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Sample records for replica exchange sampling

  1. Scalable replica-exchange framework for Wang-Landau sampling.

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P

    2014-08-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  2. Scalable replica-exchange framework for Wang-Landau sampling

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P.

    2014-08-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  3. Scalable replica-exchange framework for Wang Landau sampling

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, Thomas [University of Georgia, Athens, GA; Li, Ying Wai [ORNL; Wuest, Thomas [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA

    2014-01-01

    We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we apply it to lattice spin models, the self-assembly process in amphiphilic solutions, and the adsorption of molecules on surfaces. While of general, current interest, the latter phenomena are challenging to study computationally because of multiple structural transitions occurring over a broad temperature range. We show how the parallel framework facilitates simulations of such processes and, without any loss of accuracy or precision, gives a significant speedup and allows for the study of much larger systems and much wider temperature ranges than possible with single-walker methods.

  4. Implementation of replica-exchange umbrella sampling in the DFTB + semiempirical quantum chemistry package

    Science.gov (United States)

    Ito, Shingo; Irle, Stephan; Okamoto, Yuko

    2016-07-01

    The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB + quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB + combination.

  5. Accelerating the convergence of replica exchange simulations using Gibbs sampling and adaptive temperature sets

    CERN Document Server

    Vogel, Thomas

    2015-01-01

    We recently introduced a novel replica-exchange scheme in which an individual replica can sample from states encountered by other replicas at any previous time by way of a global configuration database, enabling the fast propagation of relevant states through the whole ensemble of replicas. This mechanism depends on the knowledge of global thermodynamic functions which are measured during the simulation and not coupled to the heat bath temperatures driving the individual simulations. Therefore, this setup also allows for a continuous adaptation of the temperature set. In this paper, we will review the new scheme and demonstrate its capability. The method is particularly useful for the fast and reliable estimation of the microcanonical temperature T(U) or, equivalently, of the density of states g(U) over a wide range of energies.

  6. Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

    Science.gov (United States)

    Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

    2014-01-01

    Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

  7. Performance of replica-exchange Wang-Landau sampling for the study of spin systems

    Science.gov (United States)

    Li, Ying Wai; Eisenbach, Markus; Vogel, Thomas; Wüst, Thomas; Landau, David P.

    2014-03-01

    The recently proposed replica-exchange Wang-Landau sampling (REWL) is a novel, massively parallel Monte Carlo method which allows for the parallelization of Wang-Landau sampling based on a replica-exchange framework. The robustness of the scheme is demonstrated by its broad applicability on a variety of spin systems: from the simplest models with discrete or continuous energy domains, to complex systems captured by large-scale first principles density functional theory calculations. The accuracy of REWL is studied by comparing the thermodynamic properties with exact solutions and results obtained by the original, serial Wang-Landau sampling. The principles for the speed-up, the strong and weak scaling behavior of REWL are also investigated when different parameter settings are employed. We will show, with the aid of selected spin systems, that the method accelerates the simulations significantly with a possible improved accuracy. Phys. Rev. Lett. 110, 210603 (2013)

  8. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

    CERN Document Server

    Li, Ying Wai; Wüst, Thomas; Landau, David P

    2014-01-01

    We introduce a generic, parallel Wang-Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang-Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  9. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling

    Science.gov (United States)

    Li, Ying Wai; Vogel, Thomas; Wüst, Thomas; Landau, David P.

    2014-05-01

    We introduce a generic, parallel Wang-Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang-Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  10. A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang Landau sampling

    Energy Technology Data Exchange (ETDEWEB)

    Li, Ying Wai [ORNL; Vogel, Thomas [Los Alamos National Laboratory (LANL); Wuest, Thomas [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA

    2014-01-01

    We introduce a generic, parallel Wang Landau method that is naturally suited to implementation on massively parallel, petaflop supercomputers. The approach introduces a replica-exchange framework in which densities of states for overlapping sub-windows in energy space are determined iteratively by traditional Wang Landau sampling. The advantages and general applicability of the method are demonstrated for several distinct systems that possess discrete or continuous degrees of freedom, including those with complex free energy landscapes and topological constraints.

  11. Enhanced Conformational Sampling using Replica Exchange with Collective-Variable Tempering

    CERN Document Server

    Gil-Ley, Alejandro

    2015-01-01

    The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strength of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

  12. Evaluation of enhanced sampling provided by accelerated molecular dynamics with Hamiltonian replica exchange methods.

    Science.gov (United States)

    Roe, Daniel R; Bergonzo, Christina; Cheatham, Thomas E

    2014-04-03

    Many problems studied via molecular dynamics require accurate estimates of various thermodynamic properties, such as the free energies of different states of a system, which in turn requires well-converged sampling of the ensemble of possible structures. Enhanced sampling techniques are often applied to provide faster convergence than is possible with traditional molecular dynamics simulations. Hamiltonian replica exchange molecular dynamics (H-REMD) is a particularly attractive method, as it allows the incorporation of a variety of enhanced sampling techniques through modifications to the various Hamiltonians. In this work, we study the enhanced sampling of the RNA tetranucleotide r(GACC) provided by H-REMD combined with accelerated molecular dynamics (aMD), where a boosting potential is applied to torsions, and compare this to the enhanced sampling provided by H-REMD in which torsion potential barrier heights are scaled down to lower force constants. We show that H-REMD and multidimensional REMD (M-REMD) combined with aMD does indeed enhance sampling for r(GACC), and that the addition of the temperature dimension in the M-REMD simulations is necessary to efficiently sample rare conformations. Interestingly, we find that the rate of convergence can be improved in a single H-REMD dimension by simply increasing the number of replicas from 8 to 24 without increasing the maximum level of bias. The results also indicate that factors beyond replica spacing, such as round trip times and time spent at each replica, must be considered in order to achieve optimal sampling efficiency.

  13. Replica-exchange Wang Landau sampling: pushing the limits of Monte Carlo simulations in materials sciences

    Energy Technology Data Exchange (ETDEWEB)

    Perera, Meewanage Dilina N [ORNL; Li, Ying Wai [ORNL; Eisenbach, Markus [ORNL; Vogel, Thomas [Los Alamos National Laboratory (LANL); Landau, David P [University of Georgia, Athens

    2015-01-01

    We describe the study of thermodynamics of materials using replica-exchange Wang Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang Landau Monte Carlo method. To evaluate the performance and scalability of the method, we investigate the magnetic phase transition in body-centered cubic (bcc) iron using the classical Heisenberg model parameterized with first principles calculations. We demonstrate that our framework leads to a significant speedup without compromising the accuracy and precision and facilitates the study of much larger systems than is possible with its serial counterpart.

  14. Reordering hydrogen bonds using hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems.

    Science.gov (United States)

    Vreede, Jocelyne; Wolf, Maarten G; de Leeuw, Simon W; Bolhuis, Peter G

    2009-05-07

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in an alternating way significantly accelerates the folding process (Wolf, M. G.; de Leeuw, S. W. Biophys. J. 2008, 94, 3742). As the biasing potentials are only active during a fixed time interval, this alternating scheme does not represent a thermodynamic equilibrium. In this work, we present a Hamiltonian replica exchange molecular dynamics (REMD) scheme that aims to shuffle and reorder hydrogen bonds in the protein backbone. We therefore apply adapted hydrogen bond potentials in a Hamiltonian REMD scheme, which we call hydrogen bond switching (HS). To compare the performance of the HS to a standard REMD method, we performed HS and temperature REMD simulations of a beta-heptapeptide in methanol. Both methods sample the conformational space to a similar extent. As the HS simulation required only five replicas, while the REMD simulation required 20 replicas, the HS method is significantly more efficient. We tested the HS method also on a larger system, 16-residue polyalanine in water. Both of the simulations starting from a completely unfolded and a folded conformation resulted in an ensemble with, apart from the starting structure, similar conformational minima. We can conclude that the HS method provides an efficient way to sample the conformational space of a protein, without requiring knowledge of the folded states beforehand. In addition, these simulations revealed that convergence was hampered by replicas having a preference for specific biasing potentials. As this sorting effect is inherent to any Hamiltonian REMD method, finding a solution will result in an additional increase in the efficiency of Hamiltonian REMD methods in general.

  15. Enhanced conformational sampling of nucleic acids by a new Hamiltonian replica exchange molecular dynamics approach.

    Science.gov (United States)

    Curuksu, Jeremy; Zacharias, Martin

    2009-03-14

    Although molecular dynamics (MD) simulations have been applied frequently to study flexible molecules, the sampling of conformational states separated by barriers is limited due to currently possible simulation time scales. Replica-exchange (Rex)MD simulations that allow for exchanges between simulations performed at different temperatures (T-RexMD) can achieve improved conformational sampling. However, in the case of T-RexMD the computational demand grows rapidly with system size. A Hamiltonian RexMD method that specifically enhances coupled dihedral angle transitions has been developed. The method employs added biasing potentials as replica parameters that destabilize available dihedral substates and was applied to study coupled dihedral transitions in nucleic acid molecules. The biasing potentials can be either fixed at the beginning of the simulation or optimized during an equilibration phase. The method was extensively tested and compared to conventional MD simulations and T-RexMD simulations on an adenine dinucleotide system and on a DNA abasic site. The biasing potential RexMD method showed improved sampling of conformational substates compared to conventional MD simulations similar to T-RexMD simulations but at a fraction of the computational demand. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions including explicit solvent and ions and can be easily extended to other types of molecules.

  16. Exchange frequency in replica exchange molecular dynamics

    Science.gov (United States)

    Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.

    2008-01-01

    The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that sampling efficiency increases with increasing exchange-attempt frequency. This conclusion is contrary to a commonly expressed view in REMD. Five peptides (1-21 residues long) are studied with a spectrum of exchange-attempt rates. Convergence rates are gauged by comparing ensemble properties between fixed length test REMD simulations and longer reference simulations. To show the fundamental correlation between exchange frequency and convergence time, a simple model is designed and studied, displaying the same basic behavior of much more complex systems.

  17. Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

    Energy Technology Data Exchange (ETDEWEB)

    Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk [Department of Computer Engineering, International Balkan University, Tashko Karadza 11A, Skopje (Macedonia, The Former Yugoslav Republic of)

    2015-09-28

    In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

  18. Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations.

    Science.gov (United States)

    Zeller, Fabian; Zacharias, Martin

    2014-02-11

    The accurate calculation of potentials of mean force for ligand-receptor binding is one of the most important applications of molecular simulation techniques. Typically, the separation distance between ligand and receptor is chosen as a reaction coordinate along which a PMF can be calculated with the aid of umbrella sampling (US) techniques. In addition, restraints can be applied on the relative position and orientation of the partner molecules to reduce accessible phase space. An approach combining such phase space reduction with flattening of the free energy landscape and configurational exchanges has been developed, which significantly improves the convergence of PMF calculations in comparison with standard umbrella sampling. The free energy surface along the reaction coordinate is smoothened by iteratively adapting biasing potentials corresponding to previously calculated PMFs. Configurations are allowed to exchange between the umbrella simulation windows via the Hamiltonian replica exchange method. The application to a DNA molecule in complex with a minor groove binding ligand indicates significantly improved convergence and complete reversibility of the sampling along the pathway. The calculated binding free energy is in excellent agreement with experimental results. In contrast, the application of standard US resulted in large differences between PMFs calculated for association and dissociation pathways. The approach could be a useful alternative to standard US for computational studies on biomolecular recognition processes.

  19. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    Science.gov (United States)

    Valentim, Alexandra; Rocha, Julio C. S.; Tsai, Shan-Ho; Li, Ying Wai; Eisenbach, Markus; Fiore, Carlos E.; Landau, David P.

    2015-09-01

    We considered a higher-dimensional extension for the replica-exchange Wang- Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.

  20. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    Energy Technology Data Exchange (ETDEWEB)

    Valentim, Alexandra [University of Georgia, Athens, GA; Rocha, Julio C. S. [Universidade Federal de Minas Gerais; Tsai, Shan-Ho [University of Georgia, Athens, GA; Li, Ying Wai [ORNL; Eisenbach, Markus [ORNL; Fiore, Carlos E [University of Sao Paulo, BRAZIL; Landau, David P [University of Georgia, Athens, GA

    2015-01-01

    We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this diculty, allowing exploration of higher parameter phase space by keeping track of the joint density of states.

  1. Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space

    CERN Document Server

    Valentim, Alexandra; Tsai, Shan-Ho; Li, Ying Wai; Eisenbach, Markus; Fiore, Carlos E; Landau, David P

    2015-01-01

    We considered a higher-dimensional extension for the replica-exchange Wang-Landau algorithm to perform a random walk in the energy and magnetization space of the two-dimensional Ising model. This hybrid scheme combines the advantages of Wang-Landau and Replica-Exchange algorithms, and the one-dimensional version of this approach has been shown to be very efficient and to scale well, up to several thousands of computing cores. This approach allows us to split the parameter space of the system to be simulated into several pieces and still perform a random walk over the entire parameter range, ensuring the ergodicity of the simulation. Previous work, in which a similar scheme of parallel simulation was implemented without using replica exchange and with a different way to combine the result from the pieces, led to discontinuities in the final density of states over the entire range of parameters. From our simulations, it appears that the replica-exchange Wang-Landau algorithm is able to overcome this difficulty,...

  2. Using the multi-objective optimization replica exchange Monte Carlo enhanced sampling method for protein-small molecule docking.

    Science.gov (United States)

    Wang, Hongrui; Liu, Hongwei; Cai, Leixin; Wang, Caixia; Lv, Qiang

    2017-07-10

    In this study, we extended the replica exchange Monte Carlo (REMC) sampling method to protein-small molecule docking conformational prediction using RosettaLigand. In contrast to the traditional Monte Carlo (MC) and REMC sampling methods, these methods use multi-objective optimization Pareto front information to facilitate the selection of replicas for exchange. The Pareto front information generated to select lower energy conformations as representative conformation structure replicas can facilitate the convergence of the available conformational space, including available near-native structures. Furthermore, our approach directly provides min-min scenario Pareto optimal solutions, as well as a hybrid of the min-min and max-min scenario Pareto optimal solutions with lower energy conformations for use as structure templates in the REMC sampling method. These methods were validated based on a thorough analysis of a benchmark data set containing 16 benchmark test cases. An in-depth comparison between MC, REMC, multi-objective optimization-REMC (MO-REMC), and hybrid MO-REMC (HMO-REMC) sampling methods was performed to illustrate the differences between the four conformational search strategies. Our findings demonstrate that the MO-REMC and HMO-REMC conformational sampling methods are powerful approaches for obtaining protein-small molecule docking conformational predictions based on the binding energy of complexes in RosettaLigand.

  3. Enhanced conformational sampling using replica exchange with concurrent solute scaling and hamiltonian biasing realized in one dimension.

    Science.gov (United States)

    Yang, Mingjun; Huang, Jing; MacKerell, Alexander D

    2015-06-09

    Replica exchange (REX) is a powerful computational tool for overcoming the quasi-ergodic sampling problem of complex molecular systems. Recently, several multidimensional extensions of this method have been developed to realize exchanges in both temperature and biasing potential space or the use of multiple biasing potentials to improve sampling efficiency. However, increased computational cost due to the multidimensionality of exchanges becomes challenging for use on complex systems under explicit solvent conditions. In this study, we develop a one-dimensional (1D) REX algorithm to concurrently combine the advantages of overall enhanced sampling from Hamiltonian solute scaling and the specific enhancement of collective variables using Hamiltonian biasing potentials. In the present Hamiltonian replica exchange method, termed HREST-BP, Hamiltonian solute scaling is applied to the solute subsystem, and its interactions with the environment to enhance overall conformational transitions and biasing potentials are added along selected collective variables associated with specific conformational transitions, thereby balancing the sampling of different hierarchical degrees of freedom. The two enhanced sampling approaches are implemented concurrently allowing for the use of a small number of replicas (e.g., 6 to 8) in 1D, thus greatly reducing the computational cost in complex system simulations. The present method is applied to conformational sampling of two nitrogen-linked glycans (N-glycans) found on the HIV gp120 envelope protein. Considering the general importance of the conformational sampling problem, HREST-BP represents an efficient procedure for the study of complex saccharides, and, more generally, the method is anticipated to be of general utility for the conformational sampling in a wide range of macromolecular systems.

  4. Onsager-Machlup action-based path sampling and its combination with replica exchange for diffusive and multiple pathways.

    Science.gov (United States)

    Fujisaki, Hiroshi; Shiga, Motoyuki; Kidera, Akinori

    2010-04-07

    For sampling multiple pathways in a rugged energy landscape, we propose a novel action-based path sampling method using the Onsager-Machlup action functional. Inspired by the Fourier-path integral simulation of a quantum mechanical system, a path in Cartesian space is transformed into that in Fourier space, and an overdamped Langevin equation is derived for the Fourier components to achieve a canonical ensemble of the path at a finite temperature. To avoid "path trapping" around an initially guessed path, the path sampling method is further combined with a powerful sampling technique, the replica exchange method. The principle and algorithm of our method is numerically demonstrated for a model two-dimensional system with a bifurcated potential landscape. The results are compared with those of conventional transition path sampling and the equilibrium theory, and the error due to path discretization is also discussed.

  5. Replica trick for rare samples

    Science.gov (United States)

    Rizzo, Tommaso

    2014-05-01

    In the context of disordered systems with quenched Hamiltonians I address the problem of characterizing rare samples where the thermal average of a specific observable has a value different from the typical one. These rare samples can be selected through a variation of the replica trick which amounts to replicating the system and dividing the replicas intwo two groups containing, respectively, M and -M replicas. Replicas in the first (second) group experience a positive (negative) small field O (1/M) conjugate to the observable considered and the M →∞ limit is to be taken in the end. Applications to the random-field Ising model and to the Sherrington-Kirkpatrick model are discussed.

  6. A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events

    Science.gov (United States)

    Swenson, David W. H.; Bolhuis, Peter G.

    2014-07-01

    The multiple state transition interface sampling (TIS) framework in principle allows the simulation of a large network of complex rare event transitions, but in practice suffers from convergence problems. To improve convergence, we combine multiple state TIS [J. Rogal and P. G. Bolhuis, J. Chem. Phys. 129, 224107 (2008)] with replica exchange TIS [T. S. van Erp, Phys. Rev. Lett. 98, 268301 (2007)]. In addition, we introduce multiple interface sets, which allow more than one order parameter to be defined for each state. We illustrate the methodology on a model system of multiple independent dimers, each with two states. For reaction networks with up to 64 microstates, we determine the kinetics in the microcanonical ensemble, and discuss the convergence properties of the sampling scheme. For this model, we find that the kinetics depend on the instantaneous composition of the system. We explain this dependence in terms of the system's potential and kinetic energy.

  7. Asynchronous replica exchange software for grid and heterogeneous computing

    Science.gov (United States)

    Gallicchio, Emilio; Xia, Junchao; Flynn, William F.; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M.

    2015-11-01

    Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices.

  8. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

    Science.gov (United States)

    Gallicchio, Emilio; Xia, Junchao; Flynn, William F.; Zhang, Baofeng; Samlalsingh, Sade; Mentes, Ahmet; Levy, Ronald M.

    2015-01-01

    Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture of a software (named ASyncRE) for performing asynchronous replica exchange molecular simulations on volunteered computing grids and heterogeneous high performance clusters. The asynchronous replica exchange algorithm on which the software is based avoids centralized synchronization steps and the need for direct communication between remote processes. It allows molecular dynamics threads to progress at different rates and enables parameter exchanges among arbitrary sets of replicas independently from other replicas. ASyncRE is written in Python following a modular design conducive to extensions to various replica exchange schemes and molecular dynamics engines. Applications of the software for the modeling of association equilibria of supramolecular and macromolecular complexes on BOINC campus computational grids and on the CPU/MIC heterogeneous hardware of the XSEDE Stampede supercomputer are illustrated. They show the ability of ASyncRE to utilize large grids of desktop computers running the Windows, MacOS, and/or Linux operating systems as well as collections of high performance heterogeneous hardware devices. PMID:27103749

  9. Simulating Replica Exchange: Markov State Models, Proposal Schemes, and the Infinite Swapping Limit.

    Science.gov (United States)

    Zhang, Bin W; Dai, Wei; Gallicchio, Emilio; He, Peng; Xia, Junchao; Tan, Zhiqiang; Levy, Ronald M

    2016-08-25

    Replica exchange molecular dynamics is a multicanonical simulation technique commonly used to enhance the sampling of solvated biomolecules on rugged free energy landscapes. While replica exchange is relatively easy to implement, there are many unanswered questions about how to use this technique most efficiently, especially because it is frequently the case in practice that replica exchange simulations are not fully converged. A replica exchange cycle consists of a series of molecular dynamics steps of a set of replicas moving under different Hamiltonians or at different thermodynamic states followed by one or more replica exchange attempts to swap replicas among the different states. How the replica exchange cycle is constructed affects how rapidly the system equilibrates. We have constructed a Markov state model of replica exchange (MSMRE) using long molecular dynamics simulations of a host-guest binding system as an example, in order to study how different implementations of the replica exchange cycle can affect the sampling efficiency. We analyze how the number of replica exchange attempts per cycle, the number of MD steps per cycle, and the interaction between the two parameters affects the largest implied time scale of the MSMRE simulation. The infinite swapping limit is an important concept in replica exchange. We show how to estimate the infinite swapping limit from the diagonal elements of the exchange transition matrix constructed from MSMRE "simulations of simulations" as well as from relatively short runs of the actual replica exchange simulations.

  10. Rare events via multiple reaction channels sampled by path replica exchange

    NARCIS (Netherlands)

    Bolhuis, P.G.

    2008-01-01

    Transition path sampling (TPS) was developed for studying activated processes in complex systems with unknown reaction coordinate. Transition interface sampling (TIS) allows efficient evaluation of the rate constants. However, when the transition can occur via more than one reaction channel separate

  11. A simple asynchronous replica-exchange implementation

    CERN Document Server

    Bussi, Giovanni

    2008-01-01

    We discuss the possibility of implementing asynchronous replica-exchange (or parallel tempering) molecular dynamics. In our scheme, the exchange attempts are driven by asynchronous messages sent by one of the computing nodes, so that different replicas are allowed to perform a different number of time-steps between subsequent attempts. The implementation is simple and based on the message-passing interface (MPI). We illustrate the advantages of our scheme with respect to the standard synchronous algorithm and we benchmark it for a model Lennard-Jones liquid on an IBM-LS21 blade center cluster.

  12. Hamiltonian replica exchange molecular dynamics using soft-core interactions.

    Science.gov (United States)

    Hritz, Jozef; Oostenbrink, Chris

    2008-04-14

    To overcome the problem of insufficient conformational sampling within biomolecular simulations, we have developed a novel Hamiltonian replica exchange molecular dynamics (H-REMD) scheme that uses soft-core interactions between those parts of the system that contribute most to high energy barriers. The advantage of this approach over other H-REMD schemes is the possibility to use a relatively small number of replicas with locally larger differences between the individual Hamiltonians. Because soft-core potentials are almost the same as regular ones at longer distances, most of the interactions between atoms of perturbed parts will only be slightly changed. Rather, the strong repulsion between atoms that are close in space, which in many cases results in high energy barriers, is weakened within higher replicas of our proposed scheme. In addition to the soft-core interactions, we proposed to include multiple replicas using the same Hamiltonian/level of softness. We have tested the new protocol on the GTP and 8-Br-GTP molecules, which are known to have high energy barriers between the anti and syn conformation of the base with respect to the sugar moiety. During two 25 ns MD simulations of both systems the transition from the more stable to the less stable (but still experimentally observed) conformation is not seen at all. Also temperature REMD over 50 replicas for 1 ns did not show any transition at room temperature. On the other hand, more than 20 of such transitions are observed in H-REMD using six replicas (at three different Hamiltonians) during 6.8 ns per replica for GTP and 12 replicas (at six different Hamiltonians) during 8.7 ns per replica for 8-Br-GTP. The large increase in sampling efficiency was obtained from an optimized H-REMD scheme involving soft-core potentials, with multiple simulations using the same level of softness. The optimization of the scheme was performed by fast mimicking [J. Hritz and C. Oostenbrink, J. Chem. Phys. 127, 204104 (2007)].

