production rate depends on the solar zenith angle. Because the Titan interaction features the possibility of having the densest ionosphere located on a face not aligned with the ram flow of the magnetospheric plasma, a variety of different scenarios can be studied. The simulations show the formation of a strong magnetic draping pattern and an extended pick-up region, being highly asymmetric with respect to the direction of the convective electric field. In general, the mechanism giving rise to these structures exhibits similarities to the interaction of the ionospheres of Mars and Venus with the supersonic solar wind. The simulation results are in agreement with data from recent Cassini flybys.

  11. Molecular modeling of cationic porphyrin-anthraquinone hybrids as DNA topoisomerase IIβ inhibitors.

    Science.gov (United States)

    Arba, Muhammad; Ruslin; Ihsan, Sunandar; Tri Wahyudi, Setyanto; Tjahjono, Daryono H

    2017-12-01

    Human DNA Topoisomerase II has been regarded as a promising target in anticancer drug discovery. In the present study, we designed six porphyrin-anthraquinone hybrids bearing pyrazole or pyridine group as meso substituents and evaluated their potentials as DNA Topoisomerase IIβ inhibitor. First, we investigated the binding orientation of porphyrin hybrids into DNA topoisomerase IIβ employing AutoDock 4.2 and then performed 20-ns molecular dynamics simulations to see the dynamic stability of each porphyrin-Topo IIβ complex using Amber 14. We found that the binding of porphyrin hybrids occured through intercalation and groove binding mode in addition interaction with the amino acid residues constituting the active cavity of Topo IIβ. Each porphyrin-Topo IIβ complex was stabilized during 20-ns dynamics simulations. The MM-PBSA free energy calculation shows that the binding affinities of porphyrin hybrids were modified with the number of meso substituent. Interestingly, the affinity of all porphyrin hybrids to Topo IIβ was stronger than that of native ligand (EVP), indicating the potential of the designed porphyrin to be considered in experimental research. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Thermal simulation of a cooling system of hybrid commercial vehicles; Thermalsimulation eine Hybrid-LKW-Kuehlsystems

    Energy Technology Data Exchange (ETDEWEB)

    Stroh, Christoph; Schnoerch, Stefan; Rathberger, Christian [Magna Powertrain Engineering Center Steyr GmbH und Co. KG, St. Valentin (Austria)

    2012-11-01

    In the past few years hybrid vehicles have been in the center of automotive engineering efforts, in particular in the field of passenger cars. But hybrid powertrains will also be important for commercial trucks. This focus on hybrid vehicles leads to high demands on thermal management since the additional components in a hybrid vehicle need appropriate cooling or even heating. In the given paper the simulation of a complete cooling system of a hybrid commercial vehicle will be explained. For this virtual examination the commercial 1D thermal management software KULI will be used, a co-simulation with several programs will not be done deliberately. Yet all aspects which are relevant for a global assessment of the thermal management are considered. The main focus is put on the investigation of appropriate concepts for the fluid circuits, including low and high temperature circuits, electric water pumps, etc. Moreover, also a refrigerant circuit with a chiller for active battery cooling will be used, the appropriate control strategy is implemented as well. For simulating transient profiles a simple driving simulation model is included, using road profile, ambient conditions, and various vehicle parameters as input. In addition an engine model is included which enables the investigation of fuel consumption potentials. This simulation model shows how the thermal management of a hybrid vehicle can be investigated with a single program and with reasonable effort. (orig.)

  13. Visualizing Energy on Target: Molecular Dynamics Simulations

    Science.gov (United States)

    2017-12-01

    ARL-TR-8234 ● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics Simulations by DeCarlos E...return it to the originator. ARL-TR-8234● DEC 2017 US Army Research Laboratory Visualizing Energy on Target: Molecular Dynamics...REPORT TYPE Technical Report 3. DATES COVERED (From - To) 1 October 2015–30 September 2016 4. TITLE AND SUBTITLE Visualizing Energy on Target

  14. 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

  15. Molecular dynamics simulations and quantum chemical calculations ...

    African Journals Online (AJOL)

    Molecular dynamic simulation results indicate that the imidazoline derivative molecules uses the imidazoline ring to effectively adsorb on the surface of iron, with the alkyl hydrophobic tail forming an n shape (canopy like covering) at geometry optimization and at 353 K. The n shape canopy like covering to a large extent may ...

  16. Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae.

    Directory of Open Access Journals (Sweden)

    Lin Shi

    Full Text Available Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA and two nuclear genes (gapC and nepGS in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.

  17. Dynamic simulation of urban hybrid electric vehicles; Dynamische Simulation von Stadthybridfahrzeugen

    Energy Technology Data Exchange (ETDEWEB)

    Winke, Florian; Bargende, Michael [Stuttgart Univ. (Germany). Inst. fuer Verbrennungsmotoren und Kraftfahrwesen (IVK)

    2013-09-15

    As a result of the rising requirements on the development process of modern vehicles, simulation models for the prediction of fuel efficiency have become an irreplaceable tool in the automotive industry. Especially for the design of hybrid electric drivetrains, the increasingly short development cycles can only be met by the use of efficient simulation models. At the IVK of the University of Stuttgart, different approaches to simulating the longitudinal dynamics of hybrid electric vehicles were analysed and compared within the presented project. The focus of the investigations was on urban operation. The objective was to develop a hybrid vehicle concept that allows an equitable comparison with pure battery electric vehicles. (orig.)

  18. Simulating movement of tRNA through the ribosome during hybrid-state formation.

    Science.gov (United States)

    Whitford, Paul C; Sanbonmatsu, Karissa Y

    2013-09-28

    Biomolecular simulations provide a means for exploring the relationship between flexibility, energetics, structure, and function. With the availability of atomic models from X-ray crystallography and cryoelectron microscopy (cryo-EM), and rapid increases in computing capacity, it is now possible to apply molecular dynamics (MD) simulations to large biomolecular machines, and systematically partition the factors that contribute to function. A large biomolecular complex for which atomic models are available is the ribosome. In the cell, the ribosome reads messenger RNA (mRNA) in order to synthesize proteins. During this essential process, the ribosome undergoes a wide range of conformational rearrangements. One of the most poorly understood transitions is translocation: the process by which transfer RNA (tRNA) molecules move between binding sites inside of the ribosome. The first step of translocation is the adoption of a "hybrid" configuration by the tRNAs, which is accompanied by large-scale rotations in the ribosomal subunits. To illuminate the relationship between these rearrangements, we apply MD simulations using a multi-basin structure-based (SMOG) model, together with targeted molecular dynamics protocols. From 120 simulated transitions, we demonstrate the viability of a particular route during P/E hybrid-state formation, where there is asynchronous movement along rotation and tRNA coordinates. These simulations not only suggest an ordering of events, but they highlight atomic interactions that may influence the kinetics of hybrid-state formation. From these simulations, we also identify steric features (H74 and surrounding residues) encountered during the hybrid transition, and observe that flexibility of the single-stranded 3'-CCA tail is essential for it to reach the endpoint. Together, these simulations provide a set of structural and energetic signatures that suggest strategies for modulating the physical-chemical properties of protein synthesis by the

  19. Hybrid Simulation in Teaching Clinical Breast Examination to Medical Students.

    Science.gov (United States)

    Nassif, Joseph; Sleiman, Abdul-Karim; Nassar, Anwar H; Naamani, Sima; Sharara-Chami, Rana

    2017-10-10

    Clinical breast examination (CBE) is traditionally taught to third-year medical students using a lecture and a tabletop breast model. The opportunity to clinically practice CBE depends on patient availability and willingness to be examined by students, especially in culturally sensitive environments. We propose the use of a hybrid simulation model consisting of a standardized patient (SP) wearing a silicone breast simulator jacket and hypothesize that this, compared to traditional teaching methods, would result in improved learning. Consenting third-year medical students (N = 82) at a university-affiliated tertiary care center were cluster-randomized into two groups: hybrid simulation (breast jacket + SP) and control (tabletop breast model). Students received the standard lecture by instructors blinded to the randomization, followed by randomization group-based learning and practice sessions. Two weeks later, participants were assessed in an Objective Structured Clinical Examination (OSCE), which included three stations with SPs blinded to the intervention. The SPs graded the students on CBE completeness, and students completed a self-assessment of their performance and confidence during the examination. CBE completeness scores did not differ between the two groups (p = 0.889). Hybrid simulation improved lesion identification grades (p simulation relieved the fear of missing a lesion on CBE (p = 0.043) and increased satisfaction with the teaching method among students (p = 0.002). As a novel educational tool, hybrid simulation improves the sensitivity of CBE performed by medical students without affecting its specificity. Hybrid simulation may play a role in increasing the confidence of medical students during CBE.

  20. Hybrid model for simulation of plasma jet injection in tokamak

    Science.gov (United States)

    Galkin, Sergei A.; Bogatu, I. N.

    2016-10-01

    Hybrid kinetic model of plasma treats the ions as kinetic particles and the electrons as charge neutralizing massless fluid. The model is essentially applicable when most of the energy is concentrated in the ions rather than in the electrons, i.e. it is well suited for the high-density hyper-velocity C60 plasma jet. The hybrid model separates the slower ion time scale from the faster electron time scale, which becomes disregardable. That is why hybrid codes consistently outperform the traditional PIC codes in computational efficiency, still resolving kinetic ions effects. We discuss 2D hybrid model and code with exact energy conservation numerical algorithm and present some results of its application to simulation of C60 plasma jet penetration through tokamak-like magnetic barrier. We also examine the 3D model/code extension and its possible applications to tokamak and ionospheric plasmas. The work is supported in part by US DOE DE-SC0015776 Grant.

  1. Hybrid simulation research on formation mechanism of tungsten nanostructure induced by helium plasma irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Ito, Atsushi M., E-mail: ito.atsushi@nifs.ac.jp [National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292 (Japan); Takayama, Arimichi; Oda, Yasuhiro [National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292 (Japan); Tamura, Tomoyuki; Kobayashi, Ryo; Hattori, Tatsunori; Ogata, Shuji [Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Nagoya 466-8555 (Japan); Ohno, Noriyasu; Kajita, Shin [Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Yajima, Miyuki [National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292 (Japan); Noiri, Yasuyuki [Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Yoshimoto, Yoshihide [University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656 (Japan); Saito, Seiki [Kushiro National College of Technology, Kushiro, Hokkaido 084-0916 (Japan); Takamura, Shuichi [Aichi Institute of Technology, 1247 Yachigusa, Yakusa-cho, Toyota 470-0392 (Japan); Murashima, Takahiro [Tohoku University, 6-3, Aramaki-Aza-Aoba, Aoba-Ward, Sendai 980-8578 (Japan); Miyamoto, Mitsutaka [Shimane University, Matsue, Shimane 690-8504 (Japan); Nakamura, Hiroaki [National Institute for Fusion Science, 322-6 Oroshi-cho, Toki 509-5292 (Japan); Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)

    2015-08-15

    The generation of tungsten fuzzy nanostructure by exposure to helium plasma is one of the important problems for the use of tungsten material as divertor plates in nuclear fusion reactors. In the present paper, the formation mechanisms of the helium bubble and the tungsten fuzzy nanostructure were investigated by using several simulation methods. We proposed the four-step process which is composed of penetration step, diffusion and agglomeration step, helium bubble growth step, and fuzzy nanostructure formation step. As the fourth step, the formation of the tungsten fuzzy nanostructure was successfully reproduced by newly developed hybrid simulation combining between molecular dynamics and Monte-Carlo method. The formation mechanism of tungsten fuzzy nanostructure observed by the hybrid simulation is that concavity and convexity of the surface are enhanced by the bursting of helium bubbles in the region around the concavity.

  2. Autocorrelations in hybrid Monte Carlo simulations

    International Nuclear Information System (INIS)

    Schaefer, Stefan; Virotta, Francesco

    2010-11-01

    Simulations of QCD suffer from severe critical slowing down towards the continuum limit. This problem is known to be prominent in the topological charge, however, all observables are affected to various degree by these slow modes in the Monte Carlo evolution. We investigate the slowing down in high statistics simulations and propose a new error analysis method, which gives a realistic estimate of the contribution of the slow modes to the errors. (orig.)

  3. CFD simulation on condensation inside a Hybrid SIT

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, Byong Guk; Ryu, Sung Uk; Kim, Seok; Euh, Dong Jin [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2016-10-15

    The concept of Hybrid Safety Injection Tank system (Hybrid SIT) was proposed by Korea Atomic Energy Research Institute (KAERI) aiming at Advanced Power Reactor Plus. The main advantage of the system is the ready injection of coolant into the reactor coolant system at high pressure. In this paper, a CFD simulation is conducted as a preliminary study. In Hybrid SITs, condensation inside the tank affects its pressure rise and injection time. In an attempt to explore the condensation in detail, we manufactured a dedicated experimental facility for visualization of condensation-induced thermal mixing and conducted a preliminary CFD simulation. Its condensation models were validated first and then computational domain was constructed. The water region was modeled as a solid for stable calculation. The CFD results gave less condensation and excessive pressurization because of lack of steam penetration into the water. In the future, the water region will be modeled as liquid using a VOF model.

  4. A hybrid society model for simulating residential electricity consumption

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Minjie [School of Electrical Engineering, Beijing Jiaotong University, Beijing (China); State Power Economic Research Institute, Beijing (China); Hu, Zhaoguang [State Power Economic Research Institute, Beijing (China); Wu, Junyong; Zhou, Yuhui [School of Electrical Engineering, Beijing Jiaotong University, Beijing (China)

    2008-12-15

    In this paper, a hybrid social model of econometric model and social influence model is proposed for evaluating the influence of pricing policy and public education policy on residential habit of electricity using in power resources management. And, a hybrid society simulation platform based on the proposed model, called residential electricity consumption multi-agent systems (RECMAS), is designed for simulating residential electricity consumption by multi-agent system. RECMAS is composed of consumer agent, power supplier agent, and policy maker agent. It provides the policy makers with a useful tool to evaluate power price policies and public education campaigns in different scenarios. According to an influenced diffusion mechanism, RECMAS can simulate the residential electricity demand-supply chain and analyze impacts of the factors on residential electricity consumption. Finally, the proposed method is used to simulate urban residential electricity consumption in China. (author)

  5. A hybrid society model for simulating residential electricity consumption

    International Nuclear Information System (INIS)

    Xu, Minjie; Hu, Zhaoguang; Wu, Junyong; Zhou, Yuhui

    2008-01-01

    In this paper, a hybrid social model of econometric model and social influence model is proposed for evaluating the influence of pricing policy and public education policy on residential habit of electricity using in power resources management. And, a hybrid society simulation platform based on the proposed model, called residential electricity consumption multi-agent systems (RECMAS), is designed for simulating residential electricity consumption by multi-agent system. RECMAS is composed of consumer agent, power supplier agent, and policy maker agent. It provides the policy makers with a useful tool to evaluate power price policies and public education campaigns in different scenarios. According to an influenced diffusion mechanism, RECMAS can simulate the residential electricity demand-supply chain and analyze impacts of the factors on residential electricity consumption. Finally, the proposed method is used to simulate urban residential electricity consumption in China. (author)

  6. Monte Carlo simulation of hybrid systems: An example

    International Nuclear Information System (INIS)

    Bacha, F.; D'Alencon, H.; Grivelet, J.; Jullien, E.; Jejcic, A.; Maillard, J.; Silva, J.; Zukanovich, R.; Vergnes, J.

    1997-01-01

    Simulation of hybrid systems needs tracking of particles from the GeV (incident proton beam) range down to a fraction of eV (thermic neutrons). We show how a GEANT based Monte-Carlo program can achieve this, with a realistic computer time and accompanying tools. An example of a dedicated original actinide burner is simulated with this chain. 8 refs., 5 figs

  7. A hybrid parallel framework for the cellular Potts model simulations

    Energy Technology Data Exchange (ETDEWEB)

    Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV

    2009-01-01

    The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).

  8. Hybrid Metaheuristic Approach for Nonlocal Optimization of Molecular Systems.

    Science.gov (United States)

    Dresselhaus, Thomas; Yang, Jack; Kumbhar, Sadhana; Waller, Mark P

    2013-04-09

    Accurate modeling of molecular systems requires a good knowledge of the structure; therefore, conformation searching/optimization is a routine necessity in computational chemistry. Here we present a hybrid metaheuristic optimization (HMO) algorithm, which combines ant colony optimization (ACO) and particle swarm optimization (PSO) for the optimization of molecular systems. The HMO implementation meta-optimizes the parameters of the ACO algorithm on-the-fly by the coupled PSO algorithm. The ACO parameters were optimized on a set of small difluorinated polyenes where the parameters exhibited small variance as the size of the molecule increased. The HMO algorithm was validated by searching for the closed form of around 100 molecular balances. Compared to the gradient-based optimized molecular balance structures, the HMO algorithm was able to find low-energy conformations with a 87% success rate. Finally, the computational effort for generating low-energy conformation(s) for the phenylalanyl-glycyl-glycine tripeptide was approximately 60 CPU hours with the ACO algorithm, in comparison to 4 CPU years required for an exhaustive brute-force calculation.

  9. Hybrid organic-inorganic rotaxanes and molecular shuttles.

    Science.gov (United States)

    Lee, Chin-Fa; Leigh, David A; Pritchard, Robin G; Schultz, David; Teat, Simon J; Timco, Grigore A; Winpenny, Richard E P

    2009-03-19

    The tetravalency of carbon and its ability to form covalent bonds with itself and other elements enables large organic molecules with complex structures, functions and dynamics to be constructed. The varied electronic configurations and bonding patterns of inorganic elements, on the other hand, can impart diverse electronic, magnetic, catalytic and other useful properties to molecular-level structures. Some hybrid organic-inorganic materials that combine features of both chemistries have been developed, most notably metal-organic frameworks, dense and extended organic-inorganic frameworks and coordination polymers. Metal ions have also been incorporated into molecules that contain interlocked subunits, such as rotaxanes and catenanes, and structures in which many inorganic clusters encircle polymer chains have been described. Here we report the synthesis of a series of discrete rotaxane molecules in which inorganic and organic structural units are linked together mechanically at the molecular level. Structural units (dialkyammonium groups) in dumb-bell-shaped organic molecules template the assembly of essentially inorganic 'rings' about 'axles' to form rotaxanes consisting of various numbers of rings and axles. One of the rotaxanes behaves as a 'molecular shuttle': the ring moves between two binding sites on the axle in a large-amplitude motion typical of some synthetic molecular machine systems. The architecture of the rotaxanes ensures that the electronic, magnetic and paramagnetic characteristics of the inorganic rings-properties that could make them suitable as qubits for quantum computers-can influence, and potentially be influenced by, the organic portion of the molecule.

  10. Hybrid continuum–molecular modelling of multiscale internal gas flows

    International Nuclear Information System (INIS)

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

    2013-01-01

    We develop and apply an efficient multiscale method for simulating a large class of low-speed internal rarefied gas flows. The method is an extension of the hybrid atomistic–continuum approach proposed by Borg et al. (2013) [28] for the simulation of micro/nano flows of high-aspect ratio. The major new extensions are: (1) incorporation of fluid compressibility; (2) implementation using the direct simulation Monte Carlo (DSMC) method for dilute rarefied gas flows, and (3) application to a broader range of geometries, including periodic, non-periodic, pressure-driven, gravity-driven and shear-driven internal flows. The multiscale method is applied to micro-scale gas flows through a periodic converging–diverging channel (driven by an external acceleration) and a non-periodic channel with a bend (driven by a pressure difference), as well as the flow between two eccentric cylinders (with the inner rotating relative to the outer). In all these cases there exists a wide variation of Knudsen number within the geometries, as well as substantial compressibility despite the Mach number being very low. For validation purposes, our multiscale simulation results are compared to those obtained from full-scale DSMC simulations: very close agreement is obtained in all cases for all flow variables considered. Our multiscale simulation is an order of magnitude more computationally efficient than the full-scale DSMC for the first and second test cases, and two orders of magnitude more efficient for the third case

  11. Parallelization of quantum molecular dynamics simulation code

    International Nuclear Information System (INIS)

    Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu

    1998-02-01

    A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)

  12. Lipid Configurations from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Pezeshkian, Weria; Khandelia, Himanshu; Marsh, Derek

    2018-01-01

    of dihedral angles in palmitoyl-oleoyl phosphatidylcholine from molecular dynamics simulations of hydrated fluid bilayer membranes. We compare results from the widely used lipid force field of Berger et al. with those from the most recent C36 release of the CHARMM force field for lipids. Only the CHARMM force......The extent to which current force fields faithfully reproduce conformational properties of lipids in bilayer membranes, and whether these reflect the structural principles established for phospholipids in bilayer crystals, are central to biomembrane simulations. We determine the distribution...

  13. Trapped ion simulation of molecular spectrum

    Science.gov (United States)

    Shen, Yangchao; Lu, Yao; Zhang, Kuan; Zhang, Shuaining; Huh, Joonsuk; Kim, Kihwan

    2016-05-01

    Boson sampling had been suggested as a classically intractable and quantum mechanically manageable problem via computational complexity theory arguments. Recently, Huh and co-workers proposed theoretically a modified version of boson sampling, which is designed to simulate a molecular problem, as a practical application. Here, we report the experimental implementation of the theoretical proposal with a trapped ion system. As a first demonstration, we perform the quantum simulation of molecular vibronic profile of SO2, which incorporates squeezing, rotation and coherent displacements operations, and the collective projection measurement on phonon modes. This work was supported by the National Basic Research Program of China 11CBA00300, 2011CBA00301, National Natural Science Foundation of China 11374178, 11574002. Basic Science Research Program of Korea NRF-2015R1A6A3A04059773.

  14. Molecular Simulation of Reacting Systems; TOPICAL

    International Nuclear Information System (INIS)

    THOMPSON, AIDAN P.

    2002-01-01

    The final report for a Laboratory Directed Research and Development project entitled, Molecular Simulation of Reacting Systems is presented. It describes efforts to incorporate chemical reaction events into the LAMMPS massively parallel molecular dynamics code. This was accomplished using a scheme in which several classes of reactions are allowed to occur in a probabilistic fashion at specified times during the MD simulation. Three classes of reaction were implemented: addition, chain transfer and scission. A fully parallel implementation was achieved using a checkerboarding scheme, which avoids conflicts due to reactions occurring on neighboring processors. The observed chemical evolution is independent of the number of processors used. The code was applied to two test applications: irreversible linear polymerization and thermal degradation chemistry

  15. Kinetics from Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Stelzl, Lukas S; Hummer, Gerhard

    2017-08-08

    Transitions between metastable states govern many fundamental processes in physics, chemistry and biology, from nucleation events in phase transitions to the folding of proteins. The free energy surfaces underlying these processes can be obtained from simulations using enhanced sampling methods. However, their altered dynamics makes kinetic and mechanistic information difficult or impossible to extract. Here, we show that, with replica exchange molecular dynamics (REMD), one can not only sample equilibrium properties but also extract kinetic information. For systems that strictly obey first-order kinetics, the procedure to extract rates is rigorous. For actual molecular systems whose long-time dynamics are captured by kinetic rate models, accurate rate coefficients can be determined from the statistics of the transitions between the metastable states at each replica temperature. We demonstrate the practical applicability of the procedure by constructing master equation (Markov state) models of peptide and RNA folding from REMD simulations.

  16. An Evaluation of Molecular Dynamics Performance on the Hybrid Cray XK6 Supercomputer

    International Nuclear Information System (INIS)

    Brown, W. Michael; Nguyen, Trung D.; Fuentes-Cabrera, Miguel A.; Fowlkes, Jason Davidson; Rack, Philip D.; Berger, Mark

    2012-01-01

    For many years, the drive towards computational physics studies that match the size and time-scales of experiment has been fueled by increases in processor and interconnect performance that could be exploited with relatively little modification to existing codes. Engineering and electrical power constraints have disrupted this trend, requiring more drastic changes to both hardware and software solutions. Here, we present details of the Cray XK6 architecture that achieves increased performance with the use of GPU accelerators. We review software development efforts in the LAMMPS molecular dynamics package that have been implemented in order to utilize hybrid high performance computers. We present benchmark results for solid-state, biological, and mesoscopic systems and discuss some challenges for utilizing hybrid systems. We present some early work in improving application performance on the XK6 and performance results for the simulation of liquid copper nanostructures with the embedded atom method.

  17. Huge-scale molecular dynamics simulation of multibubble nuclei

    KAUST Repository

    Watanabe, Hiroshi

    2013-12-01

    We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up to 38.4 billion Lennard-Jones particles were performed on Fujitsu PRIMEHPC FX10, consisting of 4800 SPARC64 IXfx 1.848 GHz processors, at the Information Technology Center of the University of Tokyo, and a performance of 193 teraflops was achieved, which corresponds to a 17.0% execution efficiency. Cavitation processes were also simulated on PRIMEHPC FX10 and SGI Altix ICE 8400EX at the Institute of Solid State Physics of the University of Tokyo, which involved 1.45 billion and 22.9 million particles, respectively. Ostwald-like ripening was observed after the multibubble nuclei. Our results demonstrate that direct simulations of multiscale phenomena involving phase transitions from the atomic scale are possible and that the molecular dynamics method is a promising method that can be applied to petascale computers. © 2013 Elsevier B.V. All rights reserved.

  18. Simulation of hybrid renewable microgeneration systems for variable electricity prices

    International Nuclear Information System (INIS)

    Brandoni, C.; Renzi, M.; Caresana, F.; Polonara, F.

    2014-01-01

    This paper addresses a hybrid renewable system that consists of a micro-Combined Cooling Heat and Power (CCHP) unit and a solar energy conversion device. In addition to a traditional PV system, a High Concentrator Photovoltaic (HCPV) device, the design of which is suitable for building integration application, was also modelled and embedded in the hybrid system. The work identifies the optimal management strategies for the hybrid renewable system in an effort to minimise the primary energy usage, the carbon dioxide emissions and the operational costs for variable electricity prices that result from the day-ahead electricity market. An “ad hoc” model describes the performance of the HCPV module, PV and Internal Combustion Engine, whilst the other units were simulated based on their main characteristic parameters. The developed algorithm was applied to three different building typologies. The results indicate that the best configuration is the hybrid renewable system with PV, which can provide a yearly primary energy reduction of between 20% and 30% compared to separate production. The hybrid renewable system with HCPV becomes competitive with the PV technology when the level of solar radiation is high. - Highlights: • The paper addresses a hybrid renewable system that consists of a micro-CCHP unit and a solar energy conversion device. • Both PV and High Concentrator Photovoltaic (HCPV) systems have been modelled and embedded in the hybrid system. • The work identifies the optimal management strategies for variable electricity prices. • Hybrid renewable systems provide a yearly primary energy reduction of between 20% and 30% compared to separate production. • When the level of solar radiation is high, HCPV becomes competitive with the PV technology

  19. Investigation of the interfacial properties of polyurethane/carbon nanotube hybrid composites: A molecular dynamics study

    Science.gov (United States)

    Goclon, Jakub; Panczyk, Tomasz; Winkler, Krzysztof

    2018-03-01

    Considering the varied applications of hybrid polymer/carbon nanotube composites and the constant progress in the synthesis methods of such materials, we report a theoretical study of interfacial layer formation between pristine single-wall carbon nanotubes (SWCNTs) and polyurethane (PU) using molecular dynamic simulations. We vary the SWCNT diameter and the number of PU chains to examine various PU-SWCNT interaction patterns. Our simulations indicate the important role of intra-chain forces in PU. No regular polymeric structures could be identified on the carbon nanotube surface during the simulations. We find that increasing the SWCNT diameter results in stronger polymer binding. However, higher surface loadings of PU lead to stronger interpenetration by the polymeric segments; this effect is more apparent for SWCNTs with small diameters. Our core finding is that the attached PU binds most strongly to the carbon nanotubes with the largest diameters. Polymer dynamics reveal the loose distribution of PU chains in these systems.

  20. Hybrid simulation using mixed reality for interventional ultrasound imaging training.

    Science.gov (United States)

    Freschi, C; Parrini, S; Dinelli, N; Ferrari, M; Ferrari, V

    2015-07-01

    Ultrasound (US) imaging offers advantages over other imaging modalities and has become the most widespread modality for many diagnostic and interventional procedures. However, traditional 2D US requires a long training period, especially to learn how to manipulate the probe. A hybrid interactive system based on mixed reality was designed, implemented and tested for hand-eye coordination training in diagnostic and interventional US. A hybrid simulator was developed integrating a physical US phantom and a software application with a 3D virtual scene. In this scene, a 3D model of the probe with its relative scan plane is coherently displayed with a 3D representation of the phantom internal structures. An evaluation study of the diagnostic module was performed by recruiting thirty-six novices and four experts. The performances of the hybrid (HG) versus physical (PG) simulator were compared. After the training session, each novice was required to visualize a particular target structure. The four experts completed a 5-point Likert scale questionnaire. Seventy-eight percentage of the HG novices successfully visualized the target structure, whereas only 45% of the PG reached this goal. The mean scores from the questionnaires were 5.00 for usefulness, 4.25 for ease of use, 4.75 for 3D perception, and 3.25 for phantom realism. The hybrid US training simulator provides ease of use and is effective as a hand-eye coordination teaching tool. Mixed reality can improve US probe manipulation training.

  1. A survey of electric and hybrid vehicle simulation programs

    Science.gov (United States)

    Bevan, J.; Heimburger, D. A.; Metcalfe, M. A.

    1978-01-01

    Results of a survey conducted within the United States to determine the extent of development and capabilities of automotive performance simulation programs suitable for electric and hybrid vehicle studies are summarized. Altogether, 111 programs were identified as being in a usable state. The complexity of the existing programs spans a range from a page of simple desktop calculator instructions to 300,000 lines of a high-level programming language. The capability to simulate electric vehicles was most common, heat-engines second, and hybrid vehicles least common. Batch-operated programs are slightly more common than interactive ones, and one-third can be operated in either mode. The most commonly used language was FORTRAN, the language typically used by engineers. The higher-level simulation languages (e.g. SIMSCRIPT, GPSS, SIMULA) used by "model builders" were conspicuously lacking.

  2. Simulations for the transmutation of nuclear wastes with hybrid reactors

    International Nuclear Information System (INIS)

    Vuillier, St.

    1998-06-01

    A Monte Carlo simulation, devoted to the spallation, has been built in the framework of the hybrid systems proposed for the nuclear wastes incineration. This system GSPARTE, described the reactions evolution. It takes into account and improves the nuclear codes and the low and high energy particles transport in the GEANT code environment, adapted to the geometry of the hybrid reactors. Many applications and abacus useful for the wastes transmutation, have been realized with this system: production of thick target neutrons, source definition, material damages. (A.L.B.)

  3. Simulation and Test of a Fuel Cell Hybrid Golf Cart

    Directory of Open Access Journals (Sweden)

    Jingming Liang

    2014-01-01

    Full Text Available This paper establishes the simulation model of fuel cell hybrid golf cart (FCHGC, which applies the non-GUI mode of the Advanced Vehicle Simulator (ADVISOR and the genetic algorithm (GA to optimize it. Simulation of the objective function is composed of fuel consumption and vehicle dynamic performance; the variables are the fuel cell stack power sizes and the battery numbers. By means of simulation, the optimal parameters of vehicle power unit, fuel cell stack, and battery pack are worked out. On this basis, GUI mode of ADVISOR is used to select the rated power of vehicle motor. In line with simulation parameters, an electrical golf cart is refitted by adding a 2 kW hydrogen air proton exchange membrane fuel cell (PEMFC stack system and test the FCHGC. The result shows that the simulation data is effective but it needs improving compared with that of the real cart test.

  4. 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)

  5. Reduction Methods for Real-time Simulations in Hybrid Testing

    DEFF Research Database (Denmark)

    Andersen, Sebastian

    2016-01-01

    Hybrid testing constitutes a cost-effective experimental full scale testing method. The method was introduced in the 1960's by Japanese researchers, as an alternative to conventional full scale testing and small scale material testing, such as shake table tests. The principle of the method...... is performed on a glass fibre reinforced polymer composite box girder. The test serves as a pilot test for prospective real-time tests on a wind turbine blade. The Taylor basis is implemented in the test, used to perform the numerical simulations. Despite of a number of introduced errors in the real...... is to divide a structure into a physical substructure and a numerical substructure, and couple these in a test. If the test is conducted in real-time it is referred to as real time hybrid testing. The hybrid testing concept has developed significantly since its introduction in the 1960', both with respect...

  6. Managing resource capacity using hybrid simulation

    Science.gov (United States)

    Ahmad, Norazura; Ghani, Noraida Abdul; Kamil, Anton Abdulbasah; Tahar, Razman Mat

    2014-12-01

    Due to the diversity of patient flows and interdependency of the emergency department (ED) with other units in hospital, the use of analytical models seems not practical for ED modeling. One effective approach to study the dynamic complexity of ED problems is by developing a computer simulation model that could be used to understand the structure and behavior of the system. Attempts to build a holistic model using DES only will be too complex while if only using SD will lack the detailed characteristics of the system. This paper discusses the combination of DES and SD in order to get a better representation of the actual system than using either modeling paradigm solely. The model is developed using AnyLogic software that will enable us to study patient flows and the complex interactions among hospital resources for ED operations. Results from the model show that patients' length of stay is influenced by laboratories turnaround time, bed occupancy rate and ward admission rate.

  7. Hybrid simulation of electron cyclotron resonance heating

    Energy Technology Data Exchange (ETDEWEB)

    Ropponen, T. [Department of Physics, University of Jyvaeskylae, P.O. Box 35, FI-40014 (Finland)], E-mail: tommi.ropponen@phys.jyu.fi; Tarvainen, O. [Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Suominen, P. [CERN Geneve 23, CH-1211 (Switzerland); Koponen, T.K. [Department of Physics, University of Jyvaeskylae, Nanoscience Center, P.O. Box 35, FI-40014 (Finland); Kalvas, T.; Koivisto, H. [Department of Physics, University of Jyvaeskylae, P.O. Box 35, FI-40014 (Finland)

    2008-03-11

    Electron Cyclotron Resonance (ECR) heating is a fundamentally important aspect in understanding the physics of Electron Cyclotron Resonance Ion Sources (ECRIS). Absorption of the radio frequency (RF) microwave power by electron heating in the resonance zone depends on many parameters including frequency and electric field strength of the microwave, magnetic field structure and electron and ion density profiles. ECR absorption has been studied in the past by e.g. modelling electric field behaviour in the resonance zone and its near proximity. This paper introduces a new ECR heating code that implements damping of the microwave power in the vicinity of the resonance zone, utilizes electron density profiles and uses right hand circularly polarized (RHCP) electromagnetic waves to simulate electron heating in ECRIS plasma.

  8. Novel flavonolignan hybrid antioxidants: From enzymatic preparation to molecular rationalization.

    Science.gov (United States)

    Vavříková, Eva; Křen, Vladimír; Jezova-Kalachova, Lubica; Biler, Michal; Chantemargue, Benjamin; Pyszková, Michaela; Riva, Sergio; Kuzma, Marek; Valentová, Kateřina; Ulrichová, Jitka; Vrba, Jiří; Trouillas, Patrick; Vacek, Jan

    2017-02-15

    A series of antioxidants was designed and synthesized based on conjugation of the hepatoprotective flavonolignan silybin with l-ascorbic acid, trolox alcohol or tyrosol via a C 12 aliphatic linker. These hybrid molecules were prepared from 12-vinyl dodecanedioate-23-O-silybin using the enzymatic regioselective acylation procedure with Novozym 435 (lipase B) or with lipase PS. Voltammetric analyses showed that the silybin-ascorbic acid conjugate exhibited excellent electron donating ability, in comparison to the other conjugates. Free radical scavenging, antioxidant activities and cytoprotective action were evaluated. The silybin-ascorbic acid hybrid exhibited the best activities (IC 50  = 30.2 μM) in terms of lipid peroxidation inhibition. The promising protective action of the conjugate against lipid peroxidation can be attributed to modulated electron transfer abilities of both the silybin and ascorbate moieties, but also to the hydrophobic C 12 linker facilitating membrane insertion. This was supported experimentally and theoretically by density functional theory (DFT) and molecular dynamics (MD) calculations. The results presented here can be used in the further development of novel multipotent antioxidants and cytoprotective agents, in particular for substances acting at an aqueous/lipid interface. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  9. Creating Ruddlesden-Popper phases by hybrid molecular beam epitaxy

    International Nuclear Information System (INIS)

    Haislmaier, Ryan C.; Stone, Greg; Alem, Nasim; Engel-Herbert, Roman

    2016-01-01

    The synthesis of a 50 unit cell thick n = 4 Sr_n_+_1Ti_nO_3_n_+_1 (Sr_5Ti_4O_1_3) Ruddlesden-Popper (RP) phase film is demonstrated by sequentially depositing SrO and TiO_2 layers in an alternating fashion using hybrid molecular beam epitaxy (MBE), where Ti was supplied using titanium tetraisopropoxide (TTIP). A detailed calibration procedure is outlined for determining the shuttering times to deposit SrO and TiO_2 layers with precise monolayer doses using in-situ reflection high energy electron diffraction (RHEED) as feedback. Using optimized Sr and TTIP shuttering times, a fully automated growth of the n = 4 RP phase was carried out over a period of >4.5 h. Very stable RHEED intensity oscillations were observed over the entire growth period. The structural characterization by X-ray diffraction and high resolution transmission electron microscopy revealed that a constant periodicity of four SrTiO_3 perovskite unit cell blocks separating the double SrO rocksalt layer was maintained throughout the entire film thickness with a very little amount of planar faults oriented perpendicular to the growth front direction. These results illustrate that hybrid MBE is capable of layer-by-layer growth with atomic level precision and excellent flux stability.

  10. Creating Ruddlesden-Popper phases by hybrid molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Haislmaier, Ryan C.; Stone, Greg; Alem, Nasim; Engel-Herbert, Roman, E-mail: rue2@psu.edu [Department of Materials Science and Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802 (United States)

    2016-07-25

    The synthesis of a 50 unit cell thick n = 4 Sr{sub n+1}Ti{sub n}O{sub 3n+1} (Sr{sub 5}Ti{sub 4}O{sub 13}) Ruddlesden-Popper (RP) phase film is demonstrated by sequentially depositing SrO and TiO{sub 2} layers in an alternating fashion using hybrid molecular beam epitaxy (MBE), where Ti was supplied using titanium tetraisopropoxide (TTIP). A detailed calibration procedure is outlined for determining the shuttering times to deposit SrO and TiO{sub 2} layers with precise monolayer doses using in-situ reflection high energy electron diffraction (RHEED) as feedback. Using optimized Sr and TTIP shuttering times, a fully automated growth of the n = 4 RP phase was carried out over a period of >4.5 h. Very stable RHEED intensity oscillations were observed over the entire growth period. The structural characterization by X-ray diffraction and high resolution transmission electron microscopy revealed that a constant periodicity of four SrTiO{sub 3} perovskite unit cell blocks separating the double SrO rocksalt layer was maintained throughout the entire film thickness with a very little amount of planar faults oriented perpendicular to the growth front direction. These results illustrate that hybrid MBE is capable of layer-by-layer growth with atomic level precision and excellent flux stability.

  11. A Hybrid Imperative and Functional Molecular Mechanics Application

    Directory of Open Access Journals (Sweden)

    Thomas Deboni

    1996-01-01

    Full Text Available Molecular mechanics applications model the interactions among large ensembles of discrete particles. They are used where probabilistic methods are inadequate, such as drug chemistry. This methodology is difficult to parallelize with good performance, due to its poor locality, uneven partitions, and dynamic behavior. Imperative programs have been written that attempt this on shared and distributed memory machines. Given such a program, the computational kernel can be rewritten in Sisal, a functional programming language, and integrated with the rest of the imperative program under the Sisal Foreign Language Interface. This allows minimal effort and maximal return from parallelization work, and leaves the work appropriate to imperative implementation in its original form. We describe such an effort, focusing on the parts of the application that are appropriate for Sisal implementation, the specifics of mixed-language programming, and the complex performance behavior of the resulting hybrid code.

  12. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Yuqi; Wang, Jinan; Shao, Qiang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn; Zhu, Weiliang, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203 (China); Shi, Jiye, E-mail: qshao@mail.shcnc.ac.cn, E-mail: Jiye.Shi@ucb.com, E-mail: wlzhu@mail.shcnc.ac.cn [UCB Pharma, 216 Bath Road, Slough SL1 4EN (United Kingdom)

    2015-03-28

    The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.

  13. Computer simulation of molecular sorption in zeolites

    International Nuclear Information System (INIS)

    Calmiano, Mark Daniel

    2001-01-01

    The work presented in this thesis encompasses the computer simulation of molecular sorption. In Chapter 1 we outline the aims and objectives of this work. Chapter 2 follows in which an introduction to sorption in zeolites is presented, with discussion of structure and properties of the main zeolites studied. Chapter 2 concludes with a description of the principles and theories of adsorption. In Chapter 3 we describe the methodology behind the work carried out in this thesis. In Chapter 4 we present our first computational study, that of the sorption of krypton in silicalite. We describe work carried out to investigate low energy sorption sites of krypton in silicalite where we observe krypton to preferentially sorb into straight and sinusoidal channels over channel intersections. We simulate single step type I adsorption isotherms and use molecular dynamics to study the diffusion of krypton and obtain division coefficients and the activation energy. We compare our results to previous experimental and computational studies where we show our work to be in good agreement. In Chapter 5 we present a systematic study of the sorption of oxygen and nitrogen in five lithium substituted zeolites using a transferable interatomic potential that we have developed from ab initio calculations. We show increased loading of nitrogen compared to oxygen in all five zeolites studied as expected and simulate adsorption isotherms, which we compare to experimental and simulated data in the literature. In Chapter 6 we present work on the sorption of ferrocene in the zeolite NaY. We show that a simulated, low energy sorption site for ferrocene is correctly located by comparing to X-ray powder diffraction results for this same system. The thesis concludes with some overall conclusions and discussion of opportunities for future work. (author)

  14. Modular modeling and simulation of hybrid power trains; Modulare Modellbildung und Simulation von hybriden Antriebstraengen

    Energy Technology Data Exchange (ETDEWEB)

    Kelz, Gerald; Hirschberg, Wolfgang [Inst. fuer Fahrzeugtechnik, Technische Univ. Graz (Austria)

    2009-07-01

    The power train of a hybrid vehicle is considerably more complex than that of conventional vehicles. Whilst the topology of a conventional vehicle is normally fixed, the arrangement of the power train components for innovative propulsion systems is a flexible one. The aim is to find those topologies and configurations which are optimal for the intended use. Fuel consumption potentials can be derived with the aid of vehicle longitudinal dynamics simulation. Mostly these simulations are carried out using commercial software which is optimized for the standard topology and do not offer the flexibility to calculate arbitrary topologies. This article covers the modular modeling and the fuel consumption simulation of complex hybrid power trains for topology analysis. A component library for the development of arbitrary hybrid propulsion systems is introduced. The focus lies on an efficient and fast modeling which provides exact simulation results. Several models of power train components are introduced. (orig.)

  15. Molecular models and simulations of layered materials

    International Nuclear Information System (INIS)

    Kalinichev, Andrey G.; Cygan, Randall Timothy; Heinz, Hendrik; Greathouse, Jeffery A.

    2008-01-01

    The micro- to nano-sized nature of layered materials, particularly characteristic of naturally occurring clay minerals, limits our ability to fully interrogate their atomic dispositions and crystal structures. The low symmetry, multicomponent compositions, defects, and disorder phenomena of clays and related phases necessitate the use of molecular models and modern simulation methods. Computational chemistry tools based on classical force fields and quantum-chemical methods of electronic structure calculations provide a practical approach to evaluate structure and dynamics of the materials on an atomic scale. Combined with classical energy minimization, molecular dynamics, and Monte Carlo techniques, quantum methods provide accurate models of layered materials such as clay minerals, layered double hydroxides, and clay-polymer nanocomposites

  16. Hybrid simulation of a 900 Mwe nuclear plant

    International Nuclear Information System (INIS)

    Constantieux, Thierry; Deat, Max.

    1979-01-01

    To analyse the effects on PWRs of transients originating from the network, specific means of calculation must be elaborated. One of them which was conceived and set up on a hybrid computer by FRAMATOME and the FRENCH ATOMIC ENERGY COMMISSION, is described in this paper. The method chosen to validate this code is fairly original, since it consisted in carrying out a long duration test on a plan and in simulating this on the hybrid computer; then in carefully comparing the recorded data of the test with the results of the simulation. The quality of the results, thus obtained shows that a relatively unsophisticated model is able to give a good idea of actual process behavior, but only if the types of transients to be studied with the code are well identified before its elaboration

  17. Diffusion and dispersion characteristics of hybridized discontinuous Galerkin methods for under-resolved turbulence simulations

    Science.gov (United States)

    Moura, Rodrigo; Fernandez, Pablo; Mengaldo, Gianmarco

    2017-11-01

    We investigate the dispersion and diffusion characteristics of hybridized discontinuous Galerkin (DG) methods. This provides us with insights to develop robust and accurate high-order DG discretizations for under-resolved flow simulations. Using the eigenanalysis technique introduced in (Moura et al., JCP, 2015 and Mengaldo et al., Computers & Fluids, 2017), we present a dispersion-diffusion analysis for the linear advection-diffusion equation. The effect of the accuracy order, the Riemann flux and the viscous stabilization are investigated. Next, we examine the diffusion characteristics of hybridized DG methods for under-resolved turbulent flows. The implicit large-eddy simulation (iLES) of the inviscid and viscous Taylor-Green vortex (TGV) problems are considered to this end. The inviscid case is relevant in the limit of high Reynolds numbers Re , i.e. negligible molecular viscosity, while the viscous case explores the effect of Re on the accuracy and robustness of the simulations. The TGV cases considered here are particularly crucial to under-resolved turbulent free flows away from walls. We conclude the talk with a discussion on the connections between hybridized and standard DG methods for under-resolved flow simulations.

  18. Hybrid Simulations of Plasma-Neutral-Dust Interactions at Enceladus

    International Nuclear Information System (INIS)

    Omidi, N.; Russell, C. T.; Jia, Y. D.; Tokar, R. L.; Farrell, W. M.; Kurth, W. S.; Gurnett, D. A.; Leisner, J. S.

    2010-01-01

    Through ejection from its southern hemisphere, Enceladus is a dominant source of neutral gas and dust in Saturn's inner magnetosphere. The interaction of the corotating plasma with the gas and dust modifies the plasma environment around Enceladus. We use 3-D hybrid (kinetic ions, fluid electrons) simulations to examine the effects of gas and dust on the nature of the interaction region and use Cassini observations to constrain their properties.

  19. Viscosity calculations at molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kirova, E M; Norman, G E

    2015-01-01

    Viscosity and diffusion are chosen as an example to demonstrate the universality of diagnostics methods in the molecular dynamics method. To emphasize the universality, three diverse systems are investigated, which differ from each other drastically: liquids with embedded atom method and pairwise interatomic interaction potentials and dusty plasma with a unique multiparametric interparticle interaction potential. Both the Einstein-Helfand and Green-Kubo relations are used. Such a particular process as glass transition is analysed at the simulation of the aluminium melt. The effect of the dust particle charge fluctuation is considered. The results are compared with the experimental data. (paper)

  20. Chain networking revealed by molecular dynamics simulation

    Science.gov (United States)

    Zheng, Yexin; Tsige, Mesfin; Wang, Shi-Qing

    Based on Kremer-Grest model for entangled polymer melts, we demonstrate how the response of a polymer glass depends critically on the chain length. After quenching two melts of very different chain lengths (350 beads per chain and 30 beads per chain) into deeply glassy states, we subject them to uniaxial extension. Our MD simulations show that the glass of long chains undergoes stable necking after yielding whereas the system of short chains is unable to neck and breaks up after strain localization. During ductile extension of the polymer glass made of long chain significant chain tension builds up in the load-bearing strands (LBSs). Further analysis is expected to reveal evidence of activation of the primary structure during post-yield extension. These results lend support to the recent molecular model 1 and are the simulations to demonstrate the role of chain networking. This work is supported, in part, by a NSF Grant (DMR-EAGER-1444859)

  1. Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator

    Science.gov (United States)

    Suh, Donghyuk; Radak, Brian K.; Chipot, Christophe; Roux, Benoît

    2018-01-01

    Molecular dynamics (MD) trajectories based on classical equations of motion can be used to sample the configurational space of complex molecular systems. However, brute-force MD often converges slowly due to the ruggedness of the underlying potential energy surface. Several schemes have been proposed to address this problem by effectively smoothing the potential energy surface. However, in order to recover the proper Boltzmann equilibrium probability distribution, these approaches must then rely on statistical reweighting techniques or generate the simulations within a Hamiltonian tempering replica-exchange scheme. The present work puts forth a novel hybrid sampling propagator combining Metropolis-Hastings Monte Carlo (MC) with proposed moves generated by non-equilibrium MD (neMD). This hybrid neMD-MC propagator comprises three elementary elements: (i) an atomic system is dynamically propagated for some period of time using standard equilibrium MD on the correct potential energy surface; (ii) the system is then propagated for a brief period of time during what is referred to as a "boosting phase," via a time-dependent Hamiltonian that is evolved toward the perturbed potential energy surface and then back to the correct potential energy surface; (iii) the resulting configuration at the end of the neMD trajectory is then accepted or rejected according to a Metropolis criterion before returning to step 1. A symmetric two-end momentum reversal prescription is used at the end of the neMD trajectories to guarantee that the hybrid neMD-MC sampling propagator obeys microscopic detailed balance and rigorously yields the equilibrium Boltzmann distribution. The hybrid neMD-MC sampling propagator is designed and implemented to enhance the sampling by relying on the accelerated MD and solute tempering schemes. It is also combined with the adaptive biased force sampling algorithm to examine. Illustrative tests with specific biomolecular systems indicate that the method can yield

  2. Molecular Simulation of Adsorption in Microporous Materials

    Directory of Open Access Journals (Sweden)

    Yiannourakou M.

    2013-11-01

    Full Text Available The development of industrial software, the decreasing cost of computing time, and the availability of well-tested forcefields make molecular simulation increasingly attractive for chemical engineers. We present here several applications of Monte-Carlo simulation techniques, applied to the adsorption of fluids in microporous solids such as zeolites and model carbons (pores < 2 nm. Adsorption was computed in the Grand Canonical ensemble with the MedeA®-GIBBS software, using energy grids to decrease computing time. MedeA®-GIBBS has been used for simulations in the NVT or NPT ensembles to obtain the density and fugacities of fluid phases. Simulation results are compared with experimental pure component isotherms in zeolites (hydrocarbon gases, water, alkanes, aromatics, ethanethiol, etc., and mixtures (methane-ethane, n-hexane-benzene, over a large range of temperatures. Hexane/benzene selectivity inversions between silicalite and Na-faujasites are well predicted with published forcefields, providing an insight on the underlying mechanisms. Also, the adsorption isotherms in Na-faujasites for light gases or ethane-thiol are well described. Regarding organic adsorbents, models of mature kerogen or coal were built in agreement with known chemistry of these systems. Obtaining realistic kerogen densities with the simple relaxation approach considered here is encouraging for the investigation of other organic systems. Computing excess sorption curves in qualitative agreement with those recently measured on dry samples of gas shale is also favorable. Although still preliminary, such applications illustrate the strength of molecular modeling in understanding complex systems in conditions where experiments are difficult.

  3. An Investigation of a Hybrid Mixing Timescale Model for PDF Simulations of Turbulent Premixed Flames

    Science.gov (United States)

    Zhou, Hua; Kuron, Mike; Ren, Zhuyin; Lu, Tianfeng; Chen, Jacqueline H.

    2016-11-01

    Transported probability density function (TPDF) method features the generality for all combustion regimes, which is attractive for turbulent combustion simulations. However, the modeling of micromixing due to molecular diffusion is still considered to be a primary challenge for TPDF method, especially in turbulent premixed flames. Recently, a hybrid mixing rate model for TPDF simulations of turbulent premixed flames has been proposed, which recovers the correct mixing rates in the limits of flamelet regime and broken reaction zone regime while at the same time aims to properly account for the transition in between. In this work, this model is employed in TPDF simulations of turbulent premixed methane-air slot burner flames. The model performance is assessed by comparing the results from both direct numerical simulation (DNS) and conventional constant mechanical-to-scalar mixing rate model. This work is Granted by NSFC 51476087 and 91441202.

  4. Two dimensional hybrid simulation of a curved bow shock

    International Nuclear Information System (INIS)

    Thomas, V.A.; Winske, D.

    1990-01-01

    Results are presented from two dimensional hybrid simulations of curved collisionless supercritical shocks, retaining both quasi-perpendicular and quasi-parallel sections of the shock in order to study the character and origin of the foreshock ion population. The simulations demonstrate that the foreshock ion population is dominated by ions impinging upon the quasi-parallel side of the shock, while nonlocal transport from the quasi-perpendicular side of the shock into the foreshock region is minimal. Further, it is shown that the ions gain energy by drifting significantly in the direction of the convection electric field through multiple shock encounters

  5. Hybrid Multilevel Monte Carlo Simulation of Stochastic Reaction Networks

    KAUST Repository

    Moraes, Alvaro

    2015-01-01

    even more, we want to achieve this objective with near optimal computational work. We first introduce a hybrid path-simulation scheme based on the well-known stochastic simulation algorithm (SSA)[3] and the tau-leap method [2]. Then, we introduce a Multilevel Monte Carlo strategy that allows us to achieve a computational complexity of order O(T OL−2), this is the same computational complexity as in an exact method but with a smaller constant. We provide numerical examples to show our results.

  6. Hybrid and electric advanced vehicle systems (heavy) simulation

    Science.gov (United States)

    Hammond, R. A.; Mcgehee, R. K.

    1981-01-01

    A computer program to simulate hybrid and electric advanced vehicle systems (HEAVY) is described. It is intended for use early in the design process: concept evaluation, alternative comparison, preliminary design, control and management strategy development, component sizing, and sensitivity studies. It allows the designer to quickly, conveniently, and economically predict the performance of a proposed drive train. The user defines the system to be simulated using a library of predefined component models that may be connected to represent a wide variety of propulsion systems. The development of three models are discussed as examples.

  7. A molecular dynamics simulation study of chloroform

    Science.gov (United States)

    Tironi, Ilario G.; van Gunsteren, Wilfred F.

    Three different chloroform models have been investigated using molecular dynamics computer simulation. The thermodynamic, structural and dynamic properties of the various models were investigated in detail. In particular, the potential energies, diffusion coefficients and rotational correlation times obtained for each model are compared with experiment. It is found that the theory of rotational Brownian motion fails in describing the rotational diffusion of chloroform. The force field of Dietz and Heinzinger was found to give good overall agreement with experiment. An extended investigation of this chloroform model has been performed. Values are reported for the isothermal compressibility, the thermal expansion coefficient and the constant volume heat capacity. The values agree well with experiment. The static and frequency dependent dielectric permittivity were computed from a 1·2 ns simulation conducted under reaction field boundary conditions. Considering the fact that the model is rigid with fixed partial charges, the static dielectric constant and Debye relaxation time compare well with experiment. From the same simulation the shear viscosity was computed using the off-diagonal elements of the pressure tensor, both via an Einstein type relation and via a Green-Kubo equation. The calculated viscosities show good agreement with experimental values. The excess Helmholtz energy is calculated using the thermodynamic integration technique and simulations of 50 and 80 ps. The value obtained for the excess Helmholtz energy matches the theoretical value within a few per cent.

  8. A Lookahead Behavior Model for Multi-Agent Hybrid Simulation

    Directory of Open Access Journals (Sweden)

    Mei Yang

    2017-10-01

    Full Text Available In the military field, multi-agent simulation (MAS plays an important role in studying wars statistically. For a military simulation system, which involves large-scale entities and generates a very large number of interactions during the runtime, the issue of how to improve the running efficiency is of great concern for researchers. Current solutions mainly use hybrid simulation to gain fewer updates and synchronizations, where some important continuous models are maintained implicitly to keep the system dynamics, and partial resynchronization (PR is chosen as the preferable state update mechanism. However, problems, such as resynchronization interval selection and cyclic dependency, remain unsolved in PR, which easily lead to low update efficiency and infinite looping of the state update process. To address these problems, this paper proposes a lookahead behavior model (LBM to implement a PR-based hybrid simulation. In LBM, a minimal safe time window is used to predict the interactions between implicit models, upon which the resynchronization interval can be efficiently determined. Moreover, the LBM gives an estimated state value in the lookahead process so as to break the state-dependent cycle. The simulation results show that, compared with traditional mechanisms, LBM requires fewer updates and synchronizations.

  9. Dynamic Garment Simulation based on Hybrid Bounding Volume Hierarchy

    Directory of Open Access Journals (Sweden)

    Zhu Dongyong

    2016-12-01

    Full Text Available In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to do the secondary segmentation to collect the human body’s upper arms, lower arms, upper legs, lower legs, trunk, hip and woman’s chest as the elementary units of dynamic clothing simulation. According to different shapes of these elementary units, it chooses the closest and most efficient hybrid bounding box to specify these units, such as cylinder bounding box and elliptic cylinder bounding box. During the process of constructing these bounding boxes, it uses the least squares method and slices of the human body to get the related parameters. This approach makes it possible to use the least amount of bounding boxes to create close collision detection regions for the appearance of the human body. A spring-mass model based on a triangular mesh of the clothing model is finally constructed for dynamic simulation. The simulation result shows the feasibility and superiority of the method described.

  10. A hybrid particle–field molecular dynamics approach: a route toward efficient coarse-grained models for biomembranes

    International Nuclear Information System (INIS)

    Milano, Giuseppe; De Nicola, Antonio; Kawakatsu, Toshihiro

    2013-01-01

    This paper gives an overview of the coarse-grained models of phospholipids recently developed by the authors in the frame of a hybrid particle–field molecular dynamics technique. This technique employs a special class of coarse-grained models that are gaining popularity because they allow simulations of large scale systems and, at the same time, they provide sufficiently detailed chemistry for the mapping scheme adopted. The comparison of the computational costs of our approach with standard molecular dynamics simulations is a function of the system size and the number of processors employed in the parallel calculations. Due to the low amount of data exchange, the larger the number of processors, the better are the performances of the hybrid particle–field models. This feature makes these models very promising ones in the exploration of several problems in biophysics. (paper)

  11. Exact Turbulence Law in Collisionless Plasmas: Hybrid Simulations

    Science.gov (United States)

    Hellinger, P.; Verdini, A.; Landi, S.; Franci, L.; Matteini, L.

    2017-12-01

    An exact vectorial law for turbulence in homogeneous incompressible Hall-MHD is derived and tested in two-dimensional hybrid simulations of plasma turbulence. The simulations confirm the validity of the MHD exact law in the kinetic regime, the simulated turbulence exhibits a clear inertial range on large scales where the MHD cascade flux dominates. The simulation results also indicate that in the sub-ion range the cascade continues via the Hall term and that the total cascade rate tends to decrease at around the ion scales, especially in high-beta plasmas. This decrease is like owing to formation of non-thermal features, such as collisionless ion energization, that can not be retained in the Hall MHD approximation.

  12. Evolution and molecular control of hybrid incompatibility in plants

    Directory of Open Access Journals (Sweden)

    Chen Chen

    2016-08-01

    Full Text Available Postzygotic reproductive isolation (RI plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with parasitic selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities.

  13. Molecular evidence for natural hybridization in the mangrove genus avicennia

    International Nuclear Information System (INIS)

    Huang, L.; Huang Y; Shi, S.; Zhou, R

    2014-01-01

    Hybridization has been observed in several multi-species genera of mangroves; however, there has been no report on hybridization in Avicennia in the Indo-West Pacific region. In this study, we sequenced 5 low-copy nuclear genes of Avicennia marina, A. rumphiana and 2 individuals of their putative hybrid in the Southeast Asia region to test the hypothesis of natural hybridization between these 2 species. We demonstrated that both putative hybrid individuals possessed two types of sequences at each of the 5 genes, perfectly corresponding to those of A. marina and A. rumphiana, confirming the hybridization between these 2 Avicennia species, and the 2 hybrid individuals are most likely F1 hybrids. Sequencing of the chloroplast trnH-psbA regions indicated that A. marina was the maternal parent of the two hybrid individuals. (author)

  14. STEM image simulation with hybrid CPU/GPU programming

    International Nuclear Information System (INIS)

    Yao, Y.; Ge, B.H.; Shen, X.; Wang, Y.G.; Yu, R.C.

    2016-01-01

    STEM image simulation is achieved via hybrid CPU/GPU programming under parallel algorithm architecture to speed up calculation on a personal computer (PC). To utilize the calculation power of a PC fully, the simulation is performed using the GPU core and multi-CPU cores at the same time to significantly improve efficiency. GaSb and an artificial GaSb/InAs interface with atom diffusion have been used to verify the computation. - Highlights: • STEM image simulation is achieved by hybrid CPU/GPU programming under parallel algorithm architecture to speed up the calculation in the personal computer (PC). • In order to fully utilize the calculation power of the PC, the simulation is performed by GPU core and multi-CPU cores at the same time so efficiency is improved significantly. • GaSb and artificial GaSb/InAs interface with atom diffusion have been used to verify the computation. The results reveal some unintuitive phenomena about the contrast variation with the atom numbers.

  15. STEM image simulation with hybrid CPU/GPU programming

    Energy Technology Data Exchange (ETDEWEB)

    Yao, Y., E-mail: yaoyuan@iphy.ac.cn; Ge, B.H.; Shen, X.; Wang, Y.G.; Yu, R.C.

    2016-07-15

    STEM image simulation is achieved via hybrid CPU/GPU programming under parallel algorithm architecture to speed up calculation on a personal computer (PC). To utilize the calculation power of a PC fully, the simulation is performed using the GPU core and multi-CPU cores at the same time to significantly improve efficiency. GaSb and an artificial GaSb/InAs interface with atom diffusion have been used to verify the computation. - Highlights: • STEM image simulation is achieved by hybrid CPU/GPU programming under parallel algorithm architecture to speed up the calculation in the personal computer (PC). • In order to fully utilize the calculation power of the PC, the simulation is performed by GPU core and multi-CPU cores at the same time so efficiency is improved significantly. • GaSb and artificial GaSb/InAs interface with atom diffusion have been used to verify the computation. The results reveal some unintuitive phenomena about the contrast variation with the atom numbers.

  16. Hybrid Computational Simulation and Study of Terahertz Pulsed Photoconductive Antennas

    Science.gov (United States)

    Emadi, R.; Barani, N.; Safian, R.; Nezhad, A. Zeidaabadi

    2016-11-01

    A photoconductive antenna (PCA) has been numerically investigated in the terahertz (THz) frequency band based on a hybrid simulation method. This hybrid method utilizes an optoelectronic solver, Silvaco TCAD, and a full-wave electromagnetic solver, CST. The optoelectronic solver is used to find the accurate THz photocurrent by considering realistic material parameters. Performance of photoconductive antennas and temporal behavior of the excited photocurrent for various active region geometries such as bare-gap electrode, interdigitated electrodes, and tip-to-tip rectangular electrodes are investigated. Moreover, investigations have been done on the center of the laser illumination on the substrate, substrate carrier lifetime, and diffusion photocurrent associated with the carriers temperature, to achieve efficient and accurate photocurrent. Finally, using the full-wave electromagnetic solver and the calculated photocurrent obtained from the optoelectronic solver, electromagnetic radiation of the antenna and its associated detected THz signal are calculated and compared with a measurement reference for verification.

  17. Hybrid Simulation of the Interaction of Europa's Atmosphere with the Jovian Plasma: Multiprocessor Simulations

    Science.gov (United States)

    Dols, V. J.; Delamere, P. A.; Bagenal, F.; Cassidy, T. A.; Crary, F. J.

    2014-12-01

    We model the interaction of Europa's tenuous atmosphere with the plasma of Jupiter's torus with an improved version of our hybrid plasma code. In a hybrid plasma code, the ions are treated as kinetic Macro-particles moving under the Lorentz force and the electrons as a fluid leading to a generalized formulation of Ohm's law. In this version, the spatial simulation domain is decomposed in 2 directions and is non-uniform in the plasma convection direction. The code is run on a multi-processor supercomputer that offers 16416 cores and 2GB Ram per core. This new version allows us to tap into the large memory of the supercomputer and simulate the full interaction volume (Reuropa=1561km) with a high spatial resolution (50km). Compared to Io, Europa's atmosphere is about 100 times more tenuous, the ambient magnetic field is weaker and the density of incident plasma is lower. Consequently, the electrodynamic interaction is also weaker and substantial fluxes of thermal torus ions might reach and sputter the icy surface. Molecular O2 is the dominant atmospheric product of this surface sputtering. Observations of oxygen UV emissions (specifically the ratio of OI 1356A / 1304A emissions) are roughly consistent with an atmosphere that is composed predominantely of O2 with a small amount of atomic O. Galileo observations along flybys close to Europa have revealed the existence of induced currents in a conducting ocean under the icy crust. They also showed that, from flyby to flyby, the plasma interaction is very variable. Asymmetries of the plasma density and temperature in the wake of Europa were also observed and still elude a clear explanation. Galileo mag data also detected ion cyclotron waves, which is an indication of heavy ion pickup close to the moon. We prescribe an O2 atmosphere with a vertical density column consistent with UV observations and model the plasma properties along several Galileo flybys of the moon. We compare our results with the magnetometer

  18. Quantum chemical approaches: semiempirical molecular orbital and hybrid quantum mechanical/molecular mechanical techniques.

    Science.gov (United States)

    Bryce, Richard A; Hillier, Ian H

    2014-01-01

    The use of computational quantum chemical methods to aid drug discovery is surveyed. An overview of the various computational models spanning ab initio, density function theory, semiempirical molecular orbital (MO), and hybrid quantum mechanical (QM)/molecular mechanical (MM) methods is given and their strengths and weaknesses are highlighted, focussing on the challenge of obtaining the accuracy essential for them to make a meaningful contribution to drug discovery. Particular attention is given to hybrid QM/MM and semiempirical MO methods which have the potential to yield the necessary accurate predictions of macromolecular structure and reactivity. These methods are shown to have advanced the study of many aspects of substrate-ligand interactions relevant to drug discovery. Thus, the successful parametrization of semiempirical MO methods and QM/MM methods can be used to model noncovalent substrate-protein interactions, and to lead to improved scoring functions. QM/MM methods can be used in crystal structure refinement and are particularly valuable for modelling covalent protein-ligand interactions and can thus aid the design of transition state analogues. An extensive collection of examples from the areas of metalloenzyme structure, enzyme inhibition, and ligand binding affinities and scoring functions are used to illustrate the power of these techniques.

  19. Scalable Quantum Simulation of Molecular Energies

    Directory of Open Access Journals (Sweden)

    P. J. J. O’Malley

    2016-07-01

    Full Text Available We report the first electronic structure calculation performed on a quantum computer without exponentially costly precompilation. We use a programmable array of superconducting qubits to compute the energy surface of molecular hydrogen using two distinct quantum algorithms. First, we experimentally execute the unitary coupled cluster method using the variational quantum eigensolver. Our efficient implementation predicts the correct dissociation energy to within chemical accuracy of the numerically exact result. Second, we experimentally demonstrate the canonical quantum algorithm for chemistry, which consists of Trotterization and quantum phase estimation. We compare the experimental performance of these approaches to show clear evidence that the variational quantum eigensolver is robust to certain errors. This error tolerance inspires hope that variational quantum simulations of classically intractable molecules may be viable in the near future.

  20. Molecular dynamic simulation study of molten cesium

    Directory of Open Access Journals (Sweden)

    Yeganegi Saeid

    2017-01-01

    Full Text Available Molecular dynamics simulations were performed to study thermodynamics and structural properties of expanded caesium fluid. Internal pressure, radial distribution functions (RDFs, coordination numbers and diffusion coefficients have been calculated at temperature range 700–1600 K and pressure range 100–800 bar. We used the internal pressure to predict the metal–non-metal transition occurrence region. RDFs were calculated at wide ranges of temperature and pressure. The coordination numbers decrease and positions of the first peak of RDFs slightly increase as the temperature increases and pressure decreases. The calculated self-diffusion coefficients at various temperatures and pressures show no distinct boundary between Cs metallic fluid and its expanded fluid where it continuously increases with temperature.

  1. Simulation with quantum mechanics/molecular mechanics for drug discovery.

    Science.gov (United States)

    Barbault, Florent; Maurel, François

    2015-10-01

    Biological macromolecules, such as proteins or nucleic acids, are (still) molecules and thus they follow the same chemical rules that any simple molecule follows, even if their size generally renders accurate studies unhelpful. However, in the context of drug discovery, a detailed analysis of ligand association is required for understanding or predicting their interactions and hybrid quantum mechanics/molecular mechanics (QM/MM) computations are relevant tools to help elucidate this process. In this review, the authors explore the use of QM/MM for drug discovery. After a brief description of the molecular mechanics (MM) technique, the authors describe the subtractive and additive techniques for QM/MM computations. The authors then present several application cases in topics involved in drug discovery. QM/MM have been widely employed during the last decades to study chemical processes such as enzyme-inhibitor interactions. However, despite the enthusiasm around this area, plain MM simulations may be more meaningful than QM/MM. To obtain reliable results, the authors suggest fixing several keystone parameters according to the underlying chemistry of each studied system.

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

    KAUST Repository

    Joya, Khurram Saleem

    2015-06-29

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

  3. Molecular data highlight hybridization in squirrel monkeys (Saimiri, Cebidae

    Directory of Open Access Journals (Sweden)

    Jeferson Carneiro

    Full Text Available Abstract Hybridization has been reported increasingly frequently in recent years, fueling the debate on its role in the evolutionary history of species. Some studies have shown that hybridization is very common in captive New World primates, and hybrid offspring have phenotypes and physiological responses distinct from those of the "pure" parents, due to gene introgression. Here we used the TA15 Alu insertion to investigate hybridization in the genus Saimiri. Our results indicate the hybridization of Saimiri boliviensis peruviensis with S. sciureus macrodon, and S. b. boliviensis with S. ustus. Unexpectedly, some hybrids of both S. boliviensis peruviensis and S. b. boliviensis were homozygous for the absence of the insertion, which indicates that the hybrids were fertile.

  4. Large scale molecular simulations of nanotoxicity.

    Science.gov (United States)

    Jimenez-Cruz, Camilo A; Kang, Seung-gu; Zhou, Ruhong

    2014-01-01

    The widespread use of nanomaterials in biomedical applications has been accompanied by an increasing interest in understanding their interactions with tissues, cells, and biomolecules, and in particular, on how they might affect the integrity of cell membranes and proteins. In this mini-review, we present a summary of some of the recent studies on this important subject, especially from the point of view of large scale molecular simulations. The carbon-based nanomaterials and noble metal nanoparticles are the main focus, with additional discussions on quantum dots and other nanoparticles as well. The driving forces for adsorption of fullerenes, carbon nanotubes, and graphene nanosheets onto proteins or cell membranes are found to be mainly hydrophobic interactions and the so-called π-π stacking (between aromatic rings), while for the noble metal nanoparticles the long-range electrostatic interactions play a bigger role. More interestingly, there are also growing evidences showing that nanotoxicity can have implications in de novo design of nanomedicine. For example, the endohedral metallofullerenol Gd@C₈₂(OH)₂₂ is shown to inhibit tumor growth and metastasis by inhibiting enzyme MMP-9, and graphene is illustrated to disrupt bacteria cell membranes by insertion/cutting as well as destructive extraction of lipid molecules. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using the cytotoxicity of nanoparticles against cancer or bacteria cells. © 2014 Wiley Periodicals, Inc.

  5. Classical molecular dynamics simulation of nuclear fuels

    International Nuclear Information System (INIS)

    Devanathan, R.; Krack, M.; Bertolus, M.

    2015-01-01

    Molecular dynamics simulation using forces calculated from empirical potentials, commonly called classical molecular dynamics, is well suited to study primary damage production by irradiation, defect interactions with fission gas atoms, gas bubble nucleation, grain boundary effects on defect and gas bubble evolution in nuclear fuel, and the resulting changes in thermomechanical properties. This enables one to obtain insights into fundamental mechanisms governing the behaviour of nuclear fuel, as well as parameters that can be used as inputs for mesoscale models. The interaction potentials used for the force calculations are generated by fitting properties of interest to experimental data and electronic structure calculations (see Chapter 12). We present here the different types of potentials currently available for UO 2 and illustrations of applications to the description of the behaviour of this material under irradiation. The results obtained from the present generation of potentials for UO 2 are qualitatively similar, but quantitatively different. There is a need to refine these existing potentials to provide a better representation of the performance of polycrystalline fuel under a variety of operating conditions, develop models that are equipped to handle deviations from stoichiometry, and validate the models and assumptions used. (authors)

  6. Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing

    Science.gov (United States)

    Wiehle, S.; Plaschke, F.; Angelopoulos, V.; Auster, H.; Glassmeier, K.; Kriegel, H.; Motschmann, U. M.; Mueller, J.

    2010-12-01

    The interaction of the highly dynamic solar wind with the Moon is simulated with the A.I.K.E.F. (Adaptive Ion Kinetic Electron Fluid) code for the ARTEMIS P1 flyby on February 13, 2010. The A.I.K.E.F. hybrid plasma simulation code is the improved version of the Braunschweig code. It is able to automatically increase simulation grid resolution in areas of interest during runtime, which greatly increases resolution as well as performance. As the Moon has no intrinsic magnetic field and no ionosphere, the solar wind particles are absorbed at its surface, resulting in the formation of the lunar wake at the nightside. The solar wind magnetic field is basically convected through the Moon and the wake is slowly filled up with solar wind particles. However, this interaction is strongly influenced by the highly dynamic solar wind during the flyby. This is considered by a dynamic variation of the upstream conditions in the simulation using OMNI solar wind measurement data. By this method, a very good agreement between simulation and observations is achieved. The simulations show that the stationary structure of the lunar wake constitutes a tableau vivant in space representing the well-known Friedrichs diagram for MHD waves.

  7. Nonlinear hybrid simulation of toroidicity-induced alfven eigenmode

    International Nuclear Information System (INIS)

    Fu, G.Y.; Park, W.

    1994-11-01

    Gyrokinetic/Magnetohydrodynamics hybrid simulations have been carried out using MH3D-K code to study the nonlinear saturation of the toroidicity-induced Alfven eigenmode driven by energetic particles in a tokamak plasma. It is shown that the wave particle trapping is the nonlinear saturation mechanism for the parameters considered. The corresponding density profile flattening of hot particles is observed. The saturation amplitude is proportional to the square of linear growth rate. In addition to TAE modes, a new n = 1, m = 0 global Alfven eigenmode is shown to be excited by the energetic particles

  8. Effective permeability in micropores from molecular simulations

    International Nuclear Information System (INIS)

    Botan, A.; Vermorel, R.; Brochard, L.; Hantal, G.; Pellenq, R.

    2012-01-01

    Document available in extended abstract form only. Despite many years' efforts and a large numbers of proposed models, the description of transport properties in clays is still an open question. The reason for this is that structurally clay is an extremely heterogeneous material. The pore size varies from a few to 20 angstroms for interlayer (micro) porosity, from 20 A to 500 A for interparticle (meso) porosity, and 500 A to μm and more for natural (macro) fractures. One further problem with the description of the transport properties is the presence of adsorption/desorption processes onto clay particles, which are coupled with swelling/shrinkage of the particles. Any volumetric changes in the particles affect the meso-pore aperture, and thus, the total permeability of the system. The various processes affecting the permeability occur on different spatial and temporal scales, that requires a multi-scale modeling approach. The most complete model to date is a dual porosity mode. Here the total flow is often written as a sum of the macropore flow and micropore flow. The flow through macro-pores is generally considered to be laminar and obeys Darcy's law, whereas flow through the matrix (micropore flow) may be modeled using Fick's law. The micropore flow involves both Knudsen and surface diffusion mechanisms. An accurate accounting of adsorption-desorption processes or the consideration of binary mixture greatly complicate analytical description. The goal of this study is to improve macro-scale model, the dual porosity model, for the transport properties of fluids in micropores from molecular simulations. The main idea is that we reproduce an experimental set-up used for permeability measurements, as illustrated in Figure 1. High density and low density regions are settled at each end of the membrane that allows to attain a steady flow. The densities in these regions are controlled by Grand Canonical Monte Carlo simulation; the molecular motions are described by

  9. Sizing and Simulation of PV-Wind Hybrid Power System

    Directory of Open Access Journals (Sweden)

    Mustafa Engin

    2013-01-01

    Full Text Available A sizing procedure is developed for hybrid system with the aid of mathematical models for photovoltaic cell, wind turbine, and battery that are readily present in the literature. This sizing procedure can simulate the annual performance of different kinds of photovoltaic-wind hybrid power system structures for an identified set of renewable resources, which fulfills technical limitations with the lowest energy cost. The output of the program will display the performance of the system during the year, the total cost of the system, and the best size for the PV-generator, wind generator, and battery capacity. Security lightning application is selected, whereas system performance data and environmental operating conditions are measured and stored. This hybrid system, which includes a PV, wind turbine, inverter, and a battery, was installed to supply energy to 24 W lamps, considering that the renewable energy resources of this site where the system was installed were 1700 Wh/m2/day solar radiation and 3.43 m/s yearly average wind speed. Using the measured variables, the inverter and charge regulator efficiencies were calculated as 90% and 98%, respectively, and the overall system’s electrical efficiency is calculated as 72%. Life cycle costs per kWh are found to be $0.89 and LLP = 0.0428.

  10. Hybrid simulation of electrode plasmas in high-power diodes

    International Nuclear Information System (INIS)

    Welch, Dale R.; Rose, David V.; Bruner, Nichelle; Clark, Robert E.; Oliver, Bryan V.; Hahn, Kelly D.; Johnston, Mark D.

    2009-01-01

    New numerical techniques for simulating the formation and evolution of cathode and anode plasmas have been successfully implemented in a hybrid code. The dynamics of expanding electrode plasmas has long been recognized as a limiting factor in the impedance lifetimes of high-power vacuum diodes and magnetically insulated transmission lines. Realistic modeling of such plasmas is being pursued to aid in understanding the operating characteristics of these devices as well as establishing scaling relations for reliable extrapolation to higher voltages. Here, in addition to kinetic and fluid modeling, a hybrid particle-in-cell technique is described that models high density, thermal plasmas as an inertial fluid which transitions to kinetic electron or ion macroparticles above a prescribed energy. The hybrid technique is computationally efficient and does not require resolution of the Debye length. These techniques are first tested on a simple planar diode then applied to the evolution of both cathode and anode plasmas in a high-power self-magnetic pinch diode. The impact of an intense electron flux on the anode surface leads to rapid heating of contaminant material and diode impedance loss.

  11. Conformation analysis of trehalose. Molecular dynamics simulation and molecular mechanics

    International Nuclear Information System (INIS)

    Donnamaira, M.C.; Howard, E.I.; Grigera, J.R.

    1992-09-01

    Conformational analysis of the disaccharide trehalose is done by molecular dynamics and molecular mechanics. In spite of the different force fields used in each case, comparison between the molecular dynamics trajectories of the torsional angles of glycosidic linkage and energy conformational map shows a good agreement between both methods. By molecular dynamics it is observed a moderate mobility of the glycosidic linkage. The demands of computer time is comparable in both cases. (author). 6 refs, 4 figs

  12. Global gyrokinetic and fluid hybrid simulations of tokamaks and stellarators

    Energy Technology Data Exchange (ETDEWEB)

    Cole, Michael David John

    2016-07-15

    Achieving commercial production of electricity by magnetic confinement fusion requires improvements in energy and particle confinement. In order to better understand and optimise confinement, numerical simulations of plasma phenomena are useful. One particularly challenging regime is that in which long wavelength MHD phenomena interact with kinetic phenomena. In such a regime, global electromagnetic gyrokinetic simulations are necessary. In this regime, computational requirements have been excessive for Eulerian methods, while Particle-in-Cell (PIC) methods have been particularly badly affected by the 'cancellation problem', a numerical problem resulting from the structure of the electromagnetic gyrokinetic equations. A number of researchers have been working on mitigating this problem with some significant successes. Another alternative to mitigating the problem is to move to a hybrid system of fluid and gyrokinetic equations. At the expense of reducing the physical content of the numerical model, particularly electron kinetic physics, it is possible in this way to perform global electromagnetic PIC simulations retaining ion gyrokinetic effects but eliminating the cancellation problem. The focus of this work has been the implementation of two such hybrid models into the gyrokinetic code EUTERPE. The two models treat electrons and the entire bulk plasma respectively as a fluid. Both models are additionally capable of considering the self-consistent interaction of an energetic ion species, described gyrokinetically, with the perturbed fields. These two models have been successfully benchmarked in linear growth rate and frequency against other codes for a Toroidal Alfven Eigenmode (TAE) case in both the linear and non-linear regimes. The m=1 internal kink mode, which is particularly challenging in terms of the fully gyrokinetic cancellation problem, has also been successfully benchmarked using the hybrid models with the MHD eigenvalue code CKA. Non

  13. Global gyrokinetic and fluid hybrid simulations of tokamaks and stellarators

    International Nuclear Information System (INIS)

    Cole, Michael David John

    2016-01-01

    Achieving commercial production of electricity by magnetic confinement fusion requires improvements in energy and particle confinement. In order to better understand and optimise confinement, numerical simulations of plasma phenomena are useful. One particularly challenging regime is that in which long wavelength MHD phenomena interact with kinetic phenomena. In such a regime, global electromagnetic gyrokinetic simulations are necessary. In this regime, computational requirements have been excessive for Eulerian methods, while Particle-in-Cell (PIC) methods have been particularly badly affected by the 'cancellation problem', a numerical problem resulting from the structure of the electromagnetic gyrokinetic equations. A number of researchers have been working on mitigating this problem with some significant successes. Another alternative to mitigating the problem is to move to a hybrid system of fluid and gyrokinetic equations. At the expense of reducing the physical content of the numerical model, particularly electron kinetic physics, it is possible in this way to perform global electromagnetic PIC simulations retaining ion gyrokinetic effects but eliminating the cancellation problem. The focus of this work has been the implementation of two such hybrid models into the gyrokinetic code EUTERPE. The two models treat electrons and the entire bulk plasma respectively as a fluid. Both models are additionally capable of considering the self-consistent interaction of an energetic ion species, described gyrokinetically, with the perturbed fields. These two models have been successfully benchmarked in linear growth rate and frequency against other codes for a Toroidal Alfven Eigenmode (TAE) case in both the linear and non-linear regimes. The m=1 internal kink mode, which is particularly challenging in terms of the fully gyrokinetic cancellation problem, has also been successfully benchmarked using the hybrid models with the MHD eigenvalue code CKA. Non-linear simulations

  14. Software development infrastructure for the HYBRID modeling and simulation project

    International Nuclear Information System (INIS)

    Epiney, Aaron S.; Kinoshita, Robert A.; Kim, Jong Suk; Rabiti, Cristian; Greenwood, M. Scott

    2016-01-01

    One of the goals of the HYBRID modeling and simulation project is to assess the economic viability of hybrid systems in a market that contains renewable energy sources like wind. The idea is that it is possible for the nuclear plant to sell non-electric energy cushions, which absorb (at least partially) the volatility introduced by the renewable energy sources. This system is currently modeled in the Modelica programming language. To assess the economics of the system, an optimization procedure is trying to find the minimal cost of electricity production. The RAVEN code is used as a driver for the whole problem. It is assumed that at this stage, the HYBRID modeling and simulation framework can be classified as non-safety “research and development” software. The associated quality level is Quality Level 3 software. This imposes low requirements on quality control, testing and documentation. The quality level could change as the application development continues.Despite the low quality requirement level, a workflow for the HYBRID developers has been defined that include a coding standard and some documentation and testing requirements. The repository performs automated unit testing of contributed models. The automated testing is achieved via an open-source python script called BuildingsP from Lawrence Berkeley National Lab. BuildingsPy runs Modelica simulation tests using Dymola in an automated manner and generates and runs unit tests from Modelica scripts written by developers. In order to assure effective communication between the different national laboratories a biweekly videoconference has been set-up, where developers can report their progress and issues. In addition, periodic face-face meetings are organized intended to discuss high-level strategy decisions with management. A second means of communication is the developer email list. This is a list to which everybody can send emails that will be received by the collective of the developers and managers

  15. Software development infrastructure for the HYBRID modeling and simulation project

    Energy Technology Data Exchange (ETDEWEB)

    Epiney, Aaron S. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert A. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kim, Jong Suk [Idaho National Lab. (INL), Idaho Falls, ID (United States); Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Greenwood, M. Scott [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2016-09-01

    One of the goals of the HYBRID modeling and simulation project is to assess the economic viability of hybrid systems in a market that contains renewable energy sources like wind. The idea is that it is possible for the nuclear plant to sell non-electric energy cushions, which absorb (at least partially) the volatility introduced by the renewable energy sources. This system is currently modeled in the Modelica programming language. To assess the economics of the system, an optimization procedure is trying to find the minimal cost of electricity production. The RAVEN code is used as a driver for the whole problem. It is assumed that at this stage, the HYBRID modeling and simulation framework can be classified as non-safety “research and development” software. The associated quality level is Quality Level 3 software. This imposes low requirements on quality control, testing and documentation. The quality level could change as the application development continues.Despite the low quality requirement level, a workflow for the HYBRID developers has been defined that include a coding standard and some documentation and testing requirements. The repository performs automated unit testing of contributed models. The automated testing is achieved via an open-source python script called BuildingsP from Lawrence Berkeley National Lab. BuildingsPy runs Modelica simulation tests using Dymola in an automated manner and generates and runs unit tests from Modelica scripts written by developers. In order to assure effective communication between the different national laboratories a biweekly videoconference has been set-up, where developers can report their progress and issues. In addition, periodic face-face meetings are organized intended to discuss high-level strategy decisions with management. A second means of communication is the developer email list. This is a list to which everybody can send emails that will be received by the collective of the developers and managers

  16. Real-Time ECG Simulation for Hybrid Mock Circulatory Loops.

    Science.gov (United States)

    Korn, Leonie; Rüschen, Daniel; Zander, Niklas; Leonhardt, Steffen; Walter, Marian

    2018-02-01

    Classically, mock circulatory loops only simulate mechanical properties of the circulation. To connect the hydraulic world with electrophysiology, we present a real-time electrical activity model of the heart and show how to integrate this model into a real-time mock loop simulation. The model incorporates a predefined conduction pathway and a simplified volume conductor to solve the bidomain equations and the forward problem of electrocardiography, resulting in a physiological simulation of the electrocardiogram (ECG) at arbitrary electrode positions. A complete physiological simulation of the heart's excitation would be too CPU intensive. Thus, in our model, complexity was reduced to allow real-time simulation of ECG-triggered medical systems in vitro; this decreases time and cost in the development process. Conversely, the presented model can still be adapted to various pathologies by locally changing the properties of the heart's conduction pathway. To simulate the ECG, the heart is divided into suitable areas, which are innervated by the hierarchically structured conduction system. To distinguish different cardiac regions, a segmentation of the heart was performed. In these regions, Prim's algorithm was applied to identify the directed minimal spanning trees for conduction orientation. Each node of the tree was assigned to a cardiac action potential generated by its hybrid automaton to represent the heart's conduction system by the spatial distribution of action potentials. To generate the ECG output, the bidomain equations were implemented and a simple model of the volume conductor of the body was used to solve the forward problem of electrocardiography. As a result, the model simulates potentials at arbitrary electrode positions in real-time. To verify the developed real-time ECG model, measurements were made within a hybrid mock circulatory loop, including a simple ECG-triggered ventricular assist device control. The model's potential value is to simulate

  17. Molecular automata assembly: principles and simulation of bacterial membrane construction.

    Science.gov (United States)

    Lahoz-Beltra, R

    1997-01-01

    The motivation to understand the basic rules and principles governing molecular self-assembly may be relevant to explain in the context of molecular biology the self-organization and biological functions exhibited within cells. This paper presents a molecular automata model to simulate molecular self-assembly introducing the concept of molecular programming to simulate the biological function or operation performed by an assembled molecular state machine. The method is illustrated modelling Escherichia coli membrane construction including the assembly and operation of ATP synthase as well as the assembly of the bacterial flagellar motor. Flagellar motor operation was simulated using a different approach based on state machine definition used in virtual reality systems. The proposed methodology provides a modelling framework for simulation of biological functions performed by cellular components and other biological systems suitable to be modelled as molecular state machines.

  18. Hybrid simulations of current-carrying instabilities in Z-pinch plasmas with sheared axial flow

    International Nuclear Information System (INIS)

    Sotnikov, Vladimir I.; Makhin, Volodymyr; Bauer, Bruno S.; Hellinger, Petr; Travnicek, Pavel; Fiala, Vladimir; Leboeuf, Jean-Noel

    2002-01-01

    The development of instabilities in z-pinch plasmas has been studied with three-dimensional (3D) hybrid simulations. Plasma equilibria without and with sheared axial flow have been considered. Results from the linear phase of the hybrid simulations compare well with linear Hall magnetohydrodynamics (MHD) calculations for sausage modes. The hybrid simulations show that sheared axial flow has a stabilizing effect on the development of both sausage and kink modes

  19. Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the Great Barrier Reef

    KAUST Repository

    He, Song; Johansen, Jacob L.; Hoey, Andrew S.; Pappas, Melissa; Berumen, Michael L.

    2017-01-01

    To date, more than 81 species of tropical coral reef fish have been reported to hybridize in nature, spanning multiple families, including the Chaetodontidae, Pomacanthidae, and Labridae. Hybridization, however, is seemingly rare among benthic nesting species that engage in pair spawning, such as the Pomacentridae. Here, we present evidence for the first molecularly confirmed record of hybridization within the genus Dascyllus; D. aruanus and D. reticulatus. Interestingly, although many hybridization events are attributed to peripheral range effects or areas of limited overlap among otherwise allopatric species, this hybrid individual was collected from the northern Great Barrier Reef, centrally located within the distribution ranges of both species. The hybrid exhibited coloration and meristic counts intermediate between D. aruanus and D. reticulatus. Diagnostic genetic markers and subsequent microsatellites analysis confirmed that this individual was a hybrid offspring of D. aruanus and D. reticulatus, with the latter providing the maternal contribution. The occurrence of the D. aruanus × D. reticulatus hybrid on the Great Barrier Reef represents an exception to the otherwise species-specific haplotypes. The nuclear diagnostic marker which was identified during this study could serve as a hybrid indicator and benefit future hybrid investigations for hybridization between these two species.

  20. Molecular confirmation of hybridization between Dascyllus reticulatus × Dascyllus aruanus from the Great Barrier Reef

    KAUST Repository

    He, Song

    2017-11-17

    To date, more than 81 species of tropical coral reef fish have been reported to hybridize in nature, spanning multiple families, including the Chaetodontidae, Pomacanthidae, and Labridae. Hybridization, however, is seemingly rare among benthic nesting species that engage in pair spawning, such as the Pomacentridae. Here, we present evidence for the first molecularly confirmed record of hybridization within the genus Dascyllus; D. aruanus and D. reticulatus. Interestingly, although many hybridization events are attributed to peripheral range effects or areas of limited overlap among otherwise allopatric species, this hybrid individual was collected from the northern Great Barrier Reef, centrally located within the distribution ranges of both species. The hybrid exhibited coloration and meristic counts intermediate between D. aruanus and D. reticulatus. Diagnostic genetic markers and subsequent microsatellites analysis confirmed that this individual was a hybrid offspring of D. aruanus and D. reticulatus, with the latter providing the maternal contribution. The occurrence of the D. aruanus × D. reticulatus hybrid on the Great Barrier Reef represents an exception to the otherwise species-specific haplotypes. The nuclear diagnostic marker which was identified during this study could serve as a hybrid indicator and benefit future hybrid investigations for hybridization between these two species.

  1. 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.

  2. Molecular Characterization of Natural Hybrids Formed between Five Related Indigenous Clade 6 Phytophthora Species

    Science.gov (United States)

    Burgess, Treena I.

    2015-01-01

    Most Phytophthora hybrids characterized to date have emerged from nurseries and managed landscapes, most likely generated as a consequence of biological invasions associated with the movement of living plants and germplasm for ornamental, horticultural and agricultural purposes. Presented here is evidence for natural hybridization among a group of five closely related indigenous clade 6 Phytophthora species isolated from waterways and riparian ecosystems in Western Australia. Molecular characterization of hybrids consisted of cloning and sequencing two nuclear genes (ITS and ASF), sequencing of two further nuclear loci (BT and HSP) and of two mitochondrial loci (COI and NADH). Additionally, phenotypic traits including morphology of sporangia and optima and maxima temperatures for growth were also determined. In most cases the nuclear genes were biparentally and in all cases the mtDNA were uniparentally inherited, indicating hybrid formation through sexual crosses. Some isolates bear the molecular signature of three parents suggesting additional hybrid events, although it cannot be determined from the data if these were sequential or simultaneous. These species and their hybrids co-exist in riparian ecosystems and waterways where their ability for rapid asexual proliferation would enable them to rapidly colonize green plant litter. The apparent ease of hybridization could eventually lead to the merging of species through introgression. However, at this point in time, species integrity has been maintained and a more likely scenario is that the hybrids are not stable evolutionary lineages, but rather transient hybrid clones. PMID:26248187

  3. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-01

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  4. Approximation of quantum observables by molecular dynamics simulations

    KAUST Repository

    Sandberg, Mattias

    2016-01-06

    In this talk I will discuss how to estimate the uncertainty in molecular dynamics simulations. Molecular dynamics is a computational method to study molecular systems in materials science, chemistry, and molecular biology. The wide popularity of molecular dynamics simulations relies on the fact that in many cases it agrees very well with experiments. If we however want the simulation to predict something that has no comparing experiment, we need a mathematical estimate of the accuracy of the computation. In the case of molecular systems with few particles, such studies are made by directly solving the Schrodinger equation. In this talk I will discuss theoretical results on the accuracy between quantum mechanics and molecular dynamics, to be used for systems that are too large to be handled computationally by the Schrodinger equation.

  5. On simulation of local fluxes in molecular junctions

    Science.gov (United States)

    Cabra, Gabriel; Jensen, Anders; Galperin, Michael

    2018-05-01

    We present a pedagogical review of the current density simulation in molecular junction models indicating its advantages and deficiencies in analysis of local junction transport characteristics. In particular, we argue that current density is a universal tool which provides more information than traditionally simulated bond currents, especially when discussing inelastic processes. However, current density simulations are sensitive to the choice of basis and electronic structure method. We note that while discussing the local current conservation in junctions, one has to account for the source term caused by the open character of the system and intra-molecular interactions. Our considerations are illustrated with numerical simulations of a benzenedithiol molecular junction.