  13. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-01-15

    A Hamiltonian Replica-Exchange Molecular Dynamics (REMD) simulation method has been developed that employs a two-dimensional backbone and one-dimensional side chain biasing potential specifically to promote conformational transitions in peptides. To exploit the replica framework optimally, the level of the biasing potential in each replica was appropriately adapted during the simulations. This resulted in both high exchange rates between neighboring replicas and improved occupancy/flow of all conformers in each replica. The performance of the approach was tested on several peptide and protein systems and compared with regular MD simulations and previous REMD studies. Improved sampling of relevant conformational states was observed for unrestrained protein and peptide folding simulations as well as for refinement of a loop structure with restricted mobility of loop flanking protein regions.

  14. A replica exchange transition interface sampling method with multiple interface sets for investigating networks of rare events

    NARCIS (Netherlands)

    Swenson, D.W.H.; Bolhuis, P.G.

    2014-01-01

    The multiple state transition interface sampling (TIS) framework in principle allows the simulation of a large network of complex rare event transitions, but in practice suffers from convergence problems. To improve convergence, we combine multiple state TIS [J. Rogal and P. G. Bolhuis, J. Chem. Phy

  15. Hamiltonian replica-exchange in GROMACS: a flexible implementation

    OpenAIRE

    Bussi, Giovanni

    2013-01-01

    A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field co...

  16. Hamiltonian replica-exchange in GROMACS: a flexible implementation

    CERN Document Server

    Bussi, Giovanni

    2013-01-01

    A simple and general implementation of Hamiltonian replica exchange for the popular molecular-dynamics software GROMACS is presented. In this implementation, arbitrarily different Hamiltonians can be used for the different replicas without incurring in any significant performance penalty. The implementation was validated on a simple toy model - alanine dipeptide in water - and applied to study the rearrangement of an RNA tetraloop, where it was used to compare recently proposed force-field corrections.

  17. Replica exchange Monte Carlo applied to hard spheres.

    Science.gov (United States)

    Odriozola, Gerardo

    2009-10-14

    In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HSs). The idea behind the proposal is expanding volume instead of increasing temperature to let crowded systems characterized by dominant repulsive interactions to unblock, and so, to produce sampling from disjoint configurations. The method produces, in a single parallel run, the complete HS equation of state. Thus, the first order fluid-solid transition is captured. The obtained results well agree with previous calculations. This approach seems particularly useful to treat purely entropy-driven systems such as hard body and nonadditive hard mixtures, where temperature plays a trivial role.

  18. Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

    Science.gov (United States)

    Huang, Kun; García, Angel E

    2014-10-14

    The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

  19. Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange.

    Science.gov (United States)

    Zacharias, Martin

    2008-03-01

    Coarse-grained elastic network models (ENM) of proteins can be used efficiently to explore the global mobility of a protein around a reference structure. A new Hamiltonian-replica exchange molecular dynamics (H-RexMD) method has been designed that effectively combines information extracted from an ENM analysis with atomic-resolution MD simulations. The ENM analysis is used to construct a distance-dependent penalty (flooding or biasing) potential that can drive the structure away from its current conformation in directions compatible with the ENM model. Various levels of the penalty or biasing potential are added to the force field description of the MD simulation along the replica coordinate. One replica runs at the original force field. By focusing the penalty potential on the relevant soft degrees of freedom the method avoids the rapid increase of the replica number with increasing system size to cover a desired temperature range in conventional (temperature) RexMD simulations. The application to domain motions in lysozyme of bacteriophage T4 and to peptide folding indicates significantly improved conformational sampling compared to conventional MD simulations.

  20. Efficient parallel implementations of QM/MM-REMD (quantum mechanical/molecular mechanics-replica-exchange MD) and umbrella sampling: isomerization of H2O2 in aqueous solution.

    Science.gov (United States)

    Fedorov, Dmitri G; Sugita, Yuji; Choi, Cheol Ho

    2013-07-03

    An efficient parallel implementation of QM/MM-based replica-exchange molecular dynamics (REMD) as well as umbrella samplings techniques was proposed by adopting the generalized distributed data interface (GDDI). Parallelization speed-up of 40.5 on 48 cores was achieved, making our QM/MM-MD engine a robust tool for studying complex chemical dynamics in solution. They were comparatively used to study the torsional isomerization of hydrogen peroxide in aqueous solution. All results by QM/MM-REMD and QM/MM umbrella sampling techniques yielded nearly identical potentials of mean force (PMFs) regardless of the particular QM theories for solute, showing that the overall dynamics are mainly determined by solvation. Although the entropic penalty of solvent rearrangements exists in cisoid conformers, it was found that both strong intermolecular hydrogen bonding and dipole-dipole interactions preferentially stabilize them in solution, reducing the torsional free-energy barrier at 0° by about 3 kcal/mol as compared to that in gas phase.

  1. Protein-ligand docking using hamiltonian replica exchange simulations with soft core potentials.

    Science.gov (United States)

    Luitz, Manuel P; Zacharias, Martin

    2014-06-23

    Molecular dynamics (MD) simulations in explicit solvent allow studying receptor-ligand binding processes including full flexibility of the binding partners and an explicit inclusion of solvation effects. However, in MD simulations, the search for an optimal ligand-receptor complex geometry is frequently trapped in locally stable non-native binding geometries. A Hamiltonian replica-exchange (H-REMD)-based protocol has been designed to enhance the sampling of putative ligand-receptor complexes. It is based on softening nonbonded ligand-receptor interactions along the replicas and one reference replica under the control of the original force field. The efficiency of the method has been evaluated on two receptor-ligand systems and one protein-peptide complex. Starting from misplaced initial docking geometries, the H-REMD method reached in each case the known binding geometry significantly faster than a standard MD simulation. The approach could also be useful to identify and evaluate alternative binding geometries in a given binding region with small relative differences in binding free energy.

  2. Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

    Science.gov (United States)

    Ostermeir, Katja; Zacharias, Martin

    2014-12-01

    Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations.

  3. Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.

    Science.gov (United States)

    Meng, Yilin; Dashti, Danial Sabri; Roitberg, Adrian E

    2011-09-13

    Alchemical free energy calculations play a very important role in the field of molecular modeling. Efforts have been made to improve the accuracy and precision of those calculations. One of the efforts is to employ a Hamiltonian replica exchange molecular dynamics (H-REMD) method to enhance conformational sampling. In this paper, we demonstrated that HREMD method not only improves convergence in alchemical free energy calculations but also can be used to compute free energy differences directly via the Free Energy Perturbation (FEP)algorithm. We show a direct mapping between the H-REMD and the usual FEP equations, which are then used directly to compute free energies. The H-REMD alchemical free energy calculation (Replica exchange Free Energy Perturbation, REFEP) was tested on predicting the pK(a) value of the buried Asp26 in thioredoxin. We compare the results of REFEP with TI and regular FEP simulations. REFEP calculations converged faster than those from TI and regular FEP simulations. The final predicted pK(a) value from the H-REMD simulation was also very accurate, only 0.4 pK(a) unit above the experimental value. Utilizing the REFEP algorithm significantly improves conformational sampling, and this in turn improves the convergence of alchemical free energy simulations.

  4. Isobaric Molecular Dynamics Version of the Generalized Replica Exchange Method (gREM): Liquid-Vapor Equilibrium.

    Science.gov (United States)

    Małolepsza, Edyta; Secor, Maxim; Keyes, Tom

    2015-10-22

    A prescription for sampling isobaric generalized ensembles with molecular dynamics is presented and applied to the generalized replica exchange method (gREM), which was designed to simulate first-order phase transitions. The properties of the isobaric gREM ensemble are discussed, and a study is presented for the liquid-vapor equilibrium of the guest molecules given for gas hydrate formation with the mW water model. Phase diagrams, critical parameters, and a law of corresponding states are obtained.

  5. Replica exchange simulations of the three-dimensional Ising spin glass: static and dynamic properties

    Science.gov (United States)

    Yucesoy, Burcu; Machta, Jonathan; Katzgraber, Helmut G.

    2012-02-01

    We present the results of a large-scale numerical study of the equilibrium three-dimensional Ising spin glass with Gaussian disorder. Using replica exchange (parallel tempering) Monte Carlo, we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the replica exchange Monte Carlo method. The correlation between static and dynamic observables for 5000 disorder realizations (N <=10^3 spins) down to very low temperatures (T 0.2Tc) is examined. Our results show that autocorrelation times are directly correlated with the roughness of the free energy landscape. We also discuss the size dependence of several static quantities.

  6. Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins.

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Landau, David P

    2016-11-01

    We have studied the folding of ribonuclease A by mapping it onto coarse-grained lattice protein models. With replica exchange Wang-Landau sampling, we calculated the free energy vs end-to-end distance as a function of temperature. A mapping to the famous hydrophobic-polar (HP) model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, extending the HP model with an additional "neutral" monomer type (i.e., a mapping to the three-letter H0P model) has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.

  7. Replica-exchange Wang-Landau simulations of the H0P lattice protein model

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Li, Ying Wai; Landau, David P.

    The hydrophobic-polar (HP) lattice protein model has been the subject of intensive investigation in an effort to aid our understanding of protein folding. However, the high ground state degeneracies caused by its simplification stands in contrast to the generally unique native states of natural proteins. Here we proposed a simple modification, by introducing a new type of ``neutral'' monomer, 0, i.e. neither hydrophobic nor polar, thus rendering the model more realistic without increasing the difficulties of sampling significantly. With the replica exchange Wang-Landau (REWL) scheme we investigated several widely studied HP proteins and their H0P counterparts. Dramatic differences in both ground state and thermodynamic properties have been found. For example, the H0P version of Crambin shows more clear two-step folding and 3 order of magnitudes less ground state degeneracy than its HP counterpart. Supported by NSF.

  8. Characterizing folding funnels with replica exchange Wang-Landau simulation of lattice proteins

    Science.gov (United States)

    Shi, Guangjie; Wüst, Thomas; Landau, David P.

    2016-11-01

    We have studied the folding of ribonuclease A by mapping it onto coarse-grained lattice protein models. With replica exchange Wang-Landau sampling, we calculated the free energy vs end-to-end distance as a function of temperature. A mapping to the famous hydrophobic-polar (HP) model shows a relatively shallow folding funnel and flat free energy minimum, reflecting the high degeneracy of the ground state. In contrast, extending the HP model with an additional "neutral" monomer type (i.e., a mapping to the three-letter H0P model) has a well developed, rough free energy funnel with a low degeneracy ground state. In both cases, folding funnels are asymmetric with temperature dependent shape.

  9. Replica exchange molecular dynamics optimization of tensor network states for quantum many-body systems.

    Science.gov (United States)

    Liu, Wenyuan; Wang, Chao; Li, Yanbin; Lao, Yuyang; Han, Yongjian; Guo, Guang-Can; Zhao, Yong-Hua; He, Lixin

    2015-03-01

    Tensor network states (TNS) methods combined with the Monte Carlo (MC) technique have been proven a powerful algorithm for simulating quantum many-body systems. However, because the ground state energy is a highly non-linear function of the tensors, it is easy to get stuck in local minima when optimizing the TNS of the simulated physical systems. To overcome this difficulty, we introduce a replica-exchange molecular dynamics optimization algorithm to obtain the TNS ground state, based on the MC sampling technique, by mapping the energy function of the TNS to that of a classical mechanical system. The method is expected to effectively avoid local minima. We make benchmark tests on a 1D Hubbard model based on matrix product states (MPS) and a Heisenberg J1-J2 model on square lattice based on string bond states (SBS). The results show that the optimization method is robust and efficient compared to the existing results.

  10. Multiple replica repulsion technique for efficient conformational sampling of biological systems.

    Science.gov (United States)

    Malevanets, Anatoly; Wodak, Shoshana J

    2011-08-17

    Here, we propose a technique for sampling complex molecular systems with many degrees of freedom. The technique, termed "multiple replica repulsion" (MRR), does not suffer from poor scaling with the number of degrees of freedom associated with common replica exchange procedures and does not require sampling at high temperatures. The algorithm involves creation of multiple copies (replicas) of the system, which interact with one another through a repulsive potential that can be applied to the system as a whole or to portions of it. The proposed scheme prevents oversampling of the most populated states and provides accurate descriptions of conformational perturbations typically associated with sampling ground-state energy wells. The performance of MRR is illustrated for three systems of increasing complexity. A two-dimensional toy potential surface is used to probe the sampling efficiency as a function of key parameters of the procedure. MRR simulations of the Met-enkephalin pentapeptide, and the 76-residue protein ubiquitin, performed in presence of explicit water molecules and totaling 32 ns each, investigate the ability of MRR to characterize the conformational landscape of the peptide, and the protein native basin, respectively. Results obtained for the enkephalin peptide reflect more closely the extensive conformational flexibility of this peptide than previously reported simulations. Those obtained for ubiquitin show that conformational ensembles sampled by MRR largely encompass structural fluctuations relevant to biological recognition, which occur on the microsecond timescale, or are observed in crystal structures of ubiquitin complexes with other proteins. MRR thus emerges as a very promising simple and versatile technique for modeling the structural plasticity of complex biological systems. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Studying the Early Stages of Protein Aggregation Using Replica Exchange Molecular Dynamics Simulations.

    Science.gov (United States)

    Shea, Joan-Emma; Levine, Zachary A

    2016-01-01

    The simulation of protein aggregation poses several computational challenges due to the disparate time and lengths scales that are involved. This chapter focuses on the use of atomistically detailed simulations to probe the initial steps of aggregation, with an emphasis on the Tau peptide as a model system, run under a replica exchange molecular dynamics protocol.

  12. Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations.

    Science.gov (United States)

    Jiang, Wei; Roux, Benoît

    2010-07-01

    Free Energy Perturbation with Replica Exchange Molecular Dynamics (FEP/REMD) offers a powerful strategy to improve the convergence of free energy computations. In particular, it has been shown previously that a FEP/REMD scheme allowing random moves within an extended replica ensemble of thermodynamic coupling parameters "lambda" can improve the statistical convergence in calculations of absolute binding free energy of ligands to proteins [J. Chem. Theory Comput. 2009, 5, 2583]. In the present study, FEP/REMD is extended and combined with an accelerated MD simulations method based on Hamiltonian replica-exchange MD (H-REMD) to overcome the additional problems arising from the existence of kinetically trapped conformations within the protein receptor. In the combined strategy, each system with a given thermodynamic coupling factor lambda in the extended ensemble is further coupled with a set of replicas evolving on a biased energy surface with boosting potentials used to accelerate the inter-conversion among different rotameric states of the side chains in the neighborhood of the binding site. Exchanges are allowed to occur alternatively along the axes corresponding to the thermodynamic coupling parameter lambda and the boosting potential, in an extended dual array of coupled lambda- and H-REMD simulations. The method is implemented on the basis of new extensions to the REPDSTR module of the biomolecular simulation program CHARMM. As an illustrative example, the absolute binding free energy of p-xylene to the nonpolar cavity of the L99A mutant of T4 lysozyme was calculated. The tests demonstrate that the dual lambda-REMD and H-REMD simulation scheme greatly accelerates the configurational sampling of the rotameric states of the side chains around the binding pocket, thereby improving the convergence of the FEP computations.

  13. Protein-Ligand Binding from Distancefield Distances and Hamiltonian Replica Exchange Simulations.

    Science.gov (United States)

    de Ruiter, Anita; Oostenbrink, Chris

    2013-02-12

    The calculation of protein-ligand binding free energies is an important goal in the field of computational chemistry. Applying path-sampling methods for this purpose involves calculating the associated potential of mean force (PMF) and gives insight into the binding free energy along the binding process. Without a priori knowledge about the binding path, sampling reversible binding can be difficult to achieve. To alleviate this problem, we introduce the distancefield (DF) as a reaction coordinate for such calculations. DF is a grid-based method in which the shortest distance between the binding site and a ligand is determined avoiding routes that pass through the protein. Combining this reaction coordinate with Hamiltonian replica exchange molecular dynamics (HREMD) allows for the reversible binding of the ligand to the protein. A comparison is made between umbrella sampling using regular distance restraints and HREMD with DF restraints to study aspirin binding to the protein phospholipase A2. Although the free energies of binding are similar for both methods, the increased sampling with HREMD has a significant influence on the shape of the PMF. A remarkable agreement between the calculated binding free energies from the PMF and the experimental estimate is obtained.

  14. Water hexamer: Self-consistent phonons versus reversible scaling versus replica exchange molecular dynamics

    CERN Document Server

    Brown, Sandra E

    2014-01-01

    Classical free energies for the cage and prism isomers of water hexamer computed by the self- consistent phonons (SCP) method and reversible scaling (RS) method are presented for several flexible water potentials. Both methods have been augmented with a rotational correction for improved accuracy when working with clusters. Comparison of the SCP results with the RS results suggests a fairly broad temperature range over which the SCP approximation can be expected to give accurate results for systems of water clusters, and complements a previously reported assessment of SCP. Discrepancies between the SCP and RS results presented here, and recently published replica exchange molecular dynamics (REMD) results bring into question the convergence of the REMD and accompanying replica exchange path integral molecular dynamics results. In addition to the ever-present specter of unconverged results, several possible sources for the discrepancy are explored based on inherent characteristics of the methods used.

  15. General Formalism of Mass Scaling Approach for Replica-Exchange Molecular Dynamics and its Application

    Science.gov (United States)

    Nagai, Tetsuro

    2017-01-01

    Replica-exchange molecular dynamics (REMD) has demonstrated its efficiency by combining trajectories of a wide range of temperatures. As an extension of the method, the author formalizes the mass-manipulating replica-exchange molecular dynamics (MMREMD) method that allows for arbitrary mass scaling with respect to temperature and individual particles. The formalism enables the versatile application of mass-scaling approaches to the REMD method. The key change introduced in the novel formalism is the generalized rules for the velocity and momentum scaling after accepted replica-exchange attempts. As an application of this general formalism, the refinement of the viscosity-REMD (V-REMD) method [P. H. Nguyen, https://doi.org/10.1063/1.3369626" xlink:type="simple">J. Chem. Phys. 132, 144109 (2010)] is presented. Numerical results are provided using a pilot system, demonstrating easier and more optimized applicability of the new version of V-REMD as well as the importance of adherence to the generalized velocity scaling rules. With the new formalism, more sound and efficient simulations will be performed.

  16. Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics.

    Science.gov (United States)

    Jo, Sunhwan; Chipot, Christophe; Roux, Benoît

    2015-05-12

    The performance and accuracy of different simulation schemes for estimating the entropy inferred from free energy calculations are tested. The results obtained from replica-exchange molecular dynamics (REMD) simulations based on a simplified toy model are compared to exact numerically derived ones to assess accuracy and convergence. It is observed that the error in entropy estimation decreases by at least an order of magnitude and the quantities of interest converge much faster when the simulations are coupled via a temperature REMD algorithm and the trajectories from different temperatures are combined. Simulations with the infinite-swapping method and its variants show some improvement over the traditional nearest-neighbor REMD algorithms, but they are more computationally expensive. To test the methodologies further, the free energy profile for the reversible association of two methane molecules in explicit water was calculated and decomposed into its entropic and enthalpic contributions. Finally, a strategy based on umbrella sampling computations carried out via simultaneous temperature and Hamiltonian REMD simulations is shown to yield the most accurate entropy estimation. The entropy profile between the two methane molecules displays the characteristic signature of a hydrophobic interaction.

  17. Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Nanyu Han

    Full Text Available Neuraminidase (NA of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1 was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150 of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

  18. Plasticity of 150-loop in influenza neuraminidase explored by Hamiltonian replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Han, Nanyu; Mu, Yuguang

    2013-01-01

    Neuraminidase (NA) of influenza is a key target for antiviral inhibitors, and the 150-cavity in group-1 NA provides new insight in treating this disease. However, NA of 2009 pandemic influenza (09N1) was found lacking this cavity in a crystal structure. To address the issue of flexibility of the 150-loop, Hamiltonian replica exchange molecular dynamics simulations were performed on different groups of NAs. Free energy landscape calculated based on the volume of 150-cavity indicates that 09N1 prefers open forms of 150-loop. The turn A (residues 147-150) of the 150-loop is discovered as the most dynamical motif which induces the inter-conversion of this loop among different conformations. In the turn A, the backbone dynamic of residue 149 is highly related with the shape of 150-loop, thus can function as a marker for the conformation of 150-loop. As a contrast, the closed conformation of 150-loop is more energetically favorable in N2, one of group-2 NAs. The D147-H150 salt bridge is found having no correlation with the conformation of 150-loop. Instead the intimate salt bridge interaction between the 150 and 430 loops in N2 variant contributes the stabilizing factor for the closed form of 150-loop. The clustering analysis elaborates the structural plasticity of the loop. This enhanced sampling simulation provides more information in further structural-based drug discovery on influenza virus.

  19. Perovskite Quantum Dots Modeled Using ab Initio and Replica Exchange Molecular Dynamics

    KAUST Repository

    Buin, Andrei

    2015-06-18

    © 2015 American Chemical Society. Organometal halide perovskites have recently attracted tremendous attention at both the experimental and theoretical levels. Much of this work has been dedicated to bulk material studies, yet recent experimental work has shown the formation of highly efficient quantum-confined nanocrystals with tunable band edges. Here we investigate perovskite quantum dots from theory, predicting an upper bound of the Bohr radius of 45 Å that agrees well with literature values. When the quantum dots are stoichiometric, they are trap-free and have nearly symmetric contributions to confinement from the valence and conduction bands. We further show that surface-associated conduction bandedge states in perovskite nanocrystals lie below the bulk states, which could explain the difference in Urbach tails between mesoporous and planar perovskite films. In addition to conventional molecular dynamics (MD), we implement an enhanced phase-space sampling algorithm, replica exchange molecular dynamics (REMD). We find that in simulation of methylammonium orientation and global minima, REMD outperforms conventional MD. To the best of our knowledge, this is the first REMD implementation for realistic-sized systems in the realm of DFT calculations.

  20. Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.

    Science.gov (United States)

    Chebaro, Yassmine; Dong, Xiao; Laghaei, Rozita; Derreumaux, Philippe; Mousseau, Normand

    2009-01-08

    Current approaches aimed at determining the free energy surface of all-atom medium-size proteins in explicit solvent are slow and are not sufficient to converge to equilibrium properties. To ensure a proper sampling of the configurational space, it is preferable to use reduced representations such as implicit solvent and/or coarse-grained protein models, which are much lighter computationally. Each model must be verified, however, to ensure that it can recover experimental structures and thermodynamics. Here we test the coarse-grained implicit solvent OPEP model with replica exchange molecular dynamics (REMD) on six peptides ranging in length from 10 to 28 residues: two alanine-based peptides, the second beta-hairpin from protein G, the Trp-cage and zinc-finger motif, and a dimer of a coiled coil peptide. We show that REMD-OPEP recovers the proper thermodynamics of the systems studied, with accurate structural description of the beta-hairpin and Trp-cage peptides (within 1-2 A from experiments). The light computational burden of REMD-OPEP, which enables us to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.

  1. Replica-exchange Wang-Landau simulations of the H0P model of protein folding

    Science.gov (United States)

    Shi, Guangjie; Landau, David P.; Wüst, Thomas; Li, Ying Wai Li

    2015-03-01

    The hydrophobic-polar (HP) model has served as a coarse-grained lattice protein folding model attracting scientists from various disciplines. However, simplification into H and P monomers may yield high ground state degeneracies which stands in contrast to the generally unique native states of natural proteins. We propose a simple modification, by introducing a new type of ``neutral'' monomer, 0, i.e. neither hydrophobic nor polar, rendering the model more realistic without increasing the difficulties of sampling significantly. With the newly developed parallel Wang-Landau (replica exchange Wang-Landau) scheme and an innovative method of estimating the ground state degeneracies, we investigated some widely studied HP proteins and their H0P counterparts. Dramatic differences in ground state and thermodynamic properties have been observed, e.g. the estimation of ground state degeneracy for the 46mer is 460,000 for the HP version and only 20 for the H0P mapping. Similarly, the specific heat and structural properties: radius of gyration and etc. show more pronounced signals associated with folding. Supported by NSF.