  6. A molecular fragment cheminformatics roadmap for mesoscopic simulation.

    Science.gov (United States)

    Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

    2014-12-01

    Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and

  7. Accelerating Climate and Weather Simulations through Hybrid Computing

    Science.gov (United States)

    Zhou, Shujia; Cruz, Carlos; Duffy, Daniel; Tucker, Robert; Purcell, Mark

    2011-01-01

    Unconventional multi- and many-core processors (e.g. IBM (R) Cell B.E.(TM) and NVIDIA (R) GPU) have emerged as effective accelerators in trial climate and weather simulations. Yet these climate and weather models typically run on parallel computers with conventional processors (e.g. Intel, AMD, and IBM) using Message Passing Interface. To address challenges involved in efficiently and easily connecting accelerators to parallel computers, we investigated using IBM's Dynamic Application Virtualization (TM) (IBM DAV) software in a prototype hybrid computing system with representative climate and weather model components. The hybrid system comprises two Intel blades and two IBM QS22 Cell B.E. blades, connected with both InfiniBand(R) (IB) and 1-Gigabit Ethernet. The system significantly accelerates a solar radiation model component by offloading compute-intensive calculations to the Cell blades. Systematic tests show that IBM DAV can seamlessly offload compute-intensive calculations from Intel blades to Cell B.E. blades in a scalable, load-balanced manner. However, noticeable communication overhead was observed, mainly due to IP over the IB protocol. Full utilization of IB Sockets Direct Protocol and the lower latency production version of IBM DAV will reduce this overhead.

  8. Hybrid neural network bushing model for vehicle dynamics simulation

    International Nuclear Information System (INIS)

    Sohn, Jeong Hyun; Lee, Seung Kyu; Yoo, Wan Suk

    2008-01-01

    Although the linear model was widely used for the bushing model in vehicle suspension systems, it could not express the nonlinear characteristics of bushing in terms of the amplitude and the frequency. An artificial neural network model was suggested to consider the hysteretic responses of bushings. This model, however, often diverges due to the uncertainties of the neural network under the unexpected excitation inputs. In this paper, a hybrid neural network bushing model combining linear and neural network is suggested. A linear model was employed to represent linear stiffness and damping effects, and the artificial neural network algorithm was adopted to take into account the hysteretic responses. A rubber test was performed to capture bushing characteristics, where sine excitation with different frequencies and amplitudes is applied. Random test results were used to update the weighting factors of the neural network model. It is proven that the proposed model has more robust characteristics than a simple neural network model under step excitation input. A full car simulation was carried out to verify the proposed bushing models. It was shown that the hybrid model results are almost identical to the linear model under several maneuvers

  9. A hybrid flight control for a simulated raptor-30 v2 helicopter

    International Nuclear Information System (INIS)

    Khizer, A.N.

    2015-01-01

    This paper presents a hybrid flight control system for a single rotor simulated Raptor-30 V2 helicopter. Hybrid intelligent control system, combination of the conventional and intelligent control methodologies, is applied to small model helicopter. The proposed hybrid control used PID as a traditional control and fuzzy as an intelligent control so as to take the maximum advantage of advanced control theory. The helicopter model used; comes from X-Plane flight simulator and their hybrid flight control system was simulated using MATLAB/SIMULINK in a simulation platform. X-Plane is also used to visualize the performance of this proposed autopilot design. Through a series of numerous experiments, the operation of hybrid control system was investigated. Results verified that the proposed hybrid control has an excellent performance at hovering flight mode. (author)

  10. A hybrid simulation model for a stable auroral arc

    Directory of Open Access Journals (Sweden)

    P. Janhunen

    Full Text Available We present a new type of hybrid simulation model, intended to simulate a single stable auroral arc in the latitude/altitude plane. The ionospheric ions are treated as particles, the electrons are assumed to follow a Boltzmann response and the magnetospheric ions are assumed to be so hot that they form a background population unaffected by the electric fields that arise. The system is driven by assumed parallel electron energisation causing a primary negative charge cloud and an associated potential structure to build up. The results show how a closed potential structure and density depletion of an auroral arc build up and how they decay after the driver is turned off. The model also produces upgoing energetic ion beams and predicts strong static perpendicular electric fields to be found in a relatively narrow altitude range (~ 5000–11 000 km.

    Key words. Magnetospheric physics (magnetosphere-ionosphere interactions; auroral phenomena – Space plasma physics (numerical simulation studies

  11. A new approach to flow simulation using hybrid models

    Science.gov (United States)

    Solgi, Abazar; Zarei, Heidar; Nourani, Vahid; Bahmani, Ramin

    2017-11-01

    The necessity of flow prediction in rivers, for proper management of water resource, and the need for determining the inflow to the dam reservoir, designing efficient flood warning systems and so forth, have always led water researchers to think about models with high-speed response and low error. In the recent years, the development of Artificial Neural Networks and Wavelet theory and using the combination of models help researchers to estimate the river flow better and better. In this study, daily and monthly scales were used for simulating the flow of Gamasiyab River, Nahavand, Iran. The first simulation was done using two types of ANN and ANFIS models. Then, using wavelet theory and decomposing input signals of the used parameters, sub-signals were obtained and were fed into the ANN and ANFIS to obtain hybrid models of WANN and WANFIS. In this study, in addition to the parameters of precipitation and flow, parameters of temperature and evaporation were used to analyze their effects on the simulation. The results showed that using wavelet transform improved the performance of the models in both monthly and daily scale. However, it had a better effect on the monthly scale and the WANFIS was the best model.

  12. Hybrid framework for the simulation of stochastic chemical kinetics

    International Nuclear Information System (INIS)

    Duncan, Andrew; Erban, Radek; Zygalakis, Konstantinos

    2016-01-01

    Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

  13. Hybrid framework for the simulation of stochastic chemical kinetics

    Science.gov (United States)

    Duncan, Andrew; Erban, Radek; Zygalakis, Konstantinos

    2016-12-01

    Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the "fast" reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

  14. Hybrid framework for the simulation of stochastic chemical kinetics

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, Andrew, E-mail: a.duncan@imperial.ac.uk [Department of Mathematics, Imperial College, South Kensington Campus, London, SW7 2AZ (United Kingdom); Erban, Radek, E-mail: erban@maths.ox.ac.uk [Mathematical Institute, University of Oxford, Radcliffe Observatory Quarter, Woodstock Road, Oxford, OX2 6GG (United Kingdom); Zygalakis, Konstantinos, E-mail: k.zygalakis@ed.ac.uk [School of Mathematics, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD (United Kingdom)

    2016-12-01

    Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when one or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.

  15. Hybrid fast Hankel transform implementation for optics simulation

    Science.gov (United States)

    Davis, Paul K.

    2013-09-01

    The most compute intensive part of a full optics simulation, especially including diffraction effects, is the Fourier transform between pupil and image spaces. This is typically performed as a two dimensional fast discrete transform. For a nearly radially symmetric system there are advantages to using polar coordinates, in which case the radial transform becomes a Hankel transform, using Bessel functions instead of circular functions. However, there are special difficulties in calculating and handling Bessel functions. Several solutions have been proposed. We present a hybrid Hankel transform which divides the domain, calculating a portion using Bessel function approximations but converting most of the domain into a one dimensional Fourier transform which can be handled by standard methods.

  16. Hybrid simulation techniques applied to the earth's bow shock

    Science.gov (United States)

    Winske, D.; Leroy, M. M.

    1985-01-01

    The application of a hybrid simulation model, in which the ions are treated as discrete particles and the electrons as a massless charge-neutralizing fluid, to the study of the earth's bow shock is discussed. The essentials of the numerical methods are described in detail; movement of the ions, solution of the electromagnetic fields and electron fluid equations, and imposition of appropriate boundary and initial conditions. Examples of results of calculations for perpendicular shocks are presented which demonstrate the need for a kinetic treatment of the ions to reproduce the correct ion dynamics and the corresponding shock structure. Results for oblique shocks are also presented to show how the magnetic field and ion motion differ from the perpendicular case.

  17. Monte Carlo simulation of lower hybrid current drive in tokamaks

    International Nuclear Information System (INIS)

    Sipilae, S.K.; Heikkinen, J.A.

    1994-01-01

    In the report a method for noninductive current drive studies based on three-dimensional simulation of test particle orbits is presented. A Monte Carlo momentum diffusion operator is developed to model the wave-particle interaction. The scheme can be utilised in studies of current drive efficiency as well as in examining the current density profiles caused by waves with a finite parallel wave number spectrum and a nonuniform power deposition profile in a toroidal configuration space of arbitrary shape. Calculations performed with a uniform poorer deposition profile of lower hybrid waves for axisymmetric magnetic configurations having different aspect ratios and poloidal cross-section shape confirm the semianalytic estimates for the current drive efficiency based on the solutions of the flux surface averaged Fokker-Planck equation for configurations with circular poloidal cross section. The consequences of the combined effect of radial diffusion, magnetic trapping and radially nonhomogeneous power deposition and background plasma parameter profiles are investigated

  18. Classical molecular dynamics simulation of electronically non-adiabatic processes.

    Science.gov (United States)

    Miller, William H; Cotton, Stephen J

    2016-12-22

    Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born-Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides "quantization" of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

  19. Molecular simulation of polar molecules interaction with MOFs family materials

    International Nuclear Information System (INIS)

    De Toni, M.

    2012-01-01

    The topic of this thesis is the adsorption of simple molecular fluids in nano-porous materials. Many industrial processes are based on this phenomenon, including ionic exchange, selective separation and heterogeneous catalysis. I used molecular simulation to study the adsorption properties of polar molecules of industrial interest (CO 2 and H 2 O) in a new class of crystalline microporous hybrid organic-inorganic materials called Metal-Organic Frameworks (MOFs). They have exceptional adsorption properties due to their topological variety and their versatility, allowed by the large range of possibilities offered by organic and coordination chemistry and functionalizations. I first studied the adsorption of CO 2 in a family of materials called IRMOFs, which share the same topology but have different porous volume, in order to characterize the effect of confinement on their adsorption performance. In particular, a general behavior has been highlighted: the critical temperature decreases when the confinement increases. Then, I looked at a recently synthesized cationic MOF called Zn2(CBTACN). After having localized the extra-framework halogen anions in the unit cell of the material, something which was not possible experimentally, I characterized CO 2 adsorption in this system first as a pure gas and then as a component of different mixtures. Finally, I was interested in the hydrothermal stability of MOFs, a crucial issue for their use in industrial applications. I observed the hydration mechanism of system that is analogous to the MOF-5 (IRMOF-0h) and shed light on some collaborative effects of the attack of water that were unknown to in the literature. (author)

  20. Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

    Science.gov (United States)

    Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

    2014-07-15

    Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Molecular-scale simulation of electroluminescence in a multilayer white organic light-emitting diode

    DEFF Research Database (Denmark)

    Mesta, Murat; Carvelli, Marco; de Vries, Rein J

    2013-01-01

    we show that it is feasible to carry out Monte Carlo simulations including all of these molecular-scale processes for a hybrid multilayer organic light-emitting diode combining red and green phosphorescent layers with a blue fluorescent layer. The simulated current density and emission profile......In multilayer white organic light-emitting diodes the electronic processes in the various layers--injection and motion of charges as well as generation, diffusion and radiative decay of excitons--should be concerted such that efficient, stable and colour-balanced electroluminescence can occur. Here...

  2. Control-relevant modeling and simulation of a SOFC-GT hybrid system

    Directory of Open Access Journals (Sweden)

    Rambabu Kandepu

    2006-07-01

    Full Text Available In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

  3. Control-relevant modeling and simulation of a SOFC-GT hybrid system

    OpenAIRE

    Rambabu Kandepu; Lars Imsland; Christoph Stiller; Bjarne A. Foss; Vinay Kariwala

    2006-01-01

    In this paper, control-relevant models of the most important components in a SOFC-GT hybrid system are described. Dynamic simulations are performed on the overall hybrid system. The model is used to develop a simple control structure, but the simulations show that more elaborate control is needed.

  4. Simulation of hybrid vehicle propulsion with an advanced battery model

    Energy Technology Data Exchange (ETDEWEB)

    Nallabolu, S.; Kostetzer, L.; Rudnyi, E. [CADFEM GmbH, Grafing (Germany); Geppert, M.; Quinger, D. [LION Smart GmbH, Frieding (Germany)

    2011-07-01

    In the recent years there has been observed an increasing concern about global warming and greenhouse gas emissions. In addition to the environmental issues the predicted scarcity of oil supplies and the dramatic increase in oil price puts new demands on vehicle design. As a result energy efficiency and reduced emission have become one of main selling point for automobiles. Hybrid electric vehicles (HEV) have therefore become an interesting technology for the governments and automotive industries. HEV are more complicated compared to conventional vehicles due to the fact that these vehicles contain more electrical components such as electric machines, power electronics, electronic continuously variable transmissions (CVT), and embedded powertrain controllers. Advanced energy storage devices and energy converters, such as Li-ion batteries, ultracapacitors, and fuel cells are also considered. A detailed vehicle model used for an energy flow analysis and vehicle performance simulation is necessary. Computer simulation is indispensible to facilitate the examination of the vast hybrid electric vehicle design space with the aim to predict the vehicle performance over driving profiles, estimate fuel consumption and the pollution emissions. There are various types of mathematical models and simulators available to perform system simulation of vehicle propulsion. One of the standard methods to model the complete vehicle powertrain is ''backward quasistatic modeling''. In this method vehicle subsystems are defined based on experiential models in the form of look-up tables and efficiency maps. The interaction between adjacent subsystems of the vehicle is defined through the amount of power flow. Modeling the vehicle subsystems like motor, engine, gearbox and battery is under this technique is based on block diagrams. The vehicle model is applied in two case studies to evaluate the vehicle performance and fuel consumption. In the first case study the affect

  5. Biocompatible magnetic and molecular dual-targeting polyelectrolyte hybrid hollow microspheres for controlled drug release.

    Science.gov (United States)

    Du, Pengcheng; Zeng, Jin; Mu, Bin; Liu, Peng

    2013-05-06

    Well-defined biocompatible magnetic and molecular dual-targeting polyelectrolyte hybrid hollow microspheres have been accomplished via the layer-by-layer (LbL) self-assembly technique. The hybrid shell was fabricated by the electrostatic interaction between the polyelectrolyte cation, chitosan (CS), and the hybrid anion, citrate modified ferroferric oxide nanoparticles (Fe3O4-CA), onto the uniform polystyrene sulfonate microsphere templates. Then the magnetic hybrid core/shell composite particles were modified with a linear, functional poly(ethylene glycol) (PEG) monoterminated with a biotargeting molecule (folic acid (FA)). Afterward the dual targeting hybrid hollow microspheres were obtained after etching the templates by dialysis. The dual targeting hybrid hollow microspheres exhibit exciting pH response and stability in high salt-concentration media. Their pH-dependent controlled release of the drug molecule (anticancer drug, doxorubicin (DOX)) was also investigated in different human body fluids. As expected, the cell viability of the HepG2 cells which decreased more rapidly was treated by the FA modified hybrid hollow microspheres rather than the unmodified one in the in vitro study. The dual-targeting hybrid hollow microspheres demonstrate selective killing of the tumor cells. The precise magnetic and molecular targeting properties and pH-dependent controlled release offers promise for cancer treatment.

  6. A wind turbine hybrid simulation framework considering aeroelastic effects

    Science.gov (United States)

    Song, Wei; Su, Weihua

    2015-04-01

    In performing an effective structural analysis for wind turbine, the simulation of turbine aerodynamic loads is of great importance. The interaction between the wake flow and the blades may impact turbine blades loading condition, energy yield and operational behavior. Direct experimental measurement of wind flow field and wind profiles around wind turbines is very helpful to support the wind turbine design. However, with the growth of the size of wind turbines for higher energy output, it is not convenient to obtain all the desired data in wind-tunnel and field tests. In this paper, firstly the modeling of dynamic responses of large-span wind turbine blades will consider nonlinear aeroelastic effects. A strain-based geometrically nonlinear beam formulation will be used for the basic structural dynamic modeling, which will be coupled with unsteady aerodynamic equations and rigid-body rotations of the rotor. Full wind turbines can be modeled by using the multi-connected beams. Then, a hybrid simulation experimental framework is proposed to potentially address this issue. The aerodynamic-dominant components, such as the turbine blades and rotor, are simulated as numerical components using the nonlinear aeroelastic model; while the turbine tower, where the collapse of failure may occur under high level of wind load, is simulated separately as the physical component. With the proposed framework, dynamic behavior of NREL's 5MW wind turbine blades will be studied and correlated with available numerical data. The current work will be the basis of the authors' further studies on flow control and hazard mitigation on wind turbine blades and towers.

  7. Simulation study of two-ion hybrid resonance heating

    International Nuclear Information System (INIS)

    Riyopoulos, S.; Tajima, T.

    1986-02-01

    A one-dimensional low-noise, low-frequency electromagnetic particle simulation code that is appropriate for investigation of ion cyclotron resonance heating (ICRH) is developed. Retaining the hyperbolicity of the electromagnetic waves and exploiting nearly one-dimensional characteristics (perpendicular to the external magnetic field) of the ICRH, we use the guiding center electron approximation for the transverse electronic current calculation. We observe mode conversion of the incoming magnetosonic wave into the electrostatic ion-ion hybrid mode accompanied by strong ion-heating. The dependence of this heating on the different plasma parameters is examined through a series of simulations, focusing mainly on wave incidence from the high field side. Because K/sub parallel/ = 0 in our runs, the conventional Landau damping cannot explain the ion heating. Non-linear mechanisms for energy transfer are discussed. Our numerical results demonstrate the importance of the non-linear wave particle interaction for energy transfer are discussed. Our numerical results demonstrate the importance of the non-linear wave particle interaction for energy absorption during radio frequency heating in the ion cyclotron regime. 32 refs., 17 figs

  8. Simulation of electric vehicles with hybrid power systems

    Science.gov (United States)

    Burke, A. F.; Cole, G. H.

    Computer programs for the simulation of the operation of electric vehicles with hybrid power systems are described. These programs treat cases in which high energy density ultracapacitors or high power density pulse batteries are used to load level the main energy storage battery in the vehicle. A generalized control strategy for splitting the power between the main battery and the pulse power devices is implemented such that the user can specify the nominal battery power as a function of the state-of-charge of the ultracapacitor or pulse power battery. The programs display graphically on the screen, as they run, the power from both the main battery and the pulse power device and the state-of-charge of the pulse power device. After each run is completed, a summary is printed out from which the effect of load leveling the battery on vehicle range and energy consumption can be determined. Default input files are provided with the programs so various combinations of vehicles, driveline components, and batteries of special current interest to the EV community can be run with either type of pulse power device. Typical simulation results are shown including cases in which the pulse power devices are connected in parallel with the main battery without interface electronics.

  9. Molecular Dynamic Modeling and Simulation for Polymers

    National Research Council Canada - National Science Library

    Harrell, Anthony

    2003-01-01

    ... the mechanical properties of polymers. In particular, the goal was to develop insights as to how a molecular level structure is connected to the bulk properties of materials assuming homogeneity...

  10. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori; Takagi, Fumiko; Shimada, Takashi; Ito, Nobuyasu

    2011-01-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We

  11. Hybrid Simulation Modeling to Estimate U.S. Energy Elasticities

    Science.gov (United States)

    Baylin-Stern, Adam C.

    This paper demonstrates how an U.S. application of CIMS, a technologically explicit and behaviourally realistic energy-economy simulation model which includes macro-economic feedbacks, can be used to derive estimates of elasticity of substitution (ESUB) and autonomous energy efficiency index (AEEI) parameters. The ability of economies to reduce greenhouse gas emissions depends on the potential for households and industry to decrease overall energy usage, and move from higher to lower emissions fuels. Energy economists commonly refer to ESUB estimates to understand the degree of responsiveness of various sectors of an economy, and use estimates to inform computable general equilibrium models used to study climate policies. Using CIMS, I have generated a set of future, 'pseudo-data' based on a series of simulations in which I vary energy and capital input prices over a wide range. I then used this data set to estimate the parameters for transcendental logarithmic production functions using regression techniques. From the production function parameter estimates, I calculated an array of elasticity of substitution values between input pairs. Additionally, this paper demonstrates how CIMS can be used to calculate price-independent changes in energy-efficiency in the form of the AEEI, by comparing energy consumption between technologically frozen and 'business as usual' simulations. The paper concludes with some ideas for model and methodological improvement, and how these might figure into future work in the estimation of ESUBs from CIMS. Keywords: Elasticity of substitution; hybrid energy-economy model; translog; autonomous energy efficiency index; rebound effect; fuel switching.

  12. Numerical simulation of collision-free plasma using Vlasov hybrid simulation

    International Nuclear Information System (INIS)

    Nunn, D.

    1990-01-01

    A novel scheme for the numerical simulation of wave particle interactions in space plasmas has been developed. The method, termed VHS or Vlasov Hybrid Simulation, is applicable to hot collision free plasmas in which the unperturbed distribution functions is smooth and free of delta function singularities. The particle population is described as a continuous Vlasov fluid in phase space-granularity and collisional effects being ignored. In traditional PIC/CIC codes the charge/current due to each simulation particle is assigned to a fixed spatial grid. In the VHS method the simulation particles sample the Vlasov fluid and provide information about the value of distribution function (F(r,v) at random points in phase space. Values of F are interpolated from the simulation particles onto a fixed grid in velocity/position or phase space. With distribution function defined on a phase space grid the plasma charge/current field is quickly calculated. The simulation particles serve only to provide information, and thus the particle population may be dynamic. Particles no longer resonant with the wavefield may be discarded from the simulation, and new particles may be inserted into the Vlasov fluid where required

  13. Visualizing functional motions of membrane transporters with molecular dynamics simulations.

    Science.gov (United States)

    Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

    2013-01-29

    Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

  14. Genetic molecular analysis of Coffea arabica (Rubiaceae hybrids using SRAP markers

    Directory of Open Access Journals (Sweden)

    Manoj Kumar Mishra

    2011-06-01

    Full Text Available In Coffea arabica (arabica coffee, the phenotypic as well as genetic variability has been found low because of the narrow genetic basis and self fertile nature of the species. Because of high similarity in phenotypic appearance among the majority of arabica collections, selection of parental lines for inter-varietals hybridization and identification of resultant hybrids at an early stage of plant growth is difficult. DNA markers are known to be reliable in identifying closely related cultivars and hybrids. Sequence Related Amplified Polymorphism (SRAP is a new molecular marker technology developed based on PCR. In this paper, sixty arabica-hybrid progenies belonging to six crosses were analyzed using 31 highly polymorphic SRAP markers. The analysis revealed seven types of SRAP marker profiles which are useful in discriminating the parents and hybrids. The number of bands amplified per primer pair ranges from 6.13 to 8.58 with average number of seven bands. Among six hybrid combinations, percentage of bands shared between hybrids and their parents ranged from 66.29% to 85.71% with polymorphic bands varied from 27.64% to 60.0%. Percentage of hybrid specific fragments obtained in various hybrid combinations ranged from 0.71% to 10.86% and ascribed to the consequence of meiotic recombination. Based on the similarity index calculation, it was observed that F1 hybrids share maximum number of bands with the female parent compared to male parent. The results obtained in the present study revealed the effectiveness of SRAP technique in cultivar identification and hybrid analysis in this coffee species. Rev. Biol. Trop. 59 (2: 607-617. Epub 2011 June 01.

  15. Molecular simulation of ionic liquids: current status and future opportunities

    International Nuclear Information System (INIS)

    Maginn, E J

    2009-01-01

    Ionic liquids are salts that are liquid near ambient conditions. Interest in these unusual compounds has exploded in the last decade, both at the academic and commercial level. Molecular simulations based on classical potentials have played an important role in helping researchers understand how condensed phase properties of these materials are linked to chemical structure and composition. Simulations have also predicted many properties and unexpected phenomena that have subsequently been confirmed experimentally. The beneficial impact molecular simulations have had on this field is due in large part to excellent timing. Just when computing power and simulation methods matured to the point where complex fluids could be studied in great detail, a new class of materials virtually unknown to experimentalists came on the scene and demanded attention. This topical review explores some of the history of ionic liquid molecular simulations, and then gives examples of the recent use of molecular dynamics and Monte Carlo simulation in understanding the structure of ionic liquids, the sorption of small molecules in ionic liquids, the nature of ionic liquids in the vapor phase and the dynamics of ionic liquids. This review concludes with a discussion of some of the outstanding problems facing the ionic liquid modeling community and how condensed phase molecular simulation experts not presently working on ionic liquids might help advance the field. (topical review)

  16. Molecular dynamics simulations of RNA motifs

    Czech Academy of Sciences Publication Activity Database

    Csaszar, K.; Špačková, Naďa; Šponer, Jiří; Leontis, N. B.

    2002-01-01

    Roč. 223, - (2002), s. 154 ISSN 0065-7727. [Annual Meeting of the American Chemistry Society /223./. 07.04.2002-11.04.2002, Orlando ] Institutional research plan: CEZ:AV0Z5004920 Keywords : molecular dynamics * RNA * hydration Subject RIV: BO - Biophysics

  17. Hybrid Multilevel Monte Carlo Simulation of Stochastic Reaction Networks

    KAUST Repository

    Moraes, Alvaro

    2015-01-07

    Stochastic reaction networks (SRNs) is a class of continuous-time Markov chains intended to describe, from the kinetic point of view, the time-evolution of chemical systems in which molecules of different chemical species undergo a finite set of reaction channels. This talk is based on articles [4, 5, 6], where we are interested in the following problem: given a SRN, X, defined though its set of reaction channels, and its initial state, x0, estimate E (g(X(T))); that is, the expected value of a scalar observable, g, of the process, X, at a fixed time, T. This problem lead us to define a series of Monte Carlo estimators, M, such that, with high probability can produce values close to the quantity of interest, E (g(X(T))). More specifically, given a user-selected tolerance, TOL, and a small confidence level, η, find an estimator, M, based on approximate sampled paths of X, such that, P (|E (g(X(T))) − M| ≤ TOL) ≥ 1 − η; even more, we want to achieve this objective with near optimal computational work. We first introduce a hybrid path-simulation scheme based on the well-known stochastic simulation algorithm (SSA)[3] and the tau-leap method [2]. Then, we introduce a Multilevel Monte Carlo strategy that allows us to achieve a computational complexity of order O(T OL−2), this is the same computational complexity as in an exact method but with a smaller constant. We provide numerical examples to show our results.

  18. SIMULATION OF WIRELESS SENSOR NETWORK WITH HYBRID TOPOLOGY

    Directory of Open Access Journals (Sweden)

    J. Jaslin Deva Gifty

    2016-03-01

    Full Text Available The design of low rate Wireless Personal Area Network (WPAN by IEEE 802.15.4 standard has been developed to support lower data rates and low power consuming application. Zigbee Wireless Sensor Network (WSN works on the network and application layer in IEEE 802.15.4. Zigbee network can be configured in star, tree or mesh topology. The performance varies from topology to topology. The performance parameters such as network lifetime, energy consumption, throughput, delay in data delivery and sensor field coverage area varies depending on the network topology. In this paper, designing of hybrid topology by using two possible combinations such as star-tree and star-mesh is simulated to verify the communication reliability. This approach is to combine all the benefits of two network model. The parameters such as jitter, delay and throughput are measured for these scenarios. Further, MAC parameters impact such as beacon order (BO and super frame order (SO for low power consumption and high channel utilization, has been analysed for star, tree and mesh topology in beacon disable mode and beacon enable mode by varying CBR traffic loads.

  19. Hybrid Methods for Muon Accelerator Simulations with Ionization Cooling

    Energy Technology Data Exchange (ETDEWEB)

    Kunz, Josiah [Anderson U.; Snopok, Pavel [Fermilab; Berz, Martin [Michigan State U.; Makino, Kyoko [Michigan State U.

    2018-03-28

    Muon ionization cooling involves passing particles through solid or liquid absorbers. Careful simulations are required to design muon cooling channels. New features have been developed for inclusion in the transfer map code COSY Infinity to follow the distribution of charged particles through matter. To study the passage of muons through material, the transfer map approach alone is not sufficient. The interplay of beam optics and atomic processes must be studied by a hybrid transfer map--Monte-Carlo approach in which transfer map methods describe the deterministic behavior of the particles, and Monte-Carlo methods are used to provide corrections accounting for the stochastic nature of scattering and straggling of particles. The advantage of the new approach is that the vast majority of the dynamics are represented by fast application of the high-order transfer map of an entire element and accumulated stochastic effects. The gains in speed are expected to simplify the optimization of cooling channels which is usually computationally demanding. Progress on the development of the required algorithms and their application to modeling muon ionization cooling channels is reported.

  20. A hybrid computer simulation of reactor spatial dynamics

    International Nuclear Information System (INIS)

    Hinds, H.W.

    1977-08-01

    The partial differential equations describing the one-speed spatial dynamics of thermal neutron reactors were converted to a set of ordinary differential equations, using finite-difference approximations for the spatial derivatives. The variables were then normalized to a steady-state reference condition in a novel manner, to yield an equation set particularly suitable for implementation on a hybrid computer. One Applied Dynamics AD/FIVE analog-computer console is capable of solving, all in parallel, up to 30 simultaneous differential equations. This corresponds roughly to eight reactor nodes, each with two active delayed-neutron groups. To improve accuracy, an increase in the number of nodes is usually required. Using the Hsu-Howe multiplexing technique, an 8-node, one-dimensional module was switched back and forth between the left and right halves of the reactor, to simulate a 16-node model, also in one dimension. These two versions (8 or 16 nodes) of the model were tested on benchmark problems of the loss-of-coolant type, which were also solved using the digital code FORSIM, with two energy groups and 26 nodes. Good agreement was obtained between the two solution techniques. (author)

  1. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    Wintec

    Near IR spectral region (1000–2500 nm) shows the elimination of water in the compound which ... 1-Butyl 3-methyl imidazolium bromide; molecular material; phosphotungstic acid; near IR. ..... attributable to the first overtone of hydroxyl groups,.

  2. Molecular Dynamics Simulations of Kinetic Models for Chiral Dominance in Soft Condensed Matter

    DEFF Research Database (Denmark)

    Toxvaerd, Søren

    2001-01-01

    Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality......Molecular dynamics simulation, models for isomerization kinetics, origin of biomolecular chirality...

  3. Wind Solar Hybrid System Rectifier Stage Topology Simulation

    OpenAIRE

    Anup M. Gakare; Subhash Kamdi

    2014-01-01

    This paper presents power-control strategies of a grid-connected hybrid generation system with versatile power transfer. The hybrid system allows maximum utilization of freely available renewable sources like wind and photovoltaic energies. This paper presents a new system configuration of the multi input rectifier stage for a hybrid wind and photovoltaic energy system. This configuration allows the two sources to supply the load simultaneously depending on the availability of...

  4. Molecular dynamics simulations of ballistic He penetration into W fuzz

    NARCIS (Netherlands)

    Klaver, T. P. C.; Nordlund, K.; Morgan, T. W.; Westerhof, E.; Thijsse, B. J.; van de Sanden, M. C. M.

    2016-01-01

    Results are presented of large-scale Molecular Dynamics simulations of low-energy He bombardment of W nanorods, or so-called ‘fuzz’ structures. The goal of these simulations is to see if ballistic He penetration through W fuzz offers a more realistic scenario for how He moves through fuzz layers

  5. Dynamic Modeling and Simulation of a Switched Reluctance Motor in a Series Hybrid Electric Vehicle

    OpenAIRE

    Siavash Sadeghi; Mojtaba Mirsalim; Arash Hassanpour Isfahani

    2010-01-01

    Dynamic behavior analysis of electric motors is required in order to accuratelyevaluate the performance, energy consumption and pollution level of hybrid electricvehicles. Simulation tools for hybrid electric vehicles are divided into steady state anddynamic models. Tools with steady-state models are useful for system-level analysiswhereas tools that utilize dynamic models give in-depth information about the behavior ofsublevel components. For the accurate prediction of hybrid electric vehicl...

  6. One-dimensional hybrid-direct kinetic simulation of the discharge plasma in a Hall thruster

    International Nuclear Information System (INIS)

    Hara, Kentaro; Boyd, Iain D.; Kolobov, Vladimir I.

    2012-01-01

    In order to model the non-equilibrium plasma within the discharge region of a Hall thruster, the velocity distribution functions (VDFs) must be obtained accurately. A direct kinetic (DK) simulation method that directly solves the plasma Boltzmann equation can achieve better resolution of VDFs in comparison to particle simulations, such as the particle-in-cell (PIC) method that inherently include statistical noise. In this paper, a one-dimensional hybrid-DK simulation, which uses a DK simulation for heavy species and a fluid model for electrons, is developed and compared to a hybrid-PIC simulation. Time-averaged results obtained from the hybrid-DK simulation are in good agreement with hybrid-PIC results and experimental data. It is shown from a comparison of using a kinetic simulation and solving the continuity equation that modeling of the neutral atoms plays an important role for simulations of the Hall thruster discharge plasma. In addition, low and high frequency plasma oscillations are observed. Although the kinetic nature of electrons is not resolved due to the use of a fluid model, the hybrid-DK model provides spatially and temporally well-resolved plasma properties and an improved resolution of VDFs for heavy species with less statistical noise in comparison to the hybrid-PIC method.

  7. Dynamic Modeling and Simulation on a Hybrid Power System for Electric Vehicle Applications

    Directory of Open Access Journals (Sweden)

    Hong-Wen He

    2010-11-01

    Full Text Available Hybrid power systems, formed by combining high-energy-density batteries and high-power-density ultracapacitors in appropriate ways, provide high-performance and high-efficiency power systems for electric vehicle applications. This paper first establishes dynamic models for the ultracapacitor, the battery and a passive hybrid power system, and then based on the dynamic models a comparative simulation between a battery only power system and the proposed hybrid power system was done under the UDDS (Urban Dynamometer Driving Schedule. The simulation results showed that the hybrid power system could greatly optimize and improve the efficiency of the batteries and their dynamic current was also decreased due to the participation of the ultracapacitors, which would have a good influence on batteries’ cycle life. Finally, the parameter matching for the passive hybrid power system was studied by simulation and comparisons.

  8. Molecular identification of hybrids from a former hot spot of Potamogeton hybrid diversity

    Czech Academy of Sciences Publication Activity Database

    Kaplan, Zdeněk; Fehrer, Judith

    2013-01-01

    Roč. 105, Feb 2013 (2013), s. 34-40 ISSN 0304-3770 R&D Projects: GA ČR GA206/09/0291 Institutional support: RVO:67985939 Keywords : hybridization * taxonomy * diversity Subject RIV: EF - Botanics Impact factor: 1.471, year: 2013

  9. Molecular simulation for novel carbon buckyball materials

    Directory of Open Access Journals (Sweden)

    Hasan R. Obayes

    2015-12-01

    Full Text Available The discovery of buckyballs was unexpected because the researchers were delivering carbon plasmas to reproduce and describe unidentified interstellar matter. Density functional theory was done to study and design the structure of [8]circulene and three new buckyballs with molecular dimensions of less than a nanometer. Cyclic polymerization reactions can be utilized to prepare new buckyballs, and this process also produces molecules of hydrogen. All reactions are spontaneous and exothermic as per the estimations to the values of entropy, Gibbs energy, and enthalpy changes. The results demonstrate that the most symmetric buckyball is the most stable, and the molecular dimensions are less than a nanometer. The new buckyballs are characterized by the high efficiency of their energy gaps, making it potentially useful for solar cell applications.

  10. Molecular dynamics simulation of a chemical reaction

    International Nuclear Information System (INIS)

    Gorecki, J.; Gryko, J.

    1988-06-01

    Molecular dynamics is used to study the chemical reaction A+A→B+B. It is shown that the reaction rate constant follows the Arrhenius law both for Lennard-Jones and hard sphere interaction potentials between substrate particles. A. For the denser systems the reaction rate is proportional to the value of the radial distribution function at the contact point of two hard spheres. 10 refs, 4 figs

  11. Mountain bicycle frame testing as an example of practical implementation of hybrid simulation using RTFEM

    Science.gov (United States)

    Mucha, Waldemar; Kuś, Wacław

    2018-01-01

    The paper presents a practical implementation of hybrid simulation using Real Time Finite Element Method (RTFEM). Hybrid simulation is a technique for investigating dynamic material and structural properties of mechanical systems by performing numerical analysis and experiment at the same time. It applies to mechanical systems with elements too difficult or impossible to model numerically. These elements are tested experimentally, while the rest of the system is simulated numerically. Data between the experiment and numerical simulation are exchanged in real time. Authors use Finite Element Method to perform the numerical simulation. The following paper presents the general algorithm for hybrid simulation using RTFEM and possible improvements of the algorithm for computation time reduction developed by the authors. The paper focuses on practical implementation of presented methods, which involves testing of a mountain bicycle frame, where the shock absorber is tested experimentally while the rest of the frame is simulated numerically.

  12. Applications of Cerius2, software of molecular simulation

    International Nuclear Information System (INIS)

    Fernandez G, M.E.; Perez A, M.; Gutierrez W, C.E.

    2007-01-01

    Most of the investigations have a theoretical sustenance based on molecular simulation. The area of application of molecular simulation is very wide, in the Materials Technology Department assigned to the Applied Sciences Management have been treated problems about metallic nano structures, glasses, interfaces, and molecules, to sustain and to explain some of the experimental results. Energy calculations are carried out to determine minimum energy structures, for later on to carry out calculations of some of their properties; as well as the images simulation of Electron microscopy and X-ray diffraction. (Author)

  13. AceCloud: Molecular Dynamics Simulations in the Cloud.

    Science.gov (United States)

    Harvey, M J; De Fabritiis, G

    2015-05-26

    We present AceCloud, an on-demand service for molecular dynamics simulations. AceCloud is designed to facilitate the secure execution of large ensembles of simulations on an external cloud computing service (currently Amazon Web Services). The AceCloud client, integrated into the ACEMD molecular dynamics package, provides an easy-to-use interface that abstracts all aspects of interaction with the cloud services. This gives the user the experience that all simulations are running on their local machine, minimizing the learning curve typically associated with the transition to using high performance computing services.

  14. [Use of ITS and ISSR markers in the molecular characterisation of Pleurotus djamor hybrid strains].

    Science.gov (United States)

    Aguilar Doroteo, Leticia; Zárate Segura, Paola Berenice; Villanueva Arce, Ramón; Yáñez Fernández, Jorge; Garín Aguilar, María Eugenia; Guadarrama Mendoza, Paula Cecilia; Valencia Del Toro, Gustavo

    Molecular characterisation of wild type Pleurotus species is important for germplasm conservation and its further use for genetic improvement. No molecular studies have been performed with monokaryons used for producing hybrid strains, either with the reconstituted strains obtained by pairing those monokaryons. The molecular characterisation of parental dikaryons, hybrid, and reconstituted strains as well as monokaryotic strains, is therefore of utmost importance. To carry out the molecular identification of Pleurotus djamor strains, i.e. dikaryotic wild type strains, hybrid strains, and the monokaryotic strains used for the hybrid formation. Five wild type strains of P. djamor from different states in Mexico were collected and molecularly identified by sequencing the ITS1-5.8-ITS2 region using ITS1 and ITS4 universal oligonucleotides. Four hybrid strains were obtained by pairing neohaplonts of two wild type strains selected. Six ISSR markers were used for the molecular characterisation of monokaryotic and dikaryotic strains. Using the ITS markers, an amplified product of 700bp was obtained in five wild type strains, with a 99-100% similarity with P. djamor. A total of 95 fragments were obtained using the ISSR markers, with 99% of polymorphism. Wild type strains were identified as P. djamor, and were clearly grouped with Mexican strains from other states of Mexico. ISSR markers allowed the generation of polymorphic bands in monokaryotic and dikaryotic strains, splitting both types of strains. The high degree of polymorphism indicates the genetic diversity of P. djamor, an advantage in mushroom production and in the improving of the species. Copyright © 2017 Asociación Española de Micología. Publicado por Elsevier España, S.L.U. All rights reserved.

  15. Numerical Simulations of Flow and Fuel Regression Rate Coupling in Hybrid Rocket Motors

    Directory of Open Access Journals (Sweden)

    Marius STOIA-DJESKA

    2017-03-01

    Full Text Available The hybrid propulsion offers some remarkable advantages like high safety and high specific impulse and thus it is considered a promising technology for the next generation launchers and space systems. The purpose of this work is to validate a design tool for hybrid rocket motors (HRM through numerical simulations.

  16. Insight into Electrospinning via Molecular Simulations.

    Czech Academy of Sciences Publication Activity Database

    Jirsák, Jan; Moučka, F.; Nezbeda, Ivo

    2014-01-01

    Roč. 53, č. 19 (2014), s. 8257-8264 ISSN 0888-5885 Grant - others:GA MŠk(CZ) LM2010005 Institutional support: RVO:67985858 Keywords : dynamics simulations * liquid water * fields Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 2.587, year: 2014

  17. Novel applications of array comparative genomic hybridization in molecular diagnostics.

    Science.gov (United States)

    Cheung, Sau W; Bi, Weimin

    2018-05-31

    In 2004, the implementation of array comparative genomic hybridization (array comparative genome hybridization [CGH]) into clinical practice marked a new milestone for genetic diagnosis. Array CGH and single-nucleotide polymorphism (SNP) arrays enable genome-wide detection of copy number changes in a high resolution, and therefore microarray has been recognized as the first-tier test for patients with intellectual disability or multiple congenital anomalies, and has also been applied prenatally for detection of clinically relevant copy number variations in the fetus. Area covered: In this review, the authors summarize the evolution of array CGH technology from their diagnostic laboratory, highlighting exonic SNP arrays developed in the past decade which detect small intragenic copy number changes as well as large DNA segments for the region of heterozygosity. The applications of array CGH to human diseases with different modes of inheritance with the emphasis on autosomal recessive disorders are discussed. Expert commentary: An exonic array is a powerful and most efficient clinical tool in detecting genome wide small copy number variants in both dominant and recessive disorders. However, whole-genome sequencing may become the single integrated platform for detection of copy number changes, single-nucleotide changes as well as balanced chromosomal rearrangements in the near future.

  18. Hybrid gold nanoparticles in molecular imaging and radiotherapy

    International Nuclear Information System (INIS)

    Katti, K.V.; Kannan, R.; Katti, K.; Kattumuri, V.; Pandrapragada, R.; Rahing, V.; Cutler, C.; Boote, E.; Casteel, S.W.; Smith, C.J.; Robertson, J.D.; Jurrison, S.

    2006-01-01

    Metallic nanoparticles, because of their size, chemical and physical properties, are particularly attractive as therapeutic probes in treating cancer. Central to any clinical advances in nanoparticulate based therapy will be to produce hybrid nanoparticles that can be targeted to vascular, extracellular or cell surface receptors. Development of hybrid nanoparticles that specifically target cancer vasculature has received considerable attention. Most cancers have leaky vasculature and the defective vascular architecture, created due to the rapid vascularisation necessary to serve fast growing cancers, in combination with poor lymphatic drainage allows increased permeation and retention effects. The leaky vasculature, because of higher porosity and permeability, serve as natural high affinity targets to metallic nanoparticles. Another attractive approach toward the application of nanotechnology to nanomedicine is the utility of nanoparticles that display inherent therapeutic properties. For example radioactive gold nanoparticles present attractive prospects in therapy of cancer. The radioactive properties of Au-198 (β(max) = 0.96 MeV; t(1/2) = 2.7 d) and Au-199 (β(max) 0.46 MeV; t(1/2) = 3.14 d) make them ideal candidates for use in radiotherapeutic applications. In addition, they both have imageable gamma emissions for dosimetry and pharmacokinetic studies and Au-199 can be made carrier-free by indirect methods. Gold nanoparticles are of interest for treatment of disease as they can deliver agents directly into cells and cellular components with a higher concentration of radioactivity, e.g. higher dose of radioactivity, to cancerous tumor cells

  19. Molecular Organization Induced Anisotropic Properties of Perylene - Silica Hybrid Nanoparticles.

    Science.gov (United States)

    Sriramulu, Deepa; Turaga, Shuvan Prashant; Bettiol, Andrew Anthony; Valiyaveettil, Suresh

    2017-08-10

    Optically active silica nanoparticles are interesting owing to high stability and easy accessibility. Unlike previous reports on dye loaded silica particles, here we address an important question on how optical properties are dependent on the aggregation-induced segregation of perylene molecules inside and outside the silica nanoparticles. Three differentially functionalized fluorescent perylene - silica hybrid nanoparticles are prepared from appropriate ratios of perylene derivatives and tetraethyl orthosilicate (TEOS) and investigated the structure property correlation (P-ST, P-NP and P-SF). The particles differ from each other on the distribution, organization and intermolecular interaction of perylene inside or outside the silica matrix. Structure and morphology of all hybrid nanoparticles were characterized using a range of techniques such as electron microscope, optical spectroscopic measurements and thermal analysis. The organizations of perylene in three different silica nanoparticles were explored using steady-state fluorescence, fluorescence anisotropy, lifetime measurements and solid state polarized spectroscopic studies. The interactions and changes in optical properties of the silica nanoparticles in presence of different amines were tested and quantified both in solution and in vapor phase using fluorescence quenching studies. The synthesized materials can be regenerated after washing with water and reused for sensing of amines.

  20. Generation of hybrid meshes for the simulation of petroleum reservoirs; Generation de maillages hybrides pour la simulation de reservoirs petroliers

    Energy Technology Data Exchange (ETDEWEB)

    Balaven-Clermidy, S.

    2001-12-01

    Oil reservoir simulations study multiphase flows in porous media. These flows are described and evaluated through numerical schemes on a discretization of the reservoir domain. In this thesis, we were interested in this spatial discretization and a new kind of hybrid mesh has been proposed where the radial nature of flows in the vicinity of wells is directly taken into account in the geometry. Our modular approach described wells and their drainage area through radial circular meshes. These well meshes are inserted in a structured reservoir mesh (a Corner Point Geometry mesh) made up with hexahedral cells. Finally, in order to generate a global conforming mesh, proper connections are realized between the different kinds of meshes through unstructured transition ones. To compute these transition meshes that we want acceptable in terms of finite volume methods, an automatic method based on power diagrams has been developed. Our approach can deal with a homogeneous anisotropic medium and allows the user to insert vertical or horizontal wells as well as secondary faults in the reservoir mesh. Our work has been implemented, tested and validated in 2D and 2D1/2. It can also be extended in 3D when the geometrical constraints are simplicial ones: points, segments and triangles. (author)

  1. Molecular sieving through a graphene nanopore: non-equilibrium molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Chengzhen Sun; Bofeng Bai

    2017-01-01

    Two-dimensional graphene nanopores have shown great promise as ultra-permeable molecular sieves based on their size-sieving effects.We design a nitrogen/hydrogen modified graphene nanopore and conduct a transient non-equilibrium molecular dynamics simulation on its molecular sieving effects.The distinct time-varying molecular crossing numbers show that this special nanopore can efficiently sieve CO2 and H2S molecules from CH4 molecules with high selectivity.By analyzing the molecular structure and pore functionalization-related molecular orientation and permeable zone in the nanopore,density distribution in the molecular adsorption layer on the graphene surface,as well as other features,the molecular sieving mechanisms of graphene nanopores are revealed.Finally,several implications on the design of highly-efficient graphene nanopores,especially for determining the porosity and chemical functionalization,as gas separation membranes are summarized based on the identified phenomena and mechanisms.

  2. Molecular dynamics simulation of ribosome jam

    KAUST Repository

    Matsumoto, Shigenori

    2011-09-01

    We propose a coarse-grained molecular dynamics model of ribosome molecules to study the dependence of translation process on environmental parameters. We found the model exhibits traffic jam property, which is consistent with an ASEP model. We estimated the influence of the temperature and concentration of molecules on the hopping probability used in the ASEP model. Our model can also treat environmental effects on the translation process that cannot be explained by such cellular automaton models. © 2010 Elsevier B.V. All rights reserved.

  3. Molecular and morphological approaches for species delimitation and hybridization investigations of two Cichla species

    Directory of Open Access Journals (Sweden)

    Andrea A. F. Mourão

    Full Text Available ABSTRACT The hybridization is a widely-discussed issue in several studies with fish species. For some authors, hybridization may be related with diversification and speciation of several groups, or also with the extinction of populations or species. Difficulties to differentiate species and hybrids may be a problem to correctly apply a management of wild species, because hybrid lineages, especially the advanced ones, may resemble the parental species. The genus Cichla Bloch & Schneider, 1801 constitutes an interesting experimental model, considering that hybridization and taxonomic uncertainties hinder a correct identification. Considering these problems, in this study, we developed genetic methodologies and applied meristic and morphometric approaches in wild samples in order to identify species and for test a possible hybridization between Cichla kelberi Kullander & Ferreira, 2006 and Cichla piquiti Kullander & Ferreira, 2006. For this, C. kelberi, C. piquiti and potential hybrid ( carijó individuals were collected in Paraná and Tietê rivers (SP, Brazil. For meristic and morphometric methods, the individuals were analyzed using the statistical software Pcord 5:31, while for molecular methods, primers for PCR-multiplex were designed and enzyme for PCR-RFLP were selected, under the species-specific nucleotide. All results indicated that the carijó is not an interspecific hybrid, because it presented identical genetic pattern and morphology closed to C. piquiti. Thus, we propose that carijó is a C. piquiti morphotype. In addition, this study promotes a new molecular tool that could be used in future research, monitoring and management programs of the genus Cichla.

  4. Co-Simulation of Hybrid Systems with SpaceEx and Uppaal

    DEFF Research Database (Denmark)

    Bogomolov, Sergiy; Greitschus, Marius; Jensen, Peter Gjøl

    2015-01-01

    The Functional Mock-up Interface (FMI) is an industry standard which enables co-simulation of complex heterogeneous systems using multiple simulation engines. In this paper, we show how to use FMI in order to co-simulate hybrid systems modeled in the model checkers SPACEEX and UPPAAL. We show how...

  5. A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition

    International Nuclear Information System (INIS)

    Zheng Zheming; Stephens, Ryan M.; Braatz, Richard D.; Alkire, Richard C.; Petzold, Linda R.

    2008-01-01

    A hybrid multiscale kinetic Monte Carlo (HMKMC) method for speeding up the simulation of copper electrodeposition is presented. The fast diffusion events are simulated deterministically with a heterogeneous diffusion model which considers site-blocking effects of additives. Chemical reactions are simulated by an accelerated (tau-leaping) method for discrete stochastic simulation which adaptively selects exact discrete stochastic simulation for the appropriate reaction whenever that is necessary. The HMKMC method is seen to be accurate and highly efficient

  6. Hybrid simulation of reactor kinetics in CANDU reactors using a modal approach

    International Nuclear Information System (INIS)

    Monaghan, B.M.; McDonnell, F.N.; Hinds, H.W.T.; m.

    1980-01-01

    A hybrid computer model for simulating the behaviour of large CANDU (Canada Deuterium Uranium) reactor cores is presented. The main dynamic variables are expressed in terms of weighted sums of a base set of spatial natural-mode functions with time-varying co-efficients. This technique, known as the modal or synthesis approach, permits good three-dimensional representation of reactor dynamics and is well suited to hybrid simulation. The hybrid model provides improved man-machine interaction and real-time capability. The model was used in two applications. The first studies the transient that follows a loss of primary coolant and reactor shutdown; the second is a simulation of the dynamics of xenon, a fission product which has a high absorption cross-section for neutrons and thus has an important effect on reactor behaviour. Comparison of the results of the hybrid computer simulation with those of an all-digital one is good, within 1% to 2%

  7. Molecular dynamics simulation of propagating cracks

    Science.gov (United States)

    Mullins, M.

    1982-01-01

    Steady state crack propagation is investigated numerically using a model consisting of 236 free atoms in two (010) planes of bcc alpha iron. The continuum region is modeled using the finite element method with 175 nodes and 288 elements. The model shows clear (010) plane fracture to the edge of the discrete region at moderate loads. Analysis of the results obtained indicates that models of this type can provide realistic simulation of steady state crack propagation.

  8. Fate of bulk and trace organics during a simulated aquifer recharge and recovery (ARR)-ozone hybrid process

    KAUST Repository

    Yoon, Min

    2013-11-01

    The attenuation of bulk organic matter and trace organic contaminants (TOrCs) was evaluated for various aquifer recharge and recovery (ARR)-ozone (O3) hybrid treatment process combinations using soil-batch reactor and bench-scale ozonation experiments as a proof of concept prior to pilot and/or field studies. In water reclamation and especially potable reuse, refractory bulk organic matter and TOrCs are of potential health concern in recycled waters. In this study, the role of biotransformation of bulk organic matter and TOrCs was investigated considering different simulated treatment combinations, including soil passage (ARR) alone, ARR after ozonation (O3-ARR), and ARR prior to ozonation (ARR-O3). During oxic (aerobic) ARR simulations, soluble microbial-like substances (e.g., higher molecular weight polysaccharides and proteins) were easily removed while (lower molecular weight) humic substances and aromatic organic matter were not efficiently removed. During ARR-ozone treatment simulations, removals of bulk organic matter and TOrCs were rapid and effective compared to ARR alone. A higher reduction of effluent-derived organic matter, including aromatic organic matter and humic substances, was observed in the ARR-O3 hybrid followed by the O3-ARR hybrid. An enhanced attenuation of recalcitrant TOrCs was observed while increasing the ozone dose slightly (O3: DOC=1). TOrC removal efficiency also increased during the post-ozone treatment combination (i.e., ARR-O3). In addition, the carcinogenic wastewater disinfection byproduct N-nitrosodimethylamine (NDMA) was eliminated below the method reporting limit (<5ngL-1) both during ARR treatment alone and the ARR-ozone hybrid. © 2013 Elsevier Ltd.

  9. Full wave simulations of lower hybrid wave propagation in tokamaks

    International Nuclear Information System (INIS)

    Wright, J. C.; Bonoli, P. T.; Phillips, C. K.; Valeo, E.; Harvey, R. W.

    2009-01-01

    Lower hybrid (LH) waves have the attractive property of damping strongly via electron Landau resonance on relatively fast tail electrons at (2.5-3)xv te , where v te ≡ (2T e /m e ) 1/2 is the electron thermal speed. Consequently these waves are well-suited to driving current in the plasma periphery where the electron temperature is lower, making LH current drive (LHCD) a promising technique for off-axis (r/a≥0.60) current profile control in reactor grade plasmas. Established techniques for computing wave propagation and absorption use WKB expansions with non-Maxwellian self-consistent distributions.In typical plasma conditions with electron densities of several 10 19 m -3 and toroidal magnetic fields strengths of 4 Telsa, the perpendicular wavelength is of the order of 1 mm and the parallel wavelength is of the order of 1 cm. Even in a relatively small device such as Alcator C-Mod with a minor radius of 22 cm, the number of wavelengths that must be resolved requires large amounts of computational resources for the full wave treatment. These requirements are met with a massively parallel version of the TORIC full wave code that has been adapted specifically for the simulation of LH waves [J. C. Wright, et al., Commun. Comput. Phys., 4, 545 (2008), J. C. Wright, et al., Phys. Plasmas 16 July (2009)]. This model accurately represents the effects of focusing and diffraction that occur in LH propagation. It is also coupled with a Fokker-Planck solver, CQL3D, to provide self-consistent distribution functions for the plasma dielectric as well as a synthetic hard X-ray (HXR) diagnostic for direct comparisons with experimental measurements of LH waves.The wave solutions from the TORIC-LH zero FLR model will be compared to the results from ray tracing from the GENRAY/CQL3D code via the synthetic HXR diagnostic and power deposition.

  10. Simulation of carbon sputtering due to molecular hydrogen impact

    International Nuclear Information System (INIS)

    Laszlo, J.

    1993-01-01

    Simulated results are compared to experimental data on the sputtering yield of carbon due to atomic and to molecular hydrogen impact. The experimental sputtering yields of carbon (graphite) due to low energy hydrogen bombardment have been found to be higher than the simulated ones. Efforts are made to obtain high enough simulated yields by considering the formation of dimer, H 2 and D 2 molecules in the primary beam. The molecular beam model applies full neutralization and full dissociation at the surface. The simulation of sputtering yields of target materials up to Z 2 ≤ 30 is also included for the low primary energy regime for deuterium projectiles. It is found that, although the sputtering yields really tend to increase, the effect of molecule formation in the beam in itself cannot be made responsible for the deviation between measured and simulated sputtering yields. (orig.)

  11. Stereochemical errors and their implications for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Freddolino Peter L

    2011-05-01

    Full Text Available Abstract Background Biological molecules are often asymmetric with respect to stereochemistry, and correct stereochemistry is essential to their function. Molecular dynamics simulations of biomolecules have increasingly become an integral part of biophysical research. However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations. Results Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules. Conclusions Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.

  12. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    International Nuclear Information System (INIS)

    Marchetti, Luca; Priami, Corrado; Thanh, Vo Hong

    2016-01-01

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  13. HRSSA – Efficient hybrid stochastic simulation for spatially homogeneous biochemical reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Marchetti, Luca, E-mail: marchetti@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); Priami, Corrado, E-mail: priami@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy); University of Trento, Department of Mathematics (Italy); Thanh, Vo Hong, E-mail: vo@cosbi.eu [The Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Piazza Manifattura, 1, 38068 Rovereto (Italy)

    2016-07-15

    This paper introduces HRSSA (Hybrid Rejection-based Stochastic Simulation Algorithm), a new efficient hybrid stochastic simulation algorithm for spatially homogeneous biochemical reaction networks. HRSSA is built on top of RSSA, an exact stochastic simulation algorithm which relies on propensity bounds to select next reaction firings and to reduce the average number of reaction propensity updates needed during the simulation. HRSSA exploits the computational advantage of propensity bounds to manage time-varying transition propensities and to apply dynamic partitioning of reactions, which constitute the two most significant bottlenecks of hybrid simulation. A comprehensive set of simulation benchmarks is provided for evaluating performance and accuracy of HRSSA against other state of the art algorithms.

  14. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (S P n), and physical measurement to verify the performance of our study method on both accuracy and efficiency. PMID:20445737

  15. Study on Photon Transport Problem Based on the Platform of Molecular Optical Simulation Environment

    Directory of Open Access Journals (Sweden)

    Kuan Peng

    2010-01-01

    Full Text Available As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SPn, and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  16. Study on photon transport problem based on the platform of molecular optical simulation environment.

    Science.gov (United States)

    Peng, Kuan; Gao, Xinbo; Liang, Jimin; Qu, Xiaochao; Ren, Nunu; Chen, Xueli; Ma, Bin; Tian, Jie

    2010-01-01

    As an important molecular imaging modality, optical imaging has attracted increasing attention in the recent years. Since the physical experiment is usually complicated and expensive, research methods based on simulation platforms have obtained extensive attention. We developed a simulation platform named Molecular Optical Simulation Environment (MOSE) to simulate photon transport in both biological tissues and free space for optical imaging based on noncontact measurement. In this platform, Monte Carlo (MC) method and the hybrid radiosity-radiance theorem are used to simulate photon transport in biological tissues and free space, respectively, so both contact and noncontact measurement modes of optical imaging can be simulated properly. In addition, a parallelization strategy for MC method is employed to improve the computational efficiency. In this paper, we study the photon transport problems in both biological tissues and free space using MOSE. The results are compared with Tracepro, simplified spherical harmonics method (SP(n)), and physical measurement to verify the performance of our study method on both accuracy and efficiency.

  17. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles

    Science.gov (United States)

    Petrini, Paula A.; Silva, Ricardo M. L.; de Oliveira, Rafael F.; Merces, Leandro; Bof Bufon, Carlos C.

    2018-06-01

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscopy. The incorporation of molecular materials in devices is not a trivial task as the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (k CuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensembles have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (k CuPc = 4.5 ± 0.5). These values suggest a mild contribution of the molecular orientation on the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology.

  18. Hybrid nanomembrane-based capacitors for the determination of the dielectric constant of semiconducting molecular ensembles.

    Science.gov (United States)

    Petrini, Paula Andreia; Lopes da Silva, Ricardo Magno; de Oliveira, Rafael Furlan; Merces, Leandro; Bufon, Carlos César Bof

    2018-04-06

    Considerable advances in the field of molecular electronics have been achieved over the recent years. One persistent challenge, however, is the exploitation of the electronic properties of molecules fully integrated into devices. Typically, the molecular electronic properties are investigated using sophisticated techniques incompatible with a practical device technology, such as the scanning tunneling microscope (STM). The incorporation of molecular materials in devices is not a trivial task since the typical dimensions of electrical contacts are much larger than the molecular ones. To tackle this issue, we report on hybrid capacitors using mechanically-compliant nanomembranes to encapsulate ultrathin molecular ensembles for the investigation of molecular dielectric properties. As the prototype material, copper (II) phthalocyanine (CuPc) has been chosen as information on its dielectric constant (kCuPc) at the molecular scale is missing. Here, hybrid nanomembrane-based capacitors containing metallic nanomembranes, insulating Al2O3 layers, and the CuPc molecular ensemble have been fabricated and evaluated. The Al2O3 is used to prevent short circuits through the capacitor plates as the molecular layer is considerably thin (< 30 nm). From the electrical measurements of devices with molecular layers of different thicknesses, the CuPc dielectric constant has been reliably determined (kCuPc = 4.5 ± 0.5). These values suggest a mild contribution of molecular orientation in the CuPc dielectric properties. The reported nanomembrane-based capacitor is a viable strategy for the dielectric characterization of ultrathin molecular ensembles integrated into a practical, real device technology. © 2018 IOP Publishing Ltd.

  19. Molecular dynamics simulation of laser shock phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, Ichirou [Japan Atomic Energy Research Inst., Kansai Research Establishment, Advanced Photon Research Center, Neyagawa, Osaka (Japan).

    2001-10-01

    Recently, ultrashort-pulse lasers with high peak power have been developed, and their application to materials processing is expected as a tool of precision microfabrication. When a high power laser irradiates, a shock wave propagates into the material and dislocations are generated. In this paper, laser shock phenomena of the metal were analyzed using the modified molecular dynamics method, which has been developed by Ohmura and Fukumoto. The main results obtained are summarized as follows: (1) The shock wave induced by the Gaussian beam irradiation propagates radially from the surface to the interior. (2) A lot of dislocations are generated at the solid-liquid interface by the propagation of a shock wave. (3) Some dislocations are moved instantaneously with the velocity of the longitudinal wave when the shock wave passes, and their velocity is not larger than the transverse velocity after the shock wave has passed. (author)

  20. Molecular simulations of CO2 at interfaces

    DEFF Research Database (Denmark)

    Silvestri, Alessandro

    trapping mechanisms that act over dierent time scales, where eectiveness is determined by phenomena that occur at the interfaces between CO2, pore uids and the pore surfaces. Solid theoretical understanding of the nanoscale interactions that result from the interplay of intermolecular and surface forces...... variety of conditions: pressure, temperature, pore solution salinity and various mineral surfaces. However, achieving representative subsurface conditions in experiments is challenging and reported data are aected by experimental uncertainties and sometimes are contradictory. Molecular modelling...... rock record and the formations are generally porous so their probable response to CO2 sequestration needs to be investigated. However, despite the large number of geologic sequestration publications on water{rock interactions over the last decade, studies on carbonate reservoirs remain scarce...

  1. Fabrication of hybrid molecular devices using multi-layer graphene break junctions

    Science.gov (United States)

    Island, J. O.; Holovchenko, A.; Koole, M.; Alkemade, P. F. A.; Menelaou, M.; Aliaga-Alcalde, N.; Burzurí, E.; van der Zant, H. S. J.

    2014-11-01

    We report on the fabrication of hybrid molecular devices employing multi-layer graphene (MLG) flakes which are patterned with a constriction using a helium ion microscope or an oxygen plasma etch. The patterning step allows for the localization of a few-nanometer gap, created by electroburning, that can host single molecules or molecular ensembles. By controlling the width of the sculpted constriction, we regulate the critical power at which the electroburning process begins. We estimate the flake temperature given the critical power and find that at low powers it is possible to electroburn MLG with superconducting contacts in close proximity. Finally, we demonstrate the fabrication of hybrid devices with superconducting contacts and anthracene-functionalized copper curcuminoid molecules. This method is extendable to spintronic devices with ferromagnetic contacts and a first step towards molecular integrated circuits.

  2. Novel flavonolignan hybrid antioxidants: From enzymatic preparation to molecular rationalization

    Czech Academy of Sciences Publication Activity Database

    Vavříková, Eva; Křen, Vladimír; Ježová-Kalachová, Lubica; Biler, M.; Chantemargue, B.; Pyszková, M.; Riva, S.; Kuzma, Marek; Valentová, Kateřina; Ulrichová, J.; Vrba, J.; Trouillas, P.; Vacek, J.

    2017-01-01

    Roč. 127, FEB 15 (2017), s. 263-274 ISSN 0223-5234 R&D Projects: GA MŠk(CZ) LD14096; GA MŠk(CZ) LD15084; GA ČR(CZ) GA15-03037S Institutional support: RVO:61388971 Keywords : Silybin * Vitamin C * Enzymatic coupling Subject RIV: CE - Biochemistry OBOR OECD: Biochemistry and molecular biology Impact factor: 4.519, year: 2016

  3. A dynamic simulation tool for the battery-hybrid hydrogen fuel cell vehicle

    Energy Technology Data Exchange (ETDEWEB)

    Moore, R.M. [Hawaii Natural Energy Institute, University of Hawaii, Manoa (United States); Ramaswamy, S.; Cunningham, J.M. [California Univ., Berkeley, CA (United States); Hauer, K.H. [xcellvision, Major-Hirst-Strasse 11, 38422 Wolfsburg (Germany)

    2006-10-15

    This paper describes a dynamic fuel cell vehicle simulation tool for the battery-hybrid direct-hydrogen fuel cell vehicle. The emphasis is on simulation of the hybridized hydrogen fuel cell system within an existing fuel cell vehicle simulation tool. The discussion is focused on the simulation of the sub-systems that are unique to the hybridized direct-hydrogen vehicle, and builds on a previous paper that described a simulation tool for the load-following direct-hydrogen vehicle. The configuration of the general fuel cell vehicle simulation tool has been previously presented in detail, and is only briefly reviewed in the introduction to this paper. Strictly speaking, the results provided in this paper only serve as an example that is valid for the specific fuel cell vehicle design configuration analyzed. Different design choices may lead to different results, depending strongly on the parameters used and choices taken during the detailed design process required for this highly non-linear and n-dimensional system. The primary purpose of this paper is not to provide a dynamic simulation tool that is the ''final word'' for the ''optimal'' hybrid fuel cell vehicle design. The primary purpose is to provide an explanation of a simulation method for analyzing the energetic aspects of a hybrid fuel cell vehicle. (Abstract Copyright [2006], Wiley Periodicals, Inc.)

  4. Activity coefficients from molecular simulations using the OPAS method

    Science.gov (United States)

    Kohns, Maximilian; Horsch, Martin; Hasse, Hans

    2017-10-01

    A method for determining activity coefficients by molecular dynamics simulations is presented. It is an extension of the OPAS (osmotic pressure for the activity of the solvent) method in previous work for studying the solvent activity in electrolyte solutions. That method is extended here to study activities of all components in mixtures of molecular species. As an example, activity coefficients in liquid mixtures of water and methanol are calculated for 298.15 K and 323.15 K at 1 bar using molecular models from the literature. These dense and strongly interacting mixtures pose a significant challenge to existing methods for determining activity coefficients by molecular simulation. It is shown that the new method yields accurate results for the activity coefficients which are in agreement with results obtained with a thermodynamic integration technique. As the partial molar volumes are needed in the proposed method, the molar excess volume of the system water + methanol is also investigated.

  5. Molecular dynamics simulation of bubble nucleation in explosive boiling

    International Nuclear Information System (INIS)

    Zou Yu; Chinese Academy of Sciences, Beijing; Huai Xiulan; Liang Shiqiang

    2009-01-01

    Molecular dynamics (MD) simulation is carried out for the bubble nucleation of liquid nitrogen in explosive boiling. The heat is transferred into the simulation system by rescaling the velocity of the molecules. The results indicate that the initial equilibrium temperature of liquid and molecular cluster size affect the energy conversion in the process of bubble nucleation. The potential energy of the system violently varies at the beginning of the bubble nucleation, and then varies around a fixed value. At the end of bubble nucleation, the potential energy of the system slowly increases. In the bubble nucleation of explosive boiling, the lower the initial equilibrium temperature, the larger the size of the molecular cluster, and the more the heat transferred into the system of the simulation cell, causing the increase potential energy in a larger range. (authors)

  6. A study on optimization of hybrid drive train using Advanced Vehicle Simulator (ADVISOR)

    Energy Technology Data Exchange (ETDEWEB)

    Same, Adam; Stipe, Alex; Grossman, David; Park, Jae Wan [Department of Mechanical and Aeronautical Engineering, University of California, Davis, One Shields Ave, Davis, CA 95616 (United States)

    2010-10-01

    This study investigates the advantages and disadvantages of three hybrid drive train configurations: series, parallel, and ''through-the-ground'' parallel. Power flow simulations are conducted with the MATLAB/Simulink-based software ADVISOR. These simulations are then applied in an application for the UC Davis SAE Formula Hybrid vehicle. ADVISOR performs simulation calculations for vehicle position using a combined backward/forward method. These simulations are used to study how efficiency and agility are affected by the motor, fuel converter, and hybrid configuration. Three different vehicle models are developed to optimize the drive train of a vehicle for three stages of the SAE Formula Hybrid competition: autocross, endurance, and acceleration. Input cycles are created based on rough estimates of track geometry. The output from these ADVISOR simulations is a series of plots of velocity profile and energy storage State of Charge that provide a good estimate of how the Formula Hybrid vehicle will perform on the given course. The most noticeable discrepancy between the input cycle and the actual velocity profile of the vehicle occurs during deceleration. A weighted ranking system is developed to organize the simulation results and to determine the best drive train configuration for the Formula Hybrid vehicle. Results show that the through-the-ground parallel configuration with front-mounted motors achieves an optimal balance of efficiency, simplicity, and cost. ADVISOR is proven to be a useful tool for vehicle power train design for the SAE Formula Hybrid competition. This vehicle model based on ADVISOR simulation is applicable to various studies concerning performance and efficiency of hybrid drive trains. (author)

  7. Simulation of molecular transitions using classical trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Donoso, A.; Martens, C. C. [University of California, California (United States)

    2001-03-01

    In the present work, we describe the implementation of a semiclassical method to study physical-chemical processes in molecular systems where electronic state transitions and quantum coherence play a dominant role. The method is based on classical trajectory propagation on the underlying coupled electronic surfaces and is derived from the semiclassical limit of the quantum Liouville equation. Unlike previous classical trajectory-based methods, quantum electronic coherence are treated naturally within this approach as complex weighted trajectory ensembles propagating on the average electronic surfaces. The method is tested on a model problem consisting of one-dimensional motion on two crossing electronic surfaces. Excellent agreement is obtained when compared to the exact results obtained by wave packet propagation. The method is applied to model quantum wave packet interferometry, where two wave packets, differing only in a relative phase, collide in the region where the two electronic surfaces cross. The dependence of the resulting population transfer on the initial relative phase of the wave packets is perfectly captured by our classical trajectory method. Comparison with an alternative method, surface hopping, shows that our approach is appropriate for modelling quantum interference phenomena. [Spanish] En este trabajo se describe la implementacion de un metodo semiclasico para estudiar procesos fisicos-quimicos en sistemas moleculares donde las transiciones entre estados electronicos y las coherencias cuanticas juegan un papel predominante. El metodo se basa en la propagacion de trayectorias clasicas sobre las correspondientes superficies electronicas acopladas y se deriva a partir del limite semiclasico de la ecuacion cuantica de Liouville. A diferencia de metodos previos basados en trayectoria clasica, dentro de este esquema, las coherencias electronicas cuanticas son tratadas de manera natural como ensamble de trayectorias con pesos complejos, moviendose en

  8. Filaments in simulations of molecular cloud formation

    Energy Technology Data Exchange (ETDEWEB)

    Gómez, Gilberto C.; Vázquez-Semadeni, Enrique [Centro de Radioastronomía y Astrofísica, Universidad Nacional Autónoma de México, Campus Morelia Apartado Postal 3-72, 58090 Morelia, Michoacán (Mexico)

    2014-08-20

    We report on the filaments that develop self-consistently in a new numerical simulation of cloud formation by colliding flows. As in previous studies, the forming cloud begins to undergo gravitational collapse because it rapidly acquires a mass much larger than the average Jeans mass. Thus, the collapse soon becomes nearly pressureless, proceeding along its shortest dimension first. This naturally produces filaments in the cloud and clumps within the filaments. The filaments are not in equilibrium at any time, but instead are long-lived flow features through which the gas flows from the cloud to the clumps. The filaments are long-lived because they accrete from their environment while simultaneously accreting onto the clumps within them; they are essentially the locus where the flow changes from accreting in two dimensions to accreting in one dimension. Moreover, the clumps also exhibit a hierarchical nature: the gas in a filament flows onto a main, central clump but other, smaller-scale clumps form along the infalling gas. Correspondingly, the velocity along the filament exhibits a hierarchy of jumps at the locations of the clumps. Two prominent filaments in the simulation have lengths ∼15 pc and masses ∼600 M {sub ☉} above density n ∼ 10{sup 3} cm{sup –3} (∼2 × 10{sup 3} M {sub ☉} at n > 50 cm{sup –3}). The density profile exhibits a central flattened core of size ∼0.3 pc and an envelope that decays as r {sup –2.5} in reasonable agreement with observations. Accretion onto the filament reaches a maximum linear density rate of ∼30 M {sub ☉} Myr{sup –1} pc{sup –1}.

  9. The simulation of molecular clouds formation in the Milky Way

    Science.gov (United States)

    Khoperskov, S. A.; Vasiliev, E. O.; Sobolev, A. M.; Khoperskov, A. V.

    2013-01-01

    Using 3D hydrodynamic calculations we simulate formation of molecular clouds in the Galaxy. The simulations take into account molecular hydrogen chemical kinetics, cooling and heating processes. Comprehensive gravitational potential accounts for contributions from the stellar bulge, two- and four-armed spiral structure, stellar disc, dark halo and takes into account self-gravitation of the gaseous component. Gas clouds in our model form in the spiral arms due to shear and wiggle instabilities and turn into molecular clouds after t ≳ 100 Myr. At the times t ˜ 100-300 Myr the clouds form hierarchical structures and agglomerations with the sizes of 100 pc and greater. We analyse physical properties of the simulated clouds and find that synthetic statistical distributions like mass spectrum, `mass-size' relation and velocity dispersion are close to those observed in the Galaxy. The synthetic l-v (galactic longitude-radial velocity) diagram of the simulated molecular gas distribution resembles observed one and displays a structure with appearance similar to molecular ring of the Galaxy. Existence of this structure in our modelling can be explained by superposition of emission from the galactic bar and the spiral arms at ˜3-4 kpc.

  10. Partial multicanonical algorithm for molecular dynamics and Monte Carlo simulations.

    Science.gov (United States)

    Okumura, Hisashi

    2008-09-28

    Partial multicanonical algorithm is proposed for molecular dynamics and Monte Carlo simulations. The partial multicanonical simulation samples a wide range of a part of the potential-energy terms, which is necessary to sample the conformational space widely, whereas a wide range of total potential energy is sampled in the multicanonical algorithm. Thus, one can concentrate the effort to determine the weight factor only on the important energy terms in the partial multicanonical simulation. The partial multicanonical, multicanonical, and canonical molecular dynamics algorithms were applied to an alanine dipeptide in explicit water solvent. The canonical simulation sampled the states of P(II), C(5), alpha(R), and alpha(P). The multicanonical simulation covered the alpha(L) state as well as these states. The partial multicanonical simulation also sampled the C(7) (ax) state in addition to the states that were sampled by the multicanonical simulation. In the partial multicanonical simulation, furthermore, backbone dihedral angles phi and psi rotated more frequently than those in the multicanonical and canonical simulations. These results mean that the partial multicanonical algorithm has a higher sampling efficiency than the multicanonical and canonical algorithms.

  11. The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

    Science.gov (United States)

    Chen, Jundong

    2018-03-01

    Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

  12. Hybrid Light-Matter States in a Molecular and Material Science Perspective.

    Science.gov (United States)

    Ebbesen, Thomas W

    2016-11-15

    The notion that light and matter states can be hybridized the way s and p orbitals are mixed is a concept that is not familiar to most chemists and material scientists. Yet it has much potential for molecular and material sciences that is just beginning to be explored. For instance, it has already been demonstrated that the rate and yield of chemical reactions can be modified and that the conductivity of organic semiconductors and nonradiative energy transfer can be enhanced through the hybridization of electronic transitions. The hybridization is not limited to electronic transitions; it can be applied for instance to vibrational transitions to selectively perturb a given bond, opening new possibilities to change the chemical reactivity landscape and to use it as a tool in (bio)molecular science and spectroscopy. Such results are not only the consequence of the new eigenstates and energies generated by the hybridization. The hybrid light-matter states also have unusual properties: they can be delocalized over a very large number of molecules (up to ca. 10 5 ), and they become dispersive or momentum-sensitive. Importantly, the hybridization occurs even in the absence of light because it is the zero-point energies of the molecular and optical transitions that generate the new light-matter states. The present work is not a review but rather an Account from the author's point of view that first introduces the reader to the underlying concepts and details of the features of hybrid light-matter states. It is shown that light-matter hybridization is quite easy to achieve: all that is needed is to place molecules or a material in a resonant optical cavity (e.g., between two parallel mirrors) under the right conditions. For vibrational strong coupling, microfluidic IR cells can be used to study the consequences for chemistry in the liquid phase. Examples of modified properties are given to demonstrate the full potential for the molecular and material sciences. Finally an

  13. Applications of Cerius2, software of molecular simulation; Aplicaciones de Cerius2, software de simulacion molecular

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez G, M E; Perez A, M; Gutierrez W, C E [ININ, 52750 La Marquesa, Estado de Mexico (Mexico)

    2007-07-01

    Most of the investigations have a theoretical sustenance based on molecular simulation. The area of application of molecular simulation is very wide, in the Materials Technology Department assigned to the Applied Sciences Management have been treated problems about metallic nano structures, glasses, interfaces, and molecules, to sustain and to explain some of the experimental results. Energy calculations are carried out to determine minimum energy structures, for later on to carry out calculations of some of their properties; as well as the images simulation of Electron microscopy and X-ray diffraction. (Author)

  14. Hybridization improved bacteria resistance in abalone: Evidence from physiological and molecular responses.

    Science.gov (United States)

    Liang, Shuang; Luo, Xuan; You, Weiwei; Ke, Caihuan

    2018-01-01

    Hybridization is an effective way of improving germplasm in abalone, as it often generates benign traits in the hybrids. The hybrids of Haliotis discus hannai and H. gigantea have shown heterosis in terms of disease resistance than one or both parental species. In the present study, to elucidate the physiological and molecular mechanism of this heterosis, we analyzed the dynamic changes of several immune indexes including survival rate, total circulating haemocyte count (THC), phagocytic activity, reactive oxygen species level (ROS) and phenoloxidase activity (PO) in two parental species, H. discus hannai (DD) and H. gigantea (GG), and their reciprocal hybrids H. discus hannai ♀ × H. gigantea ♂ (DG), H. gigantea ♀ × H. discus hannai ♂ (GD) challenged with a mixture of Vibrio harveyi, V. alginolyticus and V. parahaemolyticus (which have been demonstrated to be pathogenic to abalone). Besides, we cloned and analyzed three important immune genes: heat shock protein 70 (hsp70), ferritin and cold shock domain protein (csdp) in H. discus hannai and H. gigantea, then further investigated their mRNA level changes in the four abalone genotypes after bacterial challenge. Results showed that these physiological and molecular parameters were significantly induced by bacterial exposure, and their changing patterns were obviously different between the four genotypes: (1) Survival rates of the two hybrids were higher than both parental species after bacterial exposure; (2) DG had higher THC than the other three genotypes; (3) Phagocytosis responded slower in the hybrids than in the parental species; (4) DD's ROS level was lower than the other three genotypes at 48 h post infection; (5) Phenoloxidase activity was lower in DD during the infection compared to the other genotypes; (6) mRNA levels of hsp70 and csdp, were always lower in at least one parental species (DD) than in the hybrids after the bacterial exposure. Results from this study indicate that the hybrids

  15. Molecular Simulation Studies of Covalently and Ionically Grafted Nanoparticles

    Science.gov (United States)

    Hong, Bingbing

    Solvent-free covalently- or ionically-grafted nanoparticles (CGNs and IGNs) are a new class of organic-inorganic hybrid composite materials exhibiting fluid-like behaviors around room temperature. With similar structures to prior systems, e.g. nanocomposites, neutral or charged colloids, ionic liquids, etc, CGNs and IGNs inherit the functionality of inorganic nanopariticles, the facile processibility of polymers, as well as conductivity and nonvolatility from their constituent materials. In spite of the extensive prior experimental research having covered synthesis and measurements of thermal and dynamic properties, little progress in understanding of these new materials at the molecular level has been achieved, because of the lack of simulation work in this new area. Atomistic and coarse-grained molecular dynamics simulations have been performed in this thesis to investigate the thermodynamics, structure, and dynamics of these systems and to seek predictive methods predictable for their properties. Starting from poly(ethylene oxide) oligomers (PEO) melts, we established atomistic models based on united-atom representations of methylene. The Green-Kubo and Einstein-Helfand formulas were used to calculate the transport properties. The simulations generate densities, viscosities, diffusivities, in good agreement with experimental data. The chain-length dependence of the transport properties suggests that neither Rouse nor reptation models are applicable in the short-chain regime investigated. Coupled with thermodynamic integration methods, the models give good predictions of pressure-composition-density relations for CO 2 + PEO oligomers. Water effects on the Henry's constant of CO 2 in PEO have also been investigated. The dependence of the calculated Henry's constants on the weight percentage of water falls on a temperature-dependent master curve, irrespective of PEO chain length. CGNs are modeled by the inclusion of solid-sphere nanoparticles into the atomistic

  16. Reliable prediction of adsorption isotherms via genetic algorithm molecular simulation.

    Science.gov (United States)

    LoftiKatooli, L; Shahsavand, A

    2017-01-01

    Conventional molecular simulation techniques such as grand canonical Monte Carlo (GCMC) strictly rely on purely random search inside the simulation box for predicting the adsorption isotherms. This blind search is usually extremely time demanding for providing a faithful approximation of the real isotherm and in some cases may lead to non-optimal solutions. A novel approach is presented in this article which does not use any of the classical steps of the standard GCMC method, such as displacement, insertation, and removal. The new approach is based on the well-known genetic algorithm to find the optimal configuration for adsorption of any adsorbate on a structured adsorbent under prevailing pressure and temperature. The proposed approach considers the molecular simulation problem as a global optimization challenge. A detailed flow chart of our so-called genetic algorithm molecular simulation (GAMS) method is presented, which is entirely different from traditions molecular simulation approaches. Three real case studies (for adsorption of CO 2 and H 2 over various zeolites) are borrowed from literature to clearly illustrate the superior performances of the proposed method over the standard GCMC technique. For the present method, the average absolute values of percentage errors are around 11% (RHO-H 2 ), 5% (CHA-CO 2 ), and 16% (BEA-CO 2 ), while they were about 70%, 15%, and 40% for the standard GCMC technique, respectively.

  17. Molecular Dynamics Simulations of displacement cascades in metallic systems

    International Nuclear Information System (INIS)

    Doan, N.V.; Tietze, H.

    1995-01-01

    We use Molecular Dynamics Computer Simulations to investigate defect production induced by energetic displacement cascades up to 10 keV in pure metals (Cu, Ni) and in ordered intermetallic alloys NiAl, Ni 3 Al. Various model potentials were employed to describe the many-body nature of the interactions: the RGL (Rosato-Guillope-Legrand) model was used in pure Cu and Ni simulations; the modified version of the Vitek, Ackland and Cserti potentials (due to Gao, Bacon and Ackland) in Ni 3 Al and the EAM potentials of Foiles and Daw modified by Rubini and Ballone in NiAl, Ni 3 Al were used in alloy simulations. Atomic mixing and disordering were studied into details owing to imaging techniques and determined at different phases of the cascades. Some mixing mechanisms were identified. Our results were compared with existing data and those obtained by similar Molecular Dynamics Simulations available in the literature. (orig.)

  18. Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Wedberg, Nils Hejle Rasmus Ingemar; O'Connell, John P.; Peters, Günther H.J.

    2010-01-01

    A method is proposed for obtaining thermodynamic properties via Kirkwood–Buff (KB) integrals from molecular simulations. In order to ensure that the KB integration converges, the pair distribution function is extrapolated to large distances using the extension method of Verlet, which enforces...... of state fitted to simulation results. Good agreement is achieved for both fluids at densities larger than 1.5 times the critical density....

  19. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

    International Nuclear Information System (INIS)

    Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

    2017-01-01

    Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

  20. Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes

    Science.gov (United States)

    Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten

    2017-11-01

    Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.

  1. Vision-Augmented Molecular Dynamics Simulation of Nanoindentation

    Directory of Open Access Journals (Sweden)

    Rajab Al-Sayegh

    2015-01-01

    Full Text Available We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

  2. Hybrid programming model for implicit PDE simulations on multicore architectures

    KAUST Repository

    Kaushik, Dinesh; Keyes, David E.; Balay, Satish; Smith, Barry F.

    2011-01-01

    The complexity of programming modern multicore processor based clusters is rapidly rising, with GPUs adding further demand for fine-grained parallelism. This paper analyzes the performance of the hybrid (MPI+OpenMP) programming model in the context of an implicit unstructured mesh CFD code. At the implementation level, the effects of cache locality, update management, work division, and synchronization frequency are studied. The hybrid model presents interesting algorithmic opportunities as well: the convergence of linear system solver is quicker than the pure MPI case since the parallel preconditioner stays stronger when hybrid model is used. This implies significant savings in the cost of communication and synchronization (explicit and implicit). Even though OpenMP based parallelism is easier to implement (with in a subdomain assigned to one MPI process for simplicity), getting good performance needs attention to data partitioning issues similar to those in the message-passing case. © 2011 Springer-Verlag.

  3. Gas-Transport-Property Performance of Hybrid Carbon Molecular Sieve−Polymer Materials

    KAUST Repository

    Das, Mita

    2010-10-06

    High-performance hybrid materials using carbon molecular sieve materials and 6FDA-6FpDA were produced. A detailed analysis of the effects of casting processes and the annealing temperature is reported. Two existing major obstacles, sieve agglomeration and residual stress, were addressed in this work, and subsequently a new membrane formation technique was developed to produce high-performing membranes. The successfully improved interfacial region of the hybrid membranes allows the sieves to increase the selectivity of the membranes above the neat polymer properties. Furthermore, an additional performance enhancement was seen with increased sieve loading in the hybrid membranes, leading to an actual performance above the upper bound for pure polymer membranes. The membranes were also tested under a mixed-gas environment, which further demonstrated promising results. © 2010 American Chemical Society.

  4. Ab initio molecular dynamics simulation of laser melting of silicon

    NARCIS (Netherlands)

    Silvestrelli, P.-L.; Alavi, A.; Parrinello, M.; Frenkel, D.

    1996-01-01

    The method of ab initio molecular dynamics, based on finite temperature density functional theory, is used to simulate laser heating of crystal silicon. We have found that a high concentration of excited electrons dramatically weakens the covalent bond. As a result, the system undergoes a melting

  5. Microsecond atomic-scale molecular dynamics simulations of polyimides

    NARCIS (Netherlands)

    Lyulin, S.V.; Gurtovenko, A.A.; Larin, S.V.; Nazarychev, V.M.; Lyulin, A.V.

    2013-01-01

    We employ microsecond atomic-scale molecular dynamics simulations to get insight into the structural and thermal properties of heat-resistant bulk polyimides. As electrostatic interactions are essential for the polyimides considered, we propose a two-step equilibration protocol that includes long

  6. Refrigeration Cycle Design for Refrigerant Mixtures by Molecular Simulation

    Czech Academy of Sciences Publication Activity Database

    Smith, W.R.; Francová, Magda; Kowalski, M.; Nezbeda, Ivo

    2010-01-01

    Roč. 75, č. 4 (2010), s. 383-391 ISSN 0010-0765 R&D Projects: GA AV ČR IAA400720710 Grant - others:NSERC(CA) OGP1041 Institutional research plan: CEZ:AV0Z40720504 Keywords : refrigerants * molecular simulation s * vapor–liquid equilibrium Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.853, year: 2010

  7. Thermodynamic Models from Fluctuation Solution Theory Analysis of 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 GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

  8. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  9. Energy conservation in molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren; Heilmann, Ole; Dyre, J. C.

    2012-01-01

    Classical Newtonian dynamics is analytic and the energy of an isolated system is conserved. The energy of such a system, obtained by the discrete “Verlet” algorithm commonly used in molecular dynamics simulations, fluctuates but is conserved in the mean. This is explained by the existence...

  10. Molecular dynamics simulations of lipid vesicle fusion in atomic detail

    NARCIS (Netherlands)

    Knecht, Volker; Marrink, Siewert-Jan

    The fusion of a membrane-bounded vesicle with a target membrane is a key step in intracellular trafficking, exocytosis, and drug delivery. Molecular dynamics simulations have been used to study the fusion of small unilamellar vesicles composed of a dipalmitoyl-phosphatidylcholine (DPPC)/palmitic

  11. Molecular Simulations of Halomethanes at the Air/Ice Interface

    Czech Academy of Sciences Publication Activity Database

    Habartová, Alena; Hormain, L.; Pluhařová, Eva; Briquez, S.; Monnerville, M.; Toubin, C.; Roeselová, Martina

    2015-01-01

    Roč. 119, č. 39 (2015), s. 10052-10059 ISSN 1089-5639 R&D Projects: GA ČR GA13-06181S Institutional support: RVO:61388963 Keywords : molecular dynamics simulations * water models * ice Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.883, year: 2015

  12. Molecular dynamics simulations on PGLa using NMR orientational constraints

    Energy Technology Data Exchange (ETDEWEB)

    Sternberg, Ulrich, E-mail: ulrich.sternberg@partner.kit.edu; Witter, Raiker [Tallinn University of Technology, Technomedicum (Estonia)

    2015-11-15

    NMR data obtained by solid state NMR from anisotropic samples are used as orientational constraints in molecular dynamics simulations for determining the structure and dynamics of the PGLa peptide within a membrane environment. For the simulation the recently developed molecular dynamics with orientational constraints technique (MDOC) is used. This method introduces orientation dependent pseudo-forces into the COSMOS-NMR force field. Acting during a molecular dynamics simulation these forces drive molecular rotations, re-orientations and folding in such a way that the motional time-averages of the tensorial NMR properties are consistent with the experimentally measured NMR parameters. This MDOC strategy does not depend on the initial choice of atomic coordinates, and is in principle suitable for any flexible and mobile kind of molecule; and it is of course possible to account for flexible parts of peptides or their side-chains. MDOC has been applied to the antimicrobial peptide PGLa and a related dimer model. With these simulations it was possible to reproduce most NMR parameters within the experimental error bounds. The alignment, conformation and order parameters of the membrane-bound molecule and its dimer were directly derived with MDOC from the NMR data. Furthermore, this new approach yielded for the first time the distribution of segmental orientations with respect to the membrane and the order parameter tensors of the dimer systems. It was demonstrated the deuterium splittings measured at the peptide to lipid ratio of 1/50 are consistent with a membrane spanning orientation of the peptide.

  13. Numerical Simulation of Transitional, Hypersonic Flows using a Hybrid Particle-Continuum Method

    Science.gov (United States)

    Verhoff, Ashley Marie

    Analysis of hypersonic flows requires consideration of multiscale phenomena due to the range of flight regimes encountered, from rarefied conditions in the upper atmosphere to fully continuum flow at low altitudes. At transitional Knudsen numbers there are likely to be localized regions of strong thermodynamic nonequilibrium effects that invalidate the continuum assumptions of the Navier-Stokes equations. Accurate simulation of these regions, which include shock waves, boundary and shear layers, and low-density wakes, requires a kinetic theory-based approach where no prior assumptions are made regarding the molecular distribution function. Because of the nature of these types of flows, there is much to be gained in terms of both numerical efficiency and physical accuracy by developing hybrid particle-continuum simulation approaches. The focus of the present research effort is the continued development of the Modular Particle-Continuum (MPC) method, where the Navier-Stokes equations are solved numerically using computational fluid dynamics (CFD) techniques in regions of the flow field where continuum assumptions are valid, and the direct simulation Monte Carlo (DSMC) method is used where strong thermodynamic nonequilibrium effects are present. Numerical solutions of transitional, hypersonic flows are thus obtained with increased physical accuracy relative to CFD alone, and improved numerical efficiency is achieved in comparison to DSMC alone because this more computationally expensive method is restricted to those regions of the flow field where it is necessary to maintain physical accuracy. In this dissertation, a comprehensive assessment of the physical accuracy of the MPC method is performed, leading to the implementation of a non-vacuum supersonic outflow boundary condition in particle domains, and more consistent initialization of DSMC simulator particles along hybrid interfaces. The relative errors between MPC and full DSMC results are greatly reduced as a

  14. Molecular dynamics simulations of oscillatory flows in microfluidic channels

    DEFF Research Database (Denmark)

    Hansen, J.S.; Ottesen, Johnny T.

    2006-01-01

    In this paper we apply the direct non-equilibrium molecular dynamics technique to oscillatory flows of fluids in microscopic channels. Initially, we show that the microscopic simulations resemble the macroscopic predictions based on the Navier–Stokes equation very well for large channel width, high...... density and low temperature. Further simulations for high temperature and low density show that the non-slip boundary condition traditionally used in the macroscopic equation is greatly compromised when the fluid–wall interactions are the same as the fluid–fluid interactions. Simulations of a system...

  15. Target Molecular Simulations of RecA Family Protein Filaments

    Directory of Open Access Journals (Sweden)

    Yeng-Tseng Wang

    2012-06-01

    Full Text Available Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88 such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87 and five zero rotary residues (I71, K74, E82, R83 and K88 in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism.

  16. Molecular-dynamics simulations of urea nucleation from aqueous solution.

    Science.gov (United States)

    Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

    2015-01-06

    Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete.

  17. Molecular-dynamics simulations of urea nucleation from aqueous solution

    Science.gov (United States)

    Salvalaglio, Matteo; Perego, Claudio; Giberti, Federico; Mazzotti, Marco; Parrinello, Michele

    2015-01-01

    Despite its ubiquitous character and relevance in many branches of science and engineering, nucleation from solution remains elusive. In this framework, molecular simulations represent a powerful tool to provide insight into nucleation at the molecular scale. In this work, we combine theory and molecular simulations to describe urea nucleation from aqueous solution. Taking advantage of well-tempered metadynamics, we compute the free-energy change associated to the phase transition. We find that such a free-energy profile is characterized by significant finite-size effects that can, however, be accounted for. The description of the nucleation process emerging from our analysis differs from classical nucleation theory. Nucleation of crystal-like clusters is in fact preceded by large concentration fluctuations, indicating a predominant two-step process, whereby embryonic crystal nuclei emerge from dense, disordered urea clusters. Furthermore, in the early stages of nucleation, two different polymorphs are seen to compete. PMID:25492932

  18. Analysis and simulation of the SLD WIC [Warm Iron Calorimeter] PADS hybrid preamplifier circuitry

    International Nuclear Information System (INIS)

    Fox, J.D.; Horelick, D.