  2. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

  3. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis.

    Science.gov (United States)

    Xia, Junchao; Flynn, William F; Gallicchio, Emilio; Zhang, Bin W; He, Peng; Tan, Zhiqiang; Levy, Ronald M

    2015-09-05

    We describe methods to perform replica exchange molecular dynamics (REMD) simulations asynchronously (ASyncRE). The methods are designed to facilitate large scale REMD simulations on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters. We have implemented these methods on NSF (National Science Foundation) XSEDE (Extreme Science and Engineering Discovery Environment) clusters and BOINC (Berkeley Open Infrastructure for Network Computing) distributed computing networks at Temple University and Brooklyn College at CUNY (the City University of New York). They are also being implemented on the IBM World Community Grid. To illustrate the methods, we have performed extensive (more than 60 ms in aggregate) simulations for the beta-cyclodextrin-heptanoate host-guest system in the context of one- and two-dimensional ASyncRE, and we used the results to estimate absolute binding free energies using the binding energy distribution analysis method. We propose ways to improve the efficiency of REMD simulations: these include increasing the number of exchanges attempted after a specified molecular dynamics (MD) period up to the fast exchange limit and/or adjusting the MD period to allow sufficient internal relaxation within each thermodynamic state. Although ASyncRE simulations generally require long MD periods (>picoseconds) per replica exchange cycle to minimize the overhead imposed by heterogeneous computing networks, we found that it is possible to reach an efficiency similar to conventional synchronous REMD, by optimizing the combination of the MD period and the number of exchanges attempted per cycle.

  4. Massively parallelized replica-exchange simulations of polymers on GPUs

    CERN Document Server

    Groß, Jonathan; Bachmann, Michael

    2011-01-01

    We discuss the advantages of parallelization by multithreading on graphics processing units (GPUs) for parallel tempering Monte Carlo computer simulations of an exemplified bead-spring model for homopolymers. Since the sampling of a large ensemble of conformations is a prerequisite for the precise estimation of statistical quantities such as typical indicators for conformational transitions like the peak structure of the specific heat, the advantage of a strong increase in performance of Monte Carlo simulations cannot be overestimated. Employing multithreading and utilizing the massive power of the large number of cores on GPUs, being available in modern but standard graphics cards, we find a rapid increase in efficiency when porting parts of the code from the central processing unit (CPU) to the GPU.

  5. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Science.gov (United States)

    Doi, Hideo; Yasuoka, Kenji

    2017-05-01

    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  6. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics.

    Science.gov (United States)

    Wang, Kai; Chodera, John D; Yang, Yanzhi; Shirts, Michael R

    2013-12-01

    We present a method to identify small molecule ligand binding sites and poses within a given protein crystal structure using GPU-accelerated Hamiltonian replica exchange molecular dynamics simulations. The Hamiltonians used vary from the physical end state of protein interacting with the ligand to an unphysical end state where the ligand does not interact with the protein. As replicas explore the space of Hamiltonians interpolating between these states, the ligand can rapidly escape local minima and explore potential binding sites. Geometric restraints keep the ligands from leaving the vicinity of the protein and an alchemical pathway designed to increase phase space overlap between intermediates ensures good mixing. Because of the rigorous statistical mechanical nature of the Hamiltonian exchange framework, we can also extract binding free energy estimates for all putative binding sites. We present results of this methodology applied to the T4 lysozyme L99A model system for three known ligands and one non-binder as a control, using an implicit solvent. We find that our methodology identifies known crystallographic binding sites consistently and accurately for the small number of ligands considered here and gives free energies consistent with experiment. We are also able to analyze the contribution of individual binding sites to the overall binding affinity. Our methodology points to near term potential applications in early-stage structure-guided drug discovery.

  7. How Is cis-trans Isomerization Controlled in Dronpa Mutants? A Replica Exchange Molecular Dynamics Study.

    Science.gov (United States)

    Moors, Samuel L C; Michielssens, Servaas; Flors, Cristina; Dedecker, Peter; Hofkens, Johan; Ceulemans, Arnout

    2008-06-01

    The reversibly photoactivatable green fluorescent protein analog Dronpa holds great promise as a marker for various new cellular imaging applications. Using a replica exchange method which combines both Hamiltonian and temperature exchanges, the ground-state dynamics of Dronpa and two mutants with increased switching kinetics, Val157Gly and Met159Thr, were compared. The dominant chromophore state was found to be the cis isomer in all three proteins. The simulation data suggest that both mutations strongly increase the chromophore flexibility and cis-trans isomerization rate. We identify three key amino acids, Val157, Met159, and Phe173, which are able to impede the bottom hula-twist transition path, depending on their position and rotameric state. We believe our insights will help to understand the switching process and provide useful information for the design of new variants with improved fluorescence properties.

  8. Protein-Ligand Binding Potential of Mean Force Calculations with Hamiltonian Replica Exchange on Alchemical Interaction Grids

    CERN Document Server

    Minh, David D L

    2015-01-01

    A binding potential of mean force (BPMF) is a free energy of noncovalent association in which one binding partner is flexible and the other is rigid. I have developed a method to calculate BPMFs for protein-ligand systems. The method is based on replica exchange sampling from multiple thermodynamic states at different temperatures and protein-ligand interaction strengths. Protein-ligand interactions are represented by interpolating precomputed electrostatic and van der Waals grids. Using a simple estimator for thermodynamic length, thermodynamic states are initialized at approximately equal intervals. The method is demonstrated on the Astex diverse set, a database of 85 protein-ligand complexes relevant to pharmacy or agriculture. Fifteen independent simulations of each complex were started using poses from crystallography, docking, or the lowest-energy pose observed in the other simulations. Benchmark simulations completed within three days on a single processor. Overall, protocols initialized using the ther...

  9. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations : Application in the refinement of de novo models

    NARCIS (Netherlands)

    Fan, Hao; Periole, Xavier; Mark, Alan E.

    2012-01-01

    The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, spe

  10. A hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper.

    Science.gov (United States)

    Cukier, Robert I

    2011-01-28

    Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] hamiltonian temperature replica exchange method (HTREM), which scales the hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer

  11. A Hamiltonian replica exchange method for building protein-protein interfaces applied to a leucine zipper

    Science.gov (United States)

    Cukier, Robert I.

    2011-01-01

    Leucine zippers consist of alpha helical monomers dimerized (or oligomerized) into alpha superhelical structures known as coiled coils. Forming the correct interface of a dimer from its monomers requires an exploration of configuration space focused on the side chains of one monomer that must interdigitate with sites on the other monomer. The aim of this work is to generate good interfaces in short simulations starting from separated monomers. Methods are developed to accomplish this goal based on an extension of a previously introduced [Su and Cukier, J. Phys. Chem. B 113, 9595, (2009)] Hamiltonian temperature replica exchange method (HTREM), which scales the Hamiltonian in both potential and kinetic energies that was used for the simulation of dimer melting curves. The new method, HTREM_MS (MS designates mean square), focused on interface formation, adds restraints to the Hamiltonians for all but the physical system, which is characterized by the normal molecular dynamics force field at the desired temperature. The restraints in the nonphysical systems serve to prevent the monomers from separating too far, and have the dual aims of enhancing the sampling of close in configurations and breaking unwanted correlations in the restrained systems. The method is applied to a 31-residue truncation of the 33-residue leucine zipper (GCN4-p1) of the yeast transcriptional activator GCN4. The monomers are initially separated by a distance that is beyond their capture length. HTREM simulations show that the monomers oscillate between dimerlike and monomerlike configurations, but do not form a stable interface. HTREM_MS simulations result in the dimer interface being faithfully reconstructed on a 2 ns time scale. A small number of systems (one physical and two restrained with modified potentials and higher effective temperatures) are sufficient. An in silico mutant that should not dimerize because it lacks charged residues that provide electrostatic stabilization of the dimer

  12. Structure and thermodynamics of amylin dimer studied by Hamiltonian-temperature replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2011-03-31

    The loss of the insulin-producing β-cells in the pancreatic islets of Langerhans, responsible for type-II diabetes, is associated with islet amyloid deposits. The main component of these deposits is the amyloid fibrils formed by the 37-residue human islet amyloid polypeptide (hIAPP also known as amylin). Although the fibrils are well characterized by cross β structure, the structure of the transient oligomers formed in the early stage of aggregation remains elusive. In this study, we apply the Hamiltonian-temperature replica exchange molecular dynamics to characterize the structure and thermodynamics of a full-length hIAPP dimer in both the presence and the absence of the Cys2-Cys7 disulfide bond. We compare these results with those obtained on the monomeric and dimeric forms of rat IAPP (rIAPP) with a disulfide bridge which differ from the hIAPP by 6 amino acids in the C-terminal region, but it is unable to form fibrils. Using a coarse-grained protein force field (OPEP-the Optimized Potential for Efficient peptide structure Prediction) running for a total of 10-28 μs per system studied, we show that sequences sample α-helical structure in the N-terminal region but that the length of this secondary element is shorter and less stable for the chains without the disulfide bridge (residues 5-16 for hIAPP with the bridge vs 10-16 for hIAPP without the bridge). This α-helix is known to be an important transient stage in the formation of oligomers. In the C-terminal, the amyloidogenic region of hIAPP, β-strands are seen for residues 17-26 and 30-35. On the contrary, no significant β-sheet content in the C-terminal is observed for either the monomeric or the dimeric rIAPP. These numerical results are fully consistent with recent experimental findings that the N-terminal residues are not part of the fibril by forming α-helical structure but rather play a significant role in stabilizing the amyloidogenic region available for the fibrillation.

  13. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    CERN Document Server

    Wabik, Jacek; Gront, Dominik; Kouza, Maksim; Kolinski, Andrzej

    2013-01-01

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  14. Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

    Directory of Open Access Journals (Sweden)

    Andrzej Koliński

    2013-05-01

    Full Text Available We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  15. Combining coarse-grained protein models with replica-exchange all-atom molecular dynamics.

    Science.gov (United States)

    Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

    2013-05-10

    We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems.

  16. Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation.

    Science.gov (United States)

    Xue, Xu; Yongjun, Wang; Zhihong, Li

    2015-01-21

    Riboswitches are cis-acting RNA fragments that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket, representing an inviting new class of biomolecular target for the development of antibiotics. To understand the folding mechanism of SAM-II riboswitch, occurring predominantly in proteobacteria, a 100ns replica-exchange molecular dynamics simulation in explicit solvent is performed. Our results show that this RNA pseudoknot has multiple folding pathways, and various intermediate structures. The resultant riboswitch conformational transition map is well consistent with the recent fluorescence measurement, which confirms the dynamical properties of this pseudoknot. Moreover, a novel transition pathway is predicted. The global folding dynamics is mainly coupled with the helix rather than the loop region. The potential folding pathways of the riboswitch presented here should lead to a deeper understanding of the folding mechanism of the riboswitch, as well as the conformational change of RNA pseudoknot.

  17. Replica exchange molecular dynamics study of the truncated amyloid beta (11-40) trimer in solution.

    Science.gov (United States)

    Ngo, Son Tung; Hung, Huynh Minh; Truong, Duc Toan; Nguyen, Minh Tho

    2017-01-18

    Amyloid beta (Aβ) oligomers are neurotoxic compounds that destroy the brain of Alzheimer's disease patients. Recent studies indicated that the trimer is one of the most cytotoxic forms of low molecular weight Aβ oligomers. As there was limited information about the structure of the Aβ trimer, either by experiment or by computation, we determined in this work the structure of the 3Aβ11-40 oligomer for the first time using the temperature replica exchange molecular dynamics simulations in the presence of an explicit solvent. More than 20.0 μs of MD simulations were performed. The probability of the β-content and random coil structure of the solvated trimer amounts to 42 ± 6 and 49 ± 7% which is in good agreement with experiments. Intermolecular interactions in central hydrophobic cores play a key role in stabilizing the oligomer. Intermolecular polar contacts between D23 and residues 24-29 replace the salt bridge D23-K28 to secure the loop region. The hydrophilic region of the N-terminus is maintained by the intermolecular polar crossing contacts H13A-Q15B and H13B-Q15C. The difference in the free energy of binding between the constituting monomers and the others amounts to -36 ± 8 kcal mol(-1). The collision cross section of the representative structures of the trimer was computed to be 1330 ± 47 Å(2), which is in good agreement with previous experiments.

  18. Seismic wavefield imaging based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Ishikawa, Daichi; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2016-11-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas that have capital functions. To reduce the number and severity of secondary disasters, it is important to evaluate seismic hazards rapidly by analyzing the seismic responses of individual structures to input ground motions. We propose a method that integrates physics-based and data-driven approaches in order to obtain a seismic wavefield for use as input to a seismic response analysis. The new contribution of this study is the use of the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for estimation of a seismic wavefield, together with a one-dimensional (1-D) local subsurface structure and source information. Numerical tests were conducted to verify the proposed method, using synthetic observation data obtained from analytical solutions for two horizontally-layered subsurface structure models. The geometries of the observation sites were determined from the dense seismic observation array called the Metropolitan Seismic Observation network (MeSO-net), which has been in operation in the Tokyo metropolitan area in Japan since 2007. The results of the numerical tests show that the proposed method is able to search the parameters related to the source and the local subsurface structure in a broader parameter space than the Metropolis method, which is an ordinary MCMC method. The proposed method successfully reproduces a seismic wavefield consistent with a true wavefield. In contrast, ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce a true wavefield, even in the low frequency bands. This suggests that it is essential to employ both physics-based and data-driven approaches in seismic wavefield imaging, utilizing seismograms from a dense seismic array. The REMC method

  19. Seismic wavefield imaging based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Ishikawa, Daichi; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2017-01-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas that have capital functions. To reduce the number and severity of secondary disasters, it is important to evaluate seismic hazards rapidly by analysing the seismic responses of individual structures to input ground motions. We propose a method that integrates physics-based and data-driven approaches in order to obtain a seismic wavefield for use as input to a seismic response analysis. The new contribution of this study is the use of the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for estimation of a seismic wavefield, together with a 1-D local subsurface structure and source information. Numerical tests were conducted to verify the proposed method, using synthetic observation data obtained from analytical solutions for two horizontally layered subsurface structure models. The geometries of the observation sites were determined from the dense seismic observation array called the Metropolitan Seismic Observation network, which has been in operation in the Tokyo metropolitan area in Japan since 2007. The results of the numerical tests show that the proposed method is able to search the parameters related to the source and the local subsurface structure in a broader parameter space than the Metropolis method, which is an ordinary MCMC method. The proposed method successfully reproduces a seismic wavefield consistent with a true wavefield. In contrast, ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce a true wavefield, even in the low frequency bands. This suggests that it is essential to employ both physics-based and data-driven approaches in seismic wavefield imaging, utilizing seismograms from a dense seismic array. The REMC method, which provides not only

  20. Comparing three stochastic search algorithms for computational protein design: Monte Carlo, replica exchange Monte Carlo, and a multistart, steepest-descent heuristic.

    Science.gov (United States)

    Mignon, David; Simonson, Thomas

    2016-07-15

    Computational protein design depends on an energy function and an algorithm to search the sequence/conformation space. We compare three stochastic search algorithms: a heuristic, Monte Carlo (MC), and a Replica Exchange Monte Carlo method (REMC). The heuristic performs a steepest-descent minimization starting from thousands of random starting points. The methods are applied to nine test proteins from three structural families, with a fixed backbone structure, a molecular mechanics energy function, and with 1, 5, 10, 20, 30, or all amino acids allowed to mutate. Results are compared to an exact, "Cost Function Network" method that identifies the global minimum energy conformation (GMEC) in favorable cases. The designed sequences accurately reproduce experimental sequences in the hydrophobic core. The heuristic and REMC agree closely and reproduce the GMEC when it is known, with a few exceptions. Plain MC performs well for most cases, occasionally departing from the GMEC by 3-4 kcal/mol. With REMC, the diversity of the sequences sampled agrees with exact enumeration where the latter is possible: up to 2 kcal/mol above the GMEC. Beyond, room temperature replicas sample sequences up to 10 kcal/mol above the GMEC, providing thermal averages and a solution to the inverse protein folding problem. © 2016 Wiley Periodicals, Inc.

  1. A replica exchange Monte Carlo algorithm for protein folding in the HP model

    Directory of Open Access Journals (Sweden)

    Shmygelska Alena

    2007-09-01

    Full Text Available Abstract Background The ab initio protein folding problem consists of predicting protein tertiary structure from a given amino acid sequence by minimizing an energy function; it is one of the most important and challenging problems in biochemistry, molecular biology and biophysics. The ab initio protein folding problem is computationally challenging and has been shown to be NP MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaat0uy0HwzTfgDPnwy1egaryqtHrhAL1wy0L2yHvdaiqaacqWFneVtcqqGqbauaaa@3961@-hard even when conformations are restricted to a lattice. In this work, we implement and evaluate the replica exchange Monte Carlo (REMC method, which has already been applied very successfully to more complex protein models and other optimization problems with complex energy landscapes, in combination with the highly effective pull move neighbourhood in two widely studied Hydrophobic Polar (HP lattice models. Results We demonstrate that REMC is highly effective for solving instances of the square (2D and cubic (3D HP protein folding problem. When using the pull move neighbourhood, REMC outperforms current state-of-the-art algorithms for most benchmark instances. Additionally, we show that this new algorithm provides a larger ensemble of ground-state structures than the existing state-of-the-art methods. Furthermore, it scales well with sequence length, and it finds significantly better conformations on long biological sequences and sequences with a provably unique ground-state structure, which is believed to be a characteristic of real proteins. We also present evidence that our REMC algorithm can fold sequences which exhibit significant interaction between termini in the hydrophobic core relatively easily. Conclusion We demonstrate that REMC utilizing the pull move

  2. Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: application in the refinement of de novo models.

    Science.gov (United States)

    Fan, Hao; Periole, Xavier; Mark, Alan E

    2012-07-01

    The efficiency of using a variant of Hamiltonian replica-exchange molecular dynamics (Chaperone H-replica-exchange molecular dynamics [CH-REMD]) for the refinement of protein structural models generated de novo is investigated. In CH-REMD, the interaction between the protein and its environment, specifically, the electrostatic interaction between the protein and the solvating water, is varied leading to cycles of partial unfolding and refolding mimicking some aspects of folding chaperones. In 10 of the 15 cases examined, the CH-REMD approach sampled structures in which the root-mean-square deviation (RMSD) of secondary structure elements (SSE-RMSD) with respect to the experimental structure was more than 1.0 Å lower than the initial de novo model. In 14 of the 15 cases, the improvement was more than 0.5 Å. The ability of three different statistical potentials to identify near-native conformations was also examined. Little correlation between the SSE-RMSD of the sampled structures with respect to the experimental structure and any of the scoring functions tested was found. The most effective scoring function tested was the DFIRE potential. Using the DFIRE potential, the SSE-RMSD of the best scoring structures was on average 0.3 Å lower than the initial model. Overall the work demonstrates that targeted enhanced-sampling techniques such as CH-REMD can lead to the systematic refinement of protein structural models generated de novo but that improved potentials for the identification of near-native structures are still needed.

  3. The conformational landscape of tartrate-based inhibitors of the TACE enzyme as revealed by Hamiltonian Replica Exchange simulation.

    Science.gov (United States)

    Guardiani, Carlo; Procacci, Piero

    2013-06-21

    The inhibitors of the Tumor Necrosis Factor-α Converting Enzyme represent promising tools for the treatment of Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. In this work, using Hamiltonian Replica Exchange Molecular Dynamics simulations and atomistic force field we perform an accurate structural characterization of a group of tartrate-based inhibitors. The simulations highlight a correlation between the conformational landscape in bulk solvent and inhibition potency. Since the structures in bulk solvent are much more compact than the crystallographic bound state, we formulate the hypothesis of a two-step docking mechanism: (i) formation of an intermediate between the compact, hydroxyl exposing conformations in solution and the catalytic zinc ion; (ii) structural rearrangement in the active site of TACE of the zinc-tethered drug in the final binding conformation.

  4. Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study.

    Science.gov (United States)

    Perera, Dilina; Vogel, Thomas; Landau, David P

    2016-10-01

    Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, the results were found to be sensitive to the particular choice of interatomic potential.

  5. Magnetic phase transition in coupled spin-lattice systems: A replica-exchange Wang-Landau study

    Science.gov (United States)

    Perera, Dilina; Vogel, Thomas; Landau, David P.

    2016-10-01

    Coupled, dynamical spin-lattice models provide a unique test ground for simulations investigating the finite-temperature magnetic properties of materials under the direct influence of the lattice vibrations. These models are constructed by combining a coordinate-dependent interatomic potential with a Heisenberg-like spin Hamiltonian, facilitating the treatment of both the atomic coordinates and the spins as explicit phase variables. Using a model parameterized for bcc iron, we study the magnetic phase transition in these complex systems via the recently introduced, massively parallel replica-exchange Wang-Landau Monte Carlo method. Comparison with the results obtained from rigid lattice (spin-only) simulations shows that the transition temperature as well as the amplitude of the peak in the specific heat curve is marginally affected by the lattice vibrations. Moreover, the results were found to be sensitive to the particular choice of interatomic potential.

  6. Recovering kinetics from a simplified protein folding model using replica exchange simulations: a kinetic network and effective stochastic dynamics.

    Science.gov (United States)

    Zheng, Weihua; Andrec, Michael; Gallicchio, Emilio; Levy, Ronald M

    2009-08-27

    We present an approach to recover kinetics from a simplified protein folding model at different temperatures using the combined power of replica exchange (RE), a kinetic network, and effective stochastic dynamics. While RE simulations generate a large set of discrete states with the correct thermodynamics, kinetic information is lost due to the random exchange of temperatures. We show how we can recover the kinetics of a 2D continuous potential with an entropic barrier by using RE-generated discrete states as nodes of a kinetic network. By choosing the neighbors and the microscopic rates between the neighbors appropriately, the correct kinetics of the system can be recovered by running a kinetic simulation on the network. We fine-tune the parameters of the network by comparison with the effective drift velocities and diffusion coefficients of the system determined from short-time stochastic trajectories. One of the advantages of the kinetic network model is that the network can be built on a high-dimensional discretized state space, which can consist of multiple paths not consistent with a single reaction coordinate.

  7. Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations.

    Science.gov (United States)

    Olson, Mark A; Lee, Michael S; Yeh, In-Chul

    2017-01-28

    This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale. We found the GBSW implicit membrane model to produce results of limited accuracy in conformational properties of the peptide when compared to the NMR structure, yet the model resolution is sufficient to determine the effect of sequence differentiation on peptide-membrane integration. © 2016 Wiley Periodicals, Inc.

  8. Structure, dynamics, and function of the hammerhead ribozyme in bulk water and at a clay mineral surface from replica exchange molecular dynamics.

    Science.gov (United States)

    Swadling, Jacob B; Wright, David W; Suter, James L; Coveney, Peter V

    2015-03-01

    Compared with proteins, the relationship between structure, dynamics, and function of RNA enzymes (known as ribozymes) is far less well understood, despite the fact that ribozymes are found in many organisms and are often conceived as "molecular fossils" of the first self-replicating molecules to have arisen on Earth. To investigate how ribozymal function is governed by structure and dynamics, we study the full hammerhead ribozyme in bulk water and in an aqueous clay mineral environment by computer simulation using replica-exchange molecular dynamics. Through extensive sampling of the major conformational states of the hammerhead ribozyme, we are able to show that the hammerhead manifests a free-energy landscape reminiscent of that which is well known in proteins, exhibiting a "funnel" topology that guides the ribozyme into its globally most stable conformation. The active-site geometry is found to be closely correlated to the tertiary structure of the ribozyme, thereby reconciling conflicts between previously proposed mechanisms for the self-scission of the hammerhead. The conformational analysis also accounts for the differences reported experimentally in the catalytic activity of the hammerhead ribozyme, which is reduced when interacting with clay minerals as compared with bulk water.

  9. Replica exchange molecular dynamics simulation of cross-fibrillation of IAPP and PrP106-126.

    Science.gov (United States)

    Chua, Khi Pin; Chew, Lock Yue; Mu, Yuguang

    2016-08-01

    Aggregation of proteins into amyloid is the central hallmark of a number of protein diseases. Most studies were carried out on the aggregation between proteins of similar species. However, it was observed that some patients with certain protein disease can easily acquire another unrelated protein disease. As such, it is also important to examine aggregation between proteins of different species. Usually aggregation between proteins of the same species can be attributed to the similarity between their respective amino acid sequences. In this article, we were motivated by an experimental study of aggregation between amylin (Islet Amyloid Polypeptide, IAPP) and prion106-126 (PrP106-126) fragment (JACS, 2013, 135, 13582-9). It was found that the two non-homologous peptides can aggregate quickly to form fibrils in the presence of negatively charged lipid bilayer. We attempted to elucidate the molecular mechanism of the early stage of dimerization of these two peptides through extensive replica exchange molecular dynamics simulations. Conformations consisting of various degrees of β-sheets structures, both intra-chain and inter-chain, were found in the simulations. The conformations of the aggregated complex are very diverse, which suggests that the cross-species fibrils formed between the two proteins are highly polymorphic. The driving forces are mainly hydrophobic interactions, including aromatic-aliphatic interactions. The palindromic region of PrP106-126 and SNNFGAIL region of IAPP were found to play important roles in the interaction. Our study sheds insight into the exciting research of protein cross-fibrillation. Proteins 2016; 84:1134-1146. © 2016 Wiley Periodicals, Inc.

  10. Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

    Science.gov (United States)

    Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

    2017-03-15

    The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

  11. A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins.

    Science.gov (United States)

    Meli, Massimiliano; Colombo, Giorgio

    2013-06-06

    Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD) simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named "hot spots", are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues) and Protein A (62 residues), using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  12. A Hamiltonian Replica Exchange Molecular Dynamics (MD Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins

    Directory of Open Access Journals (Sweden)

    Massimiliano Meli

    2013-06-01

    Full Text Available Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named “hot spots”, are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues and Protein A (62 residues, using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  13. Effect of the disulfide bond on the monomeric structure of human amylin studied by combined Hamiltonian and temperature replica exchange molecular dynamics simulations.

    Science.gov (United States)

    Laghaei, Rozita; Mousseau, Normand; Wei, Guanghong

    2010-05-27

    The human Islet amyloid polypeptide (hIAPP or amylin) is a 37-residue peptide hormone that is normally cosecreted with insulin by the pancreatic beta-cells. In patients with type 2 diabetes, hIAPP deposits as amyloid fibrils in the extracellular spaces of the pancreatic islets. Recent experimental studies show that the intramolecular disulfide bond between Cys2 and Cys7 plays a central role in the process of fibril formation. However, the effect of the disulfide bond on the intrinsic structural properties of monomeric hIAPP is yet to be determined. In this study, we characterize the atomic structure and the thermodynamics of full-length hIAPP in the presence and absence of a disulfide bond using extensive combined Hamiltonian and temperature replica exchange molecular dynamics simulations (HT-REMD) with a coarse grained protein force field. Our simulations show that HT-REMD is more efficient in sampling than temperature REMD. On the basis of a total simulation time of 28 mus, we find that, although native hIAPP (in the presence of a disulfide bond) essentially adopts a disordered conformation in solution, consistent with the signal measured by ultraviolet-circular dichroism (UV-CD) spectroscopy, it also transiently samples alpha-helical structure for residues 5-16. In comparison with the N-terminal region, the C-terminal region is highly disordered and populates a much lesser content of isolated beta-strand conformation for residues 22-26 and 30-35. Moreover, the absence of the disulfide bond greatly decreases the extent of helix formed throughout residues 5-9 in favor of random coil and beta-sheet structure. Implications of the stabilization of N-terminal helical structure by disulfide bond on the initialization of hIAPP amyloid formation are discussed.

  14. Seismic wavefield imaging in the Tokyo metropolitan area, Japan, based on the replica exchange Monte Carlo method

    Science.gov (United States)

    Kano, Masayuki; Nagao, Hiromichi; Nagata, Kenji; Ito, Shin-ichi; Sakai, Shin'ichi; Nakagawa, Shigeki; Hori, Muneo; Hirata, Naoshi

    2017-04-01

    Earthquakes sometimes cause serious disasters not only directly by ground motion itself but also secondarily by infrastructure damage, particularly in densely populated urban areas. To reduce these secondary disasters, it is important to rapidly evaluate seismic hazards by analyzing the seismic responses of individual structures due to the input ground motions. Such input motions are estimated utilizing an array of seismometers that are distributed more sparsely than the structures. We propose a methodology that integrates physics-based and data-driven approaches in order to obtain the seismic wavefield to be input into seismic response analysis. This study adopts the replica exchange Monte Carlo (REMC) method, which is one of the Markov chain Monte Carlo (MCMC) methods, for the estimation of the seismic wavefield together with one-dimensional local subsurface structure and source information. Numerical tests show that the REMC method is able to search the parameters related to the source and the local subsurface structure in broader parameter space than the Metropolis method, which is an ordinary MCMC method. The REMC method well reproduces the seismic wavefield consistent with the true one. In contrast, the ordinary kriging, which is a classical data-driven interpolation method for spatial data, is hardly able to reproduce the true wavefield even at low frequencies. This indicates that it is essential to take both physics-based and data-driven approaches into consideration for seismic wavefield imaging. Then the REMC method is applied to the actual waveforms observed by a dense seismic array MeSO-net (Metropolitan Seismic Observation network), in which 296 accelerometers are continuously in operation with several kilometer intervals in the Tokyo metropolitan area, Japan. The estimated wavefield within a frequency band of 0.10-0.20 Hz is absolutely consistent with the observed waveforms. Further investigation suggests that the seismic wavefield is successfully

  15. Cellulose Acetate Replica Cleaning Study of Genesis Non-Flight Sample 3CZ00327

    Science.gov (United States)

    Kuhlman, K. R.; Schmeling, M.; Gonzalez, C. P.; Allton, J. H.; Burnett, D. S.

    2014-01-01

    The Genesis mission collected solar wind and brought it back to Earth in order to provide precise knowledge of solar isotopic and elemental compositions. The ions in the solar wind were stopped in the collectors at depths on the order of 10 to a few hundred nanometers. This shallow implantation layer is critical for scientific analysis of the composition of the solar wind and must be preserved throughout sample handling, cleaning, processing, distribution, preparation and analysis. We are working interactively with the community of scientists analyzing Genesis samples, using our unique laboratory facilities -- and, where needed, our unique cleaning techniques -- to significantly enhance the science return from the Genesis mission. This work is motivated by the need to understand the submicron contamination on the collectors in the Genesis payload as recovered from the crash site in the Utah desert, and -- perhaps more importantly -- how to remove it. That is, we are evaluating the effectiveness of the wet-chemical "cleaning" steps used by various investigators, to enable them to design improved methods of stripping terrestrial contamination from surfaces while still leaving the solar-wind signal intact.

  16. Structural and thermodynamics characters of isolated α-syn12 peptide: long-time temperature replica-exchange molecular dynamics in aqueous solution

    Institute of Scientific and Technical Information of China (English)

    Zanxia Cao; Lei Liu; Ping Wu; Jihua Wang

    2011-01-01

    The structural and thermodynamics characters of α-syn12 (residues 1-12 of the human α-synuclein protein) peptide in aqueous solution were investigated through temperature replica-exchange molecular dynamics (T-REMD) simulations with the GROMOS 43A1 force field. The two independent T-REMD simulations were completed starting from an initial conformational α-helix and an irregular structure,respectively. Each replica was run for 300ns. The structural and thermodynamics characters were studied based on parameters such as distributions of backbone dihedral angles, free energy surface, stability of folded β-hairpin structure, and favorite conformations. The results showed that the isolated α-syn12 peptide in water adopted four different conformational states: the first state was a β-hairpin ensemble with Turno-6 and four hydrogen bonds, the second state was a β-hairpin ensemble with two turns (Turn9-6 and Turn5-2) and three hydrogen bonds, the third state was a disordered structure with both Turn8-5 and Turn5-2, and the last state was a π-helix ensemble. Meanwhile, we studied the free energy change of α-syn12 peptide from the unfolded state to the β-hairpin state, which was in good agreement with the experiments and molecular dynamics simulations for some other peptides. We also analyzed the driving force of the peptide transition.The results indicated that the driving forces were high solvent exposure of hydrophobic Leu8 and hydrophobic residues in secondary structure. To our knowledge, this was the first report to study the isolated α-syn12 peptide in water by T-REMD.

  17. Reordering hydrogen bonds using Hamiltonian replica exchange enhances sampling of conformational changes in biomolecular systems

    NARCIS (Netherlands)

    Vreede, J.; Wolf, M.G.; de Leeuw, S.W.; Bolhuis, P.G.

    2009-01-01

    Hydrogen bonds play an important role in stabilizing (meta-)stable states in protein folding. Hence, they can potentially be used as a way to bias these states in molecular simulation methods. Previously, Wolf et al. showed that applying repulsive and attractive hydrogen bond biasing potentials in a

  18. Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

    Science.gov (United States)

    2011-12-01

    and Biochemistry , U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland §Computational Sciences and Engineering Branch...of motion of a system with constraints: molecular dynamics of n- alkanes . J. Comput. Phys. 1977, 23, 327–341. (29) Feig, M.; Karanicolas, J.; Brooks, C

  19. Are Bosonic Replicas Faulty?

    CERN Document Server

    Osipov, Vladimir Al

    2007-01-01

    Motivated by the ongoing discussion about a seeming asymmetry in the performance of fermionic and bosonic replicas, we present an exact, nonperturbative approach to zero-dimensional replica field theories belonging to the broadly interpreted "beta=2" Dyson symmetry class. We then utilise the formalism developed to demonstrate that the bosonic replicas do correctly reproduce the microscopic spectral density in the QCD inspired chiral Gaussian unitary ensemble. This disproves the myth that the bosonic replica field theories are intrinsically faulty.

  20. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Directory of Open Access Journals (Sweden)

    Tong Zhang

    Full Text Available Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III Hexamine ions or Mg(2+ ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III Hexamine ions were found to bind stronger with the loop than Mg(2+ ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+ ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III Hexamine ions on CorA ions transportation.

  1. Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

    Science.gov (United States)

    De Simone, Alfonso; Derreumaux, Philippe

    2010-04-01

    The self-assembly of proteins and peptides into amyloid fibrils is connected to over 40 pathological conditions including neurodegenerative diseases and systemic amyloidosis. Diffusible, low molecular weight protein and peptide oligomers that form in the early steps of aggregation appear to be the harmful cytotoxic species in the molecular etiology of these diseases. So far, the structural characterization of these oligomers has remained elusive owing to their transient and dynamic features. We here address, by means of full atomistic replica exchange molecular dynamics simulations, the energy landscape of heptamers of the amyloidogenic peptide NHVTLSQ from the beta-2 microglobulin protein. The simulations totaling 5 μs show that low molecular weight oligomers in explicit solvent consist of β-barrels in equilibrium with amorphous states and fibril-like assemblies. The results, also accounting for the influence of the pH on the conformational properties, provide a strong evidence of the formation of transient β-barrel assemblies in the early aggregation steps of amyloid-forming systems. Our findings are discussed in terms of oligomers cytotoxicity.

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

    Science.gov (United States)

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

    2015-11-10

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

  3. Initial binding of ions to the interhelical loops of divalent ion transporter CorA: replica exchange molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Tong; Mu, Yuguang

    2012-01-01

    Crystal structures of Thermotoga maritima magnesium transporter CorA, reported in 2006, revealed its homo-pentameric constructions. However, the structure of the highly conserved extracellular interhelical loops remains unsolved, due to its high flexibility. We have explored the configurations of the loops through extensive replica exchange molecular dynamics simulations in explicit solvent model with the presence of either Co(III) Hexamine ions or Mg(2+) ions. We found that there are multiple binding sites available on the interhelical loops in which the negatively charged residues, E316 and E320, are located notably close to the positively charged ions during the simulations. Our simulations resolved the distinct binding patterns of the two kinds of ions: Co(III) Hexamine ions were found to bind stronger with the loop than Mg(2+) ions with binding free energy -7.3 kJ/mol lower, which is nicely consistent with the previous data. Our study provides an atomic basis description of the initial binding process of Mg(2+) ions on the extracellular interhelical loops of CorA and the detailed inhibition mechanism of Co(III) Hexamine ions on CorA ions transportation.

  4. Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods.

    Science.gov (United States)

    Gai, Lili; Vogel, Thomas; Maerzke, Katie A; Iacovella, Christopher R; Landau, David P; Cummings, Peter T; McCabe, Clare

    2013-08-07

    Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ε) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results.

  5. Examining the phase transition behavior of amphiphilic lipids in solution using statistical temperature molecular dynamics and replica-exchange Wang-Landau methods

    Science.gov (United States)

    Gai, Lili; Vogel, Thomas; Maerzke, Katie A.; Iacovella, Christopher R.; Landau, David P.; Cummings, Peter T.; McCabe, Clare

    2013-08-01

    Two different techniques - replica-exchange Wang-Landau (REWL) and statistical temperature molecular dynamics (STMD) - were applied to systematically study the phase transition behavior of self-assembling lipids as a function of temperature using an off-lattice lipid model. Both methods allow the direct calculation of the density of states with improved efficiency compared to the original Wang-Landau method. A 3-segment model of amphiphilic lipids solvated in water has been studied with varied particle interaction energies (ɛ) and lipid concentrations. The phase behavior of the lipid molecules with respect to bilayer formation has been characterized through the calculation of the heat capacity as a function of temperature, in addition to various order parameters and general visual inspection. The simulations conducted by both methods can go to very low temperatures with the whole system exhibiting well-ordered structures. With optimized parameters, several bilayer phases are observed within the temperature range studied, including gel phase bilayers with frozen water, mixed water (i.e., frozen and liquid water), and liquid water, and a more fluid bilayer with liquid water. The results obtained from both methods, STMD and REWL, are consistently in excellent agreement with each other, thereby validating both the methods and the results.

  6. Hamiltonian replica-permutation method and its applications to an alanine dipeptide and amyloid-β(29-42) peptides.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2013-11-05

    We propose the Hamiltonian replica-permutation method (RPM) (or multidimensional RPM) for molecular dynamics and Monte Carlo simulations, in which parameters in the Hamiltonian are permuted among more than two replicas with the Suwa-Todo algorithm. We apply the Coulomb RPM, which is one of realization of the Hamiltonian RPM, to an alanine dipeptide and to two amyloid-β(29-42) molecules. The Hamiltonian RPM realizes more efficient sampling than the Hamiltonian replica-exchange method. We illustrate the protein misfolding funnel of amyloid-β(29-42) and reveal its dimerization pathways.

  7. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Damjanović, Ana; Brooks, Bernard R

    2014-07-08

    We present a new computational approach for constant pH simulations in explicit solvent based on the combination of the enveloping distribution sampling (EDS) and Hamiltonian replica exchange (HREX) methods. Unlike constant pH methods based on variable and continuous charge models, our method is based on discrete protonation states. EDS generates a hybrid Hamiltonian of different protonation states. A smoothness parameter s is used to control the heights of energy barriers of the hybrid-state energy landscape. A small s value facilitates state transitions by lowering energy barriers. Replica exchange between EDS potentials with different s values allows us to readily obtain a thermodynamically accurate ensemble of multiple protonation states with frequent state transitions. The analysis is performed with an ensemble obtained from an EDS Hamiltonian without smoothing, s = ∞, which strictly follows the minimum energy surface of the end states. The accuracy and efficiency of this method is tested on aspartic acid, lysine, and glutamic acid, which have two protonation states, a histidine with three states, a four-residue peptide with four states, and snake cardiotoxin with eight states. The pKa values estimated with the EDS-HREX method agree well with the experimental pKa values. The mean absolute errors of small benchmark systems range from 0.03 to 0.17 pKa units, and those of three titratable groups of snake cardiotoxin range from 0.2 to 1.6 pKa units. This study demonstrates that EDS-HREX is a potent theoretical framework, which gives the correct description of multiple protonation states and good calculated pKa values.

  8. Crystal Ball Replica

    Science.gov (United States)

    Ajamian, John

    2016-09-01

    The A2 collaboration of the Institute for Nuclear Physics of Johannes Gutenberg University performs research on (multiple) meson photoproduction and nucleon structure and dynamics using a high energy polarized photon beam at specific targets. Particles scattered from the target are detected in the Crystal Ball, or CB. The CB is composed of 672 NaI crystals that surround the target and can analyze particle type and energy of ejected particles. Our project was to create a replica of the CB that could display what was happening in real time on a 3 Dimensional scale replica. Our replica was constructed to help explain the physics to the general public, be used as a tool when calibrating each of the 672 NaI crystals, and to better analyze the electron showering of particles coming from the target. This poster will focus on the hardware steps necessary to construct the replica and wire the 672 programmable LEDS in such a way that they can be mapped to correspond to the Crystal Ball elements. George Washington NSF Grant.

  9. Hyper-V Replica essentials

    CERN Document Server

    Krstevski, Vangel

    2013-01-01

    a in various deployment scenarios.Hyper-V Replica Essentials is for Windows Server administrators who want to improve their system availability and speed up disaster recovery. You will need experience in Hyper-V deployment because Hyper-V Replica is built in the Hyper-V platform.

  10. Ion exchange properties of Wyodak premium coal samples

    Energy Technology Data Exchange (ETDEWEB)

    Vorres, K.S.

    1993-08-23

    Low rank coals (lignite and subbituminous) contain exchangeable cations. A sample of {minus}20+200 mesh Argonne Premium Wyodak coal was washed with nitric acid in a burette fitted with a coarse glass frit at the base of the graduations to remove the exchangeable cations from the system. The eluent was passed to a flow-through pH electrode and a titration curve was obtained on a computer file. A series of electrodes (pH, calcium, sodium and potassium) were used in separate experiments to follow the elution from the coal. Some implications for coal structure are also indicated.

  11. SRF Cavity Surface Topography Characterization Using Replica Techniques

    Energy Technology Data Exchange (ETDEWEB)

    C. Xu, M.J. Kelley, C.E. Reece

    2012-07-01

    To better understand the roll of topography on SRF cavity performance, we seek to obtain detailed topographic information from the curved practical cavity surfaces. Replicas taken from a cavity interior surface provide internal surface molds for fine Atomic Force Microscopy (AFM) and stylus profilometry. In this study, we confirm the replica resolution both on surface local defects such as grain boundary and etching pits and compare the surface uniform roughness with the aid of Power Spectral Density (PSD) where we can statistically obtain roughness parameters at different scales. A series of sampling locations are at the same magnetic field chosen at the same latitude on a single cell cavity to confirm the uniformity. Another series of sampling locations at different magnetic field amplitudes are chosen for this replica on the same cavity for later power loss calculation. We also show that application of the replica followed by rinsing does not adversely affect the cavity performance.

  12. Bayesian ensemble refinement by replica simulations and reweighting.

    Science.gov (United States)

    Hummer, Gerhard; Köfinger, Jürgen

    2015-12-28

    We describe different Bayesian ensemble refinement methods, examine their interrelation, and discuss their practical application. With ensemble refinement, the properties of dynamic and partially disordered (bio)molecular structures can be characterized by integrating a wide range of experimental data, including measurements of ensemble-averaged observables. We start from a Bayesian formulation in which the posterior is a functional that ranks different configuration space distributions. By maximizing this posterior, we derive an optimal Bayesian ensemble distribution. For discrete configurations, this optimal distribution is identical to that obtained by the maximum entropy "ensemble refinement of SAXS" (EROS) formulation. Bayesian replica ensemble refinement enhances the sampling of relevant configurations by imposing restraints on averages of observables in coupled replica molecular dynamics simulations. We show that the strength of the restraints should scale linearly with the number of replicas to ensure convergence to the optimal Bayesian result in the limit of infinitely many replicas. In the "Bayesian inference of ensembles" method, we combine the replica and EROS approaches to accelerate the convergence. An adaptive algorithm can be used to sample directly from the optimal ensemble, without replicas. We discuss the incorporation of single-molecule measurements and dynamic observables such as relaxation parameters. The theoretical analysis of different Bayesian ensemble refinement approaches provides a basis for practical applications and a starting point for further investigations.

  13. Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

    Science.gov (United States)

    Jiang, Wei; Luo, Yun; Maragliano, Luca; Roux, Benoît

    2012-11-13

    An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to enhance the sampling of each simulation. In the present application, US/H-REMD is carried out in a two-dimensional (2D) space and exchanges are attempted alternatively along the two axes corresponding to the two order parameters. The US/H-REMD strategy is implemented on the basis of parallel/parallel multiple copy protocol at the MPI level, and therefore can fully exploit computing power of large-scale supercomputers. Here the novel technique is illustrated using the leadership supercomputer IBM Blue Gene/P with an application to a typical biomolecular calculation of general interest, namely the binding of calcium ions to the small protein Calbindin D9k. The free energy landscape associated with two order parameters, the distance between the ion and its binding pocket and the root-mean-square deviation (rmsd) of the binding pocket relative the crystal structure, was calculated using the US/H-REMD method. The results are then used to estimate the absolute binding free energy of calcium ion to Calbindin D9k. The tests demonstrate that the 2D US/H-REMD scheme greatly accelerates the configurational sampling of the binding pocket, thereby improving the convergence of the potential of mean force calculation.

  14. Genealogies of regular exchangeable coalescents with applications to sampling

    CERN Document Server

    Limic, Vlada

    2010-01-01

    This article considers a model of genealogy corresponding to a regular exchangeable coalescent (also known as Xi-coalescent) started from a large finite configuration, and undergoing neutral mutations. Asymptotic expressions for the number of active lineages were obtained by the author in a previous work. Analogous results for the number of active mutation-free lineages and the combined lineage lengths are derived using the same martingale-based technique. They are given in terms of convergence in probability, while extensions to convergence in moments and convergence almost surely are discussed. The above mentioned results have direct consequences on the sampling theory in the Xi-coalescent setting. In particular, the regular Xi-coalescents that come down from infinity (i.e., with locally finite genealogies), have an asymptotically equal number of families under the corresponding infinite alleles and infinite sites models. In special cases, quantitative asymptotic formulae for the number of families that con...

  15. Replica trick and string winding

    Science.gov (United States)

    Prudenziati, Andrea; Trancanelli, Diego

    2017-07-01

    We apply the replica trick to compute the entropy of a cylinder amplitude in string theory. We focus on the contribution from nonperturbative winding modes and impose tadpole cancellation to understand the correct prescription for integrating over moduli. Choosing the entangling surface to cut longitudinally over the whole length of the cylinder, we obtain an answer that is interpreted as the entropy of a density matrix. We recast this result in target space language, in both the open and closed string picture.

  16. Replica trick and string winding

    CERN Document Server

    Prudenziati, Andrea

    2016-01-01

    We apply the replica trick to compute the entropy of a cylinder amplitude in string theory. We focus on the contribution from non-perturbative winding modes and impose tadpole cancellation to understand the correct prescription for integrating over moduli. Choosing the entangling surface to cut longitudinally over the whole length of the cylinder, we obtain an answer that is interpreted as the entropy of a density matrix. We recast this result in target space language, both in the open and closed string picture.