    1990-10-01

    The SLD PADS electronics consist of over 9000 channels of charge-sensitive preamplifiers followed by integrated sample/hold data storage, digitizing, and readout circuitry. This paper uses computer simulation techniques to analyze critical performance parameters of the preamplifier hybrid including its interactions with the detector system. Simulation results are presented and verified with measured performance. 6 refs., 9 figs

  19. Comparative molecular modeling study of Arabidopsis NADPH-dependent thioredoxin reductase and its hybrid protein.

    Directory of Open Access Journals (Sweden)

    Yuno Lee

    Full Text Available 2-Cys peroxiredoxins (Prxs play important roles in the protection of chloroplast proteins from oxidative damage. Arabidopsis NADPH-dependent thioredoxin reductase isotype C (AtNTRC was identified as efficient electron donor for chloroplastic 2-Cys Prx-A. There are three isotypes (A, B, and C of thioredoxin reductase (TrxR in Arabidopsis. AtNTRA contains only TrxR domain, but AtNTRC consists of N-terminal TrxR and C-terminal thioredoxin (Trx domains. AtNTRC has various oligomer structures, and Trx domain is important for chaperone activity. Our previous experimental study has reported that the hybrid protein (AtNTRA-(Trx-D, which was a fusion of AtNTRA and Trx domain from AtNTRC, has formed variety of structures and shown strong chaperone activity. But, electron transfer mechanism was not detected at all. To find out the reason of this problem with structural basis, we performed two different molecular dynamics (MD simulations on AtNTRC and AtNTRA-(Trx-D proteins with same cofactors such as NADPH and flavin adenine dinucleotide (FAD for 50 ns. Structural difference has found from superimposition of two structures that were taken relatively close to average structure. The main reason that AtNTRA-(Trx-D cannot transfer the electron from TrxR domain to Trx domain is due to the difference of key catalytic residues in active site. The long distance between TrxR C153 and disulfide bond of Trx C387-C390 has been observed in AtNTRA-(Trx-D because of following reasons: i unstable and unfavorable interaction of the linker region, ii shifted Trx domain, and iii different or weak interface interaction of Trx domains. This study is one of the good examples for understanding the relationship between structure formation and reaction activity in hybrid protein. In addition, this study would be helpful for further study on the mechanism of electron transfer reaction in NADPH-dependent thioredoxin reductase proteins.

  20. Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

    International Nuclear Information System (INIS)

    Brown, W. Michael; Wang, Peng; Plimpton, Steven J.; Tharrington, Arnold N.

    2011-01-01

    The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - (1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory, (2) minimizing the amount of code that must be ported for efficient acceleration, (3) utilizing the available processing power from both many-core CPUs and accelerators, and (4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.

  1. Molecular packing in 1-hexanol-DMPC bilayers studied by molecular dynamics simulation

    DEFF Research Database (Denmark)

    Pedersen, U.R.; Peters, Günther H.j.; Westh, P.

    2007-01-01

    The structure and molecular packing density of a “mismatched” solute, 1-hexanol, in lipid membranes of dimyristoyl phosphatidylcholine (DMPC) was studied by molecular dynamics simulations. We found that the average location and orientation of the hexanol molecules matched earlier experimental data...... on comparable systems. The local density or molecular packing in DMPC–hexanol was elucidated through the average Voronoi volumes of all heavy (non-hydrogen) atoms. Analogous analysis was conducted on trajectories from simulations of pure 1-hexanol and pure (hydrated) DMPC bilayers. The results suggested...... of the alcohol upon partitioning and an even stronger loosening in the packing of the lipid. Furthermore, analysis of Voronoi volumes along the membrane normal identifies a distinctive depth dependence of the changes in molecular packing. The outer (interfacial) part of the lipid acyl chains (up to C8...

  2. Measurement bias of fluid velocity in molecular simulations

    International Nuclear Information System (INIS)

    Tysanner, Martin W.; Garcia, Alejandro L.

    2004-01-01

    In molecular simulations of fluid flow, the measurement of mean fluid velocity is considered to be a straightforward computation, yet there is some ambiguity in its definition. We show that in systems far from equilibrium, such as those with large temperature or velocity gradients, two commonly used definitions give slightly different results. Specifically, a bias can arise when computing the mean fluid velocity by measuring the mean particle velocity in a cell and averaging this mean over samples. We show that this bias comes from the correlation of momentum and density fluctuations in non-equilibrium fluids, obtain an analytical expression for predicting it, and discuss what system characteristics (e.g., number of particles per cell, temperature gradients) reduce or magnify the error. The bias has a physical origin so although we demonstrate it by direct simulation Monte Carlo (DSMC) computations, the same effect will be observed with other particle-based simulation methods, such as molecular dynamics and lattice gases

  3. 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...

  4. Using Whole Mount in situ Hybridization to Link Molecular and Organismal Biology

    OpenAIRE

    Jacobs, Nicole L.; Albertson, R. Craig; Wiles, Jason R.

    2011-01-01

    Whole mount in situ hybridization (WISH) is a common technique in molecular biology laboratories used to study gene expression through the localization of specific mRNA transcripts within whole mount specimen. This technique (adapted from Albertson and Yelick, 2005) was used in an upper level undergraduate Comparative Vertebrate Biology laboratory classroom at Syracuse University. The first two thirds of the Comparative Vertebrate Biology lab course gave students the opportunity to study the ...

  5. Molecular ferroelectric contributions to anomalous hysteresis in hybrid perovskite solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Frost, Jarvist M.; Butler, Keith T.; Walsh, Aron, E-mail: a.walsh@bath.ac.uk [Centre for Sustainable Chemical Technologies and Department of Chemistry, University of Bath, Claverton Down, Bath BA2 7AY (United Kingdom)

    2014-08-01

    We report a model describing the molecular orientation disorder in CH{sub 3}NH{sub 3}PbI{sub 3}, solving a classical Hamiltonian parametrised with electronic structure calculations, with the nature of the motions informed by ab initio molecular dynamics. We investigate the temperature and static electric field dependence of the equilibrium ferroelectric (molecular) domain structure and resulting polarisability. A rich domain structure of twinned molecular dipoles is observed, strongly varying as a function of temperature and applied electric field. We propose that the internal electrical fields associated with microscopic polarisation domains contribute to hysteretic anomalies in the current-voltage response of hybrid organic-inorganic perovskite solar cells due to variations in electron-hole recombination in the bulk.

  6. Hybrid High-Fidelity Modeling of Radar Scenarios Using Atemporal, Discrete-Event, and Time-Step Simulation

    Science.gov (United States)

    2016-12-01

    10 Figure 1.8 High-efficiency and high-fidelity radar system simulation flowchart . 15 Figure 1.9...Methodology roadmaps: experimental-design flowchart showing hybrid sensor models integrated from three simulation categories, followed by overall...simulation display and output produced by Java Simkit program . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89 Figure 4.5 Hybrid

  7. Prediction of industrial tomato hybrids from agronomic traits and ISSR molecular markers.

    Science.gov (United States)

    Figueiredo, A S T; Resende, J T V; Faria, M V; Da-Silva, P R; Fagundes, B S; Morales, R G F

    2016-05-13

    Heterosis is a highly relevant phenomenon in plant breeding. This condition is usually established in hybrids derived from crosses of highly divergent parents. The success of a breeder in obtaining heterosis is directly related to the correct identification of genetically contrasting parents. Currently, the diallel cross is the most commonly used methodology to detect contrasting parents; however, it is a time- and cost-consuming procedure. Therefore, new tools capable of performing this task quickly and accurately are required. Thus, the purpose of this study was to estimate the genetic divergence in industrial tomato lines, based on agronomic traits, and to compare with estimates obtained using inter-simple sequence repeat (ISSR) molecular markers. The genetic divergence among 10 industrial tomato lines, based on nine morphological characters and 12 ISSR primers was analyzed. For data analysis, Pearson and Spearman correlation coefficients were calculated between the genetic dissimilarity measures estimated by Mahalanobis distance and Jaccard's coefficient of genetic dissimilarity from the heterosis estimates, combining ability, and means of important traits of industrial tomato. The ISSR markers efficiently detected contrasting parents for hybrid production in tomato. Parent RVTD-08 was indicated as the most divergent, both by molecular and morphological markers, that positively contributed to increased heterosis and by the specific combining ability in the crosses in which it participated. The genetic dissimilarity estimated by ISSR molecular markers aided the identification of the best hybrids of the experiment in terms of total fruit yield, pulp yield, and soluble solids content.

  8. Pitfall in quantum mechanical/molecular mechanical molecular dynamics simulation of small solutes in solution.

    Science.gov (United States)

    Hu, Hao; Liu, Haiyan

    2013-05-30

    Developments in computing hardware and algorithms have made direct molecular dynamics simulation with the combined quantum mechanical/molecular mechanical methods affordable for small solute molecules in solution, in which much improved accuracy can be obtained via the quantum mechanical treatment of the solute molecule and even sometimes water molecules in the first solvation shell. However, unlike the conventional molecular mechanical simulations of large molecules, e.g., proteins, in solutions, special care must be taken in the technical details of the simulation, including the thermostat of the solute/solvent system, so that the conformational space of the solute molecules can be properly sampled. We show here that the common setup for classical molecular mechanical molecular dynamics simulations, such as the Berendsen or single Nose-Hoover thermostat, and/or rigid water models could lead to pathological sampling of the solutes' conformation. In the extreme example of a methanol molecule in aqueous solution, improper and sluggish setups could generate two peaks in the distribution of the O-H bond length. We discuss the factors responsible for this somewhat unexpected result and evoke a simple and ancient technical fix-up to resolve this problem.

  9. Uncovering molecular processes in crystal nucleation and growth by using molecular simulation.

    Science.gov (United States)

    Anwar, Jamshed; Zahn, Dirk

    2011-02-25

    Exploring nucleation processes by molecular simulation provides a mechanistic understanding at the atomic level and also enables kinetic and thermodynamic quantities to be estimated. However, whilst the potential for modeling crystal nucleation and growth processes is immense, there are specific technical challenges to modeling. In general, rare events, such as nucleation cannot be simulated using a direct "brute force" molecular dynamics approach. The limited time and length scales that are accessible by conventional molecular dynamics simulations have inspired a number of advances to tackle problems that were considered outside the scope of molecular simulation. While general insights and features could be explored from efficient generic models, new methods paved the way to realistic crystal nucleation scenarios. The association of single ions in solvent environments, the mechanisms of motif formation, ripening reactions, and the self-organization of nanocrystals can now be investigated at the molecular level. The analysis of interactions with growth-controlling additives gives a new understanding of functionalized nanocrystals and the precipitation of composite materials. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Characterization of Background Traffic in Hybrid Network Simulation

    National Research Council Canada - National Science Library

    Lauwens, Ben; Scheers, Bart; Van de Capelle, Antoine

    2006-01-01

    .... Two approaches are common: discrete event simulation and fluid approximation. A discrete event simulation generates a huge amount of events for a full-blown battlefield communication network resulting in a very long runtime...

  11. Small-scale multi-axial hybrid simulation of a shear-critical reinforced concrete frame

    Science.gov (United States)

    Sadeghian, Vahid; Kwon, Oh-Sung; Vecchio, Frank

    2017-10-01

    This study presents a numerical multi-scale simulation framework which is extended to accommodate hybrid simulation (numerical-experimental integration). The framework is enhanced with a standardized data exchange format and connected to a generalized controller interface program which facilitates communication with various types of laboratory equipment and testing configurations. A small-scale experimental program was conducted using a six degree-of-freedom hydraulic testing equipment to verify the proposed framework and provide additional data for small-scale testing of shearcritical reinforced concrete structures. The specimens were tested in a multi-axial hybrid simulation manner under a reversed cyclic loading condition simulating earthquake forces. The physical models were 1/3.23-scale representations of a beam and two columns. A mixed-type modelling technique was employed to analyze the remainder of the structures. The hybrid simulation results were compared against those obtained from a large-scale test and finite element analyses. The study found that if precautions are taken in preparing model materials and if the shear-related mechanisms are accurately considered in the numerical model, small-scale hybrid simulations can adequately simulate the behaviour of shear-critical structures. Although the findings of the study are promising, to draw general conclusions additional test data are required.

  12. Selection of a Planning Horizon for a Hybrid Microgrid Using Simulated Wind Forecasts

    Science.gov (United States)

    2014-12-01

    microgrid robustness and efficiency and may provide operators with real-time guidance and control policies for microgrid operation. ACKNOWLEDGMENTS The...A PLANNING HORIZON FOR A HYBRID MICROGRID USING SIMULATED WIND FORECASTS Mumtaz Karatas Turkish Naval Academy Tuzla, Istanbul, 34942, TURKEY Emily M...Craparo Dashi I. Singham Naval Postgraduate School 1411 Cunningham Road Monterey, CA, 93943 USA ABSTRACT Hybrid microgrids containing renewable energy

  13. Simulation based design strategy for EMC compliance of components in hybrid vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Maass, Uwe; Ndip, Ivan; Hoene, Eckard; Guttowski, Stephan [Fraunhofer-Institut fuer Zuverlaessigkeit und Mikrointegration (IZM), Berlin (Germany); Tschoban, Christian; Lang, Klaus-Dieter [Technische Univ. Berlin (Germany)

    2012-11-01

    The design of components for the power train of hybrid vehicles needs to take into account EMC compliance standards related to hazardous electromagnetic fields. Using a simulation based design strategy allows for virtual EMC tests in parallel to the mechanical / electrical power design and thus reduces (re-)design time and costs. Taking as an example a high-voltage battery for a hybrid vehicle the emitted magnetic fields outside the battery are examined. The simulation stategy is based on 3D EM simulations using a full-wave and an eddy current solver. The simulation models are based on the actual CAD data from the mechanical construction resulting in and a high geometrical aspect ratio. The impact of simulation specific aspects such as boundary conditions and excitation is given. It was found that using field simulations it is possible to identify noise sources and coupling paths as well as aid the construction of the battery. (orig.)

  14. An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays

    Directory of Open Access Journals (Sweden)

    Laurenzi Ian J

    2009-12-01

    Full Text Available Abstract Background Although oligonucleotide microarray technology is ubiquitous in genomic research, reproducibility and standardization of expression measurements still concern many researchers. Cross-hybridization between microarray probes and non-target ssDNA has been implicated as a primary factor in sensitivity and selectivity loss. Since hybridization is a chemical process, it may be modeled at a population-level using a combination of material balance equations and thermodynamics. However, the hybridization reaction network may be exceptionally large for commercial arrays, which often possess at least one reporter per transcript. Quantification of the kinetics and equilibrium of exceptionally large chemical systems of this type is numerically infeasible with customary approaches. Results In this paper, we present a robust and computationally efficient algorithm for the simulation of hybridization processes underlying microarray assays. Our method may be utilized to identify the extent to which nucleic acid targets (e.g. cDNA will cross-hybridize with probes, and by extension, characterize probe robustnessusing the information specified by MAGE-TAB. Using this algorithm, we characterize cross-hybridization in a modified commercial microarray assay. Conclusions By integrating stochastic simulation with thermodynamic prediction tools for DNA hybridization, one may robustly and rapidly characterize of the selectivity of a proposed microarray design at the probe and "system" levels. Our code is available at http://www.laurenzi.net.

  15. The effect of betaine on the foam stability: Molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Fengfeng [Chemistry Engineering Department, Zibo Vocational Institute, Zibo 255314 (China); Key laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100 (China); Liu, Guokui [Key laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100 (China); Yuan, Shiling, E-mail: shilingyuan@sdu.edu.cn [Key laboratory of Colloid and Interface Chemistry, Shandong University, Jinan 250100 (China)

    2017-06-15

    Highlights: • The reasons of betaine to enhance the stability of foam films are investigated by molecular simulation. • An electrostatic structure is formed at the air/water interface due to the electrostatic interaction. • The electrostatic structure becomes denser with the increasing concentration of betaine. - Abstract: Zwitterionic betaines are widely used as foam boosters due to these can enhance the stability of foam films. In this paper, mechanistic insights of betaine to improve the stability of alkyl-polyoxyethylene carboxylate (AEC) foam are provided by molecular simulation. In the simulation, we observe the electropositive nitrogen atoms in betaine interact with the electronegative sulfur atoms, an electrostatic structure is formed at the air/water interface. Interaction energies of the mixed surfactants are calculated by the quantum chemistry methods. The calculations show betaine-AEC and betaine–betaine possess attractive interaction, and that AEC–AEC has repulsion to each other. In the other words, the repulsion between the headgroups of anionic surfactants is relaxed by betaine. Additionally, the influence of concentration of betaine on the stability of foam films is also simulated. The RDF and coordination numbers show that the electrostatic structures become denser with the increasing concentration of betaine. Therefore, entry barrier is enhanced accordingly. The SMD simulation also demonstrates the same variation tendency of entry barrier. The simulation details provide vital supplements to experiments.

  16. On eliminating synchronous communication in molecular simulations to improve scalability

    Science.gov (United States)

    Straatsma, T. P.; Chavarría-Miranda, Daniel G.

    2013-12-01

    Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular systems as it provides access to properties that are difficult, impossible or prohibitively expensive to obtain experimentally. Many of the available software packages have been parallelized to take advantage of modern massively concurrent processing resources. The challenge in achieving parallel efficiency is commonly attributed to the fact that molecular dynamics algorithms are communication intensive. This paper illustrates how an appropriately chosen data distribution and asynchronous one-sided communication approach can be used to effectively deal with the data movement within the Global Arrays/ARMCI programming model framework. A new put_notify capability is presented here, allowing the implementation of the molecular dynamics algorithm without any explicit global or local synchronization or global data reduction operations. In addition, this push-data model is shown to very effectively allow hiding data communication behind computation. Rather than data movement or explicit global reductions, the implicit synchronization of the algorithm becomes the primary challenge for scalability. Without any explicit synchronous operations, the scalability of molecular simulations is shown to depend only on the ability to evenly balance computational load.

  17. Lattice dynamics and molecular dynamics simulation of complex materials

    International Nuclear Information System (INIS)

    Chaplot, S.L.

    1997-01-01

    In this article we briefly review the lattice dynamics and molecular dynamics simulation techniques, as used for complex ionic and molecular solids, and demonstrate a number of applications through examples of our work. These computational studies, along with experiments, have provided microscopic insight into the structure and dynamics, phase transitions and thermodynamical properties of a variety of materials including fullerene, high temperature superconducting oxides and geological minerals as a function of pressure and temperature. The computational techniques also allow the study of the structures and dynamics associated with disorder, defects, surfaces, interfaces etc. (author)

  18. MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  19. Molecular Dynamics Computer Simulations of Multidrug RND Efflux Pumps

    Directory of Open Access Journals (Sweden)

    Paolo Ruggerone

    2013-02-01

    Full Text Available Over-expression of multidrug efflux pumps of the Resistance Nodulation Division (RND protein super family counts among the main causes for microbial resistance against pharmaceuticals. Understanding the molecular basis of this process is one of the major challenges of modern biomedical research, involving a broad range of experimental and computational techniques. Here we review the current state of RND transporter investigation employing molecular dynamics simulations providing conformational samples of transporter components to obtain insights into the functional mechanism underlying efflux pump-mediated antibiotics resistance in Escherichia coli and Pseudomonas aeruginosa.

  20. Polymorphic phase transitions: Macroscopic theory and molecular simulation.

    Science.gov (United States)

    Anwar, Jamshed; Zahn, Dirk

    2017-08-01

    Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic

  1. A hybrid parallel architecture for electrostatic interactions in the simulation of dissipative particle dynamics

    Science.gov (United States)

    Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping

    2017-11-01

    In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space

  2. Strategy and gaps for modeling, simulation, and control of hybrid systems

    Energy Technology Data Exchange (ETDEWEB)

    Rabiti, Cristian [Idaho National Lab. (INL), Idaho Falls, ID (United States); Garcia, Humberto E. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Hovsapian, Rob [Idaho National Lab. (INL), Idaho Falls, ID (United States); Kinoshita, Robert [Idaho National Lab. (INL), Idaho Falls, ID (United States); Mesina, George L. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Bragg-Sitton, Shannon M. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Boardman, Richard D. [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-04-01

    The purpose of this report is to establish a strategy for modeling and simulation of candidate hybrid energy systems. Modeling and simulation is necessary to design, evaluate, and optimize the system technical and economic performance. Accordingly, this report first establishes the simulation requirements to analysis candidate hybrid systems. Simulation fidelity levels are established based on the temporal scale, real and synthetic data availability or needs, solution accuracy, and output parameters needed to evaluate case-specific figures of merit. Accordingly, the associated computational and co-simulation resources needed are established; including physical models when needed, code assembly and integrated solutions platforms, mathematical solvers, and data processing. This report first attempts to describe the figures of merit, systems requirements, and constraints that are necessary and sufficient to characterize the grid and hybrid systems behavior and market interactions. Loss of Load Probability (LOLP) and effective cost of Effective Cost of Energy (ECE), as opposed to the standard Levelized Cost of Electricty (LCOE), are introduced as technical and economical indices for integrated energy system evaluations. Financial assessment methods are subsequently introduced for evaluation of non-traditional, hybrid energy systems. Algorithms for coupled and iterative evaluation of the technical and economic performance are subsequently discussed. This report further defines modeling objectives, computational tools, solution approaches, and real-time data collection and processing (in some cases using real test units) that will be required to model, co-simulate, and optimize; (a) an energy system components (e.g., power generation unit, chemical process, electricity management unit), (b) system domains (e.g., thermal, electrical or chemical energy generation, conversion, and transport), and (c) systems control modules. Co-simulation of complex, tightly coupled

  3. Hybrid statistics-simulations based method for atom-counting from ADF STEM images

    Energy Technology Data Exchange (ETDEWEB)

    De wael, Annelies, E-mail: annelies.dewael@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); De Backer, Annick [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium); Jones, Lewys; Nellist, Peter D. [Department of Materials, University of Oxford, Parks Road, OX1 3PH Oxford (United Kingdom); Van Aert, Sandra, E-mail: sandra.vanaert@uantwerpen.be [Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp (Belgium)

    2017-06-15

    A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. - Highlights: • A hybrid method for atom-counting from ADF STEM images is introduced. • Image simulations are incorporated into a statistical framework in a reliable manner. • Limits of the existing methods for atom-counting are far exceeded. • Reliable counting results from an experimental low dose image are obtained. • Progress towards reliable quantitative analysis of beam-sensitive materials is made.

  4. 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

  5. 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.

  6. 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)

  7. Software-in-the-loop simulation of a quadcopter portion for hybrid aircraft control

    Science.gov (United States)

    Mansoor, Shoaib; Saedan, Mana

    2018-01-01

    In this paper, we present the design of the software-in-the-loop simulation framework for a quadcopter that is incorporated in our hybrid aircraft. The hybrid aircraft comprises a quad-copter and a fixed wing with one forward thrust rotor. We need to develop a split control system that utilizes a typical quadcopter controller to control four motors/propellers and a supervisor controller to control a forward thrust rotor. The supervisor controller shall take feedback signals from the quadcopter and will command the fifth rotor for stabilizing the hybrid aircraft and resolves problems like thrust saturation. The simulation simulates the control algorithm and verifies the quadcopter’s behavior using MATLAB and Simulink together. Achieving these results, we come to know how our hybrid controller will be implemented, what results to expect once the forward thrust rotor is attached to the quadcopter. The software-in-the-loop simulation of a quadcopter is one of the most effective methods for verifying overall control performance and safety of the hybrid aircraft before actual hardware implementation and flight test.

  8. Hybrid Materials Based on Magnetic Layered Double Hydroxides: A Molecular Perspective.

    Science.gov (United States)

    Abellán, Gonzalo; Martí-Gastaldo, Carlos; Ribera, Antonio; Coronado, Eugenio

    2015-06-16

    Design of functional hybrids lies at the very core of synthetic chemistry as it has enabled the development of an unlimited number of solids displaying unprecedented or even improved properties built upon the association at the molecular level of quite disparate components by chemical design. Multifunctional hybrids are a particularly appealing case among hybrid organic/inorganic materials. Here, chemical knowledge is used to deploy molecular components bearing different functionalities within a single solid so that these properties can coexist or event interact leading to unprecedented phenomena. From a molecular perspective, this can be done either by controlled assembly of organic/inorganic molecular tectons into an extended architecture of hybrid nature or by intercalation of organic moieties within the empty channels or interlamellar space offered by inorganic solids with three-dimensional (MOFs, zeolites, and mesoporous hosts) or layered structures (phosphates, silicates, metal dichalcogenides, or anionic clays). This Account specifically illustrates the use of layered double hydroxides (LDHs) in the preparation of magnetic hybrids, in line with the development of soft inorganic chemistry processes (also called "Chimie Douce"), which has significantly contributed to boost the preparation hybrid materials based on solid-state hosts and subsequent development of applications. Several features sustain the importance of LDHs in this context. Their magnetism can be manipulated at a molecular level by adequate choice of constituting metals and interlayer separation for tuning the nature and extent of magnetic interactions across and between planes. They display unparalleled versatility in accommodating a broad range of anionic species in their interlamellar space that encompasses not only simple anions but chemical systems of increasing dimensionality and functionalities. Their swelling characteristics allow for their exfoliation in organic solvents with high

  9. Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

    Science.gov (United States)

    Shen, Lin; Wu, Jingheng; Yang, Weitao

    2016-10-11

    Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

  10. The molecular dynamics simulation of ion-induced ripple growth

    International Nuclear Information System (INIS)

    Suele, P.; Heinig, K.-H.

    2009-01-01

    The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength (λ) regime BH theory fails to reproduce the results obtained by molecular dynamics. We find that at short wavelengths (λ 35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in λ long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for λ>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.

  11. Molecular simulations in electrochemistry : Electron and proton transfer reactions mediated by flavins in different molecular environments

    NARCIS (Netherlands)

    Kılıç, M.

    2014-01-01

    The aim of this thesis is to address specific questions about the role of solvent reorganization on electron transfer in different environments and about the calculation of acidity constant, as well. Particularly, we focus on molecular simulation of flavin in water and different protein (BLUF and

  12. 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

  13. Coalescence of silver unidimensional structures by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Perez A, M.; Gutierrez W, C.E.; Mondragon, G.; Arenas, J.

    2007-01-01

    The study of nanoparticles coalescence and silver nano rods phenomena by means of molecular dynamics simulation under the thermodynamic laws is reported. In this work we focus ourselves to see the conditions under which the one can be given one dimension growth of silver nano rods for the coalescence phenomenon among two nano rods or one nano rod and one particle; what allows us to study those structural, dynamic and morphological properties of the silver nano rods to different thermodynamic conditions. The simulations are carried out using the Sutton-Chen potentials of interaction of many bodies that allow to obtain appropriate results with the real physical systems. (Author)

  14. Molecular Dynamics Simulation Studies of Caffeine Aggregation in Aqueous Solution

    OpenAIRE

    Tavagnacco, Letizia; Schnupf, Udo; Mason, Philip E.; Saboungi, Marie-Louise; Cesàro, Attilio; Brady, John W.

    2011-01-01

    Molecular dynamics simulations were carried out on a system of eight independent caffeine molecules in a periodic box of water at 300 K, representing a solution near the solubility limit for caffeine at room temperature, using a newly-developed CHARMM-type force field for caffeine in water. Simulations were also conducted for single caffeine molecules in water using two different water models (TIP3P and TIP4P). Water was found to structure in a complex fashion around the planar caffeine molec...

  15. Total Correlation Function Integrals and Isothermal Compressibilities from Molecular Simulations

    DEFF Research Database (Denmark)

    Wedberg, Rasmus; Peters, Günther H.j.; Abildskov, Jens

    2008-01-01

    Generation of thermodynamic data, here compressed liquid density and isothermal compressibility data, using molecular dynamics simulations is investigated. Five normal alkane systems are simulated at three different state points. We compare two main approaches to isothermal compressibilities: (1...... in approximately the same amount of time. This suggests that computation of total correlation function integrals is a route to isothermal compressibility, as accurate and fast as well-established benchmark techniques. A crucial step is the integration of the radial distribution function. To obtain sensible results...

  16. Molecular Models for DSMC Simulations of Metal Vapor Deposition

    OpenAIRE

    Venkattraman, A; Alexeenko, Alina A

    2010-01-01

    The direct simulation Monte Carlo (DSMC) method is applied here to model the electron‐beam (e‐beam) physical vapor deposition of copper thin films. A suitable molecular model for copper‐copper interactions have been determined based on comparisons with experiments for a 2D slit source. The model for atomic copper vapor is then used in axi‐symmetric DSMC simulations for analysis of a typical e‐beam metal deposition system with a cup crucible. The dimensional and non‐dimensional mass fluxes obt...

  17. Bio-inspired algorithms applied to molecular docking simulations.

    Science.gov (United States)

    Heberlé, G; de Azevedo, W F

    2011-01-01

    Nature as a source of inspiration has been shown to have a great beneficial impact on the development of new computational methodologies. In this scenario, analyses of the interactions between a protein target and a ligand can be simulated by biologically inspired algorithms (BIAs). These algorithms mimic biological systems to create new paradigms for computation, such as neural networks, evolutionary computing, and swarm intelligence. This review provides a description of the main concepts behind BIAs applied to molecular docking simulations. Special attention is devoted to evolutionary algorithms, guided-directed evolutionary algorithms, and Lamarckian genetic algorithms. Recent applications of these methodologies to protein targets identified in the Mycobacterium tuberculosis genome are described.

  18. 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).

  19. Atomistic Molecular Dynamics Simulations of Mitochondrial DNA Polymerase γ

    DEFF Research Database (Denmark)

    Euro, Liliya; Haapanen, Outi; Róg, Tomasz

    2017-01-01

    of replisomal interactions, and functional effects of patient mutations that do not affect direct catalysis have remained elusive. Here we report the first atomistic classical molecular dynamics simulations of the human Pol γ replicative complex. Our simulation data show that DNA binding triggers remarkable......DNA polymerase γ (Pol γ) is a key component of the mitochondrial DNA replisome and an important cause of neurological diseases. Despite the availability of its crystal structures, the molecular mechanism of DNA replication, the switch between polymerase and exonuclease activities, the site...... changes in the enzyme structure, including (1) completion of the DNA-binding channel via a dynamic subdomain, which in the apo form blocks the catalytic site, (2) stabilization of the structure through the distal accessory β-subunit, and (3) formation of a putative transient replisome-binding platform...

  20. Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Junfang [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia); Rivero, Mayela [CSIRO Petroleum, PO Box 1130, Bentley, Western Australia, 6102 (Australia); Choi, S K [CSIRO Petroleum Resources, Ian Wark Laboratory, Bayview Avenue, Clayton, Victoria 3168 (Australia)

    2007-02-14

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

  1. Global Hybrid Simulations of Energetic Particle-driven Modes in Toroidal Plasmas

    International Nuclear Information System (INIS)

    Fu, G.Y.; Breslau, J.; Fredrickson, E.; Park, W.; Strauss, H.R.

    2004-01-01

    Global hybrid simulations of energetic particle-driven MHD modes have been carried out for tokamaks and spherical tokamaks using the hybrid code M3D. The numerical results for the National Spherical Tokamak Experiments (NSTX) show that Toroidal Alfven Eigenmodes are excited by beam ions with their frequencies consistent with the experimental observations. Nonlinear simulations indicate that the n=2 mode frequency chirps down as the mode moves out radially. For ITER, it is shown that the alpha-particle effects are strongly stabilizing for internal kink mode when central safety factor q(0) is sufficiently close to unity. However, the elongation of ITER plasma shape reduces the stabilization significantly

  2. Hybrid vortex simulations of wind turbines using a three-dimensional viscous-inviscid panel method

    DEFF Research Database (Denmark)

    Ramos García, Néstor; Hejlesen, Mads Mølholm; Sørensen, Jens Nørkær

    2017-01-01

    adirect calculation, whereas the contribution from the large downstream wake is calculated using a mesh-based method. Thehybrid method is first validated in detail against the well-known MEXICO experiment, using the direct filament method asa comparison. The second part of the validation includes a study......A hybrid filament-mesh vortex method is proposed and validated to predict the aerodynamic performance of wind turbinerotors and to simulate the resulting wake. Its novelty consists of using a hybrid method to accurately simulate the wakedownstream of the wind turbine while reducing...

  3. Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

    Science.gov (United States)

    Guerrero, Carlo L.; Perlado, Jose M.

    2016-03-01

    In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

  4. Simulational nanoengineering: Molecular dynamics implementation of an atomistic Stirling engine.

    Science.gov (United States)

    Rapaport, D C

    2009-04-01

    A nanoscale-sized Stirling engine with an atomistic working fluid has been modeled using molecular dynamics simulation. The design includes heat exchangers based on thermostats, pistons attached to a flywheel under load, and a regenerator. Key aspects of the behavior, including the time-dependent flows, are described. The model is shown to be capable of stable operation while producing net work at a moderate level of efficiency.

  5. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    Energy Technology Data Exchange (ETDEWEB)

    Swygenhoven, H. van [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Caro, A. [Comision Nacional de Energia Atomica, San Carlos de Bariloche (Argentina). Centro Atomico Bariloche

    1997-09-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young`s modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs.

  6. Molecular Dynamics Simulations of Tensile Behavior of Copper

    OpenAIRE

    Sainath, G.; Srinivasan, V. S.; Choudhary, B. K.; Mathew, M. D.; Jayakumar, T.

    2014-01-01

    Molecular dynamics simulations on tensile deformation of initially defect free single crystal copper nanowire oriented in {100} has been carried out at 10 K under adiabatic and isothermal loading conditions. The tensile behaviour was characterized by sharp rise in stress in elastic regime followed by sudden drop at the point of dislocation nucleation. The important finding is that the variation in dislocation density is correlated with the observed stress-strain response. Several interesting ...

  7. Geometry optimization of zirconium sulfophenylphosphonate layers by molecular simulation methods

    Czech Academy of Sciences Publication Activity Database

    Škoda, J.; Pospíšil, M.; Kovář, P.; Melánová, Klára; Svoboda, J.; Beneš, L.; Zima, Vítězslav

    2018-01-01

    Roč. 24, č. 1 (2018), s. 1-12, č. článku 10. ISSN 1610-2940 R&D Projects: GA ČR(CZ) GA14-13368S; GA ČR(CZ) GA17-10639S Institutional support: RVO:61389013 Keywords : zirconium sulfophenylphosphonate * intercalation * molecular simulation Subject RIV: CA - Inorganic Chemistry OBOR OECD: Inorganic and nuclear chemistry Impact factor: 1.425, year: 2016

  8. Machine learning molecular dynamics for the simulation of infrared spectra.

    Science.gov (United States)

    Gastegger, Michael; Behler, Jörg; Marquetand, Philipp

    2017-10-01

    Machine learning has emerged as an invaluable tool in many research areas. In the present work, we harness this power to predict highly accurate molecular infrared spectra with unprecedented computational efficiency. To account for vibrational anharmonic and dynamical effects - typically neglected by conventional quantum chemistry approaches - we base our machine learning strategy on ab initio molecular dynamics simulations. While these simulations are usually extremely time consuming even for small molecules, we overcome these limitations by leveraging the power of a variety of machine learning techniques, not only accelerating simulations by several orders of magnitude, but also greatly extending the size of systems that can be treated. To this end, we develop a molecular dipole moment model based on environment dependent neural network charges and combine it with the neural network potential approach of Behler and Parrinello. Contrary to the prevalent big data philosophy, we are able to obtain very accurate machine learning models for the prediction of infrared spectra based on only a few hundreds of electronic structure reference points. This is made possible through the use of molecular forces during neural network potential training and the introduction of a fully automated sampling scheme. We demonstrate the power of our machine learning approach by applying it to model the infrared spectra of a methanol molecule, n -alkanes containing up to 200 atoms and the protonated alanine tripeptide, which at the same time represents the first application of machine learning techniques to simulate the dynamics of a peptide. In all of these case studies we find an excellent agreement between the infrared spectra predicted via machine learning models and the respective theoretical and experimental spectra.

  9. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane

    OpenAIRE

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-01-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present new results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition...

  10. Molecular dynamics simulation of nanocrystalline nickel: structure and mechanical properties

    International Nuclear Information System (INIS)

    Swygenhoven, H. van; Caro, A.

    1997-01-01

    Molecular dynamics computer simulations of low temperature elastic and plastic deformation of Ni nanophase samples (3-7 nm) are performed. The samples are polycrystals nucleated from different seeds, with random locations and orientations. Bulk and Young's modulus, onset of plastic deformation and mechanism responsible for the plastic behaviour are studied and compared with the behaviour of coarse grained samples. (author) 1 fig., 3 refs

  11. Molecular dynamics simulation of cascade damage in gold

    International Nuclear Information System (INIS)

    Alonso, E.; Caturla, M.J.; Tang, M.; Huang, H.; Diaz de la Rubia, T.

    1997-01-01

    High-energy cascades have been simulated in gold using molecular dynamics with a modified embedded atom method potential. The results show that both vacancy and interstitial clusters form with high probability as a result of intracascade processes. The formation of clusters has been interpreted in terms of the high pressures generated in the core of the cascade during the early stages. The authors provide evidence that correlation between interstitial and vacancy clustering exists

  12. Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Kandel, Saugat; Salomon-Ferrer, Romelia; Larsen, Adrien B.; Vaidehi, Nagarajan, E-mail: nvaidehi@coh.org [Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, California 91010 (United States); Jain, Abhinandan, E-mail: Abhi.Jain@jpl.nasa.gov [Jet Propulsion Laboratory, California Institute of Technology, 4800 Oak Grove Drive, Pasadena, California 91109 (United States)

    2016-01-28

    The Internal Coordinate Molecular Dynamics (ICMD) method is an attractive molecular dynamics (MD) method for studying the dynamics of bonded systems such as proteins and polymers. It offers a simple venue for coarsening the dynamics model of a system at multiple hierarchical levels. For example, large scale protein dynamics can be studied using torsional dynamics, where large domains or helical structures can be treated as rigid bodies and the loops connecting them as flexible torsions. ICMD with such a dynamic model of the protein, combined with enhanced conformational sampling method such as temperature replica exchange, allows the sampling of large scale domain motion involving high energy barrier transitions. Once these large scale conformational transitions are sampled, all-torsion, or even all-atom, MD simulations can be carried out for the low energy conformations sampled via coarse grained ICMD to calculate the energetics of distinct conformations. Such hierarchical MD simulations can be carried out with standard all-atom forcefields without the need for compromising on the accuracy of the forces. Using constraints to treat bond lengths and bond angles as rigid can, however, distort the potential energy landscape of the system and reduce the number of dihedral transitions as well as conformational sampling. We present here a two-part solution to overcome such distortions of the potential energy landscape with ICMD models. To alleviate the intrinsic distortion that stems from the reduced phase space in torsional MD, we use the Fixman compensating potential. To additionally alleviate the extrinsic distortion that arises from the coupling between the dihedral angles and bond angles within a force field, we propose a hybrid ICMD method that allows the selective relaxing of bond angles. This hybrid ICMD method bridges the gap between all-atom MD and torsional MD. We demonstrate with examples that these methods together offer a solution to eliminate the potential

  13. A New Sythetic Hybrid (A1D5 between Gossypium herbaceum and G. raimondii and Its Morphological, Cytogenetic, Molecular Characterization.

    Directory of Open Access Journals (Sweden)

    Yuxiang Wu

    Full Text Available The diploid species G. herbaceum (A1 and G. raimondii (D5 are the progenitors of allotetraploid cotton, respectively. However, hybrids between G. herbaceum and G. raimondii haven't been reported. In the present study, hybridization between G. herbaceum and G. raimondii was explored. Morphological, cytogenetic and molecular analyses were used to assess the hybridity. The interspecific hybrid plants were successfully obtained. Most of the morphological characteristics of the hybrids were intermediate between G. herbaceum and G. raimondii. However, the color of glands, anther cases, pollen and corolla, and the state of bracteoles in hybrids were associated with the G. herbaceum. The color of staminal columns and filaments in hybrids were associated with G. raimondii. Cytogenetic analysis confirmed abnormal meiotic behavior existed in hybrids. The hybrids couldn't produce boll-set. Simple sequence repeat results found that besides the fragments inherited from the two parents, some novel bands were amplified in hybrids, indicating that potential mutations and chromosomal recombination occurred between parental genomes during hybridization. These results may provide some novel insights in speciation, genome interaction, and evolution of the tetraploid cotton species.

  14. Synthesis, Biological Evaluation, and Molecular Modeling Studies of New Oxadiazole-Stilbene Hybrids against Phytopathogenic Fungi

    Science.gov (United States)

    Jian, Weilin; He, Daohang; Song, Shaoyun

    2016-08-01

    Natural stilbenes (especially resveratrol) play important roles in plant protection by acting as both constitutive and inducible defenses. However, their exogenous applications on crops as fungicidal agents are challenged by their oxidative degradation and limited availability. In this study, a new class of resveratrol-inspired oxadiazole-stilbene hybrids was synthesized via Wittig-Horner reaction. Bioassay results indicated that some of the compounds exhibited potent fungicidal activity against Botrytis cinerea in vitro. Among these stilbene hybrids, compounds 11 showed promising inhibitory activity with the EC50 value of 144.6 μg/mL, which was superior to that of resveratrol (315.6 μg/mL). Remarkably, the considerably abnormal mycelial morphology was observed in the presence of compound 11. The inhibitory profile was further proposed by homology modeling and molecular docking studies, which showed the possible interaction of resveratrol and oxadiazole-stilbene hybrids with the cytochrome P450-dependent sterol 14α-demethylase from B. cinerea (BcCYP51) for the first time. Taken together, these results would provide new insights into the fungicidal mechanism of stilbenes, as well as an important clue for biology-oriented synthesis of stilbene hybrids with improved bioactivity against plant pathogenic fungi in crop protection.

  15. Workable male sterility systems for hybrid rice: Genetics, biochemistry, molecular biology, and utilization.

    Science.gov (United States)

    Huang, Jian-Zhong; E, Zhi-Guo; Zhang, Hua-Li; Shu, Qing-Yao

    2014-12-01

    The exploitation of male sterility systems has enabled the commercialization of heterosis in rice, with greatly increased yield and total production of this major staple food crop. Hybrid rice, which was adopted in the 1970s, now covers nearly 13.6 million hectares each year in China alone. Various types of cytoplasmic male sterility (CMS) and environment-conditioned genic male sterility (EGMS) systems have been applied in hybrid rice production. In this paper, recent advances in genetics, biochemistry, and molecular biology are reviewed with an emphasis on major male sterility systems in rice: five CMS systems, i.e., BT-, HL-, WA-, LD- and CW- CMS, and two EGMS systems, i.e., photoperiod- and temperature-sensitive genic male sterility (P/TGMS). The interaction of chimeric mitochondrial genes with nuclear genes causes CMS, which may be restored by restorer of fertility (Rf) genes. The PGMS, on the other hand, is conditioned by a non-coding RNA gene. A survey of the various CMS and EGMS lines used in hybrid rice production over the past three decades shows that the two-line system utilizing EGMS lines is playing a steadily larger role and TGMS lines predominate the current two-line system for hybrid rice production. The findings and experience gained during development and application of, and research on male sterility in rice not only advanced our understanding but also shed light on applications to other crops.

  16. Molecular dynamics simulation of carbon molecular sieve preparation for air separation

    International Nuclear Information System (INIS)

    Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh; Shariaty-Niassar, Mojtaba

    2015-01-01

    Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments

  17. Molecular dynamics simulation of carbon molecular sieve preparation for air separation

    Energy Technology Data Exchange (ETDEWEB)

    Yaghoobpour, Elham; Ahmadpour, Ali; Farhadian, Nafiseh [Ferdowsi University of Mashhad, Mashhad (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba [University of Tehran, Tehran(Iran, Islamic Republic of)

    2015-03-15

    Carbon deposition process on activated carbon (AC) in order to produce carbon molecular sieve (CMS) was simulated using molecular dynamics simulation. The proposed activated carbon for simulation includes micropores with different characteristic diameters and lengths. Three different temperatures of 773 K, 973 K, and 1,273 K were selected to investigate the optimum deposition temperature. Simulation results show that the carbon deposition process at 973 K creates the best adsorbent structure. While at lower temperature some micropore openings are blocked with carbon atoms, at higher temperature the number of deposited carbons on the micropores does not change significantly. Also, carbon deposition process confirms the pseudo-second-order kinetic model with an endothermic behavior. To evaluate the sieving property of adsorbent products, nitrogen and oxygen adsorption on the initial and final adsorbent products are examined. Results show that there is not any considerable difference between the equilibrium adsorption amounts of nitrogen and oxygen on the initial and final adsorbents especially at low pressure (P<10 atm). Although, adsorption kinetics curves of these gases change significantly after the carbon deposition process in comparison with the initial sample. These observations indicate that the final adsorbent has high selectivity towards oxygen compared with the nitrogen, so it can be called a carbon molecular sieve. All simulated results are in good agreement with experiments.

  18. Evaluation of uranium dioxide thermal conductivity using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kim, Woongkee; Kaviany, Massoud; Shim, J. H.

    2014-01-01

    It can be extended to larger space, time scale and even real reactor situation with fission product as multi-scale formalism. Uranium dioxide is a fluorite structure with Fm3m space group. Since it is insulator, dominant heat carrier is phonon, rather than electrons. So, using equilibrium molecular dynamics (MD) simulation, we present the appropriate calculation parameters in MD simulation by calculating thermal conductivity and application of it to the thermal conductivity of polycrystal. In this work, we investigate thermal conductivity of uranium dioxide and optimize the parameters related to its process. In this process, called Green Kubo formula, there are two parameters i.e correlation length and sampling interval, which effect on ensemble integration in order to obtain thermal conductivity. Through several comparisons, long correlation length and short sampling interval give better results. Using this strategy, thermal conductivity of poly crystal is obtained and comparison with that of pure crystal is made. Thermal conductivity of poly crystal show lower value that that of pure crystal. In further study, we broaden the study to transport coefficient of radiation damaged structures using molecular dynamics. Although molecular dynamics is tools for treating microscopic scale, most macroscopic issues related to nuclear materials such as voids in fuel materials and weakened mechanical properties by radiation are based on microscopic basis. Thus, research on microscopic scale would be expanded in this field and many hidden mechanism in atomic scales will be revealed via both atomic scale simulations and experiments

  19. From cellulose to kerogen: molecular simulation of a geological process.

    Science.gov (United States)

    Atmani, Lea; Bichara, Christophe; Pellenq, Roland J-M; Van Damme, Henri; van Duin, Adri C T; Raza, Zamaan; Truflandier, Lionel A; Obliger, Amaël; Kralert, Paul G; Ulm, Franz J; Leyssale, Jean-Marc

    2017-12-01

    The process by which organic matter decomposes deep underground to form petroleum and its underlying kerogen matrix has so far remained a no man's land to theoreticians, largely because of the geological (Myears) timescale associated with the process. Using reactive molecular dynamics and an accelerated simulation framework, the replica exchange molecular dynamics method, we simulate the full transformation of cellulose into kerogen and its associated fluid phase under prevailing geological conditions. We observe in sequence the fragmentation of the cellulose crystal and production of water, the development of an unsaturated aliphatic macromolecular phase and its aromatization. The composition of the solid residue along the maturation pathway strictly follows what is observed for natural type III kerogen and for artificially matured samples under confined conditions. After expulsion of the fluid phase, the obtained microporous kerogen possesses the structure, texture, density, porosity and stiffness observed for mature type III kerogen and a microporous carbon obtained by saccharose pyrolysis at low temperature. As expected for this variety of precursor, the main resulting hydrocarbon is methane. The present work thus demonstrates that molecular simulations can now be used to assess, almost quantitatively, such complex chemical processes as petrogenesis in fossil reservoirs and, more generally, the possible conversion of any natural product into bio-sourced materials and/or fuel.