  17. File-based replica management

    CERN Document Server

    Kunszt, Peter Z; Stockinger, Heinz; Stockinger, Kurt

    2005-01-01

    Data replication is one of the best known strategies to achieve high levels of availability and fault tolerance, as well as minimal access times for large, distributed user communities using a world-wide Data Grid. In certain scientific application domains, the data volume can reach the order of several petabytes; in these domains, data replication and access optimization play an important role in the manageability and usability of the Grid. In this paper, we present the design and implementation of a replica management Grid middleware that was developed within the EDG project left bracket European Data Grid Project (EDG), http://www.eu-egee.org right bracket and is designed to be extensible so that user communities can adjust its detailed behavior according to their QoS requirements.

  18. Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

    Directory of Open Access Journals (Sweden)

    Beukelaer Herman De

    2012-11-01

    Full Text Available Abstract Background Sampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The Core Hunter computer program was developed as a tool to generate such subsets based on multiple genetic measures, including both distance measures and allelic diversity indices. At first we investigate the effect of minimum (instead of the default mean distance measures on the performance of Core Hunter. Secondly, we try to gain more insight into the performance of the original Core Hunter search algorithm through comparison with several other heuristics working with several realistic datasets of varying size and allelic composition. Finally, we propose a new algorithm (Mixed Replica search for Core Hunter II with the aim of improving the diversity of the constructed core sets and their corresponding generation times. Results Our results show that the introduction of minimum distance measures leads to core sets in which all accessions are sufficiently distant from each other, which was not always obtained when optimizing mean distance alone. Comparison of the original Core Hunter algorithm, Replica Exchange Monte Carlo (REMC, with simpler heuristics shows that the simpler algorithms often give very good results but with lower runtimes than REMC. However, the performance of the simpler algorithms is slightly worse than REMC under lower sampling intensities and some heuristics clearly struggle with minimum distance measures. In comparison the new advanced Mixed Replica search algorithm (MixRep, which uses heterogeneous replicas, was able to sample core sets with equal or higher diversity scores than REMC and the simpler heuristics, often using less computation time than REMC. Conclusion The REMC search algorithm used in the original Core Hunter computer program performs well, sometimes leading to slightly better results

  19. Calorimetry Sample Exchange analysis of data report for October--December, 1988

    Energy Technology Data Exchange (ETDEWEB)

    Lyons, J.E.

    1989-12-31

    The goals of the Calorimetry Sample Exchange Program are to: discuss measurement differences; review and improve analytical measurements and methods; discuss new measurement capabilities; provide data to DOE on measurement capabilities to evaluate shipper-receiver differences; provide characterized or standard materials as necessary for exchange participants; and provide a measurement control program for plutonium analysis. A sample of PuO{sub 2} powder is available at each participating site for NDA measurement, including either or both calorimetry and high-resolution gamma-ray spectroscopy, the elements which are typically combined to provide a calorimetric assay of plutonium. The facilities measure the sample as frequently and to the level of precision which they desire, and then submit the data to the Exchange for analysis. Statistical tests are used to evaluate the data and to determine if there are significant differences from accepted values for the exchange sample or from data previously reported by that facility. This information is presented, in the form of a quarterly report, intended for use by Exchange participants in measurement control programs, or to indicate when bias corrections may be appropriate. No attempt, however, has been made to standardize methods or frequency of data collection, calibration, or operating procedures. Direct comparisons between laboratories may, therefore, be misleading since data have not bee collected to the same precision or for the same time periods. The six participating laboratories are Lawrence Livermore, Los Alamos, MRC-Mound, Westinghouse Hanford, Rocky Flats, and Savannah River.

  20. Replica symmetry breaking for anisotropic magnets with quenched disorder

    Science.gov (United States)

    Kogan, E.; Kaveh, M.

    2017-01-01

    We study critical behaviour of a magnet with cubic anisotropy and quenched scalar disorder which is taken into account by replica method. We derive to first order in ε approximation the renormalization group equations taking into account possible replica symmetry breaking. We study the stability of the replica symmetric fixed points with respect to perturbations without (in general case) replica symmetry. However, we find that if a fixed point is stable with respect to replica symmetric deviations, it is also stable with respect to deviations without replica symmetry.

  1. Replica symmetric spin glass field theory

    Energy Technology Data Exchange (ETDEWEB)

    Temesvari, T. [Research Group for Theoretical Physics of the Hungarian Academy of Sciences, Eoetvoes University, Pazmany Peter setany 1/A, H-1117 Budapest (Hungary)]. E-mail: temtam@helios.elte.hu

    2007-06-18

    A new powerful method to test the stability of the replica symmetric spin glass phase is proposed by introducing a replicon generator function g(v). Exact symmetry arguments are used to prove that its extremum is proportional to the inverse spin glass susceptibility. By the idea of independent droplet excitations a scaling form for g(v) can be derived, whereas it can be exactly computed in the mean field Sherrington-Kirkpatrick model. It is shown by a first order perturbative treatment that the replica symmetric phase is unstable down to dimensions d < or approx. 6, and the mean field scaling function proves to be very robust. Although replica symmetry breaking is escalating for decreasing dimensionality, a mechanism caused by the infrared divergent replicon propagator may destroy the mean field picture at some low enough dimension.

  2. Replica symmetric spin glass field theory

    Science.gov (United States)

    Temesvári, T.

    2007-06-01

    A new powerful method to test the stability of the replica symmetric spin glass phase is proposed by introducing a replicon generator function g(v). Exact symmetry arguments are used to prove that its extremum is proportional to the inverse spin glass susceptibility. By the idea of independent droplet excitations a scaling form for g(v) can be derived, whereas it can be exactly computed in the mean field Sherrington-Kirkpatrick model. It is shown by a first order perturbative treatment that the replica symmetric phase is unstable down to dimensions d≲6, and the mean field scaling function proves to be very robust. Although replica symmetry breaking is escalating for decreasing dimensionality, a mechanism caused by the infrared divergent replicon propagator may destroy the mean field picture at some low enough dimension.

  3. Replica Fourier Transform: Properties and applications

    Directory of Open Access Journals (Sweden)

    A. Crisanti

    2015-02-01

    Full Text Available The Replica Fourier Transform is the generalization of the discrete Fourier Transform to quantities defined on an ultrametric tree. It finds use in conjunction of the replica method used to study thermodynamics properties of disordered systems such as spin glasses. Its definition is presented in a systematic and simple form and its use illustrated with some representative examples. In particular we give a detailed discussion of the diagonalization in the Replica Fourier Space of the Hessian matrix of the Gaussian fluctuations about the mean field saddle point of spin glass theory. The general results are finally discussed for a generic spherical spin glass model, where the Hessian can be computed analytically.

  4. Two phase decision algorithm of replica allocation

    Institute of Scientific and Technical Information of China (English)

    Zuo Chaoshu; Liu Xinsong; Wang Zheng; Li Yi

    2006-01-01

    In distributed parallel server system, location and redundancy of replicas have great influence on availability and efficiency of the system. In order to improve availahility and efficiency of the system, two phase decision algorithm of replica allocation is proposed. The algorithm which makes use of auto-regression model dynamically predicts the future count of READ and WRITE operation, and then determines location and redundancy of replicas by considering availability, CPU and bands of the network. The algorithm can not only ensure the requirement of availability, but also reduce the system resources consumed by all the operations in a great scale. Analysis and test show that communication complexity and time complexity of the algorithm satisfy O( n ), resource optimizing scale increases with the increase of READ count.

  5. Generalized gravitational entropy without replica symmetry

    Science.gov (United States)

    Camps, Joan; Kelly, William R.

    2015-03-01

    We explore several extensions of the generalized entropy construction of Lewkowycz and Maldacena, including a formulation that does not rely on preserving replica symmetry in the bulk. We show that an appropriately general ansatz for the analytically continued replica metric gives us the flexibility needed to solve the gravitational field equations beyond general relativity. As an application of this observation we study EinsteinGauss-Bonnet gravity with a small Gauss-Bonnet coupling and derive the condition that the holographic entanglement entropy must be evaluated on a surface which extremizes the Jacobson-Myers entropy. We find that in both general relativity and Einstein-Gauss-Bonnet gravity replica symmetry breaking terms are permitted by the field equations, suggesting that they do not generically vanish.

  6. Generalized gravitational entropy without replica symmetry

    CERN Document Server

    Camps, Joan

    2014-01-01

    We explore several extensions of the generalized entropy construction of Lewkowycz and Maldacena, including a formulation that does not rely on preserving replica symmetry in the bulk. We show that an appropriately general ansatz for the analytically continued replica metric gives us the flexibility needed to solve the gravitational field equations beyond general relativity. As an application of this observation we study Einstein-Gauss-Bonnet gravity with a small Gauss-Bonnet coupling and derive the condition that the holographic entanglement entropy must be evaluated on a surface which extremizes the Jacobson-Myers entropy. We find that in both general relativity and Einstein-Gauss-Bonnet gravity replica symmetry breaking terms are permitted by the field equations, suggesting that they do not generically vanish.

  7. Cryogenic sample exchange NMR probe for magic angle spinning dynamic nuclear polarization

    Science.gov (United States)

    Barnes, Alexander B.; Mak-Jurkauskas, Melody L.; Matsuki, Yoh; Bajaj, Vikram S.; van der Wel, Patrick C. A.; DeRocher, Ronald; Bryant, Jeffrey; Sirigiri, Jagadishwar R.; Temkin, Richard J.; Lugtenburg, Johan; Herzfeld, Judith; Griffin, Robert G.

    2009-01-01

    We describe a cryogenic sample exchange system that dramatically improves the efficiency of magic angle spinning (MAS) dynamic nuclear polarization (DNP) experiments by reducing the time required to change samples and by improving long-term instrument stability. Changing samples in conventional cryogenic MAS DNP/NMR experiments involves warming the probe to room temperature, detaching all cryogenic, RF, and microwave connections, removing the probe from the magnet, replacing the sample, and reversing all the previous steps, with the entire cycle requiring a few hours. The sample exchange system described here — which relies on an eject pipe attached to the front of the MAS stator and a vacuum jacketed dewar with a bellowed hole — circumvents these procedures. To demonstrate the excellent sensitivity, resolution, and stability achieved with this quadruple resonance sample exchange probe, we have performed high precision distance measurements on the active site of the membrane protein bacteriorhodopsin. We also include a spectrum of the tripeptide N-f-MLF-OH at 100 K which shows 30 Hz linewidths. PMID:19356957

  8. Vertices from replica in a random matrix theory

    Energy Technology Data Exchange (ETDEWEB)

    Brezin, E [Laboratoire de Physique Theorique, Ecole Normale Superieure, 24 rue Lhomond 75231, Paris Cedex 05 (France); Hikami, S [Department of Basic Sciences, University of Tokyo, Meguro-ku, Komaba, Tokyo 153 (Japan)

    2007-11-09

    Kontsevich's work on Airy matrix integrals has led to explicit results for the intersection numbers of the moduli space of curves. In a subsequent work Okounkov rederived these results from the edge behavior of a Gaussian matrix integral. In our work we consider the correlation functions of vertices in a Gaussian random matrix theory, with an external matrix source. We deal with operator products of the form <{pi}{sub i=1}{sup n}1/N tr M{sup k{sub i}}>, in a 1/N expansion. For large values of the powers k{sub i}, in an appropriate scaling limit relating large k's to large N, universal scaling functions are derived. Furthermore, we show that the replica method applied to characteristic polynomials of the random matrices, together with a duality exchanging N and the number of points, provides a new way to recover Kontsevich's results on these intersection numbers.

  9. EXCHANGE

    Energy Technology Data Exchange (ETDEWEB)

    Boltz, J.C. (ed.)

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  10. Replica approach to mean-variance portfolio optimization

    Science.gov (United States)

    Varga-Haszonits, Istvan; Caccioli, Fabio; Kondor, Imre

    2016-12-01

    We consider the problem of mean-variance portfolio optimization for a generic covariance matrix subject to the budget constraint and the constraint for the expected return, with the application of the replica method borrowed from the statistical physics of disordered systems. We find that the replica symmetry of the solution does not need to be assumed, but emerges as the unique solution of the optimization problem. We also check the stability of this solution and find that the eigenvalues of the Hessian are positive for r  =  N/T  portfolio and T the length of the time series used to estimate the covariance matrix. At the critical point r  =  1 a phase transition is taking place. The out of sample estimation error blows up at this point as 1/(1  -  r), independently of the covariance matrix or the expected return, displaying the universality not only of the critical exponent, but also the critical point. As a conspicuous illustration of the dangers of in-sample estimates, the optimal in-sample variance is found to vanish at the critical point inversely proportional to the divergent estimation error.

  11. AN EMPIRICAL ANALYSIS OF SAMPLING INTERVAL FOR EXCHANGE RATE FORECASTING WITH NEURAL NETWORKS

    Institute of Scientific and Technical Information of China (English)

    HUANG Wei; K. K. Lai; Y. Nakamori; WANG Shouyang

    2003-01-01

    Artificial neural networks (ANNs) have been widely used as a promising alternative approach for forecast task because of their several distinguishing features. In this paper, we investigate the effect of different sampling intervals on predictive performance of ANNs in forecasting exchange rate time series. It is shown that selection of an appropriate sampling interval would permit the neural network to model adequately the financial time series. Too short or too long a sampling interval does not provide good forecasting accuracy. In addition, we discuss the effect of forecasting horizons and input nodes on the prediction performance of neural networks.

  12. RRS: Replica Registration Service for Data Grids

    Energy Technology Data Exchange (ETDEWEB)

    Shoshani, Arie; Sim, Alex; Stockinger, Kurt

    2005-07-15

    Over the last few years various scientific experiments and Grid projects have developed different catalogs for keeping track of their data files. Some projects use specialized file catalogs, others use distributed replica catalogs to reference files at different locations. Due to this diversity of catalogs, it is very hard to manage files across Grid projects, or to replace one catalog with another. In this paper we introduce a new Grid service called the Replica Registration Service (RRS). It can be thought of as an abstraction of the concepts for registering files and their replicas. In addition to traditional single file registration operations, the RRS supports collective file registration requests and keeps persistent registration queues. This approach is of particular importance for large-scale usage where thousands of files are copied and registered. Moreover, the RRS supports a set of error directives that are triggered in case of registration failures. Our goal is to provide a single uniform interface for various file catalogs to support the registration of files across multiple Grid projects, and to make Grid clients oblivious to the specific catalog used.

  13. Semiautomated Sample Preparation for Protein Stability and Formulation Screening via Buffer Exchange.

    Science.gov (United States)

    Ying, William; Levons, Jaquan K; Carney, Andrea; Gandhi, Rajesh; Vydra, Vicky; Rubin, A Erik

    2016-06-01

    A novel semiautomated buffer exchange process workflow was developed to enable efficient early protein formulation screening. An antibody fragment protein, BMSdab, was used to demonstrate the workflow. The process afforded 60% to 80% cycle time and scientist time savings and significant material efficiencies. These efficiencies ultimately facilitated execution of this stability work earlier in the drug development process, allowing this tool to inform the developability of potential candidates for development from a formulation perspective. To overcome the key technical challenges, the protein solution was buffer-exchanged by centrifuge filtration into formulations for stability screening in a 96-well plate with an ultrafiltration membrane, leveraging automated liquid handling and acoustic volume measurements to allow several cycles of exchanges. The formulations were transferred into a vacuum manifold and sterile filtered into a rack holding 96 glass vials. The vials were sealed with a capmat of individual caps and placed in stability stations. Stability of the samples prepared by this process and by the standard process was demonstrated to be comparable. This process enabled screening a number of formulations of a protein at an early pharmaceutical development stage with a short sample preparation time.

  14. Measurement of (90)Sr in environmental samples by cation-exchange and liquid scintillation counting.

    Science.gov (United States)

    Amano, H; Yanase, N

    1990-06-01

    A new method for the measurement of (90)Sr in environmental samples by cation-exchange and liquid scintillation counting is described. Strontium carbonate is purified by precipitation and ion-exchange, weighed for the determination of chemical yield, dissolved in hydrochloric acid and mixed with the liquid scintillator, Aquasol-2. Two channels of a low-background liquid scintillation counter are used to determine (90)Sr, (90)Y and (89)Sr, free from the effects of environmental tritium. The values of (90)Sr obtained by this method are in good agreement with those from ordinary (90)Y milking and the gas proportional counting method. The concentration of (90)Sr in the air at Tokai-mura in Japan has been measured by the new method.

  15. Aerospace devices for magnetic replicas

    Science.gov (United States)

    Weinstein, Roy

    1993-05-01

    Retained persistent magnetic field has been studied and improved in the superconductor YBa2Cu3O7 (Y123). During the study, trapped magnetic field, B(t), has been increased by over a factor of 10(exp 5). Methods used to improve magnetic field trapping were principally: (1) the adoption of the Melt Texturing process to increase grain size; (2) the addition of excess Y to disperse deposits of Y2BaCuO5 (Y211) and again increase grain size; (3) irradiation with high energy particles including 1H+, 3He++, 4He++, and fission fragments; and (4) utilizing temperatures below 77 K has also been quantified as a way to increase trapped field. In addition, in our study of B(t), we have found laws governing creep, activation, temperature dependence, creep vs. current flow, etc. In the range 20 K less than or equal to T less than or equal to 65 K, and for B less than 10 Tesla, a simple empirical relationship was found: B(trap) (T2) = B(trap) (T1) ((Tc - T2)/(Tc - T1))squared where Tc is the critical temperature. The highest experimental trapped field was B(trap) = 3.96 Tesla, at 65 K. We believe this to be the highest persistent field ever produced, by any method. A two component model of the persistent currents has been developed. This accurately reproduces the data, using as parameters only the magnitude of a constant surface current, J(s), and a constant volume current J(v). The model successfully predicts B(t) (xyz) for the case of maximum trapped field, for all samples observed. It has also been extended to describe the unsaturated case either zero field cooled, or field cooled. Loss of strap with time has been studied for the critical state (Bt,max), and non critical state (Bt less than Bt,max), for times from a few minutes to a few months, for unirradiated material, for irradiation by 1H+, 3He++, 4He++, high z projectiles, and neutrons, and for all materials used in the overall study. We conclude that: (1) multi Tesla trapped fields are attained; (2) fields over 10 T are

  16. Novel algorithm for distributed replicas management based on dynamic programming

    Institute of Scientific and Technical Information of China (English)

    Wang Tao; Lu Xianliang; Hou Mengshu

    2006-01-01

    Replicas can improve the data reliability in distributed system. However, the traditional algorithms for replica management are based on the assumption that all replicas have the uniform reliability, which is inaccurate in some actual systems. To address such problem, a novel algorithm is proposed based on dynamic programming to manage the number and distribution of replicas in different nodes. By using Markov model, replicas management is organized as a multi-phase process, and the recursion equations are provided. In this algorithm, the heterogeneity of nodes, the expense for maintaining replicas and the engaged space have been considered. Under these restricted conditions, this algorithm realizes high data reliability in a distributed system. The results of case analysis prove the feasibility of the algorithm.

  17. An Adaptive Replica Allocation Algorithm in Mobile Ad Hoc Networks

    Institute of Scientific and Technical Information of China (English)

    JingZheng; JinshuSu; KanYang

    2004-01-01

    In mobile ad hoc networks (MANET), nodes move freely and the distribution of access requests changes dynamically. Replica allocation in such a dynamic environment is a significant challenge. In this paoer, a dynamic adaptive replica allocation algorithm that can adapt to the nodes motion is proposed to minimize the communication cost of object access. When changes occur in the access requests of the object or the network topology, each replica node collects access requests from its neighbors and makes decisions locally to expand replica to neighbors or to relinquish the replica. The algorithm dynamically adapts the replica allocation scheme to a local optimal one. Simulation results show that our algorithms efficiently reduce the communication cost of object access in MANET environment.

  18. An Arbitrary 2D Structured Replica Control Protocol

    OpenAIRE

    Basmadjian, Robert; Meer, Hermann,

    2011-01-01

    Traditional replication protocols that logically arrange the replicas into a specific structure have reasonable availability, lower communication cost as well as system load than those that do not require any logical organisation of replicas. We propose in this paper the A2DS protocol: a single protocol that, unlike the existing proposed protocols, can be adapted to any 2D structure. Its read operation is carried out on any replica of every level of the structure whereas write operations are ...

  19. Ion-exchange preconcentration and determination of vanadium in milk samples by electrothermal atomic absorption spectrometry.

    Science.gov (United States)

    López-García, Ignacio; Viñas, Pilar; Romero-Romero, Rafael; Hernández-Córdoba, Manuel

    2009-06-15

    A new method for the electrothermal atomic absorption spectrometric determination of vanadium in milk and infant formulas using suspensions to avoid the need for previous dissolution of samples is described. Sensitivity is improved by a procedure based on preconcentration and removal of the matrix, using ion-exchange (Dowex 1X8-100). Suspensions of 15% (m/v) infant formula samples were prepared in a medium containing 0.05M sodium citrate (pH 7.2) and passed through the ion exchange column. Vanadium was eluted from the column using 1M hydrochloric acid and injected in the graphite furnace using a mixture of hydrofluoric acid plus magnesium nitrate as chemical modifiers. Calibration was carried out using multiple injection and aqueous standards prepared in the same medium. Detection limits were 0.2 ng g(-1) for infant formulas and 0.02 microg L(-1) for cow milk samples. The reliability of the procedure was checked by comparing the results obtained with those found using a previous mineralization stage and by analyzing five certified reference materials.

  20. Determination of uranium isotopes in environmental samples by anion exchange in sulfuric and hydrochloric acid media.

    Science.gov (United States)

    Popov, L

    2016-09-01

    Method for determination of uranium isotopes in various environmental samples is presented. The major advantages of the method are the low cost of the analysis, high radiochemical yields and good decontamination factors from the matrix elements, natural and man-made radionuclides. The separation and purification of uranium is attained by adsorption with strong base anion exchange resin in sulfuric and hydrochloric acid media. Uranium is electrodeposited on a stainless steel disk and measured by alpha spectrometry. The analytical method has been applied for the determination of concentrations of uranium isotopes in mineral, spring and tap waters from Bulgaria. The analytical quality was checked by analyzing reference materials.

  1. Determination of organoarsenic species in marine samples using gradient elution cation exchange HPLC-ICP-MS

    DEFF Research Database (Denmark)

    Sloth, Jens Jørgen; Larsen, Erik Huusfeldt; Julshamn, Kåre

    2003-01-01

    A method for the determination of arsenic species in marine samples using high performance liquid chromatography coupled to inductively coupled mass spectrometry (HPLC-ICP-MS) has been developed. Cation exchange HPLC with gradient elution using pyridine formate as the mobile phase was employed...... the certified limits and low detection limits of 0.002-0.005 mug g(-1) dry mass (as As) for the different arsenic species were obtained. At least 23 different organic arsenic species were detected in a scallop kidney in one analytical run of 25 min duration. The ability of our analytical method to detect...

  2. Reliability of the impression replica technique.

    Science.gov (United States)

    Falk, Anders; Vult von Steyern, Per; Fransson, Håkan; Thorén, Margareta Molin

    2015-01-01

    The aim of this study was to evaluate the reliability of the impression replica technique with a four-unit zirconia fixed dental prosthesis (FDP). Marginal and internal fit were measured by repeatedly placing the FDP on an epoxy cast using light-body silicone material corresponding to cement. All measured marginal and internal fit points showed varying values. The greatest variations were seen at the most distal margin (33 μm) and at the distal abutment of the FDP (77 μm). The results showed that the technique gives moderate variations and is a useful method to evaluate marginal and internal fit.