  20. Balancing an accurate representation of the molecular surface in generalized Born formalisms with integrator stability in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Chocholoušová, Jana; Feig, M.

    2006-01-01

    Roč. 27, č. 6 (2006), s. 719-729 ISSN 0192-8651 Keywords : molecular surface * generalized Born formalisms * molecular dynamic simulations Subject RIV: CC - Organic Chemistry Impact factor: 4.893, year: 2006

  1. A hybrid approach to simulate multiple photon scattering in X-ray imaging

    International Nuclear Information System (INIS)

    Freud, N.; Letang, J.-M.; Babot, D.

    2005-01-01

    A hybrid simulation approach is proposed to compute the contribution of scattered radiation in X- or γ-ray imaging. This approach takes advantage of the complementarity between the deterministic and probabilistic simulation methods. The proposed hybrid method consists of two stages. Firstly, a set of scattering events occurring in the inspected object is determined by means of classical Monte Carlo simulation. Secondly, this set of scattering events is used as a starting point to compute the energy imparted to the detector, with a deterministic algorithm based on a 'forced detection' scheme. For each scattering event, the probability for the scattered photon to reach each pixel of the detector is calculated using well-known physical models (form factor and incoherent scattering function approximations, in the case of Rayleigh and Compton scattering respectively). The results of the proposed hybrid approach are compared to those obtained with the Monte Carlo method alone (Geant4 code) and found to be in excellent agreement. The convergence of the results when the number of scattering events increases is studied. The proposed hybrid approach makes it possible to simulate the contribution of each type (Compton or Rayleigh) and order of scattering, separately or together, with a single PC, within reasonable computation times (from minutes to hours, depending on the number of pixels of the detector). This constitutes a substantial benefit, compared to classical simulation methods (Monte Carlo or deterministic approaches), which usually requires a parallel computing architecture to obtain comparable results

  2. A hybrid approach to simulate multiple photon scattering in X-ray imaging

    Energy Technology Data Exchange (ETDEWEB)

    Freud, N. [CNDRI, Laboratory of Nondestructive Testing using Ionizing Radiations, INSA-Lyon Scientific and Technical University, Bat. Antoine de Saint-Exupery, 20, avenue Albert Einstein, 69621 Villeurbanne Cedex (France)]. E-mail: nicolas.freud@insa-lyon.fr; Letang, J.-M. [CNDRI, Laboratory of Nondestructive Testing using Ionizing Radiations, INSA-Lyon Scientific and Technical University, Bat. Antoine de Saint-Exupery, 20, avenue Albert Einstein, 69621 Villeurbanne Cedex (France); Babot, D. [CNDRI, Laboratory of Nondestructive Testing using Ionizing Radiations, INSA-Lyon Scientific and Technical University, Bat. Antoine de Saint-Exupery, 20, avenue Albert Einstein, 69621 Villeurbanne Cedex (France)

    2005-01-01

    A hybrid simulation approach is proposed to compute the contribution of scattered radiation in X- or {gamma}-ray imaging. This approach takes advantage of the complementarity between the deterministic and probabilistic simulation methods. The proposed hybrid method consists of two stages. Firstly, a set of scattering events occurring in the inspected object is determined by means of classical Monte Carlo simulation. Secondly, this set of scattering events is used as a starting point to compute the energy imparted to the detector, with a deterministic algorithm based on a 'forced detection' scheme. For each scattering event, the probability for the scattered photon to reach each pixel of the detector is calculated using well-known physical models (form factor and incoherent scattering function approximations, in the case of Rayleigh and Compton scattering respectively). The results of the proposed hybrid approach are compared to those obtained with the Monte Carlo method alone (Geant4 code) and found to be in excellent agreement. The convergence of the results when the number of scattering events increases is studied. The proposed hybrid approach makes it possible to simulate the contribution of each type (Compton or Rayleigh) and order of scattering, separately or together, with a single PC, within reasonable computation times (from minutes to hours, depending on the number of pixels of the detector). This constitutes a substantial benefit, compared to classical simulation methods (Monte Carlo or deterministic approaches), which usually requires a parallel computing architecture to obtain comparable results.

  3. A hybrid method for flood simulation in small catchments combining hydrodynamic and hydrological techniques

    Science.gov (United States)

    Bellos, Vasilis; Tsakiris, George

    2016-09-01

    The study presents a new hybrid method for the simulation of flood events in small catchments. It combines a physically-based two-dimensional hydrodynamic model and the hydrological unit hydrograph theory. Unit hydrographs are derived using the FLOW-R2D model which is based on the full form of two-dimensional Shallow Water Equations, solved by a modified McCormack numerical scheme. The method is tested at a small catchment in a suburb of Athens-Greece for a storm event which occurred in February 2013. The catchment is divided into three friction zones and unit hydrographs of 15 and 30 min are produced. The infiltration process is simulated by the empirical Kostiakov equation and the Green-Ampt model. The results from the implementation of the proposed hybrid method are compared with recorded data at the hydrometric station at the outlet of the catchment and the results derived from the fully hydrodynamic model FLOW-R2D. It is concluded that for the case studied, the proposed hybrid method produces results close to those of the fully hydrodynamic simulation at substantially shorter computational time. This finding, if further verified in a variety of case studies, can be useful in devising effective hybrid tools for the two-dimensional flood simulations, which are lead to accurate and considerably faster results than those achieved by the fully hydrodynamic simulations.

  4. 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.

  5. Hybrid Reynolds-Averaged/Large Eddy Simulation of a Cavity Flameholder; Assessment of Modeling Sensitivities

    Science.gov (United States)

    Baurle, R. A.

    2015-01-01

    Steady-state and scale-resolving simulations have been performed for flow in and around a model scramjet combustor flameholder. The cases simulated corresponded to those used to examine this flowfield experimentally using particle image velocimetry. A variety of turbulence models were used for the steady-state Reynolds-averaged simulations which included both linear and non-linear eddy viscosity models. The scale-resolving simulations used a hybrid Reynolds-averaged / large eddy simulation strategy that is designed to be a large eddy simulation everywhere except in the inner portion (log layer and below) of the boundary layer. Hence, this formulation can be regarded as a wall-modeled large eddy simulation. This effort was undertaken to formally assess the performance of the hybrid Reynolds-averaged / large eddy simulation modeling approach in a flowfield of interest to the scramjet research community. The numerical errors were quantified for both the steady-state and scale-resolving simulations prior to making any claims of predictive accuracy relative to the measurements. The steady-state Reynolds-averaged results showed a high degree of variability when comparing the predictions obtained from each turbulence model, with the non-linear eddy viscosity model (an explicit algebraic stress model) providing the most accurate prediction of the measured values. The hybrid Reynolds-averaged/large eddy simulation results were carefully scrutinized to ensure that even the coarsest grid had an acceptable level of resolution for large eddy simulation, and that the time-averaged statistics were acceptably accurate. The autocorrelation and its Fourier transform were the primary tools used for this assessment. The statistics extracted from the hybrid simulation strategy proved to be more accurate than the Reynolds-averaged results obtained using the linear eddy viscosity models. However, there was no predictive improvement noted over the results obtained from the explicit

  6. Reactor Subsystem Simulation for Nuclear Hybrid Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    Shannon Bragg-Sitton; J. Michael Doster; Alan Rominger

    2012-09-01

    Preliminary system models have been developed by Idaho National Laboratory researchers and are currently being enhanced to assess integrated system performance given multiple sources (e.g., nuclear + wind) and multiple applications (i.e., electricity + process heat). Initial efforts to integrate a Fortran-based simulation of a small modular reactor (SMR) with the balance of plant model have been completed in FY12. This initial effort takes advantage of an existing SMR model developed at North Carolina State University to provide initial integrated system simulation for a relatively low cost. The SMR subsystem simulation details are discussed in this report.

  7. Torsional properties of hexagonal boron nitride nanotubes, carbon nanotubes and their hybrid structures: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Qi-lin, E-mail: xiongql@hust.edu.cn [Department of Mechanics, Huazhong University of Science & Technology, 1037 Luoyu Road, Wuhan 430074 (China); Hubei Key Laboratory of Engineering Structural Analysis and Safety Assessment, Luoyu Road 1037, Wuhan 430074 (China); Tian, Xiao Geng [State Key Laboratory for Mechanical Structure Strength and Vibration, Xi’an Jiaotong University, Xi’an 710049 (China)

    2015-10-15

    The torsional mechanical properties of hexagonal single-walled boron nitride nanotubes (SWBNNTs), single-walled carbon nanotubes (SWCNTs), and their hybrid structures (SWBN-CNTs) are investigated using molecular dynamics (MD) simulation. Two approaches - force approach and energy approach, are adopted to calculate the shear moduli of SWBNNTs and SWCNTs, the discrepancy between two approaches is analyzed. The results show that the shear moduli of single-walled nanotubes (SWNTs), including SWBNNTs and SWCNTs are dependent on the diameter, especially for armchair SWNTs. The armchair SWNTs show the better ability of resistance the twisting comparable to the zigzag SWNTs. The effects of diameter and length on the critical values of torque of SWNTs are obtained by comparing the torsional behaviors of SWNTs with different diameters and different lengths. It is observed that the MD results of the effect of diameter and length on the critical values of torque agrees well with the prediction of continuum shell model. The shear modulus of SWBN-CNT has a significant dependence on the percentages of SWCNT and the hybrid style has also an influence on shear modulus. The critical values of torque of SWBN-CNTs increase with the increase of the percentages of SWCNT. This phenomenon can be interpreted by the function relationship between the torque of different bonds (B-N-X, C-C-X, C-B-X, C-N-X) and the angles of bonds.

  8. A hybrid simulation approach for integrating safety behavior into construction planning: An earthmoving case study.

    Science.gov (United States)

    Goh, Yang Miang; Askar Ali, Mohamed Jawad

    2016-08-01

    One of the key challenges in improving construction safety and health is the management of safety behavior. From a system point of view, workers work unsafely due to system level issues such as poor safety culture, excessive production pressure, inadequate allocation of resources and time and lack of training. These systemic issues should be eradicated or minimized during planning. However, there is a lack of detailed planning tools to help managers assess the impact of their upstream decisions on worker safety behavior. Even though simulation had been used in construction planning, the review conducted in this study showed that construction safety management research had not been exploiting the potential of simulation techniques. Thus, a hybrid simulation framework is proposed to facilitate integration of safety management considerations into construction activity simulation. The hybrid framework consists of discrete event simulation (DES) as the core, but heterogeneous, interactive and intelligent (able to make decisions) agents replace traditional entities and resources. In addition, some of the cognitive processes and physiological aspects of agents are captured using system dynamics (SD) approach. The combination of DES, agent-based simulation (ABS) and SD allows a more "natural" representation of the complex dynamics in construction activities. The proposed hybrid framework was demonstrated using a hypothetical case study. In addition, due to the lack of application of factorial experiment approach in safety management simulation, the case study demonstrated sensitivity analysis and factorial experiment to guide future research. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Logic hybrid simulation-optimization algorithm for distillation design

    OpenAIRE

    Caballero Suárez, José Antonio

    2014-01-01

    In this paper, we propose a novel algorithm for the rigorous design of distillation columns that integrates a process simulator in a generalized disjunctive programming formulation. The optimal distillation column, or column sequence, is obtained by selecting, for each column section, among a set of column sections with different number of theoretical trays. The selection of thermodynamic models, properties estimation etc., are all in the simulation environment. All the numerical issues relat...

  10. Imaging performance of a hybrid x-ray computed tomography-fluorescence molecular tomography system using priors.

    Science.gov (United States)

    Ale, Angelique; Schulz, Ralf B; Sarantopoulos, Athanasios; Ntziachristos, Vasilis

    2010-05-01

    The performance is studied of two newly introduced and previously suggested methods that incorporate priors into inversion schemes associated with data from a recently developed hybrid x-ray computed tomography and fluorescence molecular tomography system, the latter based on CCD camera photon detection. The unique data set studied attains accurately registered data of high spatially sampled photon fields propagating through tissue along 360 degrees projections. Approaches that incorporate structural prior information were included in the inverse problem by adding a penalty term to the minimization function utilized for image reconstructions. Results were compared as to their performance with simulated and experimental data from a lung inflammation animal model and against the inversions achieved when not using priors. The importance of using priors over stand-alone inversions is also showcased with high spatial sampling simulated and experimental data. The approach of optimal performance in resolving fluorescent biodistribution in small animals is also discussed. Inclusion of prior information from x-ray CT data in the reconstruction of the fluorescence biodistribution leads to improved agreement between the reconstruction and validation images for both simulated and experimental data.

  11. 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.

  12. Molecular electronics: insight from first-principles transport simulations.

    Science.gov (United States)

    Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

    2010-01-01

    Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

  13. 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...

  14. 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

  15. Haptization of molecular dynamics simulation with thermal display

    International Nuclear Information System (INIS)

    Tamura, Yuichi; Fujiwara, Susumu; Nakamura, Hiroaki

    2010-01-01

    Thermal display, which is a type of haptic display, is effective in providing intuitive information of temperature. However, in many studies, the user has assumed a sitting position during the use of these devices. In contrast, the user generally watches 3D objects while standing and walking around in large-scale virtual reality system, In addition, in scientific visualization, the response time is very important for observing physical phenomena, especially for dynamic numerical simulation. One solution is to provide two types of thermal information: information about the rate of thermal change and information about the actual temperature. We propose a thermal display with two Peltier elements which can show above two pairs of information and the result (for example energy and temperature, as thermal information) of numerical simulation. Finally, we represent an example of visualizing and haptizing the result of molecular dynamics simulation. (author)

  16. Lightweight computational steering of very large scale molecular dynamics simulations

    International Nuclear Information System (INIS)

    Beazley, D.M.

    1996-01-01

    We present a computational steering approach for controlling, analyzing, and visualizing very large scale molecular dynamics simulations involving tens to hundreds of millions of atoms. Our approach relies on extensible scripting languages and an easy to use tool for building extensions and modules. The system is extremely easy to modify, works with existing C code, is memory efficient, and can be used from inexpensive workstations and networks. We demonstrate how we have used this system to manipulate data from production MD simulations involving as many as 104 million atoms running on the CM-5 and Cray T3D. We also show how this approach can be used to build systems that integrate common scripting languages (including Tcl/Tk, Perl, and Python), simulation code, user extensions, and commercial data analysis packages

  17. Molecular dynamics simulation of gold cluster growth during sputter deposition

    Energy Technology Data Exchange (ETDEWEB)

    Abraham, J. W., E-mail: abraham@theo-physik.uni-kiel.de; Bonitz, M., E-mail: bonitz@theo-physik.uni-kiel.de [Institut für Theoretische Physik und Astrophysik, Christian-Albrechts-Universität zu Kiel, Leibnizstraße 15, D-24098 Kiel (Germany); Strunskus, T.; Faupel, F. [Institut für Materialwissenschaft, Lehrstuhl für Materialverbunde, Christian-Albrechts-Universität zu Kiel, Kaiserstraße 2, D-24143 Kiel (Germany)

    2016-05-14

    We present a molecular dynamics simulation scheme that we apply to study the time evolution of the self-organized growth process of metal cluster assemblies formed by sputter-deposited gold atoms on a planar surface. The simulation model incorporates the characteristics of the plasma-assisted deposition process and allows for an investigation over a wide range of deposition parameters. It is used to obtain data for the cluster properties which can directly be compared with recently published experimental data for gold on polystyrene [M. Schwartzkopf et al., ACS Appl. Mater. Interfaces 7, 13547 (2015)]. While good agreement is found between the two, the simulations additionally provide valuable time-dependent real-space data of the surface morphology, some of whose details are hidden in the reciprocal-space scattering images that were used for the experimental analysis.

  18. Molecular dynamics simulations of a lithium/sodium carbonate mixture.

    Science.gov (United States)

    Ottochian, Alistar; Ricca, Chiara; Labat, Frederic; Adamo, Carlo

    2016-03-01

    The diffusion and ionic conductivity of Li x Na1-x CO3 salt mixtures were studied by means of Molecular Dynamics (MD) simulations, using the Janssen and Tissen model (Janssen and Tissen, Mol Simul 5:83-98; 1990). These salts have received particular attention due to their central role in fuel cells technology, and reliable numerical methods that could perform as important interpretative tool of experimental data are thus required but still lacking. The chosen computational model nicely reproduces the main structural behaviour of the pure Li2CO3, Na2CO3 and K2CO3 carbonates, but also of their Li/K and Li/Na mixtures. However, it fails to accurately describe dynamic properties such as activation energies of diffusion and conduction processes, outlining the need to develop more accurate models for the simulation of molten salt carbonates.

  19. A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations

    NARCIS (Netherlands)

    van Dijk, Marc; Wassenaar, Tsjerk A; Bonvin, Alexandre M J J

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  20. A flexible, grid-enabled web portal for GROMACS molecular dynamics simulations

    NARCIS (Netherlands)

    van Dijk, M.; Wassenaar, T.A.; Bonvin, A.M.J.J.

    2012-01-01

    Molecular dynamics simulations are becoming a standard part of workflows in structural biology. They are used for tasks as diverse as assessing molecular flexibility, probing conformational changes, assessing the impact of mutations, or gaining information about molecular interactions. However,

  1. Molecular dynamics simulation of thermophysical properties of undercooled liquid cobalt

    International Nuclear Information System (INIS)

    Han, X J; Wang, J Z; Chen, M; Guo, Z Y

    2004-01-01

    Molecular dynamics simulations with two different embedded-atom-method (EAM) potentials are applied to calculate the density, specific heat and self-diffusion coefficient of liquid cobalt at temperatures above and below the melting temperature. Simulation shows that Pasianot's EAM model of cobalt constructed on the basis of a hcp structure is more successful than Stoop's EAM model in the framework of a fcc structure in predicting the thermophysical properties of liquid cobalt. Simulations with Pasianot's EAM model indicate that the density fits into ρ = 7.49-9.17 x 10 -4 (T- T m ) g cm -3 , and the self-diffusion coefficient is given by D = 1.291 x 10 -7 exp(-48 795.71/RT) m 2 s -1 . Dissimilar to the linear dependence of the density and the Arrhenius dependence of the self-diffusion coefficient on temperature, the specific heat shows almost a constant value of 38.595 ± 0.084 J mol -1 K -1 within the temperature range of simulation. The simulated properties of liquid cobalt are compared with experimental data available. Comparisons show reasonable agreements between the simulated results from Pasianot's EAM model and experimental data

  2. Fabrication of molecular hybrid films of gold nanoparticle and polythiophene by covalent assembly

    Energy Technology Data Exchange (ETDEWEB)

    Sundaramurthy, Jayaraman, E-mail: jsu2@np.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore); Environmental & Water Technology Centre of Innovation, Ngee Ann Polytechnic, 599489 (Singapore); Dharmarajan, Rajarathnam [CERAR, University of South Australia, Mawson Lakes, SA 5095 (Australia); Srinivasan, M.P., E-mail: chesmp@nus.edu.sg [Department of Chemical & Biomolecular Engineering, National University of Singapore, Block E5, 4 Engineering Drive 4, 117576 (Singapore)

    2015-08-31

    This work demonstrates the fabrication of molecular hybrid films comprising gold nanoparticles (AuNPs) incorporated in covalently assembled, substituted polythiophene (poly(3-(2-bromoethoxy)ethoxymethylthiophene-2,5-diyl (PBrEEMT))) films by different surface chemistry routes. AuNPs are incorporated in the immobilized polythiophene matrix due to its affinity for amine and sulfur. The amount of AuNPs present depends on the nature of the incorporation, the extent of film coverage and interaction of thiophene and amine groups. PBrEEMT films functionalized with amine rich polyallylamine immobilize greater numbers of AuNPs due to more extensive gold–amine interactions. Covalent binding between AuNP and PBrEEMT films was accomplished by using pre-functionalised AuNPs (4-aminothiophenol functionalized AuNPs). Atomic force microscopy, field emission scanning electron microscopy and X-ray photoelectron spectroscopy were used to study the morphology and chemical constituents of assembled films. These approaches will pave the way for developing facile methods for nanoparticle incorporation and will also facilitate direct interaction of nanoparticles with the conducting polymer matrix and enhance the electrical properties of the films. - Highlights: • Covalent molecular assembly enabled the fabrication of molecular hybrid films. • Monomeric and polymeric species were employed as intermediate linkers. • Adopted approaches facilitated the direct interaction of gold nanoparticle in films. • The amount of nanoparticle incorporation depended on the extent of film coverage.

  3. Self-regulated growth of LaVO3 thin films by hybrid molecular beam epitaxy

    International Nuclear Information System (INIS)

    Zhang, Hai-Tian; Engel-Herbert, Roman; Dedon, Liv R.; Martin, Lane W.

    2015-01-01

    LaVO 3 thin films were grown on SrTiO 3 (001) by hybrid molecular beam epitaxy. A volatile metalorganic precursor, vanadium oxytriisopropoxide (VTIP), and elemental La were co-supplied in the presence of a molecular oxygen flux. By keeping the La flux fixed and varying the VTIP flux, stoichiometric LaVO 3 films were obtained for a range of cation flux ratios, indicating the presence of a self-regulated growth window. Films grown under stoichiometric conditions were found to have the largest lattice parameter, which decreased monotonically with increasing amounts of excess La or V. Energy dispersive X-ray spectroscopy and Rutherford backscattering measurements were carried out to confirm film compositions. Stoichiometric growth of complex vanadate thin films independent of cation flux ratios expands upon the previously reported self-regulated growth of perovskite titanates using hybrid molecular beam epitaxy, thus demonstrating the general applicability of this growth approach to other complex oxide materials, where a precise control over film stoichiometry is demanded by the application

  4. Modeling and Simulation of Renewable Hybrid Power System using Matlab Simulink Environment

    Directory of Open Access Journals (Sweden)

    Cristian Dragoş Dumitru

    2010-12-01

    Full Text Available The paper presents the modeling of a solar-wind-hydroelectric hybrid system in Matlab/Simulink environment. The application is useful for analysis and simulation of a real hybrid solar-wind-hydroelectric system connected to a public grid. Application is built on modular architecture to facilitate easy study of each component module influence. Blocks like wind model, solar model, hydroelectric model, energy conversion and load are implemented and the results of simulation are also presented. As an example, one of the most important studies is the behavior of hybrid system which allows employing renewable and variable in time energy sources while providing a continuous supply. Application represents a useful tool in research activity and also in teaching

  5. 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

  6. Quasi-Static Single-Component Hybrid Simulation of a Composite Structure with Multi-Axis Control

    DEFF Research Database (Denmark)

    Høgh, J.; Waldbjørn, J.; Wittrup-Schmidt, J.

    2015-01-01

    This paper presents a quasi-static hybrid simulation performed on a single component structure. Hybrid simulation is a substructural technique, where a structure is divided into two sections: a numerical section of the main structure and a physical experiment of the remainder. In previous cases...

  7. Study on driver model for hybrid truck based on driving simulator experimental results

    Directory of Open Access Journals (Sweden)

    Dam Hoang Phuc

    2018-04-01

    Full Text Available In this paper, a proposed car-following driver model taking into account some features of both the compensatory and anticipatory model representing the human pedal operation has been verified by driving simulator experiments with several real drivers. The comparison between computer simulations performed by determined model parameters with the experimental results confirm the correctness of this mathematical driver model and identified model parameters. Then the driver model is joined to a hybrid vehicle dynamics model and the moderate car following maneuver simulations with various driver parameters are conducted to investigate influences of driver parameters on vehicle dynamics response and fuel economy. Finally, major driver parameters involved in the longitudinal control of drivers are clarified. Keywords: Driver model, Driver-vehicle closed-loop system, Car Following, Driving simulator/hybrid electric vehicle (B1

  8. Molecular Dynamics Simulations of Silica Nanoparticles Grafted with Poly(ethylene oxide) Oligomer Chains

    KAUST Repository

    Hong, Bingbing; Panagiotopoulos, Athanassios Z.

    2012-01-01

    A molecular model of silica nanoparticles grafted with poly(ethylene oxide) oligomers has been developed for predicting the transport properties of nanoparticle organic-hybrid materials (NOHMs). Ungrafted silica nanoparticles in a medium of poly(ethylene

  9. 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

  10. Structure of Mercury's magnetosphere for different pressure of the solar wind: Three dimensional hybrid simulations

    Czech Academy of Sciences Publication Activity Database

    Trávníček, Pavel; Hellinger, Petr; Schriver, D.

    2007-01-01

    Roč. 34, č. 5 (2007), L05104/1-L05104/5 ISSN 0094-8276 R&D Projects: GA ČR GA205/05/1011 Institutional research plan: CEZ:AV0Z30420517 Keywords : Global simulations * Mercury's magnetosphere * solar wind * hybrid simulations * ion drift driven rings Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 2.744, year: 2007

  11. Microcanonical and hybrid simulations of lattice quantum chromodynamics with dynamical fermions

    International Nuclear Information System (INIS)

    Sinclair, D.K.

    1986-10-01

    Lattice QCD is simulated using Microcanonical and Hybrid (Micro-canonical/Langevin) methods to facilitate the inclusion of dynamical fermions (quarks). We report on simulations with 4 flavors of light dynamical quarks on a 10 3 x 6 lattice to study the finite temperature deconfinement/chiral transition which should be observable in relativistic heavy ion collisions, as a function of quark mass. A first order transition is observed at large mass, weakens at intermediate mass and strengthens for very small quark mass

  12. A survey of electric and hybrid vehicles simulation programs. Volume 2: Questionnaire responses

    Science.gov (United States)

    Bevan, J.; Heimburger, D. A.; Metcalfe, M. A.

    1978-01-01

    The data received in a survey conducted within the United States to determine the extent of development and capabilities of automotive performance simulation programs suitable for electric and hybrid vehicle studies are presented. The survey was conducted for the Department of Energy by NASA's Jet Propulsion Laboratory. Volume 1 of this report summarizes and discusses the results contained in Volume 2.

  13. Dynamic Performance Comparison for MPPT-PV Systems using Hybrid Pspice/Matlab Simulation

    Science.gov (United States)

    Aouchiche, N.; Becherif, M.; HadjArab, A.; Aitcheikh, M. S.; Ramadan, H. S.; Cheknane, A.

    2016-10-01

    The power generated by solar photovoltaic (PV) module depends on the surrounding irradiance and temperature. This paper presents a hybrid Matlab™/Pspice™ simulation model of PV system, combined with Cadence software SLPS. The hybridization is performed in order to gain the advantages of both simulation tools such as accuracy and efficiency in both Pspice electronic circuit and Matlab™ mathematical modelling respectively. For this purpose, the PV panel and the boost converter are developed using Pspice™ and hybridized with the mathematical Matlab™ model of maximum power point method controller (MPPT) through SLPS. The main objective is verify the significance of using the proposed hybrid simulation techniques in comparing the different MPPT algorithms such as the perturbation and observation (P&O), incremental of conductance (Inc-Cond) and counter reaction voltage using pilot cell (Pilot-Cell). Various simulations are performed under different atmospheric conditions in order to evaluate the dynamic behaviour for the system under study in terms of stability, efficiency and rapidity.

  14. A Hybrid Three Layer Architecture for Fire Agent Management in Rescue Simulation Environment

    Directory of Open Access Journals (Sweden)

    Alborz Geramifard

    2008-11-01

    Full Text Available This paper presents a new architecture called FAIS for imple- menting intelligent agents cooperating in a special Multi Agent environ- ment, namely the RoboCup Rescue Simulation System. This is a layered architecture which is customized for solving fire extinguishing problem. Structural decision making algorithms are combined with heuristic ones in this model, so it's a hybrid architecture.

  15. A Hybrid Three Layer Architecture for Fire Agent Management in Rescue Simulation Environment

    Directory of Open Access Journals (Sweden)

    Alborz Geramifard

    2005-06-01

    Full Text Available This paper presents a new architecture called FAIS for implementing intelligent agents cooperating in a special Multi Agent environment, namely the RoboCup Rescue Simulation System. This is a layered architecture which is customized for solving fire extinguishing problem. Structural decision making algorithms are combined with heuristic ones in this model, so it's a hybrid architecture.

  16. Advanced hybrid transient stability and EMT simulation for VSC-HVDC systems

    NARCIS (Netherlands)

    Van Der Meer, A.A.; Gibescu, M.; Van Der Meijden, M.A.M.M.; Kling, W.L.; Ferreira, J.A.

    2015-01-01

    This paper deals with advanced hybrid transient stability and electromagnetic-transient (EMT) simulation of combined ac/dc power systems containing large amounts of renewable energy sources interfaced through voltage-source converter-high-voltage direct current (VSC-HVDC). The concerning transient

  17. A hybrid Genetic and Simulated Annealing Algorithm for Chordal Ring implementation in large-scale networks

    DEFF Research Database (Denmark)

    Riaz, M. Tahir; Gutierrez Lopez, Jose Manuel; Pedersen, Jens Myrup

    2011-01-01

    The paper presents a hybrid Genetic and Simulated Annealing algorithm for implementing Chordal Ring structure in optical backbone network. In recent years, topologies based on regular graph structures gained a lot of interest due to their good communication properties for physical topology of the...

  18. Prediction of Sliding Friction Coefficient Based on a Novel Hybrid Molecular-Mechanical Model.

    Science.gov (United States)

    Zhang, Xiaogang; Zhang, Yali; Wang, Jianmei; Sheng, Chenxing; Li, Zhixiong

    2018-08-01

    Sliding friction is a complex phenomenon which arises from the mechanical and molecular interactions of asperities when examined in a microscale. To reveal and further understand the effects of micro scaled mechanical and molecular components of friction coefficient on overall frictional behavior, a hybrid molecular-mechanical model is developed to investigate the effects of main factors, including different loads and surface roughness values, on the sliding friction coefficient in a boundary lubrication condition. Numerical modelling was conducted using a deterministic contact model and based on the molecular-mechanical theory of friction. In the contact model, with given external loads and surface topographies, the pressure distribution, real contact area, and elastic/plastic deformation of each single asperity contact were calculated. Then asperity friction coefficient was predicted by the sum of mechanical and molecular components of friction coefficient. The mechanical component was mainly determined by the contact width and elastic/plastic deformation, and the molecular component was estimated as a function of the contact area and interfacial shear stress. Numerical results were compared with experimental results and a good agreement was obtained. The model was then used to predict friction coefficients in different operating and surface conditions. Numerical results explain why applied load has a minimum effect on the friction coefficients. They also provide insight into the effect of surface roughness on the mechanical and molecular components of friction coefficients. It is revealed that the mechanical component dominates the friction coefficient when the surface roughness is large (Rq > 0.2 μm), while the friction coefficient is mainly determined by the molecular component when the surface is relatively smooth (Rq < 0.2 μm). Furthermore, optimal roughness values for minimizing the friction coefficient are recommended.

  19. Synthesis and characterization of curcumin-sulfonamide hybrids: Biological evaluation and molecular docking studies

    Science.gov (United States)

    Banuppriya, Govindharasu; Sribalan, Rajendran; Padmini, Vediappen

    2018-03-01

    Curcumin-sulfonamide hybrids (4a-e) were synthesized and their in vitro antioxidant, anti-inflammatory and anticancer activities were studied. The synthesized compounds showed a very good potent activity towards antioxidant and anti-inflammatory studies rather than its parent as well as standard. These compounds have exhibited an excellent toxicity effect to the cancer cell lines such as A549 and AGS. The compounds 4a and 4c have showed good anticancer activity than curcumin. The molecular docking studies were also performed against various Epidermal Growth Factor Receptor (EGFR) enzymes. The DFT calculations were also done in order to support the docking results.

  20. Enzymatic Amplification of DNA/RNA Hybrid Molecular Beacon Signaling in Nucleic Acid Detection

    OpenAIRE

    Jacroux, Thomas; Rieck, Daniel C.; Cui, Rong; Ouyang, Yexin; Dong, Wen-Ji

    2012-01-01

    A rapid assay operable under isothermal or non-isothermal conditions is described wherein the sensitivity of a typical molecular beacon (MB) system is improved by utilizing thermostable RNase H to enzymatically cleave an MB comprised of a DNA stem and RNA loop (R/D-MB). Upon hybridization of the R/D-MB to target DNA, there was a modest increase in fluorescence intensity (~5.7x above background) due to an opening of the probe and concomitant reduction in the Förster resonance energy transfer e...

  1. Molecular dynamics simulations of solutions at constant chemical potential

    Science.gov (United States)

    Perego, C.; Salvalaglio, M.; Parrinello, M.

    2015-04-01

    Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

  2. Molecular simulation of methane adsorption characteristics on coal macromolecule

    Science.gov (United States)

    Yang, Zhiyuan; He, Xiaoxiao; Meng, Zhuoyue; Xue, Wenying

    2018-02-01

    In this paper, the molecular model of anthracite named Wender2 was selected to study the adsorption behaviour of single component CH4 and the competitive adsorption of CH4/CO2, CH4/H2O and CH4/N2. The molecular model of anthracite was established by molecular simulation software (Materials Studio 8.0), and Grand Canonical Monte Carlo (GCMC) simulations were carried out to investigate the single and binary component adsorption. The effects of pressure and temperature on the adsorption position, adsorption energy and adsorption capacity were mainly discussed. The results show that for the single component adsorption, the adsorption capacity of CH4 increases rapidly with the pressure ascending, and then tends to be stable after the first step. The low temperature is favourable for the adsorption of CH4, and the high temperature promotes desorption quantity of CH4 from the coal. Adsorbent molecules are preferentially adsorbed on the edge of coal macromolecules. The order of adsorption capacity of CH4/CO2, CH4/H2O and CH4/N2 in the binary component is H2O>CO2>CH4>N2. The change of pressure has little effect on the adsorption capacity of the adsorbent in the competitive adsorption, but it has a great influence on the adsorption capacity of the adsorbent, and there is a positive correlation between them.

  3. Hybrid Large-Eddy/Reynolds-Averaged Simulation of a Supersonic Cavity Using VULCAN

    Science.gov (United States)

    Quinlan, Jesse; McDaniel, James; Baurle, Robert A.

    2013-01-01

    Simulations of a supersonic recessed-cavity flow are performed using a hybrid large-eddy/Reynolds-averaged simulation approach utilizing an inflow turbulence recycling procedure and hybridized inviscid flux scheme. Calorically perfect air enters a three-dimensional domain at a free stream Mach number of 2.92. Simulations are performed to assess grid sensitivity of the solution, efficacy of the turbulence recycling, and the effect of the shock sensor used with the hybridized inviscid flux scheme. Analysis of the turbulent boundary layer upstream of the rearward-facing step for each case indicates excellent agreement with theoretical predictions. Mean velocity and pressure results are compared to Reynolds-averaged simulations and experimental data for each case and indicate good agreement on the finest grid. Simulations are repeated on a coarsened grid, and results indicate strong grid density sensitivity. Simulations are performed with and without inflow turbulence recycling on the coarse grid to isolate the effect of the recycling procedure, which is demonstrably critical to capturing the relevant shear layer dynamics. Shock sensor formulations of Ducros and Larsson are found to predict mean flow statistics equally well.

  4. Fabrication of reproducible, integration-compatible hybrid molecular/si electronics.

    Science.gov (United States)

    Yu, Xi; Lovrinčić, Robert; Kraynis, Olga; Man, Gabriel; Ely, Tal; Zohar, Arava; Toledano, Tal; Cahen, David; Vilan, Ayelet

    2014-12-29

    Reproducible molecular junctions can be integrated within standard CMOS technology. Metal-molecule-semiconductor junctions are fabricated by direct Si-C binding of hexadecane or methyl-styrene onto oxide-free H-Si(111) surfaces, with the lateral size of the junctions defined by an etched SiO2 well and with evaporated Pb as the top contact. The current density, J, is highly reproducible with a standard deviation in log(J) of 0.2 over a junction diameter change from 3 to 100 μm. Reproducibility over such a large range indicates that transport is truly across the molecules and does not result from artifacts like edge effects or defects in the molecular monolayer. Device fabrication is tested for two n-Si doping levels. With highly doped Si, transport is dominated by tunneling and reveals sharp conductance onsets at room temperature. Using the temperature dependence of current across medium-doped n-Si, the molecular tunneling barrier can be separated from the Si-Schottky one, which is a 0.47 eV, in agreement with the molecular-modified surface dipole and quite different from the bare Si-H junction. This indicates that Pb evaporation does not cause significant chemical changes to the molecules. The ability to manufacture reliable devices constitutes important progress toward possible future hybrid Si-based molecular electronics. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Tungsten polyoxometalate molecules as active nodes for dynamic carrier exchange in hybrid molecular/semiconductor capacitors

    International Nuclear Information System (INIS)

    Balliou, A.; Douvas, A. M.; Normand, P.; Argitis, P.; Glezos, N.; Tsikritzis, D.; Kennou, S.

    2014-01-01

    In this work we study the utilization of molecular transition metal oxides known as polyoxometalates (POMs), in particular the Keggin structure anions of the formula PW 12 O 40 3− , as active nodes for potential switching and/or fast writing memory applications. The active molecules are being integrated in hybrid Metal-Insulator/POM molecules-Semiconductor capacitors, which serve as prototypes allowing investigation of critical performance characteristics towards the design of more sophisticated devices. The charging ability as well as the electronic structure of the molecular layer is probed by means of electrical characterization, namely, capacitance-voltage and current-voltage measurements, as well as transient capacitance measurements, C (t), under step voltage polarization. It is argued that the transient current peaks observed are manifestations of dynamic carrier exchange between the gate electrode and specific molecular levels, while the transient C (t) curves under conditions of molecular charging can supply information for the rate of change of the charge that is being trapped and de-trapped within the molecular layer. Structural characterization via surface and cross sectional scanning electron microscopy as well as atomic force microscopy, spectroscopic ellipsometry, UV and Fourier-transform IR spectroscopies, UPS, and XPS contribute to the extraction of accurate electronic structure characteristics and open the path for the design of new devices with on-demand tuning of their interfacial properties via the controlled preparation of the POM layer.

  6. Membrane separation study for methane-hydrogen gas mixtures by molecular simulations

    Directory of Open Access Journals (Sweden)

    T. Kovács

    2017-06-01

    Full Text Available Direct simulation results for stationary gas transport through pure silica zeolite membranes (MFI, LTA and DDR types are presented using a hybrid, non-equilibrium molecular dynamics simulation methodology introduced recently. The intermolecular potential models for the investigated CH_4 and H_2 gases were taken from literature. For different zeolites, the same atomic (Si and O interaction parameters were used, and the membranes were constructed according to their real (MFI, LTA, or DDR crystal structures. A realistic nature of the applied potential parameters was tested by performing equilibrium adsorption simulations and by comparing the calculated results with the data of experimental adsorption isotherms. The results of transport simulations carried out at 25°C and 125°C, and at 2.5, 5 or 10 bar clearly show that the permeation selectivities of CH_4 are higher than the corresponding permeability ratios of pure components, and significantly differ from the equilibrium selectivities in mixture adsorptions. We experienced a transport selectivity in favor of CH_4 in only one case. A large discrepancy between different types of selectivity data can be attributed to dissimilar mobilities of the components in a membrane, their dependence on the loading of a membrane, and the unlike adsorption preferences of the gas molecules.

  7. Design, synthesis, conformational and molecular docking study of some novel acyl hydrazone based molecular hybrids as antimalarial and antimicrobial agents.

    Science.gov (United States)

    Kumar, Parvin; Kadyan, Kulbir; Duhan, Meenakshi; Sindhu, Jayant; Singh, Vineeta; Saharan, Baljeet Singh

    2017-11-14

    Acyl hydrazones are an important class of heterocyclic compounds promising pharmacological characteristics. Malaria is a life-threatening mosquito-borne blood disease caused by a plasmodium parasite. In some places, malaria can be treated and controlled with early diagnosis. However, some countries lack the resources to do this effectively. The present work involves the design and synthesis of some novel acyl hydrazone based molecular hybrids of 1,4-dihydropyridine and pyrazole (5a-g). These molecular hybrids were synthesised by condensation of 1,4-dihydropyridin-4-yl-phenoxyacetohydrazides with differently substituted pyrazole carbaldehyde. The final compound (5) showed two conformations (the major, E, s-cis and the minor, E, s-trans) as revealed by NMR spectral data and further supported by the energy calculations (MOPAC2016 using PM7 method). All the synthesised compounds were screened for their in vitro antimalarial activities against chloroquine-sensitive malaria parasite Plasmodium falciparum (3D7) and antimicrobial activity against Gram positive bacteria i.e. Bacillus cereus, Gram negative bacteria i.e. Escherichia coli and antifungal activity against one yeast i.e. Aspergillus niger. All these compounds were found more potent than chloroquine and clotrimazole, the standard drugs. In vitro antiplasmodial IC 50 value of the most potent compound 5d was found to be 4.40 nM which is even less than all the three reference drugs chloroquine (18.7 nM), pyrimethamine (11 nM) and artimisinin (6 nM). In silico binding study of compound 5d with plasmodial cysteine protease falcipain-2 indicated the inhibition of falcipain-2 as the probable reason for the antimalarial potency of compound 5d. All the compounds had shown good to excellent antimicrobial and antifungal activities.

  8. 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.

  9. 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.

  10. Simulation and understanding of atomic and molecular quantum crystals

    Science.gov (United States)

    Cazorla, Claudio; Boronat, Jordi

    2017-07-01

    Quantum crystals abound in the whole range of solid-state species. Below a certain threshold temperature the physical behavior of rare gases (He 4 and Ne), molecular solids (H2 and CH4 ), and some ionic (LiH), covalent (graphite), and metallic (Li) crystals can be explained only in terms of quantum nuclear effects (QNE). A detailed comprehension of the nature of quantum solids is critical for achieving progress in a number of fundamental and applied scientific fields such as planetary sciences, hydrogen storage, nuclear energy, quantum computing, and nanoelectronics. This review describes the current physical understanding of quantum crystals formed by atoms and small molecules, as well as the wide palette of simulation techniques that are used to investigate them. Relevant aspects in these materials such as phase transformations, structural properties, elasticity, crystalline defects, and the effects of reduced dimensionality are discussed thoroughly. An introduction to quantum Monte Carlo techniques, which in the present context are the simulation methods of choice, and other quantum simulation approaches (e.g., path-integral molecular dynamics and quantum thermal baths) is provided. The overarching objective of this article is twofold: first, to clarify in which crystals and physical situations the disregard of QNE may incur in important bias and erroneous interpretations. And second, to promote the study and appreciation of QNE, a topic that traditionally has been treated in the context of condensed matter physics, within the broad and interdisciplinary areas of materials science.

  11. Molecular Dynamics Simulation of Binary Fluid in a Nanochannel

    International Nuclear Information System (INIS)

    Mullick, Shanta; Ahluwalia, P. K.; Pathania, Y.

    2011-01-01

    This paper presents the results from a molecular dynamics simulation of binary fluid (mixture of argon and krypton) in the nanochannel flow. The computational software LAMMPS is used for carrying out the molecular dynamics simulations. Binary fluids of argon and krypton with varying concentration of atom species were taken for two densities 0.65 and 0.45. The fluid flow takes place between two parallel plates and is bounded by horizontal walls in one direction and periodic boundary conditions are imposed in the other two directions. To drive the flow, a constant force is applied in one direction. Each fluid atom interacts with other fluid atoms and wall atoms through Week-Chandler-Anderson (WCA) potential. The velocity profile has been looked at for three nanochannel widths i.e for 12σ, 14σ and 16σ and also for the different concentration of two species. The velocity profile of the binary fluid predicted by the simulations agrees with the quadratic shape of the analytical solution of a Poiseuille flow in continuum theory.

  12. 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.

  13. Enhancing protein adsorption simulations by using accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Christian Mücksch

    Full Text Available The atomistic modeling of protein adsorption on surfaces is hampered by the different time scales of the simulation ([Formula: see text][Formula: see text]s and experiment (up to hours, and the accordingly different 'final' adsorption conformations. We provide evidence that the method of accelerated molecular dynamics is an efficient tool to obtain equilibrated adsorption states. As a model system we study the adsorption of the protein BMP-2 on graphite in an explicit salt water environment. We demonstrate that due to the considerably improved sampling of conformational space, accelerated molecular dynamics allows to observe the complete unfolding and spreading of the protein on the hydrophobic graphite surface. This result is in agreement with the general finding of protein denaturation upon contact with hydrophobic surfaces.

  14. Empirical potential for molecular simulation of graphene nanoplatelets

    Science.gov (United States)

    Bourque, Alexander J.; Rutledge, Gregory C.

    2018-04-01

    A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ˜15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

  15. Quantum molecular dynamics simulations of thermophysical properties of fluid ethane.

    Science.gov (United States)

    Zhang, Yujuan; Wang, Cong; Zheng, Fawei; Zhang, Ping

    2012-12-01

    We have performed first-principles molecular-dynamics simulations based on density-functional theory to study the thermophysical properties of ethane under extreme conditions. We present results for the equation of state of fluid ethane in the warm dense region. The optical conductivity is calculated via the Kubo-Greenwood formula from which the dc conductivity and optical reflectivity are derived. The close correlation between the nonmetal-metal transition of ethane and its decomposition, that ethane dissociates significantly into molecular and/or atomic hydrogen and some long alkane chains, has been systematically studied by analyzing the optical conductivity spectra, pair correlation functions, electronic density of states, and charge density distribution of fluid ethane.

  16. The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Bianchi, L.

    2000-05-01

    Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

  17. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  18. Prediction Errors of Molecular Machine Learning Models Lower than Hybrid DFT Error.