  3. Spin Glass Field Theory with Replica Fourier Transforms

    Science.gov (United States)

    Pimentel, Iveta R.; De Dominicis, Cirano

    We develop a field theory for spin glasses using Replica Fourier Transforms (RFT). We present the formalism for the case of replica symmetry and the case of replica symmetry breaking on an ultrametric tree, with the number of replicas n and the number of replica symmetry breaking steps R generic integers. We show how the RFT applied to the two-replica fields allows to construct a new basis which block-diagonalizes the four-replica mass-matrix, into the replicon, anomalous and longitudinal modes. The eigenvalues are given in terms of the mass RFT and the propagators in the RFT space are obtained by inversion of the block-diagonal matrix. The formalism allows to express any i-replica vertex in the new RFT basis and hence enables to perform a standard perturbation expansion. We apply the formalism to calculate the contribution of the Gaussian fluctuations around the Parisi's solution for the free-energy of an Ising spin glass.

  4. Dimerization process of amyloid-β(29-42) studied by the Hamiltonian replica-permutation molecular dynamics simulations.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2014-10-02

    The amyloid-β peptides form amyloid fibrils which are associated with Alzheimer's disease. Amyloid-β(29-42) is its C-terminal fragment and a critical determinant of the amyloid formation rate. This fragment forms the amyloid fibril by itself. However, the fragment conformation in the fibril has yet to be determined. The oligomerization process including the dimerization process is also still unknown. The dimerization process corresponds to an early process of the amyloidogenesis. In order to investigate the dimerization process and conformations, we applied the Hamiltonian replica-permutation method, which is a better alternative to the Hamiltonian replica-exchange method, to two amyloid-β(29-42) molecules in explicit water solvent. At the first step of the dimerization process, two amyloid-β(29-42) molecules came close to each other and had intermolecular side chain contacts. When two molecules had the intermolecular side chain contacts, the amyloid-β(29-42) tended to have intramolecular secondary structures, especially β-hairpin structures. The two molecules had intermolecular β-bridge structures by coming much closer at the second step of the dimerization process. Formation of these intermolecular β-bridge structures was induced by the β-hairpin structures. The intermolecular β-sheet structures elongated at the final step. Structures of the amyloid-β(29-42) in the monomer and dimer states are also shown with the free-energy landscapes, which were obtained by performing efficient sampling in the conformational space in our simulations.

  5. Fret Replica Inspection Laser Scanner (FRILS)

    Energy Technology Data Exchange (ETDEWEB)

    Kretz, S.; Hanley, K., E-mail: steve.kretz@opg.com, E-mail: kelly.hanley@opg.com [Ontario Power Generation, Inspection Maintenance and Commercial Services, Pickering, Ontario (Canada)

    2008-07-01

    In the stress analysis of flaws and artifacts found in pressure tubes, it is crucial to have detailed knowledge of the flaw geometry. Fuel channel inspections by ultrasonic or eddy current inspection methods alone cannot provide the complete required geometry information. Replicas, which are a negative impression of surface pressure tube indications, are scanned with a laser system which will provide the additional detail required. FRILS was initially developed in 1993 to establish in-house capability of profiling indications on the inside diameter surface of pressure tubes. The need of this profiling was initially a response to the discovery of fuel bundle bearing pad fretting (FBBPF) caused by flow induced fuel bundle vibration. The benefits of the system were soon realized as a tool for profiling debris type indications. Although the primary use of FRILS is to profile FBBBF and Debris Fretting, since its inception the FRILS inspection system has become an instrumental tool in flaw assessment for: Fuel Bundle Bearing Pad Frets (FBBPF); Debris Frets; Scratches; Crevice Corrosion; Oxide Jacking; Areas of surface roughness; and, Weld Profiling. Replicas are collected via acquisition from tooling on both the Channel and Gauging Apparatus for Reactors (CIGAR) and the Advanced Non-Destructive Examination (ANDE) systems. The ANDE system is a high speed data acquisition system which includes both an ultrasonic inspection tool and a replication tool. Although both of these tools were designed to be delivered with the UDM, the platform for these tools was built with flexibility allowing for adoption to other delivery systems. These tools were based on the experience of the CIGAR inspection system. The CIGAR system has also undergone many system upgrades resulting in reduced inspection times. The FRILS system - Fret Replication Inspection Laser Scanner system was developed and has been upgraded to meet the demands of the improved inspection and replication systems. FRILS

  6. Equilibrium molecular thermodynamics from Kirkwood sampling.

    Science.gov (United States)

    Somani, Sandeep; Okamoto, Yuko; Ballard, Andrew J; Wales, David J

    2015-05-21

    We present two methods for barrierless equilibrium sampling of molecular systems based on the recently proposed Kirkwood method (J. Chem. Phys. 2009, 130, 134102). Kirkwood sampling employs low-order correlations among internal coordinates of a molecule for random (or non-Markovian) sampling of the high dimensional conformational space. This is a geometrical sampling method independent of the potential energy surface. The first method is a variant of biased Monte Carlo, where Kirkwood sampling is used for generating trial Monte Carlo moves. Using this method, equilibrium distributions corresponding to different temperatures and potential energy functions can be generated from a given set of low-order correlations. Since Kirkwood samples are generated independently, this method is ideally suited for massively parallel distributed computing. The second approach is a variant of reservoir replica exchange, where Kirkwood sampling is used to construct a reservoir of conformations, which exchanges conformations with the replicas performing equilibrium sampling corresponding to different thermodynamic states. Coupling with the Kirkwood reservoir enhances sampling by facilitating global jumps in the conformational space. The efficiency of both methods depends on the overlap of the Kirkwood distribution with the target equilibrium distribution. We present proof-of-concept results for a model nine-atom linear molecule and alanine dipeptide.

  7. Response Time Optimization for Replica Selection Service in Data Grids

    Directory of Open Access Journals (Sweden)

    Husni H.E. AL-Mistarihi

    2008-01-01

    Full Text Available Problem Statement: Data Grid architecture provides a scalable infrastructure for grid services in order to manage data files and their corresponding replicas that were distributed across the globe. The grid services are designed to support a variety of data grid applications (jobs and projects. Replica selection is a high-level service that chooses a replica location from among many distributed replicas with the minimum response time for the users' jobs. Estimating the response time accurately in the grid environment is not an easy task. The current systems expose high response time in selecting the required replicas because the response time is estimated by considering the data transfer time only. Approach: We proposed a replica selection system that selects the best replica location for the users' running jobs in a minimum response time that can be estimated by considering new factors besides the data transfer time, namely, the storage access latency and the replica requests that waiting in the storage queue. Results: The performance of the proposed system was compared with a similar system that exists in the literature namely, SimpleOptimiser. The simulation results demonstrated that our system performed better than the SimpleOptimiser on an average of 6%. Conclusions: The proposed system can select the best replica location in a lesser response time than the SimpleOptimise. The efficiency of the proposed system is 6% higher than the SimpleOptimise. The efficiency level has a high impact on the quality of service that is perceived by grid users in a data grid environment where the data files are relatively big. For example, the data files produced from the scientific applications are of the size hundreds of Terabytes.

  8. Uncertainties in Air Exchange using Continuous-Injection, Long-Term Sampling Tracer-Gas Methods

    Energy Technology Data Exchange (ETDEWEB)

    Sherman, Max H.; Walker, Iain S.; Lunden, Melissa M.

    2013-12-01

    The PerFluorocarbon Tracer (PFT) method is a low-cost approach commonly used for measuring air exchange in buildings using tracer gases. It is a specific application of the more general Continuous-Injection, Long-Term Sampling (CILTS) method. The technique is widely used but there has been little work on understanding the uncertainties (both precision and bias) associated with its use, particularly given that it is typically deployed by untrained or lightly trained people to minimize experimental costs. In this article we will conduct a first-principles error analysis to estimate the uncertainties and then compare that analysis to CILTS measurements that were over-sampled, through the use of multiple tracers and emitter and sampler distribution patterns, in three houses. We find that the CILTS method can have an overall uncertainty of 10-15percent in ideal circumstances, but that even in highly controlled field experiments done by trained experimenters expected uncertainties are about 20percent. In addition, there are many field conditions (such as open windows) where CILTS is not likely to provide any quantitative data. Even avoiding the worst situations of assumption violations CILTS should be considered as having a something like a ?factor of two? uncertainty for the broad field trials that it is typically used in. We provide guidance on how to deploy CILTS and design the experiment to minimize uncertainties.

  9. Semiautomatic exchanger of samples for carry out neutron activation analysis; Intercambiador semiautomatico de muestras para realizar analisis por activacion neutronica

    Energy Technology Data Exchange (ETDEWEB)

    Aguilar H, F.; Quintana C, G. [ININ, Carretera Mexico-Toluca s/n, 52750 Ocoyoacac, Estado de Mexico (Mexico); Torres R, C. E.; Mejia J, J. O., E-mail: fortunato.aguilar@inin.gob.mx [Instituto Tecnologico de Toluca, Av. Tecnologico s/n, Ex-Rancho La Virgen, Metepec, Estado de Mexico (Mexico)

    2015-09-15

    In this paper the design methodology and implementation of a semiautomatic exchanger of samples for the Analysis Laboratory by Neutron Activation of the Reactor department is presented. Taking into account the antecedents, the necessities of improvement are described, as well as the equipment that previously contained the Laboratory. The project of the semiautomatic exchanger of samples was developed at Instituto Nacional de Investigaciones Nucleares, with its own technology to increase independence from commercial equipment. Each element of the semiautomatic exchanger of samples is described both in the design phase as construction. The achieved results are positive and encouraging for the fulfillment of the proposed objective that is to increase the capacity of the Laboratory. (Author)

  10. Development of sample exchange robot PAM-HC for beamline BL-1A at the photon factory

    Energy Technology Data Exchange (ETDEWEB)

    Hiraki, Masahiko, E-mail: masahiko.hiraki@kek.jp [Mechanical Engineering Center, Applied Research Laboratory, KEK (High Energy Accelerator Research Organization), 1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan (Japan); Department of Accelerator Science, SOKENDAI (the Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801 Japan (Japan); Matsugaki, Naohiro; Yamada, Yusuke; Senda, Toshiya [Structural Biology research Center, Institute of Materials Structure Science, KEK (Japan); Department of Materials Structure Science, SOKENDAI (Japan)

    2016-07-27

    A macromolecular crystallography beamline, BL-1A, has been built at the Photon Factory (PF) for low energy experiments and has been operational since 2010. We have installed a sample exchange robot, PAM (PF Automated Mounting system), similar to other macromolecular crystallography beamlines. However, following the installation of a helium chamber to reduce the absorption of the diffraction signal by air, we developed a new sample exchange robot to replace PAM. The new robot, named PAM-HC (Helium Chamber), is designed with the goal of minimizing leakage of helium gas from the chamber. Here, the PAM-HC hardware and the flow of its movement are described. Furthermore, measurements of temperature changes during sample exchange are presented in this paper.

  11. High-throughput operation of sample-exchange robots with double tongs at the Photon Factory beamlines

    Science.gov (United States)

    Hiraki, Masahiko; Watanabe, Shokei; pHonda, Nobuo; Yamada, Yusuke; Matsugaki, Naohiro; Igarashi, Noriyuki; Gaponov, Yurii; Wakatsuki, Soichi

    2008-01-01

    Sample-exchange robots that can exchange cryo-pins bearing protein crystals out of experimental hutches according to user instructions have been developed. The robots were designed based on the SAM (Stanford Synchrotron Research Laboratory automated mounting) system. In order to reduce the time required for the sample exchange, the single tongs of the SAM system were modified and a double-tongs system that can hold two cryo-pins at the same time was developed. Robots with double tongs can move to the goniometer head holding the next cryo-pin with one set of tongs, dismount the experimented cryo-pin with the other set, and then mount the next pin onto the goniometer head without leaving the diffractometer area. Two different types of tongs have been installed: single tongs at beamlines BL-5A and AR-NW12A, and a double-tongs system at beamline BL-17A of the Photon Factory. The same graphical user interface software for operation of the sample-exchange robots is used at all beamlines, however, so that users do not need to consider differences between the systems. In a trial, the robot with double tongs could exchange samples within 10 s. PMID:18421164

  12. Rapid Preparation Methods of Biological Samples for Ionic Compounds Using Ion Exchange Type Monolithic Silica Spin Column

    OpenAIRE

    宮崎, 将太; 山田, 智子; 太田, 茂徳; 斉藤, 剛; 奈女良, 昭; 大平, 真義

    2010-01-01

    We developed a device comprising a spin column packed with ion exchange type (SCX and SAX) monolithic silica for extracting ionic compounds from biological samples. The methods involving the use of these spin column are not useful for the extraction of ionic analytes, but are highly reproducible for the analysis in serum and urine. This spin column enabled sample preparation in less than 10 min. Handling such as sample loading, washing, and elution of analytes, was exhibited by the centrifuga...

  13. Application of Enhanced Sampling Monte Carlo Methods for High-Resolution Protein-Protein Docking in Rosetta.

    Directory of Open Access Journals (Sweden)

    Zhe Zhang

    Full Text Available The high-resolution refinement of docked protein-protein complexes can provide valuable structural and mechanistic insight into protein complex formation complementing experiment. Monte Carlo (MC based approaches are frequently applied to sample putative interaction geometries of proteins including also possible conformational changes of the binding partners. In order to explore efficiency improvements of the MC sampling, several enhanced sampling techniques, including temperature or Hamiltonian replica exchange and well-tempered ensemble approaches, have been combined with the MC method and were evaluated on 20 protein complexes using unbound partner structures. The well-tempered ensemble method combined with a 2-dimensional temperature and Hamiltonian replica exchange scheme (WTE-H-REMC was identified as the most efficient search strategy. Comparison with prolonged MC searches indicates that the WTE-H-REMC approach requires approximately 5 times fewer MC steps to identify near native docking geometries compared to conventional MC searches.

  14. Elastomer and resin replicas for sem observation of metallic materials

    OpenAIRE

    Palin-Luc, Thierry; Sellier, E.; D?Errico, F.; Vanhaeren, M.

    2002-01-01

    International audience; The replica technique is often used to study damage evolution at the surface of specimens or industrial components and understand the physicial phenomena responsible for fatigue crack initiation before failure. Replicas are usually made from acetate cellulose film. This paper presents an alternative technique generally used by archaeologists to study lithic use-wear and bone modification. A mold is made from a dental elastomer (silicon based impression material) and a ...

  15. JavaFIRE: A Replica and File System for Grids

    Science.gov (United States)

    Petek, Marko; da Silva Gomes, Diego; Resin Geyer, Claudio Fernando; Santoro, Alberto; Gowdy, Stephen

    2012-12-01

    The work is focused on the creation of a replica and file transfers system for Computational Grids inspired on the needs of the High Energy Physics (HEP). Due to the high volume of data created by the HEP experiments, an efficient file and dataset replica system may play an important role on the computing model. Data replica systems allow the creation of copies, distributed between the different storage elements on the Grid. In the HEP context, the data files are basically immutable. This eases the task of the replica system, because given sufficient local storage resources any dataset just needs to be replicated to a particular site once. Concurrent with the advent of computational Grids, another important theme in the distributed systems area that has also seen some significant interest is that of peer-to-peer networks (p2p). P2p networks are an important and evolving mechanism that eases the use of distributed computing and storage resources by end users. One common technique to achieve faster file download from possibly overloaded storage elements over congested networks is to split the files into smaller pieces. This way, each piece can be transferred from a different replica, in parallel or not, optimizing the moments when the network conditions are better suited to the transfer. The main tasks achieved by the system are: the creation of replicas, the development of a system for replicas transfer (RFT) and for replicas location (RLS) with a different architecture that the one provided by Globus and the development of a system for file transfer in pieces on computational grids with interfaces for several storage elements. The RLS uses a p2p overlay based on the Kademlia algorithm.

  16. Injection Compression Molding of Replica Molds for Nanoimprint Lithography

    Directory of Open Access Journals (Sweden)

    Keisuke Nagato

    2014-03-01

    Full Text Available As a breakthrough in the cost and durability of molds for nanoimprint lithography (NIL, replica molds are fabricated by injection compression molding (ICM. ICM is commonly used for optical disks such as DVDs or Blu-ray disks and is also a practical fabrication method for nanostructures. In this paper, I successfully demonstrated the fabrication of cycloolefin polymer replica molds with structures smaller than 60 nm by ICM. Furthermore, ultraviolet (UV-NIL using these replica molds was demonstrated. UV-cured resist was replicated over an area of 60 mm diameter. The degree of replication by UV-NIL in the first usage of each replica mold had good repeatability. Because ICM is a high-throughput, low-cost process, the replica mold can be disposed of after a certain time for UV-NIL. This method leads to a high-integrity UV-NIL process of patterned media because multiple large-area replica molds can be fabricated simultaneously.

  17. Replica Fourier Tansforms on Ultrametric Trees, and Block-Diagonalizing Multi-Replica Matrices

    Science.gov (United States)

    de Dominicis, C.; Carlucci, D. M.; Temesvári, T.

    1997-01-01

    The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices M^{α β;γ^δ}, is shown to be dramatically simplified through the introduction of properly chosen operations on those objects. These are the Replica Fourier Transforms on ultrametric trees. Those transformations are defined and used in the present work. On montre que l'analyse d'objets vivant sur un arbre ultramétrique, en particulier, la diagonalisation par blocs d'une matrice M^{α β;γ^δ} dépendant de 4-répliques, se simplifie de façon dramatique si l'on introduit les opérations appropriées sur ces objets. Ce sont les Transformées de Fourier de Répliques sur un arbre ultramétrique. Ces transformations sont définies et utilisées dans le présent travail.

  18. Spatial Variability of Soil Cation Exchange Capacity in Hilly Tea Plantation Soils Under Different Sampling Scales

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Studies on the spatial variability of the soil cation exchange capacity (CEC) were made to provide a theoretical basis for an ecological tea plantation and management of soil fertilizer in the tea plantation. Geostatistics were used to analyze the spatial variability of soil CEC in the tea plantation site on Mengding Mountain in Sichuan Province of China on two sampling scales. It was found that, (1) on the small scale, the soil CEC was intensively spatially correlative, the rate of nugget to sill was 18.84% and the spatially dependent range was 1 818 m, and structural factors were the main factors that affected the spatial variability of the soil CEC; (2) on the microscale, the soil CEC was also consumingly spatially dependent,and the rate of nugget to sill was 16.52%, the spatially dependent range was 311 m, and the main factors affecting the spatial variability were just the same as mentioned earlier. On the small scale, soil CEC had a stronger anisotropic structure on the slope aspect, and a weaker one on the lateral side. According to the ordinary Kriging method, the equivalence of soil CEC distributed along the lateral aspect of the slope from northeast to outhwest, and the soil CEC reduced as the elevation went down. On the microscale, the anisotropic structure was different from that measured on the small scale. It had a stronger anisotropic structure on the aspect that was near the aspect of the slope, and a weaker one near the lateral aspect of the slope. The soil CEC distributed along the lateral aspect of the slope and some distributed in the form of plots.From the top to the bottom of the slope, the soil CEC increased initially, and then reduced, and finally increased.

  19. Human skulls with turquoise inlays: pre hispanic origin or replicas?; Craneos humanos con teselas de turquesa: origen prehispanico o replicas?

    Energy Technology Data Exchange (ETDEWEB)

    Silva V, Y. [FIME-UANL, Pedro A. del Alba s/n, Ciudad Universitaria, San Nicolas de los Garza, Nuevo Leon (Mexico); Castillo M, M.T.; Bautista M, J.P. [DRPMZA/INAH. Direccion de Registro Publico de Monumentos y Zonas Arqueologicas, Victoria 110, Copilco El Bajo, 04340 Mexico D.F. (Mexico); Arenas A, J. [IFUNAM, Circuito de la Investigacion Cientifica s/n, Ciudad Universitaria, 04510 Mexico D.F. (Mexico)]. e-mail: ysilva@fisica.unam.mx

    2006-07-01

    The lack of archaeological context determining if the manufacture of two human skulls adorned with turquoise inlays have pre-Columbian origin or not (replicas), led to perform other studies. Under these conditions, besides orthodox methodology commonly used to assign chronology and cultural aspects as form, style, decoration, iconography, etc., it was necessary to obtain more results based on the use of characterization techniques. The techniques employed were Scanning Electron Microscopy (SEM), X-Ray Energy Dispersive Spectroscopy (EDS), Transmission Electron Microscopy (TEM) and Fourier Transform Infrared Spectroscopy (FTIR), in order to determine the manufacture techniques and chemical composition of the materials used for the cementant. SEM analysis showed the presence of zones composed by Ca, O, C and Al. In some cases Mg, Cl, Fe and Pb were identified. High concentration of Cu was present in all samples, due to residues of turquoise inlays (CuAI{sub 6}(PO{sub 4}){sub 4}(OH){sub 8}(H{sub 2}O){sub 4}) with which the skulls were decorated. In the cementant was identified the Ca as base element of the cementant, as well as particles < 100 nm with irregular morphology and other amorphous zones. FTIR spectrums indicated the presence of organic substances that could be used as agglutinating in the cementant. The current work shows a progress identifying involved techniques in the manufacturing of two human skulls with turquoise inlays. (Author)

  20. Standard practice for production and evaluation of field metallographic replicas

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2001-01-01

    1.1 This practice covers recognized methods for the preparation and evaluation of cellulose acetate or plastic film replicas which have been obtained from metallographically prepared surfaces. It is designed for the evaluation of replicas to ensure that all significant features of a metallographically prepared surface have been duplicated and preserved on the replica with sufficient detail to permit both LM and SEM examination with optimum resolution and sensitivity. 1.2 This practice may be used as a controlling document in commercial situations. 1.3 The values stated in SI units are to be regarded as the standard. Inch-pound units given in parentheses are for information only. 1.4 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  1. Time evolution of the autocorrelation function in dynamical replica theory

    Science.gov (United States)

    Sakata, A.

    2013-04-01

    Asynchronous dynamics given by the master equation in the Sherrington-Kirkpatrick (SK) spin-glass model is studied based on dynamical replica theory (DRT) with an extension to take into account the autocorrelation function. The dynamical behaviour of the system is approximately described by dynamical equations of the macroscopic quantities: magnetization, energy contributed by randomness and the autocorrelation function. The dynamical equations under the replica symmetry assumption are derived by introducing the subshell equipartitioning assumption and exploiting the replica method. The obtained dynamical equations are compared with Monte Carlo simulations, and it is demonstrated that the proposed formula describes well the time evolution of the autocorrelation function in some parameter regions. The study offers a reasonable description of the autocorrelation function in the SK spin-glass system.

  2. Fractographic ceramic failure analysis using the replica technique

    Science.gov (United States)

    Scherrer, Susanne S.; Quinn, Janet B.; Quinn, George D.; Anselm Wiskott, H. W.

    2007-01-01

    Objectives To demonstrate the effectiveness of in vivo replicas of fractured ceramic surfaces for descriptive fractography as applied to the analysis of clinical failures. Methods The fracture surface topography of partially failed veneering ceramic of a Procera Alumina molar and an In Ceram Zirconia premolar were examined utilizing gold-coated epoxy poured replicas viewed using scanning electron microscopy. The replicas were inspected for fractographic features such as hackle, wake hackle, twist hackle, compression curl and arrest lines for determination of the direction of crack propagation and location of the origin. Results For both veneering ceramics, replicas provided an excellent reproduction of the fractured surfaces. Fine details including all characteristic fracture features produced by the interaction of the advancing crack with the material's microstructure could be recognized. The observed features are indicators of the local direction of crack propagation and were used to trace the crack's progression back to its initial starting zone (the origin). Drawbacks of replicas such as artifacts (air bubbles) or imperfections resulting from inadequate epoxy pouring were noted but not critical for the overall analysis of the fractured surfaces. Significance The replica technique proved to be easy to use and allowed an excellent reproduction of failed ceramic surfaces. It should be applied before attempting to remove any failed part remaining in situ as the fracture surface may be damaged during this procedure. These two case studies are intended as an introduction for the clinical researcher in using qualitative (descriptive) fractography as a tool for understanding fracture processes in brittle restorative materials and, secondarily, to draw conclusions as to possible design inadequacies in failed restorations. PMID:17270267

  3. Gas exchange measurement during pediatric mechanical ventilation--agreement between gas sampling at the airway and the ventilator exhaust.