    Science.gov (United States)

    Faber, Felix A; Hutchison, Luke; Huang, Bing; Gilmer, Justin; Schoenholz, Samuel S; Dahl, George E; Vinyals, Oriol; Kearnes, Steven; Riley, Patrick F; von Lilienfeld, O Anatole

    2017-11-14

    We investigate the impact of choosing regressors and molecular representations for the construction of fast machine learning (ML) models of 13 electronic ground-state properties of organic molecules. The performance of each regressor/representation/property combination is assessed using learning curves which report out-of-sample errors as a function of training set size with up to ∼118k distinct molecules. Molecular structures and properties at the hybrid density functional theory (DFT) level of theory come from the QM9 database [ Ramakrishnan et al. Sci. Data 2014 , 1 , 140022 ] and include enthalpies and free energies of atomization, HOMO/LUMO energies and gap, dipole moment, polarizability, zero point vibrational energy, heat capacity, and the highest fundamental vibrational frequency. Various molecular representations have been studied (Coulomb matrix, bag of bonds, BAML and ECFP4, molecular graphs (MG)), as well as newly developed distribution based variants including histograms of distances (HD), angles (HDA/MARAD), and dihedrals (HDAD). Regressors include linear models (Bayesian ridge regression (BR) and linear regression with elastic net regularization (EN)), random forest (RF), kernel ridge regression (KRR), and two types of neural networks, graph convolutions (GC) and gated graph networks (GG). Out-of sample errors are strongly dependent on the choice of representation and regressor and molecular property. Electronic properties are typically best accounted for by MG and GC, while energetic properties are better described by HDAD and KRR. The specific combinations with the lowest out-of-sample errors in the ∼118k training set size limit are (free) energies and enthalpies of atomization (HDAD/KRR), HOMO/LUMO eigenvalue and gap (MG/GC), dipole moment (MG/GC), static polarizability (MG/GG), zero point vibrational energy (HDAD/KRR), heat capacity at room temperature (HDAD/KRR), and highest fundamental vibrational frequency (BAML/RF). We present numerical

  19. Modelling and simulation of a hybrid solar heating system for greenhouse applications using Matlab/Simulink

    International Nuclear Information System (INIS)

    Kıyan, Metin; Bingöl, Ekin; Melikoğlu, Mehmet; Albostan, Ayhan

    2013-01-01

    Highlights: • Matlab/Simulink modelling of a solar hybrid greenhouse. • Estimation of greenhouse gas emission reductions. • Feasibility and cost analysis of the system. - Abstract: Solar energy is a major renewable energy source and hybrid solar systems are gaining increased academic and industrial attention due to the unique advantages they offer. In this paper, a mathematical model has been developed to investigate the thermal behavior of a greenhouse heated by a hybrid solar collector system. This hybrid system contains an evacuated tube solar heat collector unit, an auxiliary fossil fuel heating unit, a hot water storage unit, control and piping units. A Matlab/Simulink based model and software has been developed to predict the storage water temperature, greenhouse indoor temperature and the amount of auxiliary fuel, as a function of various design parameters of the greenhouse such as location, dimensions, and meteorological data of the region. As a case study, a greenhouse located in Şanlıurfa/Turkey has been simulated based on recent meteorological data and aforementioned hybrid system. The results of simulations performed on an annual basis indicate that revising the existing fossil fuel system with the proposed hybrid system, is economically feasible for most cases, however it requires a slightly longer payback period than expected. On the other hand, by reducing the greenhouse gas emissions significantly, it has a considerable positive environmental impact. The developed dynamic simulation method can be further used for designing heating systems for various solar greenhouses and optimizing the solar collector and thermal storage sizes

  20. Hybrid Building Performance Simulation Models for Industrial Energy Efficiency Applications

    Directory of Open Access Journals (Sweden)

    Peter Smolek

    2018-06-01

    Full Text Available In the challenge of achieving environmental sustainability, industrial production plants, as large contributors to the overall energy demand of a country, are prime candidates for applying energy efficiency measures. A modelling approach using cubes is used to decompose a production facility into manageable modules. All aspects of the facility are considered, classified into the building, energy system, production and logistics. This approach leads to specific challenges for building performance simulations since all parts of the facility are highly interconnected. To meet this challenge, models for the building, thermal zones, energy converters and energy grids are presented and the interfaces to the production and logistics equipment are illustrated. The advantages and limitations of the chosen approach are discussed. In an example implementation, the feasibility of the approach and models is shown. Different scenarios are simulated to highlight the models and the results are compared.

  1. A comparative study of leachate quality and biogas generation in simulated anaerobic and hybrid bioreactors

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Qiyong; Tian, Ying; Wang, Shen; Ko, Jae Hac, E-mail: jaehacko@pkusz.edu.cn

    2015-07-15

    Highlights: • Temporary aeration shortened the initial acid inhibition phase for methanogens. • COD decreased faster in the hybrid bioreactor than that in the anaerobic control. • Methane generations from hybrid bioreactors were 133.4 L/kg{sub vs} and 113.2 L/kg{sub vs}. • MSW settlement increased with increasing the frequency of intermittent aeration. - Abstract: Research has been conducted to compare leachate characterization and biogas generation in simulated anaerobic and hybrid bioreactor landfills with typical Chinese municipal solid waste (MSW). Three laboratory-scale reactors, an anaerobic (A1) and two hybrid bioreactors (C1 and C2), were constructed and operated for about 10 months. The hybrid bioreactors were operated in an aerobic–anaerobic mode with different aeration frequencies by providing air into the upper layer of waste. Results showed that the temporary aeration into the upper layer aided methane generation by shortening the initial acidogenic phase because of volatile fatty acids (VFAs) reduction and pH increase. Chemical oxygen demand (COD) decreased faster in the hybrid bioreactors, but the concentrations of ammonia–nitrogen in the hybrid bioreactors were greater than those in the anaerobic control. Methanogenic conditions were established within 75 d and 60 d in C1 and C2, respectively. However, high aeration frequency led to the consumption of organic matters by aerobic degradation and resulted in reducing accumulative methane volume. The temporary aeration enhanced waste settlement and the settlement increased with increasing the frequency of aeration. Methane production was inhibited in the anaerobic control; however, the total methane generations from hybrid bioreactors were 133.4 L/kg{sub vs} and 113.2 L/kg{sub vs}. As for MSW with high content of food waste, leachate recirculation right after aeration stopped was not recommended due to VFA inhibition for methanogens.

  2. Speed-up of ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo simulations by using an auxiliary potential energy surface

    International Nuclear Information System (INIS)

    Nakayama, Akira; Taketsugu, Tetsuya; Shiga, Motoyuki

    2009-01-01

    Efficiency of the ab initio hybrid Monte Carlo and ab initio path integral hybrid Monte Carlo methods is enhanced by employing an auxiliary potential energy surface that is used to update the system configuration via molecular dynamics scheme. As a simple illustration of this method, a dual-level approach is introduced where potential energy gradients are evaluated by computationally less expensive ab initio electronic structure methods. (author)

  3. Hybrid molecular–continuum methods: From prototypes to coupling software

    KAUST Repository

    Neumann, Philipp; Eckhardt, Wolfgang; Bungartz, Hans-Joachim

    2014-01-01

    In this contribution, we review software requirements in hybrid molecular-continuum simulations. For this purpose, we analyze a prototype implementation which combines two frameworks-the Molecular Dynamics framework MarDyn and the framework Peano

  4. Molecular Dynamics Simulations on Evaporation of Droplets with Dissolved Salts

    OpenAIRE

    Jin-Liang Xu; Min Chen; Xiao-Dong Wang; Bing-Bing Wang

    2013-01-01

    Molecular dynamics simulations are used to study the evaporation of water droplets containing either dissolved LiCl, NaCl or KCl salt in a gaseous surrounding (nitrogen) with a constant high temperature of 600 K. The initial droplet has 298 K temperature and contains 1,120 water molecules, 0, 40, 80 or 120 salt molecules. The effects of the salt type and concentration on the evaporation rate are examined. Three stages with different evaporation rates are observed for all cases. In the initial...

  5. Extracting the diffusion tensor from molecular dynamics simulation with Milestoning

    International Nuclear Information System (INIS)

    Mugnai, Mauro L.; Elber, Ron

    2015-01-01

    We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system—the diffusion along the backbone torsions of a solvated alanine dipeptide

  6. Molecular dynamics computer simulations based on NMR data

    International Nuclear Information System (INIS)

    Vlieg, J. de.

    1989-01-01

    In the work described in this thesis atom-atom distance information obtained from two-dimensional cuclear magnetic resonance is combined with molecular dynamics simulaitons. The simulation is used to improve the accuracy of a structure model constructed on the basis of NMR data. During the MD refinement the crude NMR structure is simultaneously optimized with respect to the atomic interaction function and to the set of atom-atom distances or other NMR information. This means that insufficient experimental data is completed with theoretical knowledge and the combination will lead to more reliable structures than would be obtained from one technique alone. (author). 191 refs.; 17 figs.; 12 schemes; 22 tabs

  7. Crystal and molecular simulation of high-performance polymers.

    Science.gov (United States)

    Colquhoun, H M; Williams, D J

    2000-03-01

    Single-crystal X-ray analyses of oligomeric models for high-performance aromatic polymers, interfaced to computer-based molecular modeling and diffraction simulation, have enabled the determination of a range of previously unknown polymer crystal structures from X-ray powder data. Materials which have been successfully analyzed using this approach include aromatic polyesters, polyetherketones, polythioetherketones, polyphenylenes, and polycarboranes. Pure macrocyclic homologues of noncrystalline polyethersulfones afford high-quality single crystals-even at very large ring sizes-and have provided the first examples of a "protein crystallographic" approach to the structures of conventionally amorphous synthetic polymers.

  8. Orientation Dependence in Molecular Dynamics Simulations of Shocked Single Crystals

    International Nuclear Information System (INIS)

    Germann, Timothy C.; Holian, Brad Lee; Lomdahl, Peter S.; Ravelo, Ramon

    2000-01-01

    We use multimillion-atom molecular dynamics simulations to study shock wave propagation in fcc crystals. As shown recently, shock waves along the direction form intersecting stacking faults by slippage along {111} close-packed planes at sufficiently high shock strengths. We find even more interesting behavior of shocks propagating in other low-index directions: for the case, an elastic precursor separates the shock front from the slipped (plastic) region. Shock waves along the direction generate a leading solitary wave train, followed (at sufficiently high shock speeds) by an elastic precursor, and then a region of complex plastic deformation. (c) 2000 The American Physical Society

  9. 3D hybrid simulation of the Titan's plasma environment

    Science.gov (United States)

    Lipatov, Alexander; Sittler, Edward, Jr.; Hartle, Richard

    2007-11-01

    Titan plays an important role as a simulation laboratory for multiscale kinetic plasma processes which are key processes in space and laboratory plasmas. A development of multiscale combined numerical methods allows us to use more realistic plasma models at Titan. In this report, we describe a Particle-Ion--Fluid-Ion--Fluid--Electron method of kinetic ion-neutral simulation code. This method takes into account charge-exchange and photoionization processes. The model of atmosphere of Titan was based on a paper by Sittler, Hartle, Vinas et al., [2005]. The background ions H^+, O^+ and pickup ions H2^+, CH4^+ and N2^+ are described in a kinetic approximation, where the electrons are approximated as a fluid. In this report we study the coupling between background ions and pickup ions on the multiple space scales determined by the ion gyroradiis. The first results of such a simulation of the dynamics of ions near Titan are discussed in this report and compared with recent measurements made by the Cassini Plasma Spectrometer (CAPS, [Hartle, Sittler et al., 2006]). E C Sittler Jr., R E Hartle, A F Vinas, R E Johnson, H T Smith and I Mueller-Wodarg, J. Geophys. Res., 110, A09302, 2005.R E Hartle, E C Sittler, F M Neubauer, R E Johnson, et al., Planet. Space Sci., 54, 1211, 2006.

  10. Simulation of Mercury's magnetosheath with a combined hybrid-paraboloid model

    Science.gov (United States)

    Parunakian, David; Dyadechkin, Sergey; Alexeev, Igor; Belenkaya, Elena; Khodachenko, Maxim; Kallio, Esa; Alho, Markku

    2017-08-01

    In this paper we introduce a novel approach for modeling planetary magnetospheres that involves a combination of the hybrid model and the paraboloid magnetosphere model (PMM); we further refer to it as the combined hybrid model. While both of these individual models have been successfully applied in the past, their combination enables us both to overcome the traditional difficulties of hybrid models to develop a self-consistent magnetic field and to compensate the lack of plasma simulation in the PMM. We then use this combined model to simulate Mercury's magnetosphere and investigate the geometry and configuration of Mercury's magnetosheath controlled by various conditions in the interplanetary medium. The developed approach provides a unique comprehensive view of Mercury's magnetospheric environment for the first time. Using this setup, we compare the locations of the bow shock and the magnetopause as determined by simulations with the locations predicted by stand-alone PMM runs and also verify the magnetic and dynamic pressure balance at the magnetopause. We also compare the results produced by these simulations with observational data obtained by the magnetometer on board the MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) spacecraft along a dusk-dawn orbit and discuss the signatures of the magnetospheric features that appear in these simulations. Overall, our analysis suggests that combining the semiempirical PMM with a self-consistent global kinetic model creates new modeling possibilities which individual models cannot provide on their own.

  11. Hybrid statistics-simulations based method for atom-counting from ADF STEM images.

    Science.gov (United States)

    De Wael, Annelies; De Backer, Annick; Jones, Lewys; Nellist, Peter D; Van Aert, Sandra

    2017-06-01

    A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Modeling and Simulation of Multi-scale Environmental Systems with Generalized Hybrid Petri Nets

    Directory of Open Access Journals (Sweden)

    Mostafa eHerajy

    2015-07-01

    Full Text Available Predicting and studying the dynamics and properties of environmental systems necessitates the construction and simulation of mathematical models entailing different levels of complexities. Such type of computational experiments often require the combination of discrete and continuous variables as well as processes operating at different time scales. Furthermore, the iterative steps of constructing and analyzing environmental models might involve researchers with different background. Hybrid Petri nets may contribute in overcoming such challenges as they facilitate the implementation of systems integrating discrete and continuous dynamics. Additionally, the visual depiction of model components will inevitably help to bridge the gap between scientists with distinct expertise working on the same problem. Thus, modeling environmental systems with hybrid Petri nets enables the construction of complex processes while keeping the models comprehensible for researchers working on the same project with significantly divergent education path. In this paper we propose the utilization of a special class of hybrid Petri nets, Generalized Hybrid Petri Nets (GHPN, to model and simulate environmental systems exposing processes interacting at different time-scales. GHPN integrate stochastic and deterministic semantics as well as other types of special basic events. Moreover, a case study is presented to illustrate the use of GHPN in constructing and simulating multi-timescale environmental scenarios.

  13. Recovery act. Development of design and simulation tool for hybrid geothermal heat pump system

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Shaojie [ClimateMaster, Inc., Oklahoma City, OK (United States); Ellis, Dan [ClimateMaster, Inc., Oklahoma City, OK (United States)

    2014-05-29

    The ground source heat pump (GSHP) system is one of the most energy efficient HVAC technologies in the current market. However, the heat imbalance may degrade the ability of the ground loop heat exchanger (GLHX) to absorb or reject heat. The hybrid GSHP system, which combines a geothermal well field with a supplemental boiler or cooling tower, can balance the loads imposed on the ground loop heat exchangers to minimize its size while retaining superior energy efficiency. This paper presents a recent simulation-based study with an intention to compare multiple common control strategies used in hybrid GSHP systems, including fixed setpoint, outside air reset, load reset, and wetbulb reset. A small office in Oklahoma City conditioned by a hybrid GSHP system was simulated with the latest version of eQUEST 3.7[1]. The simulation results reveal that the hybrid GSHP system has the excellent capability to meet the cooling and heating setpoints during the occupied hours, balance thermal loads on the ground loop, as well as improve the thermal comfort of the occupants with the undersized well field.

  14. A hybrid hydrostatic and non-hydrostatic numerical model for shallow flow simulations

    Science.gov (United States)

    Zhang, Jingxin; Liang, Dongfang; Liu, Hua

    2018-05-01

    Hydrodynamics of geophysical flows in oceanic shelves, estuaries, and rivers, are often studied by solving shallow water model equations. Although hydrostatic models are accurate and cost efficient for many natural flows, there are situations where the hydrostatic assumption is invalid, whereby a fully hydrodynamic model is necessary to increase simulation accuracy. There is a growing concern about the decrease of the computational cost of non-hydrostatic pressure models to improve the range of their applications in large-scale flows with complex geometries. This study describes a hybrid hydrostatic and non-hydrostatic model to increase the efficiency of simulating shallow water flows. The basic numerical model is a three-dimensional hydrostatic model solved by the finite volume method (FVM) applied to unstructured grids. Herein, a second-order total variation diminishing (TVD) scheme is adopted. Using a predictor-corrector method to calculate the non-hydrostatic pressure, we extended the hydrostatic model to a fully hydrodynamic model. By localising the computational domain in the corrector step for non-hydrostatic pressure calculations, a hybrid model was developed. There was no prior special treatment on mode switching, and the developed numerical codes were highly efficient and robust. The hybrid model is applicable to the simulation of shallow flows when non-hydrostatic pressure is predominant only in the local domain. Beyond the non-hydrostatic domain, the hydrostatic model is still accurate. The applicability of the hybrid method was validated using several study cases.

  15. Optimal design of supply chain network under uncertainty environment using hybrid analytical and simulation modeling approach

    Science.gov (United States)

    Chiadamrong, N.; Piyathanavong, V.

    2017-12-01

    Models that aim to optimize the design of supply chain networks have gained more interest in the supply chain literature. Mixed-integer linear programming and discrete-event simulation are widely used for such an optimization problem. We present a hybrid approach to support decisions for supply chain network design using a combination of analytical and discrete-event simulation models. The proposed approach is based on iterative procedures until the difference between subsequent solutions satisfies the pre-determined termination criteria. The effectiveness of proposed approach is illustrated by an example, which shows closer to optimal results with much faster solving time than the results obtained from the conventional simulation-based optimization model. The efficacy of this proposed hybrid approach is promising and can be applied as a powerful tool in designing a real supply chain network. It also provides the possibility to model and solve more realistic problems, which incorporate dynamism and uncertainty.

  16. A hybrid local/non-local framework for the simulation of damage and fracture

    KAUST Repository

    Azdoud, Yan

    2014-01-01

    Recent advances in non-local continuum models, notably peridynamics, have spurred a paradigm shift in solid mechanics simulation by allowing accurate mathematical representation of singularities and discontinuities. This doctoral work attempts to extend the use of this theory to a community more familiar with local continuum models. In this communication, a coupling strategy - the morphing method -, which bridges local and non-local models, is presented. This thesis employs the morphing method to ease use of the non-local model to represent problems with failure-induced discontinuities. First, we give a quick review of strategies for the simulation of discrete degradation, and suggest a hybrid local/non-local alternative. Second, we present the technical concepts involved in the morphing method and evaluate the quality of the coupling. Third, we develop a numerical tool for the simulation of the hybrid model for fracture and damage and demonstrate its capabilities on numerical model examples

  17. Functional simulations of power electronics components in series-hybrid machinery for the needs of OEM

    Energy Technology Data Exchange (ETDEWEB)

    Liukkonen, M.; Hentunen, A.; Kyyrae, J. (Department of Electrical Engineering, Helsinki University of Technology, Espoo (Finland)); Suomela, J. (Department of Automation and Systems, Helsinki University of Technology, Espoo (Finland))

    2008-07-01

    A method for rapid control prototyping of the series-hybrid transmission system is proposed in this paper. The rapid control prototyping needs simulation submodels from all system components in order to develop supervisory control software. The same simulation models can also be used to optimize the drive train. The target framework for the rapid control prototyping method is the original equipment manufacturer (OEM), where the objective is to build devices from subcontractor's components. The machinery industry, as a target group, uses high power ratings for the creation of motion, which leads to high voltage and current values used in the system. Therefore, prototyping is started with careful simulations. This paper also seeks to create a general idea about the structure of the series-hybrid power transmission and assists the start of the process for designing the supervisory control. (orig.)

  18. Coding considerations for standalone molecular dynamics simulations of atomistic structures

    Science.gov (United States)

    Ocaya, R. O.; Terblans, J. J.

    2017-10-01

    The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

  19. Molecular dynamics simulation of deformation twin in rocksalt vanadium nitride

    International Nuclear Information System (INIS)

    Fu, Tao; Peng, Xianghe; Zhao, Yinbo; Li, Tengfei; Li, Qibin; Wang, Zhongchang

    2016-01-01

    We perform molecular dynamics simulation of nano-indentation with a cylindrical indenter to investigate the formation mechanism of deformation twin in vanadium nitride (VN) with a rocksalt structure. We find that the deformation twins occur during the loading stage, and subsequently conduct a systematic analysis of nucleation, propagation and thickening of a deformation twin. We find that the nucleation of a partial dislocation and its propagation to form a stacking fault are premise of deformation twin formation. The sequential nucleation and propagation of partial dislocation on adjacent parallel {111} planes are found to cause the thickening of the deformation twin. Moreover, the deformation twins can exist in VN at room temperature. - Highlights: • MD simulations of indentation are performed to study the deformation twin in VN. • The deformation twins can occur in VN during the loading stage. • The nucleation, propagation and thickening of a deformation twin are analyzed. • The deformation twins can exist in VN at room temperature.

  20. Molecular dynamics simulation of radiation damage cascades in diamond

    Energy Technology Data Exchange (ETDEWEB)

    Buchan, J. T. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Robinson, M. [Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia); Christie, H. J.; Roach, D. L.; Ross, D. K. [Physics and Materials Research Centre, School of Computing, Science and Engineering, University of Salford, Salford, Greater Manchester M5 4WT (United Kingdom); Marks, N. A. [Department of Physics and Astronomy, Curtin University, Perth, Western Australia 6845 (Australia); Nanochemistry Research Institute, Curtin University, Perth, Western Australia 6845 (Australia)

    2015-06-28

    Radiation damage cascades in diamond are studied by molecular dynamics simulations employing the Environment Dependent Interaction Potential for carbon. Primary knock-on atom (PKA) energies up to 2.5 keV are considered and a uniformly distributed set of 25 initial PKA directions provide robust statistics. The simulations reveal the atomistic origins of radiation-resistance in diamond and provide a comprehensive computational analysis of cascade evolution and dynamics. As for the case of graphite, the atomic trajectories are found to have a fractal-like character, thermal spikes are absent and only isolated point defects are generated. Quantitative analysis shows that the instantaneous maximum kinetic energy decays exponentially with time, and that the timescale of the ballistic phase has a power-law dependence on PKA energy. Defect recombination is efficient and independent of PKA energy, with only 50% of displacements resulting in defects, superior to graphite where the same quantity is nearly 75%.

  1. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The investigation is based on the stability of the shadow energy, obtained by including the first term in the asymptotic expansion, and on the exact solution of discrete dynamics for a single harmonic mode. The exact solution of discrete dynamics for a harmonic potential with frequency ω gives a criterion...... for the limit of stability h ⩽ 2/ω. Simulations of the Lennard-Jones system and the viscous Kob-Andersen system show that one can use the limit of stability of the shadow energy or the stability criterion for a harmonic mode on the spectrum of instantaneous frequencies to determine the limit of stability of MD...

  2. Molecular dynamics simulations of field emission from a planar nanodiode

    Energy Technology Data Exchange (ETDEWEB)

    Torfason, Kristinn; Valfells, Agust; Manolescu, Andrei [School of Science and Engineering, Reykjavik University, Menntavegur 1, IS-101 Reykjavik (Iceland)

    2015-03-15

    High resolution molecular dynamics simulations with full Coulomb interactions of electrons are used to investigate field emission in planar nanodiodes. The effects of space-charge and emitter radius are examined and compared to previous results concerning transition from Fowler-Nordheim to Child-Langmuir current [Y. Y. Lau, Y. Liu, and R. K. Parker, Phys. Plasmas 1, 2082 (1994) and Y. Feng and J. P. Verboncoeur, Phys. Plasmas 13, 073105 (2006)]. The Fowler-Nordheim law is used to determine the current density injected into the system and the Metropolis-Hastings algorithm to find a favourable point of emission on the emitter surface. A simple fluid like model is also developed and its results are in qualitative agreement with the simulations.

  3. Liquid-vapor coexistence by molecular dynamics simulation

    International Nuclear Information System (INIS)

    Baranyai, Andras; Cummings, Peter T.

    2000-01-01

    We present a simple and consistent molecular dynamics algorithm for determining the equilibrium properties of a bulk liquid and its coexisting vapor phase. The simulation follows the dynamics of the two systems simultaneously while maintaining the volume and the number of particles of the composite system fixed. The thermostat can constrain either the total energy or the temperature at a desired value. Division of the extensive properties between the two phases is governed by the difference of the corresponding intensive state variables. Particle numbers are continuous variables and vary only in virtual sense, i.e., the real sizes of the two systems are the same and do not change during the course of the simulation. Calculation of the chemical potential is separate from the dynamics; thus, one can replace the particle exchange step with other method if it improves the efficiency of the code. (c) 2000 American Institute of Physics

  4. Deformation mechanisms in nanotwinned copper by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xing [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China); Lu, Cheng, E-mail: chenglu@uow.edu.au [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Tieu, Anh Kiet; Pei, Linqing; Zhang, Liang; Su, Lihong [School of Mechanical, Materials and Mechatronic Engineering, University of Wollongong, Wollongong, NSW 2522 (Australia); Zhan, Lihua [State Key Laboratory of High Performance Complex Manufacturing, Central South University, Changsha 410083 (China)

    2017-02-27

    Nanotwinned materials exhibit simultaneous ultrahigh strength and high ductility which is attributed to the interactions between dislocations and twin boundaries but the specific deformation mechanisms are rarely seen in experiments at the atomic level. Here we use large scale molecular dynamics simulations to explore this intricate interplay during the plastic deformation of nanotwinned Cu. We demonstrate that the dominant deformation mechanism transits dynamically from slip transfer to twin boundary migration to slip-twin interactions as the twin boundary orientation changes from horizontal to slant, and then to a vertical direction. Building on the fundamental physics of dislocation processes from computer simulations and combining the available experimental investigations, we unravel the underlying deformation mechanisms for nanotwinned Cu, incorporating all three distinct dislocation processes. Our results give insights into systematically engineering the nanoscale twins to fabricate nanotwinned metals or alloys that have high strength and considerable ductility.

  5. First Principles Modelling of Shape Memory Alloys Molecular Dynamics Simulations

    CERN Document Server

    Kastner, Oliver

    2012-01-01

    Materials sciences relate the macroscopic properties of materials to their microscopic structure and postulate the need for holistic multiscale research. The investigation of shape memory alloys is a prime example in this regard. This particular class of materials exhibits strong coupling of temperature, strain and stress, determined by solid state phase transformations of their metallic lattices. The present book presents a collection of simulation studies of this behaviour. Employing conceptually simple but comprehensive models, the fundamental material properties of shape memory alloys are qualitatively explained from first principles. Using contemporary methods of molecular dynamics simulation experiments, it is shown how microscale dynamics may produce characteristic macroscopic material properties. The work is rooted in the materials sciences of shape memory alloys and  covers  thermodynamical, micro-mechanical  and crystallographical aspects. It addresses scientists in these research fields and thei...

  6. Molecular dynamics simulation of thermal conductivities of superlattice nanowires

    Institute of Scientific and Technical Information of China (English)

    YANG; Juekuan(杨决宽); CHEN; Yunfei(陈云飞); YAN; Jingping(颜景平)

    2003-01-01

    Nonequilibrium molecular dynamics simulations were carried out to investigate heat transfer in superlattice nanowires. Results show that for fixed period length superlattice nanowires, the ratio of the total interfacial thermal resistance to the total thermal resistance and the effective thermal conductivities are invariant with the changes in interface numbers. Increasing the period length leads to an increase in the average interfacial thermal resistance, which indicates that the interfacial thermal resistance depends not only on the materials that constitute the alternating segments of superlattice nanowires, but also on the lattice strain throughout the segments. The modification of the lattice structure due to the lattice mismatch should be taken into account in the acoustic mismatch model. Simulation results also demonstrated the size confinement effect on the thermal conductivities for low dimensional structures, i.e. the thermal conductivities and the interfacial thermal resistance increase as the nanowire cross-sectional area increases.

  7. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    Science.gov (United States)

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  8. Synthesis and molecular modelling studies of phenyl linked oxadiazole-phenylhydrazone hybrids as potent antileishmanial agents.

    Science.gov (United States)

    Taha, Muhammad; Ismail, Nor Hadiani; Imran, Syahrul; Anouar, El Hassane; Selvaraj, Manikandan; Jamil, Waqas; Ali, Muhammad; Kashif, Syed Muhammad; Rahim, Fazal; Khan, Khalid Mohammed; Adenan, Mohd Ilham

    2017-01-27

    Molecular hybridization yielded phenyl linked oxadiazole-benzohydrazones hybrids 6-35 and were evaluated for their antileishmanial potentials. Compound 10, a 3,4-dihydroxy analog with IC 50 value of 0.95 ± 0.01 μM, was found to be the most potent antileishmanial agent (7 times more active) than the standard drug pentamidine (IC 50  = 7.02 ± 0.09 μM). The current series 6-35 conceded in the identification of thirteen (13) potent antileishmanial compounds with the IC 50 values ranging between 0.95 ± 0.01-78.6 ± 1.78 μM. Molecular docking analysis against pteridine reductase (PTR1) were also performed to probe the mode of action. Selectivity index showed that compounds with higher number of hydroxyl groups have low selectivity index. Theoretical stereochemical assignment was also done for certain derivatives by using density functional calculations. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  9. Hybrid Reynolds-Averaged/Large-Eddy Simulations of a Coaxial Supersonic Free-Jet Experiment

    Science.gov (United States)

    Baurle, Robert A.; Edwards, Jack R.

    2010-01-01

    Reynolds-averaged and hybrid Reynolds-averaged/large-eddy simulations have been applied to a supersonic coaxial jet flow experiment. The experiment was designed to study compressible mixing flow phenomenon under conditions that are representative of those encountered in scramjet combustors. The experiment utilized either helium or argon as the inner jet nozzle fluid, and the outer jet nozzle fluid consisted of laboratory air. The inner and outer nozzles were designed and operated to produce nearly pressure-matched Mach 1.8 flow conditions at the jet exit. The purpose of the computational effort was to assess the state-of-the-art for each modeling approach, and to use the hybrid Reynolds-averaged/large-eddy simulations to gather insight into the deficiencies of the Reynolds-averaged closure models. The Reynolds-averaged simulations displayed a strong sensitivity to choice of turbulent Schmidt number. The initial value chosen for this parameter resulted in an over-prediction of the mixing layer spreading rate for the helium case, but the opposite trend was observed when argon was used as the injectant. A larger turbulent Schmidt number greatly improved the comparison of the results with measurements for the helium simulations, but variations in the Schmidt number did not improve the argon comparisons. The hybrid Reynolds-averaged/large-eddy simulations also over-predicted the mixing layer spreading rate for the helium case, while under-predicting the rate of mixing when argon was used as the injectant. The primary reason conjectured for the discrepancy between the hybrid simulation results and the measurements centered around issues related to the transition from a Reynolds-averaged state to one with resolved turbulent content. Improvements to the inflow conditions were suggested as a remedy to this dilemma. Second-order turbulence statistics were also compared to their modeled Reynolds-averaged counterparts to evaluate the effectiveness of common turbulence closure

  10. Evaluation of integration methods for hybrid simulation of complex structural systems through collapse

    Science.gov (United States)

    Del Carpio R., Maikol; Hashemi, M. Javad; Mosqueda, Gilberto

    2017-10-01

    This study examines the performance of integration methods for hybrid simulation of large and complex structural systems in the context of structural collapse due to seismic excitations. The target application is not necessarily for real-time testing, but rather for models that involve large-scale physical sub-structures and highly nonlinear numerical models. Four case studies are presented and discussed. In the first case study, the accuracy of integration schemes including two widely used methods, namely, modified version of the implicit Newmark with fixed-number of iteration (iterative) and the operator-splitting (non-iterative) is examined through pure numerical simulations. The second case study presents the results of 10 hybrid simulations repeated with the two aforementioned integration methods considering various time steps and fixed-number of iterations for the iterative integration method. The physical sub-structure in these tests consists of a single-degree-of-freedom (SDOF) cantilever column with replaceable steel coupons that provides repeatable highlynonlinear behavior including fracture-type strength and stiffness degradations. In case study three, the implicit Newmark with fixed-number of iterations is applied for hybrid simulations of a 1:2 scale steel moment frame that includes a relatively complex nonlinear numerical substructure. Lastly, a more complex numerical substructure is considered by constructing a nonlinear computational model of a moment frame coupled to a hybrid model of a 1:2 scale steel gravity frame. The last two case studies are conducted on the same porotype structure and the selection of time steps and fixed number of iterations are closely examined in pre-test simulations. The generated unbalance forces is used as an index to track the equilibrium error and predict the accuracy and stability of the simulations.

  11. [Molecular classification of breast cancer patients obtained through the technique of chromogenic in situ hybridization (CISH)].

    Science.gov (United States)

    Fernández, Angel; Reigosa, Aldo

    2013-12-01

    Breast cancer is a heterogeneous disease composed of a growing number of biological subtypes, with substantial variability of the disease progression within each category. The aim of this research was to classify the samples object of study according to the molecular classes of breast cancer: luminal A, luminal B, HER2 and triple negative, as a result of the state of HER2 amplification obtained by the technique of chromogenic in situ hybridization (CISH). The sample consisted of 200 biopsies fixed in 10% formalin, processed by standard techniques up to paraffin embedding, corresponding to patients diagnosed with invasive ductal carcinoma of the breast. These biopsies were obtained from patients from private practice and the Institute of Oncology "Dr. Miguel Pérez Carreño", for immunohistochemistry (IHC) of hormone receptors and HER2 made in the Hospital Metropolitano del Norte, Valencia, Venezuela. The molecular classification of the patient's tumors considering the expression of estrogen and progesterone receptors by IHC and HER2 amplification by CISH, allowed those cases originally classified as unknown, since they had an indeterminate (2+) outcome for HER2 expression by IHC, to be grouped into the different molecular classes. Also, this classification permitted that some cases, initially considered as belonging to a molecular class, were assigned to another class, after the revaluation of the HER2 status by CISH.

  12. Dynamics and Thermodynamics of Transthyretin Association from Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Cedrix J. Dongmo Foumthuim

    2018-01-01

    Full Text Available Molecular dynamics simulations are used in this work to probe the structural stability and the dynamics of engineered mutants of transthyretin (TTR, i.e., the double mutant F87M/L110M (MT-TTR and the triple mutant F87M/L110M/S117E (3M-TTR, in relation to wild-type. Free energy analysis from end-point simulations and statistical effective energy functions are used to analyze trajectories, revealing that mutations do not have major impact on protein structure but rather on protein association, shifting the equilibria towards dissociated species. The result is confirmed by the analysis of 3M-TTR which shows dissociation within the first 10 ns of the simulation, indicating that contacts are lost at the dimer-dimer interface, whereas dimers (formed by monomers which pair to form two extended β-sheets appear fairly stable. Overall the simulations provide a detailed view of the dynamics and thermodynamics of wild-type and mutant transthyretins and a rationale of the observed effects.

  13. Hybrid Reynolds-Averaged/Large Eddy Simulation of the Flow in a Model SCRamjet Cavity Flameholder

    Science.gov (United States)

    Baurle, R. A.

    2016-01-01

    Steady-state and scale-resolving simulations have been performed for flow in and around a model scramjet combustor flameholder. Experimental data available for this configuration include velocity statistics obtained from particle image velocimetry. Several turbulence models were used for the steady-state Reynolds-averaged simulations which included both linear and non-linear eddy viscosity models. The scale-resolving simulations used a hybrid Reynolds-averaged/large eddy simulation strategy that is designed to be a large eddy simulation everywhere except in the inner portion (log layer and below) of the boundary layer. Hence, this formulation can be regarded as a wall-modeled large eddy simulation. This e ort was undertaken to not only assess the performance of the hybrid Reynolds-averaged / large eddy simulation modeling approach in a flowfield of interest to the scramjet research community, but to also begin to understand how this capability can best be used to augment standard Reynolds-averaged simulations. The numerical errors were quantified for the steady-state simulations, and at least qualitatively assessed for the scale-resolving simulations prior to making any claims of predictive accuracy relative to the measurements. The steady-state Reynolds-averaged results displayed a high degree of variability when comparing the flameholder fuel distributions obtained from each turbulence model. This prompted the consideration of applying the higher-fidelity scale-resolving simulations as a surrogate "truth" model to calibrate the Reynolds-averaged closures in a non-reacting setting prior to their use for the combusting simulations. In general, the Reynolds-averaged velocity profile predictions at the lowest fueling level matched the particle imaging measurements almost as well as was observed for the non-reacting condition. However, the velocity field predictions proved to be more sensitive to the flameholder fueling rate than was indicated in the measurements.

  14. Statistical Measures to Quantify Similarity between Molecular Dynamics Simulation Trajectories

    Directory of Open Access Journals (Sweden)

    Jenny Farmer

    2017-11-01

    Full Text Available Molecular dynamics simulation is commonly employed to explore protein dynamics. Despite the disparate timescales between functional mechanisms and molecular dynamics (MD trajectories, functional differences are often inferred from differences in conformational ensembles between two proteins in structure-function studies that investigate the effect of mutations. A common measure to quantify differences in dynamics is the root mean square fluctuation (RMSF about the average position of residues defined by C α -atoms. Using six MD trajectories describing three native/mutant pairs of beta-lactamase, we make comparisons with additional measures that include Jensen-Shannon, modifications of Kullback-Leibler divergence, and local p-values from 1-sample Kolmogorov-Smirnov tests. These additional measures require knowing a probability density function, which we estimate by using a nonparametric maximum entropy method that quantifies rare events well. The same measures are applied to distance fluctuations between C α -atom pairs. Results from several implementations for quantitative comparison of a pair of MD trajectories are made based on fluctuations for on-residue and residue-residue local dynamics. We conclude that there is almost always a statistically significant difference between pairs of 100 ns all-atom simulations on moderate-sized proteins as evident from extraordinarily low p-values.

  15. Quantum mechanical force fields for condensed phase molecular simulations

    Science.gov (United States)

    Giese, Timothy J.; York, Darrin M.

    2017-09-01

    Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

  16. Implementation of force distribution analysis for molecular dynamics simulations

    Directory of Open Access Journals (Sweden)

    Seifert Christian

    2011-04-01

    Full Text Available Abstract Background The way mechanical stress is distributed inside and propagated by proteins and other biopolymers largely defines their function. Yet, determining the network of interactions propagating internal strain remains a challenge for both, experiment and theory. Based on molecular dynamics simulations, we developed force distribution analysis (FDA, a method that allows visualizing strain propagation in macromolecules. Results To be immediately applicable to a wide range of systems, FDA was implemented as an extension to Gromacs, a commonly used package for molecular simulations. The FDA code comes with an easy-to-use command line interface and can directly be applied to every system built using Gromacs. We provide an additional R-package providing functions for advanced statistical analysis and presentation of the FDA data. Conclusions Using FDA, we were able to explain the origin of mechanical robustness in immunoglobulin domains and silk fibers. By elucidating propagation of internal strain upon ligand binding, we previously also successfully revealed the functionality of a stiff allosteric protein. FDA thus has the potential to be a valuable tool in the investigation and rational design of mechanical properties in proteins and nano-materials.

  17. Molecular simulations of hydrocarbon lubricants: Impact of molecular architecture on performance properties

    Science.gov (United States)

    Kioupis, Loukas I.

    2000-07-01

    With the increased power of modern computers, molecular modeling has been used widely and proven to be a valuable tool for elucidating the physical processes important in many industrial and engineering problems. Of particular interest to us is the rheology and physical chemistry of complex fluids, such as hydrocarbon lubricants and polymers. The goal is to provide qualitative and quantitative molecular-level explanations for the behavior of such fluids, and provide guidance in the development of new improved materials. For example, during the production of poly-α-olefin (PAO) synthetic lubricants, the number of the isomer skeletal structures that can be obtained is staggering. Which of the countless PAO isomers produce a lubricant with superior performance properties? How does it behave under different operational conditions of temperature, pressure, and shear rate? A fundamental understanding of the effect that molecular structure has on the oil's rheological and lubricant performance is first needed, in order to answer these questions. To serve this purpose, we have developed efficient molecular dynamics (MD) simulation programs, which utilize multiple time step algorithms and parallel computational techniques. This enables us to conduct simulations of typical PAO isomers and compute the viscosity, as well as several other dynamic and static properties, as a function of temperature, pressure, and shear rate. The key molecular mechanisms that determine important macroscopic properties, such as viscosity index, viscosity-pressure coefficient, traction coefficient, and shear thinning behavior are discussed. Based on this analysis, lubricant and traction fluid structures that have a high likelihood of having desirable properties are proposed. In addition, studies on simple alkane mixtures are presented, in an attempt to understand the more complex polydisperse lubricant fluids, their blends, and their interaction with additives.

  18. Microwave imaging for conducting scatterers by hybrid particle swarm optimization with simulated annealing

    International Nuclear Information System (INIS)

    Mhamdi, B.; Grayaa, K.; Aguili, T.

    2011-01-01

    In this paper, a microwave imaging technique for reconstructing the shape of two-dimensional perfectly conducting scatterers by means of a stochastic optimization approach is investigated. Based on the boundary condition and the measured scattered field derived by transverse magnetic illuminations, a set of nonlinear integral equations is obtained and the imaging problem is reformulated in to an optimization problem. A hybrid approximation algorithm, called PSO-SA, is developed in this work to solve the scattering inverse problem. In the hybrid algorithm, particle swarm optimization (PSO) combines global search and local search for finding the optimal results assignment with reasonable time and simulated annealing (SA) uses certain probability to avoid being trapped in a local optimum. The hybrid approach elegantly combines the exploration ability of PSO with the exploitation ability of SA. Reconstruction results are compared with exact shapes of some conducting cylinders; and good agreements with the original shapes are observed.

  19. Simulations of the Fuel Economy and Emissions of Hybrid Transit Buses over Planned Local Routes

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Zhiming [ORNL; LaClair, Tim J [ORNL; Daw, C Stuart [ORNL; Smith, David E [ORNL; Franzese, Oscar [ORNL

    2014-01-01

    We present simulated fuel economy and emissions city transit buses powered by conventional diesel engines and diesel-hybrid electric powertrains of varying size. Six representative city drive cycles were included in the study. In addition, we included previously published aftertreatment device models for control of CO, HC, NOx, and particulate matter (PM) emissions. Our results reveal that bus hybridization can significantly enhance fuel economy by reducing engine idling time, reducing demands for accessory loads, exploiting regenerative braking, and shifting engine operation to speeds and loads with higher fuel efficiency. Increased hybridization also tends to monotonically reduce engine-out emissions, but trends in the tailpipe (post-aftertreatment) emissions involve more complex interactions that significantly depend on motor size and drive cycle details.

  20. Synthesis, spectroscopic characterization, antimicrobial evaluation and molecular docking study of novel triazine-quinazolinone based hybrids

    Science.gov (United States)

    Dinari, Mohammad; Gharahi, Fateme; Asadi, Parvin

    2018-03-01

    A new series of 1,3,5-triazine incorporating aromatic quinazolinone moieties as a potential antimicrobial agents is reported. The first chlorine group of the cyanuric chloride (1) was replaced by aniline and the second one was replaced by various aromatic amines. The prepared monochlorotriazine was allowed to react with hydrazine and subsequently it was reacted with 2-methyl-4H-benzo[1,3]oxazin-4-one to obtain novel triazine-quinazolinone based hybrids (9a-f). The chemical structure and purity of the hybrid compounds were evaluated by different techniques such as thin layer chromatography, melting point, Fourier-transform infrared (FTIR), 1H and 13C NMR spectra and elemental analysis. Antimicrobial activity of the hybrid compounds were study by three Gram-negative bacteria (Salmonella entritidis, Escherichia coli, Pseudomonas aeruginosa) and three Gram-positive bacteria (Staphylococcus aureus, Listeria monocitogenes, Bacillus subtilis) as well as Candida albicansas a yeast-like fungus using the serial broth dilution method. Among them, compound 9d with benzenesulfonamide group showed higher antimicrobial activity with a minimum inhibitory concentration (MIC) value of 16 μg/mL. Furthermore, compounds 5d, 9a and 9b showed good activity against several tested strains. In addition, docking simulation was perform to position best antibacterial compounds in to the S. aureus dihydrofolate reductase (DHFR) active site to determine the probable binding conformations.

  1. Hybrid Network Simulation for the ATLAS Trigger and Data Acquisition (TDAQ) System

    CERN Document Server

    Bonaventura, Matias Alejandro; The ATLAS collaboration; Castro, Rodrigo Daniel; Foguelman, Daniel Jacob

    2015-01-01

    The poster shows the ongoing research in the ATLAS TDAQ group in collaboration with the University of Buenos Aires in the area of hybrid data network simulations. he Data Network and Processing Cluster filters data in real-time, achieving a rejection factor in the order of 40000x and has real-time latency constrains. The dataflow between the processing units (TPUs) and Readout System (ROS) presents a “TCP Incast”-type network pathology which TCP cannot handle it efficiently. A credits system is in place which limits rate of queries and reduces latency. This large computer network, and the complex dataflow has been modelled and simulated using a PowerDEVS, a DEVS-based simulator. The simulation has been validated and used to produce what-if scenarios in the real network. Network Simulation with Hybrid Flows: Speedups and accuracy, combined • For intensive network traffic, Discrete Event simulation models (packet-level granularity) soon becomes prohibitive: Too high computing demands. • Fluid Flow simul...

  2. Molecular Dynamics Simulation of Salt Diffusion in Polyelectrolyte Assemblies.

    Science.gov (United States)

    Zhang, Ran; Duan, Xiaozheng; Ding, Mingming; Shi, Tongfei

    2018-06-05

    The diffusion of salt ions and charged probe molecules in polyelectrolyte assemblies is often assumed to follow a theoretical hopping model, in which the diffusing ion is hopping between charged sites of chains based on electroneutrality. However, experimental verification of diffusing pathway at such microscales is difficult, and the corresponding molecular mechanisms remain elusive. In this study, we perform all-atom molecular dynamics (MD) simulations of salt diffusion in polyelectrolyte (PE) assembly of poly (sodium 4-styrenesulfonate) (PSS) and poly (diallyldimethylammonium chloride) (PDAC). Besides the ion hopping mode, the diffusing trajectories are found presenting common features of a jump process, i.e., subjecting to PE relaxation, water pockets in the structure open and close, thus the ion can move from one pocket to another. Anomalous subdiffusion of ions and water is observed due to the trapping scenarios in these water pockets. The jump events are much rarer compared with ion hopping but significantly increases salt diffusion with increasing temperature. Our result strongly indicates that salt diffusion in hydrated PDAC/PSS is a combined process of ion hopping and jump motion. This provides new molecular explanation for the coupling of salt motion with chain motion and the nonlinear increase of salt diffusion at glass transition temperature.

  3. Modelling dust polarization observations of molecular clouds through MHD simulations

    Science.gov (United States)

    King, Patrick K.; Fissel, Laura M.; Chen, Che-Yu; Li, Zhi-Yun

    2018-03-01

    The BLASTPol observations of Vela C have provided the most detailed characterization of the polarization fraction p and dispersion in polarization angles S for a molecular cloud. We compare the observed distributions of p and S with those obtained in synthetic observations of simulations of molecular clouds, assuming homogeneous grain alignment. We find that the orientation of the mean magnetic field relative to the observer has a significant effect on the p and S distributions. These distributions for Vela C are most consistent with synthetic observations where the mean magnetic field is close to the line of sight. Our results point to apparent magnetic disorder in the Vela C molecular cloud, although it can be due to either an inclination effect (i.e. observing close to the mean field direction) or significant field tangling from strong turbulence/low magnetization. The joint correlations of p with column density and of S with column density for the synthetic observations generally agree poorly with the Vela C joint correlations, suggesting that understanding these correlations requires a more sophisticated treatment of grain alignment physics.

  4. Molecular dynamics simulations of nucleation and phase transitions in molecular clusters of hexafluorides

    International Nuclear Information System (INIS)

    Xu, S.

    1993-01-01

    Molecular dynamics simulations of nucleation and phase transitions in TeF 6 and SeF 6 clusters containing 100-350 molecules were carried out. Simulations successfully reproduced the crystalline structures observed in electron diffraction studies of large clusters (containing about 10 4 molecules) of the same materials. When the clusters were cooled, they spontaneously underwent the same bcc the monoclinic phase transition in simulations as in experiment, despite the million-fold difference in the time scales involved. Other transitions observed included melting and freezing. Several new techniques based on molecular translation and orientation were introduced to identify different condensed phases, to study nucleation and phase transitions, and to define characteristic temperatures of transitions. The solid-state transition temperatures decreased with cluster size in the same way as did the melting temperature, in that the depression of transition temperature was inversely proportional to the cluster radius. Rotational melting temperatures, as inferred from the rotational diffusion of molecules, coincided with those of the solid-state transition. Nucleation in liquid-solid and bcc-monoclinic transitions started in the interior of clusters on cooling, and at the surface on heating. Transition temperatures on cooling were always lower than those on heating due to the barriers to nucleation. Linear growth rates of nuclei in freezing were an order of magnitude lower than those in the bcc-monoclinic transition. Revealing evidence about the molecular behavior associated with phase changes was found. Simulations showed the formation of the actual transition complexes along the transition pathway, i.e., the critical nuclei of the new phase. These nuclei, consisting of a few dozen molecules, were distinguishable in the midst of the surrounding matter

  5. Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1.