    Science.gov (United States)

    Smallwood, Craig D; Mehta, Nilesh M

    2013-12-01

    A variety of indirect calorimetry (IC) devices are used for gas exchange measurement and calculation of resting energy expenditure (REE) in the pediatric intensive care unit. The aim of this investigation was to compare oxygen consumption (VO2), carbon dioxide elimination (VCO2), REE and respiratory quotient (RQ) in mechanically ventilated children, obtained by 2 devices using distinct gas sampling methods. Mechanically ventilated children were targeted for IC and gas exchange measurements were recorded for a 30 min period, simultaneously using the E-COVX(®) (gas sampling at the airway) and the Vmax(®) (gas sampling at the humidifier and ventilator exhaust). Steady state gas exchange measurements by the 2 devices were tested for agreement using Spearman correlation and Bland-Altman analysis. Steady state data from both devices were available in 19 tests and were included in the analysis. The correlations coefficients for measurements by the 2 devices were r = 0.903(P < 0.001), 0.955(P < 0.001), 0.944(P < 0.001) and 0.484(P < 0.05) for VO2, VCO2, REE and RQ, respectively. The mean percentage bias (limits of agreement) for VO2, VCO2, REE and RQ values between the two methods (Vmax-E-COVX) was 0.2 (-41.8-42.3), -0.8 (-21.8-20.1), -2.2 (-33.9-29.6) and 1.9 (-21-24.9) respectively. Despite strong correlations and small mean biases for VO2, VCO2 and REE obtained by the Vmax(®) and E-COVX(®), the limits of agreement were beyond the clinically acceptable range. These devices should not be used interchangeably for gas exchange measurements in mechanically ventilated children. Copyright © 2013 Elsevier Ltd and European Society for Clinical Nutrition and Metabolism. All rights reserved.

  4. Experimental setup for the determination of exchangeable hydrogen in environmental samples using deuterium and tritium

    Energy Technology Data Exchange (ETDEWEB)

    Pastor, L.; Siclet, F. [EDF R et D (France); Peron, O.; Gegout, C.; Montavon, G.; Landesman, C. [Laboratoire SUBATECH, IN2P3/CNRS, EMN, Universite de Nantes (France); Fourre, E.; Jean-Baptiste, P. [LSCE, UMR 8112 CEA-CNRS-UVSQ/IPSL (France)

    2014-07-01

    Tritium ({sup 3}H or T) is a radioactive isotope of the element hydrogen with a half-life of 12.32 yrs. It is naturally produced in the upper atmosphere, but also by the nuclear industry. It is used in many fields like medical research and watch making. It is thus released in the environment on gaseous and liquid form by these facilities and is currently the major released radionuclide in liquid effluent from French nuclear power plants (in HTO form). Current studies dealing with the fate and behavior of tritium in the environment focus mainly on its organic form, i.e. the organically bound tritium (OBT). It is indeed more resilient in the environment than the tritiated water (HTO) as it is part of the organic matter cycle. There is nevertheless a distinction to be made between the exchangeable and the non-exchangeable fraction of OBT. When hydrogen is linked to nitrogen, sulfur or oxygen, it is considered to be exchangeable with the H contained in the surrounding solution or in the atmospheric water phase. Thus, its residence time within the molecule will be reduced and closely linked to the surrounding parameters. When hydrogen is linked to carbon, it is assumed that the link is more stable and thus the residence time in the molecule will be enhanced. It is thus important to know the fraction of exchangeable OBT when addressing the residence time of tritium in the environment. The present study aims at assessing this fraction in different environmental matrixes using deuterium and/or tritium. Compared to several others studies on exchangeable hydrogen where experiments were conducted at high temperature and/or high pressure, this study follows a different approach with experiments conducted at ambient temperature and atmospheric pressure (natural conditions) with a controlled hygrometric value within the system. The system itself consists in a glove box modified to fulfill the requirements for an efficient control on the experimental parameters (temperature

  5. Quantifying non-contact tip-sample thermal exchange parameters for accurate scanning thermal microscopy with heated microprobes

    Science.gov (United States)

    Wilson, Adam A.; Borca-Tasciuc, Theodorian

    2017-07-01

    Simplified heat-transfer models are widely employed by heated probe scanning thermal microscopy techniques for determining thermal conductivity of test samples. These parameters have generally been assumed to be independent of sample properties; however, there has been little investigation of this assumption in non-contact mode, and the impact calibration procedures have on sample thermal conductivity results has not been explored. However, there has been little investigation of the commonly used assumption that thermal exchange parameters are sample independent in non-contact mode, or of the impact calibration procedures have on sample thermal conductivity results. This article establishes conditions under which quantitative, localized, non-contact measurements using scanning thermal microscopy with heated microprobes may be most accurately performed. The work employs a three-dimensional finite element (3DFE) model validated using experimental results and no fitting parameters, to determine the dependence of a heated microprobe thermal resistance as a function of sample thermal conductivity at several values of probe-to-sample clearance. The two unknown thermal exchange parameters were determined by fitting the 3DFE simulated probe thermal resistance with the predictions of a simplified probe heat transfer model, for two samples with different thermal conductivities. This calibration procedure known in experiments as the intersection method was simulated for sample thermal conductivities in the range of 0.1-50 W m-1 K-1 and clearance values in the 260-1010 nm range. For a typical Wollaston wire microprobe geometry as simulated here, both the thermal exchange radius and thermal contact resistance were found to increase with the sample thermal conductivity in the low thermal conductivity range while they remained approximately constant for thermal conductivities >1 W m-1 K-1, with similar trends reported for all clearance values investigated. It is shown that

  6. Replica calibration artefacts for optical 3D scanning of micro parts

    DEFF Research Database (Denmark)

    De Chiffre, Leonardo; Carmignato, S.; Cantatore, Angela

    2009-01-01

    This work deals with development of calibration artefacts produced by using hard replica materials, achieving high quality geometrical reproduction of suitable reference artefacts, high stability, and high surface cooperativeness. An investigation was carried out using a replica material for dental...

  7. An automated gas exchange tank for determining gas transfer velocities in natural seawater samples

    Directory of Open Access Journals (Sweden)

    K. Schneider-Zapp

    2014-02-01

    Full Text Available In order to advance understanding of the role of seawater surfactants in the air–sea exchange of climatically active trace gases via suppression of the gas transfer velocity (kw, we constructed a fully automated, closed air-water gas exchange tank and coupled analytical system. The system allows water-side turbulence in the tank to be precisely controlled with an electronically operated baffle. Two coupled gas chromatographs and an integral equilibrator, connected to the tank in a continuous gas-tight system, allow temporal changes in the partial pressures of SF6, CH4 and N2O to be measured simultaneously in the tank water and headspace at multiple turbulence settings, during a typical experimental run of 3.25 h. PC software developed by the authors controls all operations and data acquisition, enabling the optimisation of experimental conditions with high reproducibility. The use of three gases allows three independent estimates of kw for each turbulence setting; these values are subsequently normalised to a constant Schmidt number for direct comparison. The normalised kw estimates show close agreement. Repeated experiments with MilliQ water demonstrate a typical measurement accuracy of 4% for kw. Experiments with natural seawater show that the system clearly resolves the effects on kw of spatial and temporal trends in natural surfactant activity. The system is an effective tool with which to probe the relationships between kw, surfactant activity and biogeochemical indices of primary productivity, and should assist in providing valuable new insights into the air–sea gas exchange process.

  8. An automated gas exchange tank for determining gas transfer velocities in natural seawater samples

    Directory of Open Access Journals (Sweden)

    K. Schneider-Zapp

    2014-07-01

    Full Text Available In order to advance understanding of the role of seawater surfactants in the air–sea exchange of climatically active trace gases via suppression of the gas transfer velocity (kw, we constructed a fully automated, closed air–water gas exchange tank and coupled analytical system. The system allows water-side turbulence in the tank to be precisely controlled with an electronically operated baffle. Two coupled gas chromatographs and an integral equilibrator, connected to the tank in a continuous gas-tight system, allow temporal changes in the partial pressures of SF6, CH4 and N2O to be measured simultaneously in the tank water and headspace at multiple turbulence settings, during a typical experimental run of 3.25 h. PC software developed by the authors controls all operations and data acquisition, enabling the optimisation of experimental conditions with high reproducibility. The use of three gases allows three independent estimates of kw for each turbulence setting; these values are subsequently normalised to a constant Schmidt number for direct comparison. The normalised kw estimates show close agreement. Repeated experiments with Milli-Q water demonstrate a typical measurement accuracy of 4% for kw. Experiments with natural seawater show that the system clearly resolves the effects on kw of spatial and temporal trends in natural surfactant activity. The system is an effective tool with which to probe the relationships between kw, surfactant activity and biogeochemical indices of primary productivity, and should assist in providing valuable new insights into the air–sea gas exchange process.

  9. Data-Replicas Scheduler for Heterogeneous MapReduce Cluster

    Directory of Open Access Journals (Sweden)

    Yang Yang

    2013-05-01

    Full Text Available Large scale data processing has rapidly increased in nowadays. MapReduce programming model, which is firstly mentioned in functional languages, appeared in distributed system and perform excellently in large scale data processing since 2006. Hadoop, which is the most popular framework of open-sourced MapReduce runtime environment, supplies reliable, scalable and distributed system processing large scale data across clusters of computers using this virtue programming model. In this system, files are split into many blocks and all blocks are replicated over several computers in clusters. To process these blocks efficiently, each job runs parallel and is divided into many tasks which deals with a file block. In order to fully take advantage of network bandwidth these systems, data locality is paid more and more attentions. Considering the existence of data-replica blocks, we propose a data-replicas scheduler which includes task scheduling and data allocation. The data-replicas scheduler takes fully advantage of data replicas in local Data node, reduce the costs of data transfer and improve the system performance. The results of experiments show that our scheduler not only improves the CPU ratio, but also reduces the packets that transfer in the network.

  10. Replicas in Caravaggio's paintings: the correct use of scientific analysis

    Science.gov (United States)

    Diana, Maurizio; Moioli, Pietro; Seccaroni, Claudio

    1998-05-01

    Painting techniques and materials employed by Caravaggio are analyzed by X-ray fluorescence and radiography of unquestioned genuine works and compared to replicas of his earlier work. This approach is important in the attribution of recently discovered paintings and copies from the XVII century.

  11. Replica-Based High-Performance Tuple Space Computing

    DEFF Research Database (Denmark)

    Andric, Marina; De Nicola, Rocco; Lluch Lafuente, Alberto

    2015-01-01

    We present the tuple-based coordination language RepliKlaim, which enriches Klaim with primitives for replica-aware coordination. Our overall goal is to offer suitable solutions to the challenging problems of data distribution and locality in large-scale high performance computing. In particular,...

  12. Enhanced sampling techniques in molecular dynamics simulations of biological systems.

    Science.gov (United States)

    Bernardi, Rafael C; Melo, Marcelo C R; Schulten, Klaus

    2015-05-01

    Molecular dynamics has emerged as an important research methodology covering systems to the level of millions of atoms. However, insufficient sampling often limits its application. The limitation is due to rough energy landscapes, with many local minima separated by high-energy barriers, which govern the biomolecular motion. In the past few decades methods have been developed that address the sampling problem, such as replica-exchange molecular dynamics, metadynamics and simulated annealing. Here we present an overview over theses sampling methods in an attempt to shed light on which should be selected depending on the type of system property studied. Enhanced sampling methods have been employed for a broad range of biological systems and the choice of a suitable method is connected to biological and physical characteristics of the system, in particular system size. While metadynamics and replica-exchange molecular dynamics are the most adopted sampling methods to study biomolecular dynamics, simulated annealing is well suited to characterize very flexible systems. The use of annealing methods for a long time was restricted to simulation of small proteins; however, a variant of the method, generalized simulated annealing, can be employed at a relatively low computational cost to large macromolecular complexes. Molecular dynamics trajectories frequently do not reach all relevant conformational substates, for example those connected with biological function, a problem that can be addressed by employing enhanced sampling algorithms. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent.

    Science.gov (United States)

    Li, Xianfeng; Snyder, James A; Stuart, Steven J; Latour, Robert A

    2015-10-14

    The recently developed "temperature intervals with global exchange of replicas" (TIGER2) accelerated sampling method is found to have inaccuracies when applied to systems with explicit solvation. This inaccuracy is due to the energy fluctuations of the solvent, which cause the sampling method to be less sensitive to the energy fluctuations of the solute. In the present work, the problem of the TIGER2 method is addressed in detail and a modification to the sampling method is introduced to correct this problem. The modified method is called "TIGER2 with solvent energy averaging," or TIGER2A. This new method overcomes the sampling problem with the TIGER2 algorithm and is able to closely approximate Boltzmann-weighted sampling of molecular systems with explicit solvation. The difference in performance between the TIGER2 and TIGER2A methods is demonstrated by comparing them against analytical results for simple one-dimensional models, against replica exchange molecular dynamics (REMD) simulations for sampling the conformation of alanine dipeptide and the folding behavior of (AAQAA)3 peptide in aqueous solution, and by comparing their performance in sampling the behavior of hen egg-white lysozyme in aqueous solution. The new TIGER2A method solves the problem caused by solvent energy fluctuations in TIGER2 while maintaining the two important characteristics of TIGER2, i.e., (1) using multiple replicas sampled at different temperature levels to help systems efficiently escape from local potential energy minima and (2) enabling the number of replicas used for a simulation to be independent of the size of the molecular system, thus providing an accelerated sampling method that can be used to efficiently sample systems considered too large for the application of conventional temperature REMD.

  14. Comparing generalized ensemble methods for sampling of systems with many degrees of freedom

    Science.gov (United States)

    Lincoff, James; Sasmal, Sukanya; Head-Gordon, Teresa

    2016-11-01

    We compare two standard replica exchange methods using temperature and dielectric constant as the scaling variables for independent replicas against two new corresponding enhanced sampling methods based on non-equilibrium statistical cooling (temperature) or descreening (dielectric). We test the four methods on a rough 1D potential as well as for alanine dipeptide in water, for which their relatively small phase space allows for the ability to define quantitative convergence metrics. We show that both dielectric methods are inferior to the temperature enhanced sampling methods, and in turn show that temperature cool walking (TCW) systematically outperforms the standard temperature replica exchange (TREx) method. We extend our comparisons of the TCW and TREx methods to the 5 residue met-enkephalin peptide, in which we evaluate the Kullback-Leibler divergence metric to show that the rate of convergence between two independent trajectories is faster for TCW compared to TREx. Finally we apply the temperature methods to the 42 residue amyloid-β peptide in which we find non-negligible differences in the disordered ensemble using TCW compared to the standard TREx. All four methods have been made available as software through the OpenMM Omnia software consortium (http://www.omnia.md/).

  15. Spontaneous versus explicit replica symmetry breaking in the theory of disordered systems

    Science.gov (United States)

    Mouhanna, D.; Tarjus, G.

    2010-05-01

    We investigate the relation between spontaneous and explicit replica symmetry breaking in the theory of disordered systems. On general ground, we prove the equivalence between the replicon operator associated with the stability of the replica-symmetric solution in the standard replica scheme and the operator signaling a breakdown of the solution with analytic field dependence in a scheme in which replica symmetry is explicitly broken by applied sources. This opens the possibility to study, via the recently developed functional renormalization group, unresolved questions related to spontaneous replica symmetry breaking and spin-glass behavior in finite-dimensional disordered systems.

  16. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2014-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  17. ATLAS Replica Management in Rucio: Replication Rules and Subscriptions

    CERN Document Server

    Barisits, M; The ATLAS collaboration; Garonne, V; Lassnig, M; Stewart, G; Beermann, T; Vigne, R; Goossens, L; Nairz, A; Molfetas, A

    2013-01-01

    The ATLAS Distributed Data Management system stores more than 150PB of physics data across 120 sites globally. To cope with the anticipated ATLAS workload of the coming decade, Rucio, the next-generation data management system has been developed. Replica management, as one of the keys aspects of the system, has to satisfy critical performance requirements in order to keep pace with the experiment’s high rate of continual data generation. The challenge lies in meeting these performance objectives while still giving the system users and applications a powerful toolkit to control their data workflows. In this work we present the concept, design and implementation of the replica management in Rucio. We will specifically introduce the workflows behind replication rules, their formal language definition, weighting and site selection. Furthermore we will present the subscription component, which offers functionality for users to proclaim interest in data that has not been created yet. This contribution describes t...

  18. An adaptive range-query optimization technique with distributed replicas

    Institute of Scientific and Technical Information of China (English)

    Sayar Ahmet; Pierce Marlon; Fox C.Geoffrey

    2014-01-01

    Replication is an approach often used to speed up the execution of queries submitted to a large dataset. A compile-time/run-time approach is presented for minimizing the response time of 2-dimensional range when a distributed replica of a dataset exists. The aim is to partition the query payload (and its range) into subsets and distribute those to the replica nodes in a way that minimizes a client’s response time. However, since query size and distribution characteristics of data (data dense/sparse regions) in varying ranges are not known a priori, performing efficient load balancing and parallel processing over the unpredictable workload is difficult. A technique based on the creation and manipulation of dynamic spatial indexes for query payload estimation in distributed queries was proposed. The effectiveness of this technique was demonstrated on queries for analysis of archived earthquake-generated seismic data records.

  19. Replica symmetry breaking in cold atoms and spin glasses

    Science.gov (United States)

    Rotondo, P.; Tesio, E.; Caracciolo, S.

    2015-01-01

    We consider a system composed by N atoms trapped within a multimode cavity, whose theoretical description is captured by a disordered multimode Dicke model. We show that in the resonant, zero-field limit the system exactly realizes the Sherrington-Kirkpatrick model. Upon a redefinition of the temperature, the same dynamics is realized in the dispersive, strong-field limit. This regime also gives access to spin-glass observables which can be used to detect replica symmetry breaking.

  20. DC thermal microscopy: study of the thermal exchange between a probe and a sample

    Science.gov (United States)

    Gomès, Séverine; Trannoy, Nathalie; Grossel, Philippe

    1999-09-01

    The Scanning Thermal Microscopic (SThM) probe, a thin Pt resistance wire, is used in the constant force mode of an Atomic Force Microscope (AFM). Thermal signal-distance curves for differing degrees of relative humidity and different surrounding gases demonstrate how heat is transferred from the heated probe to the sample. It is known that water affects atomic force microscopy and thermal measurements; we report here on the variation of the water interaction on the thermal coupling versus the probe temperature. Measurements were taken for several solid materials and show that the predominant heat transfer mechanisms taking part in thermal coupling are dependent on the thermal conductivity of the sample. The results have important implications for any quantitative interpretation of thermal images made in air.

  1. Who needs RDD? Combining directory listings with cell phone exchanges for an alternative telephone sampling frame

    OpenAIRE

    Guterbock, Thomas; Diop, Abdoulaye; Ellis, James; Trung Le, Kien

    2011-01-01

    Abstract The traditional Random Digit Dialing method (list-assisted RDD using a frame of landline phone numbers) is clearly under threat. The difficulty and costs of completing telephone surveys have increased due to rising rates of refusal and non-contact. The completeness of coverage of list-assisted RDD samples has diminished due to the proliferation of cell-phone only households. The ability of list-assisted RDD to capture young, mobile, unmarried, and minority households is thus dimin...

  2. Replica inference approach to unsupervised multiscale image segmentation.

    Science.gov (United States)

    Hu, Dandan; Ronhovde, Peter; Nussinov, Zohar

    2012-01-01

    We apply a replica-inference-based Potts model method to unsupervised image segmentation on multiple scales. This approach was inspired by the statistical mechanics problem of "community detection" and its phase diagram. Specifically, the problem is cast as identifying tightly bound clusters ("communities" or "solutes") against a background or "solvent." Within our multiresolution approach, we compute information-theory-based correlations among multiple solutions ("replicas") of the same graph over a range of resolutions. Significant multiresolution structures are identified by replica correlations manifest by information theory overlaps. We further employ such information theory measures (such as normalized mutual information and variation of information), thermodynamic quantities such as the system entropy and energy, and dynamic measures monitoring the convergence time to viable solutions as metrics for transitions between various solvable and unsolvable phases. Within the solvable phase, transitions between contending solutions (such as those corresponding to segmentations on different scales) may also appear. With the aid of these correlations as well as thermodynamic measures, the phase diagram of the corresponding Potts model is analyzed at both zero and finite temperatures. Optimal parameters corresponding to a sensible unsupervised segmentations appear within the "easy phase" of the Potts model. Our algorithm is fast and shown to be at least as accurate as the best algorithms to date and to be especially suited to the detection of camouflaged images.

  3. Ion-exchange molecularly imprinted polymer for the extraction of negatively charged acesulfame from wastewater samples.

    Science.gov (United States)

    Zarejousheghani, Mashaalah; Schrader, Steffi; Möder, Monika; Lorenz, Pierre; Borsdorf, Helko

    2015-09-11

    Acesulfame is a known indicator that is used to identify the introduction of domestic wastewater into water systems. It is negatively charged and highly water-soluble at environmental pH values. In this study, a molecularly imprinted polymer (MIP) was synthesized for negatively charged acesulfame and successfully applied for the selective solid phase extraction (SPE) of acesulfame from influent and effluent wastewater samples. (Vinylbenzyl)trimethylammonium chloride (VBTA) was used as a novel phase transfer reagent, which enhanced the solubility of negatively charged acesulfame in the organic solvent (porogen) and served as a functional monomer in MIP synthesis. Different molecularly imprinted polymers were synthesized to optimize the extraction capability of acesulfame. The different materials were evaluated using equilibrium rebinding experiments, selectivity experiments and scanning electron microscopy (SEM). The most efficient MIP was used in a molecularly imprinted-solid phase extraction (MISPE) protocol to extract acesulfame from wastewater samples. Using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) analysis, detection and quantification limits were achieved at 0.12μgL(-1) and 0.35μgL(-1), respectively. Certain cross selectivity for the chemical compounds containing negatively charged sulfonamide functional group was observed during selectivity experiments.

  4. Determination of plutonium in environmental samples by controlled valence in anion exchange

    DEFF Research Database (Denmark)

    Chen, Q.J.; Aarkrog, A.; Nielsen, S.P.

    1993-01-01

    is heated at 400-degrees-C and digested in aqua regia. Na2SO3 and NaNO2 have been applied to obtain the Pu4+ valence state in 0.571 N HN03 for different samples. Plutonium and thorium are coadsorbed on anionic resin from 8N HN03. The column is eluted with 8N HN03 containing fresh NaNO2 to keep the Pu4......+ state for uranium decontamination. The system of the column is changed from 8N HNO3 to concentrated HCl with 50 ml concentrated HCI containing a few milligrams of NaNO2. Further decontamination of thorium was achieved by elution with concentrated HCI instead of 9N HCl. The plutonium is successfully...

  5. Connexin composition in apposed gap junction hemiplaques revealed by matched double-replica freeze-fracture replica immunogold labeling.

    Science.gov (United States)

    Rash, John E; Kamasawa, Naomi; Davidson, Kimberly G V; Yasumura, Thomas; Pereda, Alberto E; Nagy, James I

    2012-06-01

    Despite the combination of light-microscopic immunocytochemistry, histochemical mRNA detection techniques and protein reporter systems, progress in identifying the protein composition of neuronal versus glial gap junctions, determination of the differential localization of their constituent connexin proteins in two apposing membranes and understanding human neurological diseases caused by connexin mutations has been problematic due to ambiguities introduced in the cellular and subcellular assignment of connexins. Misassignments occurred primarily because membranes and their constituent proteins are below the limit of resolution of light microscopic imaging techniques. Currently, only serial thin-section transmission electron microscopy and freeze-fracture replica immunogold labeling have sufficient resolution to assign connexin proteins to either or both sides of gap junction plaques. However, freeze-fracture replica immunogold labeling has been limited because conventional freeze fracturing allows retrieval of only one of the two membrane fracture faces within a gap junction, making it difficult to identify connexin coupling partners in hemiplaques removed by fracturing. We now summarize progress in ascertaining the connexin composition of two coupled hemiplaques using matched double-replicas that are labeled simultaneously for multiple connexins. This approach allows unambiguous identification of connexins and determination of the membrane "sidedness" and the identities of connexin coupling partners in homotypic and heterotypic gap junctions of vertebrate neurons.