    Directory of Open Access Journals (Sweden)

    Min-Sun Park

    Full Text Available Glucose transporters (GLUTs provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and cancer. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE, a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM domains and the intracellular helices (ICH domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states.

  6. On the fragmentation of filaments in a molecular cloud simulation

    Science.gov (United States)

    Chira, R.-A.; Kainulainen, J.; Ibáñez-Mejía, J. C.; Henning, Th.; Mac Low, M.-M.

    2018-03-01

    Context. The fragmentation of filaments in molecular clouds has attracted a lot of attention recently as there seems to be a close relation between the evolution of filaments and star formation. The study of the fragmentation process has been motivated by simple analytical models. However, only a few comprehensive studies have analysed the evolution of filaments using numerical simulations where the filaments form self-consistently as part of large-scale molecular cloud evolution. Aim. We address the early evolution of parsec-scale filaments that form within individual clouds. In particular, we focus on three questions: How do the line masses of filaments evolve? How and when do the filaments fragment? How does the fragmentation relate to the line masses of the filaments? Methods: We examine three simulated molecular clouds formed in kiloparsec-scale numerical simulations performed with the FLASH adaptive mesh refinement magnetohydrodynamic code. The simulations model a self-gravitating, magnetised, stratified, supernova-driven interstellar medium, including photoelectric heating and radiative cooling. We follow the evolution of the clouds for 6 Myr from the time self-gravity starts to act. We identify filaments using the DisPerSe algorithm, and compare the results to other filament-finding algorithms. We determine the properties of the identified filaments and compare them with the predictions of analytic filament stability models. Results: The average line masses of the identified filaments, as well as the fraction of mass in filamentary structures, increases fairly continuously after the onset of self-gravity. The filaments show fragmentation starting relatively early: the first fragments appear when the line masses lie well below the critical line mass of Ostriker's isolated hydrostatic equilibrium solution ( 16 M⊙ pc-1), commonly used as a fragmentation criterion. The average line masses of filaments identified in three-dimensional volume density cubes

  7. 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.

  8. Simulation of Hybrid Photovoltaic Solar Assisted Loop Heat Pipe/Heat Pump System

    Directory of Open Access Journals (Sweden)

    Nannan Dai

    2017-02-01

    Full Text Available A hybrid photovoltaic solar assisted loop heat pipe/heat pump (PV-SALHP/HP water heater system has been developed and numerically studied. The system is the combination of loop heat pipe (LHP mode and heat pump (HP mode, and the two modes can be run separately or compositely according to the weather conditions. The performances of independent heat pump (HP mode and hybrid loop heat pipe/heat pump (LHP/HP mode were simulated and compared. Simulation results showed that on typical sunny days in spring or autumn, using LHP/HP mode could save 40.6% power consumption than HP mode. In addition, the optimal switchover from LHP mode to HP mode was analyzed in different weather conditions for energy saving and the all-year round operating performances of the system were also simulated. The simulation results showed that hybrid LHP/HP mode should be utilized to save electricity on sunny days from March to November and the system can rely on LHP mode alone without any power consumption in July and August. When solar radiation and ambient temperature are low in winter, HP mode should be used

  9. Hybrid Imaging Labels: Providing the Link Between Mass Spectrometry-Based Molecular Pathology and Theranostics

    Science.gov (United States)

    Buckle, Tessa; van der Wal, Steffen; van Malderen, Stijn J.M.; Müller, Larissa; Kuil, Joeri; van Unen, Vincent; Peters, Ruud J.B.; van Bemmel, Margaretha E.M.; McDonnell, Liam A.; Velders, Aldrik H.; Koning, Frits; Vanhaeke, Frank; van Leeuwen, Fijs W. B.

    2017-01-01

    Background: Development of theranostic concepts that include inductively coupled plasma mass spectrometry (ICP-MS) and laser ablation ICP-MS (LA-ICP-MS) imaging can be hindered by the lack of a direct comparison to more standardly used methods for in vitro and in vivo evaluation; e.g. fluorescence or nuclear medicine. In this study a bimodal (or rather, hybrid) tracer that contains both a fluorescent dye and a chelate was used to evaluate the existence of a direct link between mass spectrometry (MS) and in vitro and in vivo molecular imaging findings using fluorescence and radioisotopes. At the same time, the hybrid label was used to determine whether the use of a single isotope label would allow for MS-based diagnostics. Methods: A hybrid label that contained both a DTPA chelate (that was coordinated with either 165Ho or 111In) and a Cy5 fluorescent dye was coupled to the chemokine receptor 4 (CXCR4) targeting peptide Ac-TZ14011 (hybrid-Cy5-Ac-TZ4011). This receptor targeting tracer was used to 1) validate the efficacy of (165Ho-based) mass-cytometry in determining the receptor affinity via comparison with fluorescence-based flow cytometry (Cy5), 2) evaluate the microscopic binding pattern of the tracer in tumor cells using both fluorescence confocal imaging (Cy5) and LA-ICP-MS-imaging (165Ho), 3) compare in vivo biodistribution patterns obtained with ICP-MS (165Ho) and radiodetection (111In) after intravenous administration of hybrid-Cy5-Ac-TZ4011 in tumor-bearing mice. Finally, LA-ICP-MS-imaging (165Ho) was linked to fluorescence-based analysis of excised tissue samples (Cy5). Results: Analysis with both mass-cytometry and flow cytometry revealed a similar receptor affinity, respectively 352 ± 141 nM and 245 ± 65 nM (p = 0.08), but with a much lower detection sensitivity for the first modality. In vitro LA-ICP-MS imaging (165Ho) enabled clear discrimination between CXCR4 positive and negative cells, but fluorescence microscopy was required to determine the

  10. Hybrid simulation: bringing motivation to the art of teamwork training in the operating room.

    Science.gov (United States)

    Kjellin, A; Hedman, L; Escher, C; Felländer-Tsai, L

    2014-12-01

    Crew resource management-based operating room team training will be an evident part of future surgical training. Hybrid simulation in the operating room enables the opportunity for trainees to perform higher fidelity training of technical and non-technical skills in a realistic context. We focus on situational motivation and self-efficacy, two important factors for optimal learning in light of a prototype course for teams of residents in surgery and anesthesiology and nurses. Authentic operating room teams consisting of residents in anesthesia (n = 2), anesthesia nurses (n = 3), residents in surgery (n = 2), and scrub nurses (n = 6) were, during a one-day course, exposed to four different scenarios. Their situational motivation was self-assessed (ranging from 1 = does not correspond at all to 7 = corresponds exactly) immediately after training, and their self-efficacy (graded from 1 to 7) before and after training. Training was performed in a mock-up operating theater equipped with a hybrid patient simulator (SimMan 3G; Laerdal) and a laparoscopic simulator (Lap Mentor Express; Simbionix). The functionality of the systematic hybrid procedure simulation scenario was evaluated by an exit questionnaire (graded from 1 = disagree entirely to 5 = agree completely). The trainees were mostly intrinsically motivated, engaged for their own sake, and had a rather great degree of self-determination toward the training situation. Self-efficacy among the team members improved significantly from 4 to 6 (median). Overall evaluation showed very good result with a median grading of 5. We conclude that hybrid simulation is feasible and has the possibility to train an authentic operating team in order to improve individual motivation and confidence. © The Finnish Surgical Society 2014.

  11. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    Science.gov (United States)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Kunaseth, Manaschai; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Ohmura, Satoshi; Rajak, Pankaj; Shimamura, Kohei; Vashishta, Priya

    2014-05-01

    We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 106-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of techniques

  12. A divide-conquer-recombine algorithmic paradigm for large spatiotemporal quantum molecular dynamics simulations

    International Nuclear Information System (INIS)

    Shimojo, Fuyuki; Hattori, Shinnosuke; Kalia, Rajiv K.; Mou, Weiwei; Nakano, Aiichiro; Nomura, Ken-ichi; Rajak, Pankaj; Vashishta, Priya; Kunaseth, Manaschai; Ohmura, Satoshi; Shimamura, Kohei

    2014-01-01

    We introduce an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large quantum molecular dynamics (QMD) simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). In DCR, the DC phase constructs globally informed, overlapping local-domain solutions, which in the recombine phase are synthesized into a global solution encompassing large spatiotemporal scales. For the DC phase, we design a lean divide-and-conquer (LDC) DFT algorithm, which significantly reduces the prefactor of the O(N) computational cost for N electrons by applying a density-adaptive boundary condition at the peripheries of the DC domains. Our globally scalable and locally efficient solver is based on a hybrid real-reciprocal space approach that combines: (1) a highly scalable real-space multigrid to represent the global charge density; and (2) a numerically efficient plane-wave basis for local electronic wave functions and charge density within each domain. Hybrid space-band decomposition is used to implement the LDC-DFT algorithm on parallel computers. A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786 432 cores for a 50.3 × 10 6 -atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16 661 atoms is performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles. As an example of the recombine phase, LDC-DFT electronic structures are used as a basis set to describe global photoexcitation dynamics with nonadiabatic QMD (NAQMD) and kinetic Monte Carlo (KMC) methods. The NAQMD simulations are based on the linear response time-dependent density functional theory to describe electronic excited states and a surface-hopping approach to describe transitions between the excited states. A series of

  13. DCMS: A data analytics and management system for molecular simulation.

    Science.gov (United States)

    Kumar, Anand; Grupcev, Vladimir; Berrada, Meryem; Fogarty, Joseph C; Tu, Yi-Cheng; Zhu, Xingquan; Pandit, Sagar A; Xia, Yuni

    Molecular Simulation (MS) is a powerful tool for studying physical/chemical features of large systems and has seen applications in many scientific and engineering domains. During the simulation process, the experiments generate a very large number of atoms and intend to observe their spatial and temporal relationships for scientific analysis. The sheer data volumes and their intensive interactions impose significant challenges for data accessing, managing, and analysis. To date, existing MS software systems fall short on storage and handling of MS data, mainly because of the missing of a platform to support applications that involve intensive data access and analytical process. In this paper, we present the database-centric molecular simulation (DCMS) system our team developed in the past few years. The main idea behind DCMS is to store MS data in a relational database management system (DBMS) to take advantage of the declarative query interface ( i.e. , SQL), data access methods, query processing, and optimization mechanisms of modern DBMSs. A unique challenge is to handle the analytical queries that are often compute-intensive. For that, we developed novel indexing and query processing strategies (including algorithms running on modern co-processors) as integrated components of the DBMS. As a result, researchers can upload and analyze their data using efficient functions implemented inside the DBMS. Index structures are generated to store analysis results that may be interesting to other users, so that the results are readily available without duplicating the analysis. We have developed a prototype of DCMS based on the PostgreSQL system and experiments using real MS data and workload show that DCMS significantly outperforms existing MS software systems. We also used it as a platform to test other data management issues such as security and compression.

  14. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    Directory of Open Access Journals (Sweden)

    Sposito Garrison

    2002-09-01

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

  15. Animated molecular dynamics simulations of hydrated caesium-smectite interlayers

    Science.gov (United States)

    Sutton, Rebecca; Sposito, Garrison

    2002-01-01

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

  16. Simulation of lower hybrid current drive in enhanced reversed shear plasmas in the tokamak fusion test reactor using the lower hybrid simulation code

    International Nuclear Information System (INIS)

    Kaita, R.; Bernabei, S.; Budny, R.

    1996-01-01

    The Enhanced Reversed Shear (ERS) mode has already shown great potential for improving the performance of the Tokamak Fusion Test Reactor (TFTR) and other devices. Sustaining the ERS, however, remains an outstanding problem. Lower hybrid (LH) current drive is a possible method for modifying the current profile and controlling its time evolution. To predict its effectiveness in TFTR, the Lower Hybrid Simulation Code (LSC) model is used in the TRANSP code and the Tokamak Simulation Code (TSC). Among the results from the simulations are the following. (1) Single-pass absorption is expected in TFTR ERS plasmas. The simulations show that the LH current follows isotherms of the electron temperature. The ability to control the location of the minimum in the q profile (q min ) has been demonstrated by varying the phase velocity of the launched LH waves and observing the change in the damping location. (2) LH current drive can been used to sustain the q min location. The tendency of qmin to drift inward, as the inductive current diffuses during the formation phase of the reversed shear discharge, is prevented by the LH current driven at a fixed radial location. If this results in an expanded plasma volume with improved confinement as high power neutral beam injection is applied, the high bootstrap currents induced during this phase can then maintain the larger qmin radius. (3) There should be no LH wave damping on energetic beam particles. The values of perpendicular index of refraction in the calculations never exceed about 20, while ions at TFR injection energies are resonant with waves having values closer to 100. Other issues being addressed in the study include the LH current drive efficiency in the presence of high bootstrap currents, and the effect of fast electron diffusion on LH current localization

  17. Improved signal processing approaches in an offline simulation of a hybrid brain–computer interface

    Science.gov (United States)

    Brunner, Clemens; Allison, Brendan Z.; Krusienski, Dean J.; Kaiser, Vera; Müller-Putz, Gernot R.; Pfurtscheller, Gert; Neuper, Christa

    2012-01-01

    In a conventional brain–computer interface (BCI) system, users perform mental tasks that yield specific patterns of brain activity. A pattern recognition system determines which brain activity pattern a user is producing and thereby infers the user’s mental task, allowing users to send messages or commands through brain activity alone. Unfortunately, despite extensive research to improve classification accuracy, BCIs almost always exhibit errors, which are sometimes so severe that effective communication is impossible. We recently introduced a new idea to improve accuracy, especially for users with poor performance. In an offline simulation of a “hybrid” BCI, subjects performed two mental tasks independently and then simultaneously. This hybrid BCI could use two different types of brain signals common in BCIs – event-related desynchronization (ERD) and steady-state evoked potentials (SSEPs). This study suggested that such a hybrid BCI is feasible. Here, we re-analyzed the data from our initial study. We explored eight different signal processing methods that aimed to improve classification and further assess both the causes and the extent of the benefits of the hybrid condition. Most analyses showed that the improved methods described here yielded a statistically significant improvement over our initial study. Some of these improvements could be relevant to conventional BCIs as well. Moreover, the number of illiterates could be reduced with the hybrid condition. Results are also discussed in terms of dual task interference and relevance to protocol design in hybrid BCIs. PMID:20153371

  18. Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

    Science.gov (United States)

    Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

    2015-09-15

    There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

  19. Hybrid simulation models for data-intensive systems

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00473067

    Data-intensive systems are used to access and store massive amounts of data by combining the storage resources of multiple data-centers, usually deployed all over the world, in one system. This enables users to utilize these massive storage capabilities in a simple and efficient way. However, with the growth of these systems it becomes a hard problem to estimate the effects of modifications to the system, such as data placement algorithms or hardware upgrades, and to validate these changes for potential side effects. This thesis addresses the modeling of operational data-intensive systems and presents a novel simulation model which estimates the performance of system operations. The running example used throughout this thesis is the data-intensive system Rucio, which is used as the data man- agement system of the ATLAS experiment at CERN’s Large Hadron Collider. Existing system models in literature are not applicable to data-intensive workflows, as they only consider computational workflows or make assumpti...

  20. 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.

  1. MOLECULAR DYNAMICS SIMULATIONS OF DISPLACEMENT CASCADES IN MOLYBDENUM

    International Nuclear Information System (INIS)

    Smith, Richard Whiting

    2003-01-01

    Molecular dynamics calculations have been employed to simulate displacement cascades in neutron irradiated Mo. A total of 90 simulations were conducted for PKA energies between 1 and 40 keV and temperatures from 298 to 923K. The results suggest very little effect of temperature on final defect count and configuration, but do display a temperature effect on peak defect generation prior to cascade collapse. Cascade efficiency, relative to the NRT model, is computed to lie between 1/4 and 1/3 in agreement with simulations performed on previous systems. There is a tendency for both interstitials and vacancies to cluster together following cascade collapse producing vacancy rich regions surrounded by interstitials. Although coming to rest in close proximity, the point defects comprising the clusters generally do not lie within the nearest neighbor positions of one another, except for the formation of dumbbell di-interstitials. Cascades produced at higher PKA energies (20 or 40 keV) exhibit the formation of subcascades

  2. Molecular Dynamics Simulations of Slip on Curved Surfaces

    Directory of Open Access Journals (Sweden)

    Ross D.A.

    2016-07-01

    Full Text Available We present Molecular Dynamics (MD simulations of liquid water confined within nanoscale geometries, including slit-like and cylindrical graphitic pores. These equilibrium results are used for calculating friction coefficients, which in turn can be used to calculate slip lengths. The slip length is a material property independent of the fluid flow rate. It is therefore a better quantity for study than the fluid velocity at the wall, also known as the slip velocity. Once the slip length has been found as a function of surface curvature, it can be used to parameterise Lattice Boltzmann (LB simulations. These larger scale simulations are able to tell us about how fluid transport is affected by slip in complex geometries; not just limited to single pores. Applications include flow and transport in nano-porous engine valve deposits and gas shales. The friction coefficient is found to be a function of curvature and is higher for fluid on convex surfaces and lower for concave surfaces. Both concave and convex surfaces approach the same value of the friction coefficient, which is constant above some critical radius of curvature, here found to be 7.4 ± 2.9 nm. The constant value of the friction coefficient is 10,000 ± 600 kg m−2 s−1, which is equivalent to a slip length of approximately 67 ± 4 nm.

  3. Functional Annotation of Ion Channel Structures by Molecular Simulation.

    Science.gov (United States)

    Trick, Jemma L; Chelvaniththilan, Sivapalan; Klesse, Gianni; Aryal, Prafulla; Wallace, E Jayne; Tucker, Stephen J; Sansom, Mark S P

    2016-12-06

    Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT 3 R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore. Three increasingly complex simulation analyses are described: water equilibrium densities; single-ion free-energy profiles; and computational electrophysiology. All three approaches correctly predict the 5-HT 3 R crystal structure to represent a functionally closed (i.e., non-conductive) state. We also illustrate the application of water equilibrium density simulations to annotate different conformational states of a glycine receptor. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Sequence-dependent DNA deformability studied using molecular dynamics simulations.

    Science.gov (United States)

    Fujii, Satoshi; Kono, Hidetoshi; Takenaka, Shigeori; Go, Nobuhiro; Sarai, Akinori

    2007-01-01

    Proteins recognize specific DNA sequences not only through direct contact between amino acids and bases, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetrameric sequences sandwiched between CGCG sequences. The deformability of dimeric steps obtained by the simulations is consistent with that by the crystal structures. The simulation results further showed that the conformation and deformability of the tetramers can highly depend on the flanking base pairs. The conformations of xATx tetramers show the most rigidity and are not affected by the flanking base pairs and the xYRx show by contrast the greatest flexibility and change their conformations depending on the base pairs at both ends, suggesting tetramers with the same central dimer can show different deformabilities. These results suggest that analysis of dimeric steps alone may overlook some conformational features of DNA and provide insight into the mechanism of indirect readout during protein-DNA recognition. Moreover, the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

  5. 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.)

  6. 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.

  7. Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

    Science.gov (United States)

    Hu, Pan; Yang, Bin

    2016-01-15

    Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Molecular simulation studies on thermophysical properties with application to working fluids

    CERN Document Server

    Raabe, Gabriele

    2017-01-01

    This book discusses the fundamentals of molecular simulation, starting with the basics of statistical mechanics and providing introductions to Monte Carlo and molecular dynamics simulation techniques. It also offers an overview of force-field models for molecular simulations and their parameterization, with a discussion of specific aspects. The book then summarizes the available know-how for analyzing molecular simulation outputs to derive information on thermophysical and structural properties. Both the force-field modeling and the analysis of simulation outputs are illustrated by various examples. Simulation studies on recently introduced HFO compounds as working fluids for different technical applications demonstrate the value of molecular simulations in providing predictions for poorly understood compounds and gaining a molecular-level understanding of their properties. This book will prove a valuable resource to researchers and students alike.

  9. Predictive simulation of bidirectional Glenn shunt using a hybrid blood vessel model.

    Science.gov (United States)

    Li, Hao; Leow, Wee Kheng; Chiu, Ing-Sh

    2009-01-01

    This paper proposes a method for performing predictive simulation of cardiac surgery. It applies a hybrid approach to model the deformation of blood vessels. The hybrid blood vessel model consists of a reference Cosserat rod and a surface mesh. The reference Cosserat rod models the blood vessel's global bending, stretching, twisting and shearing in a physically correct manner, and the surface mesh models the surface details of the blood vessel. In this way, the deformation of blood vessels can be computed efficiently and accurately. Our predictive simulation system can produce complex surgical results given a small amount of user inputs. It allows the surgeon to easily explore various surgical options and evaluate them. Tests of the system using bidirectional Glenn shunt (BDG) as an application example show that the results produc by the system are similar to real surgical results.

  10. Hardware-in-the-loop-simulation using the example of a compressed-natural-gas hybrid; Hardware-in-the-Loop-Simulation am Beispiel eines Erdgas-Hybridfahrzeugs

    Energy Technology Data Exchange (ETDEWEB)

    Boehm, M.; Mauk, T.; Reuss, H.C. [Univ. Stuttgart (Germany)

    2008-07-01

    This paper deals with the development of hybrid specific software for a compressed natural gas hybrid. After the presentation of the project the software development process is being illustrated. A two phase hardware-in-the-loop simulation is an important part of it. The vehicle model and the modelling process will be described. (orig.)

  11. QM/MM and classical molecular dynamics simulation of histidine-tagged peptide immobilization on nickel surface

    Energy Technology Data Exchange (ETDEWEB)

    Yang Zhenyu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080(China); Zhao Yapu [State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, Beijing 100080 (China)]. E-mail: yzhao@lnm.imech.ac.cn

    2006-05-15

    The hybrid quantum mechanics (QM) and molecular mechanics (MM) method is employed to simulate the His-tagged peptide adsorption to ionized region of nickel surface. Based on the previous experiments, the peptide interaction with one Ni ion is considered. In the QM/MM calculation, the imidazoles on the side chain of the peptide and the metal ion with several neighboring water molecules are treated as QM part calculated by 'GAMESS', and the rest atoms are treated as MM part calculated by 'TINKER'. The integrated molecular orbital/molecular mechanics (IMOMM) method is used to deal with the QM part with the transitional metal. By using the QM/MM method, we optimize the structure of the synthetic peptide chelating with a Ni ion. Different chelate structures are considered. The geometry parameters of the QM subsystem we obtained by QM/MM calculation are consistent with the available experimental results. We also perform a classical molecular dynamics (MD) simulation with the experimental parameters for the synthetic peptide adsorption on a neutral Ni(1 0 0) surface. We find that half of the His-tags are almost parallel with the substrate, which enhance the binding strength. Peeling of the peptide from the Ni substrate is simulated in the aqueous solvent and in vacuum, respectively. The critical peeling forces in the two environments are obtained. The results show that the imidazole rings are attached to the substrate more tightly than other bases in this peptide.

  12. 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

  13. Multibillion-atom Molecular Dynamics Simulations of Plasticity, Spall, and Ejecta

    Science.gov (United States)

    Germann, Timothy C.

    2007-06-01

    Modern supercomputing platforms, such as the IBM BlueGene/L at Lawrence Livermore National Laboratory and the Roadrunner hybrid supercomputer being built at Los Alamos National Laboratory, are enabling large-scale classical molecular dynamics simulations of phenomena that were unthinkable just a few years ago. Using either the embedded atom method (EAM) description of simple (close-packed) metals, or modified EAM (MEAM) models of more complex solids and alloys with mixed covalent and metallic character, simulations containing billions to trillions of atoms are now practical, reaching volumes in excess of a cubic micron. In order to obtain any new physical insights, however, it is equally important that the analysis of such systems be tractable. This is in fact possible, in large part due to our highly efficient parallel visualization code, which enables the rendering of atomic spheres, Eulerian cells, and other geometric objects in a matter of minutes, even for tens of thousands of processors and billions of atoms. After briefly describing the BlueGene/L and Roadrunner architectures, and the code optimization strategies that were employed, results obtained thus far on BlueGene/L will be reviewed, including: (1) shock compression and release of a defective EAM Cu sample, illustrating the plastic deformation accompanying void collapse as well as the subsequent void growth and linkup upon release; (2) solid-solid martensitic phase transition in shock-compressed MEAM Ga; and (3) Rayleigh-Taylor fluid instability modeled using large-scale direct simulation Monte Carlo (DSMC) simulations. I will also describe our initial experiences utilizing Cell Broadband Engine processors (developed for the Sony PlayStation 3), and planned simulation studies of ejecta and spall failure in polycrystalline metals that will be carried out when the full Petaflop Opteron/Cell Roadrunner supercomputer is assembled in mid-2008.

  14. Hybrid computer simulation of the dynamics of the Hoger Onderwijs Reactor

    International Nuclear Information System (INIS)

    Moers, J.C.; Vries, J.W. de.

    1976-01-01

    A distributed parameter model for the dynamics of the Hoger Onderwijs Reactor (HOR) at Delft is presented. The neutronic and the thermodynamic part of this model have been separately implemented on the AD4-IBM1800 Hybrid Computer of the Delft University of Technology Computation Centre. A continuous Space/Discrete Time solution method has been employed. Some test results of the simulation are included

  15. Structure of the lunar wake: Two-dimensional global hybrid simulations

    Czech Academy of Sciences Publication Activity Database

    Trávníček, Pavel; Hellinger, Petr; Schriver, D.; Bale, S. D.

    2005-01-01

    Roč. 32, - (2005), L06102/1-L06102/4 ISSN 0094-8276 R&D Projects: GA ČR(CZ) GA205/05/1011 Grant - others:ESA(XE) PRODEX 14529; NSF(US) INT- 0010111; NASA (US) NAG5-11804 Institutional research plan: CEZ:AV0Z30420517 Keywords : hybrid simulations * lunar wake Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 2.491, year: 2005

  16. Molecular dynamics simulation of displacement cascades in iron-alpha

    International Nuclear Information System (INIS)

    Vascon, R.

    1997-01-01

    Radiation damage by neutrons or ions in bcc iron has been investigated by molecular dynamics simulations using an embedded atom type many-body potential (EAM). Displacement cascades with energies of 1 to 30 keV were generated in the microcanonical system where the number of atoms (up to 1.5 million) is chosen high enough to compensate the fact that the dissipation of energy is not taken into account in our model. The defect number at the end of cascade lifetime was found to be 60 percent of the NRT standard value. This tendency is in good agreement with experimental data. However, compared with other simulations in iron, we found significant differences in the defect production and distribution. The comparison with results obtained form simulations of cascades in other metals, leads on the one hand to a higher value of the defect number in bcc iron than in fcc metals like copper or nickel, and on the other hand to a ratio, between the number of replacements and the number of defects, lower in iron ( 100). We observed the transient melting of the core of the cascade during simulations. We showed that a higher value of the initial iron crystal temperature, as the mass difference between the components of an artificial binary alloy Fe-X(X=Al,Sb,Au,U) both produce a 'cascade effect': a decrease of the number of defects and an increase of the number of replacements. We also showed up the quasi-channeling of some atoms in high energy cascades. They are at the origin of sub-cascades formation; as a result they induce an opposite effect to the 'cascade effect'. (author)

  17. Analysis of actuator delay and its effect on uncertainty quantification for real-time hybrid simulation

    Science.gov (United States)

    Chen, Cheng; Xu, Weijie; Guo, Tong; Chen, Kai

    2017-10-01

    Uncertainties in structure properties can result in different responses in hybrid simulations. Quantification of the effect of these uncertainties would enable researchers to estimate the variances of structural responses observed from experiments. This poses challenges for real-time hybrid simulation (RTHS) due to the existence of actuator delay. Polynomial chaos expansion (PCE) projects the model outputs on a basis of orthogonal stochastic polynomials to account for influences of model uncertainties. In this paper, PCE is utilized to evaluate effect of actuator delay on the maximum displacement from real-time hybrid simulation of a single degree of freedom (SDOF) structure when accounting for uncertainties in structural properties. The PCE is first applied for RTHS without delay to determine the order of PCE, the number of sample points as well as the method for coefficients calculation. The PCE is then applied to RTHS with actuator delay. The mean, variance and Sobol indices are compared and discussed to evaluate the effects of actuator delay on uncertainty quantification for RTHS. Results show that the mean and the variance of the maximum displacement increase linearly and exponentially with respect to actuator delay, respectively. Sensitivity analysis through Sobol indices also indicates the influence of the single random variable decreases while the coupling effect increases with the increase of actuator delay.

  18. Hybrid simulation of scatter intensity in industrial cone-beam computed tomography

    International Nuclear Information System (INIS)

    Thierry, R.; Miceli, A.; Hofmann, J.; Flisch, A.; Sennhauser, U.

    2009-01-01

    A cone-beam computed tomography (CT) system using a 450 kV X-ray tube has been developed to challenge the three-dimensional imaging of parts of the automotive industry in short acquisition time. Because the probability of detecting scattered photons is high regarding the energy range and the area of detection, a scattering correction becomes mandatory for generating reliable images with enhanced contrast detectability. In this paper, we present a hybrid simulator for the fast and accurate calculation of the scattering intensity distribution. The full acquisition chain, from the generation of a polyenergetic photon beam, its interaction with the scanned object and the energy deposit in the detector is simulated. Object phantoms can be spatially described in form of voxels, mathematical primitives or CAD models. Uncollided radiation is treated with a ray-tracing method and scattered radiation is split into single and multiple scattering. The single scattering is calculated with a deterministic approach accelerated with a forced detection method. The residual noisy signal is subsequently deconvoluted with the iterative Richardson-Lucy method. Finally the multiple scattering is addressed with a coarse Monte Carlo (MC) simulation. The proposed hybrid method has been validated on aluminium phantoms with varying size and object-to-detector distance, and found in good agreement with the MC code Geant4. The acceleration achieved by the hybrid method over the standard MC on a single projection is approximately of three orders of magnitude.

  19. Molecular dynamics simulation of dislocations in uranium dioxide

    Energy Technology Data Exchange (ETDEWEB)

    Fossati, Paul [CEA, DEN, DPC, SCCME, F-91191 Gif-sur-Yvette Cedex (France); Van Brutzel, Laurent, E-mail: laurent.vanbrutzel@cea.fr [CEA, DEN, DPC, SCCME, F-91191 Gif-sur-Yvette Cedex (France); Devincre, Benoît [LEM, CNRS-ONERA, 29 avenue de la Division Leclerc, F-92322 Châtillon Cedex (France)

    2013-11-15

    The plasticity of the fluorite structure in UO{sub 2} is investigated with molecular dynamics simulation and empirical potential. The stacking fault energies and the dislocation core structures with Burgers vector a/2 〈110〉 are systematically calculated. All dislocation core structures show a significant increase of the oxygen sub-lattice disorder at temperatures higher than 1500 K. The threshold stress for dislocation glide is found to decrease with increasing temperature but its values is always very high, several GPa at 0 K and several hundred of MPa at 2000 K. A relation between the dislocation mobility dependence with temperature and the increase of the oxygen sub-lattice disorder in the dislocation cores is established.

  20. Molecular dynamic simulations of the sputtering of multilayer organic systems

    CERN Document Server

    Postawa, Z; Piaskowy, J; Krantzman, K; Winograd, N; Garrison, B J

    2003-01-01

    Sputtering of organic overlayers has been modeled using molecular dynamics computer simulations. The investigated systems are composed of benzene molecules condensed into one, two and three layers on an Ag left brace 1 1 1 right brace surface. The formed organic overlayers were bombarded with 4 keV Ar projectiles at normal incidence. The development of the collision cascade in the organic overlayer was investigated. The sputtering yield, mass, internal and kinetic energy distributions of ejected particles have been analyzed as a function of the thickness of the organic layer. The results show that all emission characteristics are sensitive to the variation of layer thickness. Although most of the ejected intact benzene molecules originate from the topmost layer, the emission of particles located initially in second and third layers is significant. The analysis indicates that the metallic substrate plays a dominant role in the ejection of intact organic molecules.

  1. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS

    Energy Technology Data Exchange (ETDEWEB)

    Athanassios Z. Panagiotopoulos

    2009-09-09

    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-04-18

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

  3. Molecular dynamics simulation of annealed ZnO surfaces

    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

    The effect of thermally annealing a slab of wurtzite ZnO, terminated by two surfaces, (0001) (which is oxygen-terminated) and (0001{sup ¯}) (which is Zn-terminated), is investigated via molecular dynamics simulation by using reactive force field (ReaxFF). We found that upon heating beyond a threshold temperature of ∼700 K, surface oxygen atoms begin to sublimate from the (0001) surface. The ratio of oxygen leaving the surface at a given temperature increases as the heating temperature increases. A range of phenomena occurring at the atomic level on the (0001) surface has also been explored, such as formation of oxygen dimers on the surface and evolution of partial charge distribution in the slab during the annealing process. It was found that the partial charge distribution as a function of the depth from the surface undergoes a qualitative change when the annealing temperature is above the threshold temperature.

  4. Molecular Simulation Of Phase Equilibria For Complex Fluids

    International Nuclear Information System (INIS)

    Panagiotopoulos, Athanassios Z.

    2009-01-01

    The general area of this project was the development and application of novel molecular simulation methods for prediction of thermodynamic and structural properties of complex polymeric, surfactant and ionic fluids. Over this project period, we have made considerable progress in developing novel algorithms to meet the computational challenges presented by the strong or long-range interactions in these systems and have generated data for well-defined mod-els that can be used to test theories and compare to experimental data. Overall, 42 archival papers and many invited and contributed presentations and lectures have been based on work supported by this project. 6 PhD, 1 M.S. and 2 postdoctoral students have been associated with this work, as listed in the body of the report.

  5. Molecular dynamics simulations of cluster fission and fusion processes

    DEFF Research Database (Denmark)

    Lyalin, Andrey G.; Obolensky, Oleg I.; Solov'yov, Ilia

    2004-01-01

    Results of molecular dynamics simulations of fission reactions Na_10^2+ --> Na_7^+ +Na_3^+ and Na_18^2+ --> 2Na_9^+ are presented. The dependence of the fission barriers on the isomer structure of the parent cluster is analyzed. It is demonstrated that the energy necessary for removing homothetic...... separation of the daughter fragments begins and/or forming a "neck" between the separating fragments. A novel algorithm for modeling the cluster growth process is described. This approach is based on dynamic search for the most stable cluster isomers and allows one to find the optimized cluster geometries...... groups of atoms from the parent cluster is largely independent of the isomer form of the parent cluster. The importance of rearrangement of the cluster structure during the fission process is elucidated. This rearrangement may include transition to another isomer state of the parent cluster before actual...

  6. Molecular Dynamics Simulations for Resolving Scaling Laws of Polyethylene Melts

    Directory of Open Access Journals (Sweden)

    Kazuaki Z. Takahashi

    2017-01-01

    Full Text Available Long-timescale molecular dynamics simulations were performed to estimate the actual physical nature of a united-atom model of polyethylene (PE. Several scaling laws for representative polymer properties are compared to theoretical predictions. Internal structure results indicate a clear departure from theoretical predictions that assume ideal chain statics. Chain motion deviates from predictions that assume ideal motion of short chains. With regard to linear viscoelasticity, the presence or absence of entanglements strongly affects the duration of the theoretical behavior. Overall, the results indicate that Gaussian statics and dynamics are not necessarily established for real atomistic models of PE. Moreover, the actual physical nature should be carefully considered when using atomistic models for applications that expect typical polymer behaviors.

  7. Molecular dynamics simulations of glycerol glass-forming liquid

    International Nuclear Information System (INIS)

    Blieck, J.; Affouard, F.; Bordat, P.; Lerbret, A.; Descamps, M.

    2005-01-01

    Structural and dynamical properties of liquid glycerol have been investigated by Molecular Dynamics simulations. An improved model based on a slight reparametrisation of the all-atoms AMBER force field used in [R. Chelli, P. Procacci, G. Cardini, R.G.D. Valle, S. Califano, Phys. Chem. Chem. Phys. 1 (1999) 871] is presented. The structure remains satisfactory, qualitatively similar to that obtained from the original model. This new model is also found to reproduce significantly better the diffusion coefficient and the correlations times as they can be deduced from neutron spin echo (NSE) experiments. Structural heterogeneities revealed as a pre-peak of the static structure factor S(Q) close to Q ∼ 0.6 A -1 are observed. Our results are also found compatible with predictions of the Mode Coupling Theory

  8. Molecular dynamics simulation of hydrogen isotope injection into graphene

    International Nuclear Information System (INIS)

    Nakamura, Hiroaki; Takayama, Arimichi; Ito, Atsushi

    2007-07-01

    We reveal the hydrogen isotope effect of three chemical reactions, i.e., the reflection, the absorption and the penetration ratios, by classical molecular dynamics simulation with a modified Brenner's reactive empirical bond order (REBO) potential. We find that the reflection by π-electron does not depend on the mass of the incident isotope, but the peak of the reflection by nuclear moves to higher side of incident energy. In addition to the reflection, we also find that the absorption ratio in the positive z side of the graphene becomes larger, as the mass of the incident isotope becomes larger. On the other hand, the absorption ratio in the negative z side of the graphene becomes smaller. Last, it is found that the penetration ratio does not depend on the mass of the incident isotope because the graphene potential is not affected by the mass. (author)

  9. Acidity constants from DFT-based molecular dynamics simulations

    International Nuclear Information System (INIS)

    Sulpizi, Marialore; Sprik, Michiel

    2010-01-01

    In this contribution we review our recently developed method for the calculation of acidity constants from density functional theory based molecular dynamics simulations. The method is based on a half reaction scheme in which protons are formally transferred from solution to the gas phase. The corresponding deprotonation free energies are computed from the vertical energy gaps for insertion or removal of protons. Combined to full proton transfer reactions, the deprotonation energies can be used to estimate relative acidity constants and also the Broensted pK a when the deprotonation free energy of a hydronium ion is used as a reference. We verified the method by investigating a series of organic and inorganic acids and bases spanning a wide range of pK a values (20 units). The thermochemical corrections for the biasing potentials assisting and directing the insertion are discussed in some detail.

  10. Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics - Monte Carlo Canonical Propagation Algorithm.

    Science.gov (United States)

    Chen, Yunjie; Kale, Seyit; Weare, Jonathan; Dinner, Aaron R; Roux, Benoît

    2016-04-12

    A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method.

  11. Fluorescence in situ hybridization and molecular studies in infertile men with dysplasia of the fibrous sheath.

    Science.gov (United States)

    Baccetti, Baccio; Collodel, Giulia; Gambera, Laura; Moretti, Elena; Serafini, Francesca; Piomboni, Paola

    2005-07-01

    To perform fluorescence in situ hybridization (FISH) and molecular analysis in patients with the genetic sperm defect "dysplasia of the fibrous sheath" (DFS). Retrospective study. Regional Referral Center for Male Infertility, Siena, Italy. Twelve infertile patients with DFS sperm defects. Family history, lymphocytic karyotype, physical and hormonal assays, semen analysis. The DFS sperm phenotype was defined by light, fluorescent, and electron microscopy. Sperm chromosomal constitution was examined by FISH. Gene deletions were tested by polymerase chain reaction. The genetic sperm defect DFS was determined by transmission and scanning electron microscopy. Immunofluorescence staining of A-kinase anchoring protein 4 (AKAP4) showed a moderate and diffuse signal, revealing a disorganized and incompletely assembled fibrous sheath. In 11 of 12 DFS patients, polymerase chain reaction for detecting the presence of partial sequence of AKAP4/AKAP3 binding regions gave positive results. Fluorescence in situ hybridization was performed in decondensed sperm nuclei with probes for chromosomes 18, X, and Y. The mean disomy frequency of chromosome 18 was in the normal range, whereas the mean disomy frequencies of sex chromosomes and diploidies were twice those of controls. These results should be considered when DFS sperm are used in assisted reproductive technology, owing to the high risk of transmission of chromosomal unbalance and of DFS sperm defects to male offspring.

  12. Nanotubule and Tour Molecule Based Molecular Electronics: Suggestion for a Hybrid Approach

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash (Technical Monitor)

    1998-01-01

    Recent experimental and theoretical attempts and results indicate two distinct broad pathways towards future molecular electronic devices and architectures. The first is the approach via Tour type ladder molecules and their junctions which can be fabricated with solution phase chemical approaches. Second are fullerenes or nanotubules and their junctions which may have better conductance, switching and amplifying characteristics but can not be made through well controlled and defined chemical means. A hybrid approach combining the two pathways to take advantage of the characteristics of both is suggested. Dimension and scale of such devices would be somewhere in between isolated molecule and nanotubule based devices but it maybe possible to use self-assembly towards larger functional and logicalunits.

  13. Photoclickable dendritic molecular glue: noncovalent-to-covalent photochemical transformation of protein hybrids.

    Science.gov (United States)

    Uchida, Noriyuki; Okuro, Kou; Niitani, Yamato; Ling, Xiao; Ariga, Takayuki; Tomishige, Michio; Aida, Takuzo

    2013-03-27

    A water-soluble dendron with a fluorescein isothiocyanate (FITC) fluorescent label and bearing nine pendant guanidinium ion (Gu(+))/benzophenone (BP) pairs at its periphery (Glue(BP)-FITC) serves as a "photoclickable molecular glue". By multivalent salt-bridge formation between Gu(+) ions and oxyanions, Glue(BP)-FITC temporarily adheres to a kinesin/microtubule hybrid. Upon subsequent exposure to UV light, this noncovalent binding is made permanent via a cross-linking reaction mediated by carbon radicals derived from the photoexcited BP units. This temporal-to-permanent transformation by light occurs quickly and efficiently in this preorganized state, allowing the movements of microtubules on a kinesin-coated glass plate to be photochemically controlled. A fundamental difference between such temporal and permanent bindings was visualized by the use of "optical tweezers".

  14. Hybrid simulations of Z-Pinches in support of wire array implosion experiments at NTF

    International Nuclear Information System (INIS)

    Sotnikov, Vladimir Isaakovich; Oliver, Bryan Velten; Ivanov, Vladimir V.; LePell, Paul David; Fedin, Dmitry; Kantsyrev, Victor Leonidovich; Coverdale, Christine Anne; Travnicek, P.; Deeney, Christopher; Hellinger, P.; Jones, B.; Leboeuf, J.N.; Cowan, Thomas E.; Safronova, Alla S.

    2005-01-01

    Three-dimensional hybrid simulation of a plasma current-carrying column reveal two different regimes of sausage and kink instability development. In the first regime, with small Hall parameter, development of instabilities leads to the appearance of large-scale axial perturbations and eventually to bending of the plasma column. In the second regime, with a four-times-larger Hall parameter, small-scale perturbations dominate and no bending of the plasma column is observed. Simulation results are compared with laser probing experimental data obtained during wire array implosions on the Zebra pulse power generator at the Nevada Terawatt Facility.

  15. Adaptive multi-rate interface: development and experimental verification for real-time hybrid simulation

    DEFF Research Database (Denmark)

    Maghareh, Amin; Waldbjørn, Jacob Paamand; Dyke, Shirley J.

    2016-01-01

    Real-time hybrid simulation (RTHS) is a powerful cyber-physical technique that is a relatively cost-effective method to perform global/local system evaluation of structural systems. A major factor that determines the ability of an RTHS to represent true system-level behavior is the fidelity...... of the numerical substructure. While the use of higher-order models increases fidelity of the simulation, it also increases the demand for computational resources. Because RTHS is executed at real-time, in a conventional RTHS configuration, this increase in computational resources may limit the achievable sampling...

  16. Microstructure in two- and three-dimensional hybrid simulations of perpendicular collisionless shocks

    Czech Academy of Sciences Publication Activity Database

    Burgess, D.; Hellinger, Petr; Gingell, I.; Trávníček, Pavel M.

    2016-01-01

    Roč. 82, č. 4 (2016), 905820401/1-905820401/23 ISSN 0022-3778 Institutional support: RVO:68378289 Keywords : ion-acceleration * numerical simulations * bow shock * electron acceleration * cluster observations * self-reformation * magnetic-field * whistler waves * injection * nonstationarity Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.160, year: 2016 https://www.cambridge.org/core/ journals /journal-of-plasma-physics/article/microstructure-in-two-and-three-dimensional-hybrid-simulations-of-perpendicular-collisionless-shocks/F964EF89FB14A6504A49CFAD54970E2B

  17. Molecular Dynamics Simulation of High Density DNA Arrays

    Directory of Open Access Journals (Sweden)

    Rudolf Podgornik

    2018-01-01

    Full Text Available Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and

  18. Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

    Science.gov (United States)

    Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

    2018-01-01

    Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.

  19. Molecular Simulation of Gas Solubility in Nitrile Butadiene Rubber.

    Science.gov (United States)

    Khawaja, M; Sutton, A P; Mostofi, A A

    2017-01-12

    Molecular simulation is used to compute the solubility of small gases in nitrile butadiene rubber (NBR) with a Widom particle-insertion technique biased by local free volume. The convergence of the method is examined as a function of the number of snapshots upon which the insertions are performed and the number of insertions per snapshot and is compared to the convergence of the unbiased Widom insertion technique. The effect of varying the definition of local free volume is also investigated. The acrylonitrile content of the polymer is altered to examine its influence on the solubility of helium, CO 2 , and H 2 O, and the solubilities of polar gases are found to be enhanced relative to those of nonpolar gases, in qualitative agreement with experiment. To probe this phenomenon further, the solubilities are decomposed into contributions from the neighborhoods of different atoms, using a Voronoi cell construction, and a strong bias is found for CO 2 and H 2 O in particular to be situated near nitrogen sites in the elastomer. Temperature is shown to suppress the solubility of CO 2 and H 2 O but to increase that of helium. Increasing pressure is found to suppress the solubility of all gases but at different rates, according to a balance between their molecular sizes and electrostatic interactions with the polymer. These results are relevant to the use of NBR seals at elevated temperatures and pressures, such as in oil and gas wells.

  20. Excipient-assisted vinpocetine nanoparticles: experiments and molecular dynamic simulations.

    Science.gov (United States)

    Li, Cai-Xia; Wang, Hao-Bo; Oppong, Daniel; Wang, Jie-Xin; Chen, Jian-Feng; Le, Yuan

    2014-11-03

    Hydrophilic excipients can be used to increase the solubility and bioavailability of poorly soluble drugs. In this work, the conventional water-soluble pharmaceutical excipients hydroxypropylmethylcellulose (HPMC), polyvinylpyrrolidone (PVP), and lactose (LAC) were used as solid supports to prevent drug nanoparticles from aggregation and enhance drug dissolution. Excipient-assisted vinpocetine (VIN) nanoparticles were prepared by reactive precipitation. The analysis results indicated that HPMC was a suitable excipient to prepare VIN nanoparticles. VIN/HPMC nanoparticles had a mean size of 130 nm within a narrow distribution. The dissolution rate of VIN nanoparticles was significantly faster than those of a physical mixture of VIN/HPMC and raw VIN. VIN/HPMC nanoparticles had a higher dissolution profile than VIN/PVP and VIN/LAC nanoparticles. Besides, molecular dynamics (MD) simulation was applied to investigate the molecular interactions between VIN and excipients. The calculated results revealed that VIN interacted with excipients by Coulomb and Lennard-Jones (LJ) interactions. Few hydrogen bonds were formed between VIN and excipients. The HPMC affording smaller particle size may be a result of the stronger interactions between VIN and HPMC (mainly LJ interaction) and the property of HPMC. These characteristics may greatly influence the adsorption behavior and may be the crucial parameter for the better performance of HPMC.