  6. Biomimetic zinc oxide replica with structural color using butterfly (Ideopsis similis) wings as templates.

    Science.gov (United States)

    Zhang, Wang; Zhang, Di; Fan, Tongxiang; Ding, Jian; Gu, Jiajun; Guo, Qixin; Ogawa, Hiroshi

    2006-09-01

    Nano-structured colorful zinc oxide (ZnO) replicas were produced using the wings of the Ideopsis similis butterfly as templates. The ZnO replicas we obtained exhibit iridescence, which was clearly observed under an optical microscope (OM). Field emission scanning electron microscope analysis shows that all the microstructure details are maintained faithfully in the ZnO replica. A computer model was established to simulate the diffraction spectral results, which agreed well with the OM images.

  7. Uptake of Zn2+ ions by a fully iron-exchanged clinoptilolite. Case study of heavily contaminated drinking water samples.

    Science.gov (United States)

    Dimirkou, Anthoula

    2007-06-01

    Clinoptilolite, a natural zeolite, was used for the synthesis of a high surface area clinoptilolite (Clin)-iron (Fe) oxide system, in order to be used for the removal of Zn(2+) ions from drinking water samples. The new system was obtained by adding natural Clin in an iron nitrate solution under strongly basic conditions. The Clin-Fe system has specific surface area equal to 151 m(2)/g and is fully iron exchanged (Fe/Al=1.23). Batch adsorption experiments were carried out to determine the effectiveness of the Clin and the Clin-Fe system in removal of Zn from drinking water. Adsorption experiments were conducted by mixing 1.00 g of each of the substrates with certain volume of water samples contaminated with ten different Zn concentrations (from 7.65x10(-5) to 3.82x10(-2)M or from 5.00 to 2500 ppm Zn). For our experimental conditions, the maximum adsorbed Zn amount by Clin was 71.3mg/g, whereas by the Clin-Fe system 94.8 mg/g. The main factors that contribute to different adsorbed Zn amounts by the two solids are due to new surface species and negative charge of the Clin-Fe system. In addition, the release of counterbalanced ions (i.e. Ca(2+), Mg(2+), Na(+) and K(+)) was examined, as well as the dissolution of framework Si and Al. It was found that for most of the samples the Clin-Fe system releases lower concentrations of Ca, Mg and Na and higher concentrations of K than Clin, while the dissolution of Si/Al was limited. Changes in the composition of water samples, as well as in their pH and conductivities values were reported and explained.

  8. 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.

  9. Replica location mechanism in data grid based on ED-Chord

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    A peer-to-peer hierarchical replica location mechanism(PRLM)was designed for data grids to provide better load balancing capability and scalability.Global replica indexes of the PRLM are organized based on even distributed Chord(ED-Chord)structure.The locality can optimize queries on local replica indexes of virtual organizations.ED-Chord protocol collects the node identifiers information using a distributed method and assigns optimal identifiers for new nodes to make them more uniformly distributed in the entire identifier space.Theoretical analysis and simulations show that PRLM provides good performance,scalability and load balancing capability for replica location in data grids.

  10. Replica Analysis for Portfolio Optimization with Single-Factor Model

    Science.gov (United States)

    Shinzato, Takashi

    2017-06-01

    In this paper, we use replica analysis to investigate the influence of correlation among the return rates of assets on the solution of the portfolio optimization problem. We consider the behavior of an optimal solution for the case where the return rate is described with a single-factor model and compare the findings obtained from our proposed methods with correlated return rates with those obtained with independent return rates. We then analytically assess the increase in the investment risk when correlation is included. Furthermore, we also compare our approach with analytical procedures for minimizing the investment risk from operations research.

  11. REPLICA ORNSTEIN-ZERNIKE EQUATIONS FOR POSITIONALLY FROZEN HEISENBERG SYSTEMS

    Directory of Open Access Journals (Sweden)

    E.Lomba

    2003-01-01

    Full Text Available We present the formulation of the Replica Ornstein-Zernike equations for a model of positionally frozen disordered Heisenberg spin system. The results are obtained for various models, one in which the particle positions correspond to a frozen hard sphere fluid, another system in which the configurations are generated by a random insertion of hard spheres, a system of randomly distributed spins, and finally a system corresponding to a soft sphere fluid quenched at high and low temperatures. We will see that the orientational structure of the spin system is fairly well reproduced by the integral equation which, however, does not correctly account for the critical behaviour.

  12. Generating Scaled Replicas of Real-World Complex Networks

    CERN Document Server

    Staudt, Christian L; Safro, Ilya; Gutfraind, Alexander; Meyerhenke, Henning

    2016-01-01

    Research on generative models plays a central role in the emerging field of network science, studying how statistical patterns found in real networks can be generated by formal rules. During the last two decades, a variety of models has been proposed with an ultimate goal of achieving comprehensive realism for the generated networks. In this study, we (a) introduce a new generator, termed ReCoN; (b) explore how models can be fitted to an original network to produce a structurally similar replica, and (c) aim for producing much larger networks than the original exemplar. In a comparative experimental study, we find ReCoN often superior to many other state-of-the-art network generation methods. Our design yields a scalable and effective tool for replicating a given network while preserving important properties at both micro- and macroscopic scales and (optionally) scaling the replica by orders of magnitude in size. We recommend ReCoN as a general practical method for creating realistic test data for the enginee...

  13. Improved proteomic discovery by sample pre-fractionation using dual-column ion-exchange high performance liquid chromatography.

    Science.gov (United States)

    Havugimana, Pierre C; Wong, Peter; Emili, Andrew

    2007-02-15

    Clinically relevant biomarkers are urgently needed for improving patient diagnosis, risk stratification, prognosis and therapeutic treatments. There is a particularly compelling motivation for identifying protein-based indicators of early-stage disease for more effective interventions. Despite recent progress, the proteomic discovery process remains a daunting challenge due to the sheer heterogeneity and skewed protein abundances in biofluids. Even the most advanced mass spectrometry systems exhibit limiting overall dynamic ranges and sensitivities relative to the needs of modern biomedical applications. To this end, we report the development of a robust, rapid, and reproducible high performance ion-exchange liquid chromatography pre-fractionation method that allows for improved proteomic detection coverage of complex biological specimens using basic tandem mass spectrometry screening procedures. This form of sample simplification prior to global proteomic profiling, which we refer to collectively as 'fractionomics', increases the number and diversity of proteins that can be confidently identified in tissue and cell lysates as compared to the straight analysis of unfractionated crude extracts.

  14. Three-dimensional nanometrology of microstructures by replica molding and large-range atomic force microscopy

    DEFF Research Database (Denmark)

    Stöhr, Frederik; Michael-Lindhard, Jonas; Simons, Hugh

    2015-01-01

    We have used replica molding and large-range atomic force microscopy to characterize the threedimensional shape of high aspect ratio microstructures. Casting inverted replicas of microstructures using polydimethylsiloxane (PDMS) circumvents the inability of AFM probes to measure deep and narrow c...

  15. Finite size corrections in the random energy model and the replica approach

    Science.gov (United States)

    Derrida, Bernard; Mottishaw, Peter

    2015-01-01

    We present a systematic and exact way of computing finite size corrections for the random energy model, in its low temperature phase. We obtain explicit (though complicated) expressions for the finite size corrections of the overlap functions. In its low temperature phase, the random energy model is known to exhibit Parisi's broken symmetry of replicas. The finite size corrections given by our exact calculation can be reproduced using replicas if we make specific assumptions about the fluctuations (with negative variances!) of the number and sizes of the blocks when replica symmetry is broken. As an alternative we show that the exact expression for the non-integer moments of the partition function can be written in terms of coupled contour integrals over what can be thought of as ‘complex replica numbers’. Parisi's one step replica symmetry breaking arises naturally from the saddle point of these integrals without making any ansatz or using the replica method. The fluctuations of the ‘complex replica numbers’ near the saddle point in the imaginary direction correspond to the negative variances we observed in the replica calculation. Finally our approach allows one to see why some apparently diverging series or integrals are harmless.

  16. A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

    Science.gov (United States)

    Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

    2014-01-01

    Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

  17. A Novel General Chemistry Laboratory: Creation of Biomimetic Superhydrophobic Surfaces through Replica Molding

    Science.gov (United States)

    Verbanic, Samuel; Brady, Owen; Sanda, Ahmed; Gustafson, Carolina; Donhauser, Zachary J.

    2014-01-01

    Biomimetic replicas of superhydrophobic lotus and taro leaf surfaces can be made using polydimethylsiloxane. These replicas faithfully reproduce the microstructures of the leaves' surface and can be analyzed using contact angle goniometry, self-cleaning experiments, and optical microscopy. These simple and adaptable experiments were used to…

  18. Fabrication of free-standing replicas of fragile, laminar, chitinous biotemplates.

    Science.gov (United States)

    Lakhtakia, Akhlesh; Martín-Palma, Raúl J; Motyka, Michael A; Pantano, Carlo G

    2009-09-01

    The conformal-evaporated-film-by-rotation technique, followed by the dissolution of chitin in an aqueous solution of orthophosphoric acid, can be used to fabricate free-standing replicas of fragile, laminar, chitinous biotemplates. This novel approach was demonstrated using butterfly wings as biotemplates and GeSeSb chalcogenide glass for replicas.

  19. Generic parallel Wang-Landau sampling for complex systems

    Science.gov (United States)

    Li, Ying Wai; Vogel, Thomas; Landau, David P.; Wüst, Thomas

    2013-03-01

    We introduce a parallel realization for Wang-Landau sampling in Monte Carlo simulations based on a replica-exchange framework. The key idea is to split the entire energy range of the system under consideration into several smaller, overlapping sub intervals. The survey of configurational phase space can then be distributed over multiple processors, with exchanges of random walkers taking place in the overlapping energy windows. To demonstrate the robustness and advantages of this parallel scheme for the simulations of complex systems, we have applied it to protein adsorption problems using the HP lattice protein model[1]. The method gives significant speed-up and achieves strong scaling on small computer architectures like multi-core processors, with a possible improvement in accuracy. We believe that it could be potentially beneficial for large-scale petaflop machines.

  20. Replica analysis for the duality of the portfolio optimization problem

    Science.gov (United States)

    Shinzato, Takashi

    2016-11-01

    In the present paper, the primal-dual problem consisting of the investment risk minimization problem and the expected return maximization problem in the mean-variance model is discussed using replica analysis. As a natural extension of the investment risk minimization problem under only a budget constraint that we analyzed in a previous study, we herein consider a primal-dual problem in which the investment risk minimization problem with budget and expected return constraints is regarded as the primal problem, and the expected return maximization problem with budget and investment risk constraints is regarded as the dual problem. With respect to these optimal problems, we analyze a quenched disordered system involving both of these optimization problems using the approach developed in statistical mechanical informatics and confirm that both optimal portfolios can possess the primal-dual structure. Finally, the results of numerical simulations are shown to validate the effectiveness of the proposed method.

  1. Nontrivial Critical Fixed Point for Replica-Symmetry-Breaking Transitions

    Science.gov (United States)

    Charbonneau, Patrick; Yaida, Sho

    2017-05-01

    The transformation of the free-energy landscape from smooth to hierarchical is one of the richest features of mean-field disordered systems. A well-studied example is the de Almeida-Thouless transition for spin glasses in a magnetic field, and a similar phenomenon—the Gardner transition—has recently been predicted for structural glasses. The existence of these replica-symmetry-breaking phase transitions has, however, long been questioned below their upper critical dimension, du=6 . Here, we obtain evidence for the existence of these transitions in d

  2. Searching near-replicas of images via clustering

    Science.gov (United States)

    Chang, Edward Y.; Li, Chen; Wang, James Z.; Mork, Peter; Wiederhold, Gio

    1999-08-01

    Internet piracy has been one of the major concerns for Web publishing. In this study we present a system, RIME, that we have prototyped for detecting unauthorized image copying on the WWW. To speed up the copy detection, RIME uses a new clustering/hashing approach that first clusters similar images on adjacent disk cylinders and then builds indexes to access the clusters made in this way. Searching for the replicas of an image often takes just one IO to loop up the location of the cluster containing similar objects and one sequential file IO to read in this cluster. Our experimental results show that RIME can detect images copies both more efficiently and effectively than the traditional content- based image retrieval systems that use tree-like structures to index images. In addition, RIME copes well with image format conversion, resampling, requantization and geometric transformation.

  3. Beyond Virtual Replicas: 3D Modeling and Maltese Prehistoric Architecture

    Directory of Open Access Journals (Sweden)

    Filippo Stanco

    2013-01-01

    Full Text Available In the past decade, computer graphics have become strategic for the development of projects aimed at the interpretation of archaeological evidence and the dissemination of scientific results to the public. Among all the solutions available, the use of 3D models is particularly relevant for the reconstruction of poorly preserved sites and monuments destroyed by natural causes or human actions. These digital replicas are, at the same time, a virtual environment that can be used as a tool for the interpretative hypotheses of archaeologists and as an effective medium for a visual description of the cultural heritage. In this paper, the innovative methodology and aims and outcomes of a virtual reconstruction of the Borg in-Nadur megalithic temple, carried out by Archeomatica Project of the University of Catania, are offered as a case study for a virtual archaeology of prehistoric Malta.

  4. Internal structure analysis of particle-double network gels used in a gel organ replica

    Science.gov (United States)

    Abe, Mei; Arai, Masanori; Saito, Azusa; Sakai, Kazuyuki; Kawakami, Masaru; Furukawa, Hidemitsu

    2016-04-01

    In recent years, the fabrication of patient organ replicas using 3D printers has been attracting a great deal of attention in medical fields. However, the cost of these organ replicas is very high as it is necessary to employ very expensive 3D printers and printing materials. Here we present a new gel organ replica, of human kidney, fabricated with a conventional molding technique, using a particle-double network hydrogel (P-DN gel). The replica is transparent and has the feel of a real kidney. It is expected that gel organ replicas produced this way will be a useful tool for the education of trainee surgeons and clinical ultrasonography technologists. In addition to developing a gel organ replica, the internal structure of the P-DN gel used is also discussed. Because the P-DN gel has a complex structure comprised of two different types of network, it has not been possible to investigate them internally in detail. Gels have an inhomogeneous network structure. If it is able to get a more uniform structure, it is considered that this would lead to higher strength in the gel. In the present study we investigate the structure of P-DN gel, using the gel organ replica. We investigated the internal structure of P-DN gel using Scanning Microscopic Light Scattering (SMILS), a non-contacting and non-destructive.

  5. Fabrication of the replica templated from butterfly wing scales with complex light trapping structures

    Science.gov (United States)

    Han, Zhiwu; Li, Bo; Mu, Zhengzhi; Yang, Meng; Niu, Shichao; Zhang, Junqiu; Ren, Luquan

    2015-11-01

    The polydimethylsiloxane (PDMS) positive replica templated twice from the excellent light trapping surface of butterfly Trogonoptera brookiana wing scales was fabricated by a simple and promising route. The exact SiO2 negative replica was fabricated by using a synthesis method combining a sol-gel process and subsequent selective etching. Afterwards, a vacuum-aided process was introduced to make PDMS gel fill into the SiO2 negative replica, and the PDMS gel was solidified in an oven. Then, the SiO2 negative replica was used as secondary template and the structures in its surface was transcribed onto the surface of PDMS. At last, the PDMS positive replica was obtained. After comparing the PDMS positive replica and the original bio-template in terms of morphology, dimensions and reflectance spectra and so on, it is evident that the excellent light trapping structures of butterfly wing scales were inherited by the PDMS positive replica faithfully. This bio-inspired route could facilitate the preparation of complex light trapping nanostructure surfaces without any assistance from other power-wasting and expensive nanofabrication technologies.

  6. Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide.

    Science.gov (United States)

    Wright, Louise B; Walsh, Tiffany R

    2013-04-07

    Harnessing the properties of biomolecules, such as peptides, adsorbed on inorganic surfaces is of interest to many cross-disciplinary areas of science, ranging from biomineralisation to nanomedicine. Key to advancing research in this area is determination of the peptide conformation(s) in its adsorbed state, at the aqueous interface. Molecular simulation is one such approach for accomplishing this goal. In this respect, use of temperature-based replica-exchange molecular dynamics (T-REMD) can yield enhanced sampling of the interfacial conformations, but does so at great computational expense, chiefly because of the need to include an explicit representation of water at the interface. Here, we investigate a number of more economical variations on REMD, chiefly those based on Replica Exchange with Solvent Tempering (REST), using the aqueous quartz-binding peptide S1-(100) α-quartz interfacial system as a benchmark. We also incorporate additional implementation details specifically targeted at improving sampling of biomolecules at interfaces. We find the REST-based variants yield configurational sampling of the peptide-surface system comparable with T-REMD, at a fraction of the computational time and resource. Our findings also deliver novel insights into the binding behaviour of the S1 peptide at the quartz (100) surface that are consistent with available experimental data.

  7. Rapid isolation of plutonium in environmental solid samples using sequential injection anion exchange chromatography followed by detection with inductively coupled plasma mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Qiao Jixin, E-mail: jixin.qiao@risoe.d [Radiation Research Division, Riso National Laboratory for Sustainable Energy, Technical University of Denmark, DK-4000 Roskilde (Denmark); Hou Xiaolin; Roos, Per [Radiation Research Division, Riso National Laboratory for Sustainable Energy, Technical University of Denmark, DK-4000 Roskilde (Denmark); Miro, Manuel [Department of Chemistry, Faculty of Sciences, University of the Balearic Islands, Carretera de Valldemossa km. 7.5, E-07122 Palma de Mallorca, Illes Balears (Spain)

    2011-01-31

    This paper reports an automated analytical method for rapid determination of plutonium isotopes ({sup 239}Pu and {sup 240}Pu) in environmental solid extracts. Anion exchange chromatographic columns were incorporated in a sequential injection (SI) system to undertake the automated separation of plutonium from matrix and interfering elements. The analytical results most distinctly demonstrated that the crosslinkage of the anion exchanger is a key parameter controlling the separation efficiency. AG 1-x4 type resin was selected as the most suitable sorbent material for analyte separation. Investigation of column size effect upon the separation efficiency revealed that small-sized (2 mL) columns sufficed to handle up to 50 g of environmental soil samples. Under the optimum conditions, chemical yields of plutonium exceeded 90% and the decontamination factors for uranium, thorium and lead ranged from 10{sup 3} to 10{sup 4}. The determination of plutonium isotopes in three standard/certified reference materials (IAEA-375 soil, IAEA-135 sediment and NIST-4359 seaweed) and two reference samples (Irish Sea sediment and Danish soil) revealed a good agreement with reference/certified values. The SI column-separation method is straightforward and less labor intensive as compared with batch-wise anion exchange chromatographic procedures. Besides, the automated method features low consumption of ion-exchanger and reagents for column washing and elution, with the consequent decrease in the generation of acidic waste, thus bearing green chemical credentials.

  8. Rapid isolation of plutonium in environmental solid samples using sequential injection anion exchange chromatography followed by detection with inductively coupled plasma mass spectrometry.

    Science.gov (United States)

    Qiao, Jixin; Hou, Xiaolin; Roos, Per; Miró, Manuel

    2011-01-31

    This paper reports an automated analytical method for rapid determination of plutonium isotopes ((239)Pu and (240)Pu) in environmental solid extracts. Anion exchange chromatographic columns were incorporated in a sequential injection (SI) system to undertake the automated separation of plutonium from matrix and interfering elements. The analytical results most distinctly demonstrated that the crosslinkage of the anion exchanger is a key parameter controlling the separation efficiency. AG 1-×4 type resin was selected as the most suitable sorbent material for analyte separation. Investigation of column size effect upon the separation efficiency revealed that small-sized (2 mL) columns sufficed to handle up to 50 g of environmental soil samples. Under the optimum conditions, chemical yields of plutonium exceeded 90% and the decontamination factors for uranium, thorium and lead ranged from 10(3) to 10(4). The determination of plutonium isotopes in three standard/certified reference materials (IAEA-375 soil, IAEA-135 sediment and NIST-4359 seaweed) and two reference samples (Irish Sea sediment and Danish soil) revealed a good agreement with reference/certified values. The SI column-separation method is straightforward and less labor intensive as compared with batch-wise anion exchange chromatographic procedures. Besides, the automated method features low consumption of ion-exchanger and reagents for column washing and elution, with the consequent decrease in the generation of acidic waste, thus bearing green chemical credentials.

  9. Assessment of contemporary genetic diversity and inter-taxa/inter-region exchange of avian paramyxovirus serotype 1 in wild birds sampled in North America.

    Science.gov (United States)

    Ramey, Andrew M; Goraichuk, Iryna V; Hicks, Joseph T; Dimitrov, Kiril M; Poulson, Rebecca L; Stallknecht, David E; Bahl, Justin; Afonso, Claudio L

    2017-03-03

    Avian paramyxovirus serotype 1 (APMV-1) viruses are globally distributed, infect wild, peridomestic, and domestic birds, and sometimes lead to outbreaks of disease. Thus, the maintenance, evolution, and spread of APMV-1 viruses are relevant to avian health. In this study we sequenced the fusion gene from 58 APMV-1 isolates recovered from thirteen species of wild birds sampled throughout the USA during 2007-2014. We analyzed sequence information with previously reported data in order to assess contemporary genetic diversity and inter-taxa/inter-region exchange of APMV-1 in wild birds sampled in North America. Our results suggest that wild birds maintain previously undescribed genetic diversity of APMV-1; however, such diversity is unlikely to be pathogenic to domestic poultry. Phylogenetic analyses revealed that APMV-1 diversity detected in wild birds of North America has been found in birds belonging to numerous taxonomic host orders and within hosts inhabiting multiple geographic regions suggesting some level of viral exchange. However, our results also provide statistical support for associations between phylogenetic tree topology and host taxonomic order/region of sample origin which supports restricted exchange among taxa and geographical regions of North America for some APMV-1 sub-genotypes. We identify previously unrecognized genetic diversity of APMV-1 in wild birds in North America which is likely a function of continued viral evolution in reservoir hosts. We did not, however, find support for the emergence or maintenance of APMV-1 strains predicted to be pathogenic to poultry in wild birds of North America outside of the order Suliformes (i.e., cormorants). Furthermore, genetic evidence suggests that ecological drivers or other mechanisms may restrict viral exchange among taxa and regions of North America. Additional and more systematic sampling for APMV-1 in North America would likely provide further inference on viral dynamics for this infectious agent

  10. Sampling

    CERN Document Server

    Thompson, Steven K

    2012-01-01

    Praise for the Second Edition "This book has never had a competitor. It is the only book that takes a broad approach to sampling . . . any good personal statistics library should include a copy of this book." —Technometrics "Well-written . . . an excellent book on an important subject. Highly recommended." —Choice "An ideal reference for scientific researchers and other professionals who use sampling." —Zentralblatt Math Features new developments in the field combined with all aspects of obtaining, interpreting, and using sample data Sampling provides an up-to-date treat

  11. Use of mixed-mode ion exchange sorbent for the passive sampling of organic acids by polar organic chemical integrative sampler (POCIS).

    Science.gov (United States)

    Fauvelle, Vincent; Mazzella, Nicolas; Delmas, François; Madarassou, Karine; Eon, Mélissa; Budzinski, Hélène

    2012-12-18

    Acidic herbicides are increasingly monitored in freshwater, since their high solubility favors their rapid transfer to the water phase. Therefore, contaminant levels in the water can vary rapidly and passive sampling would be preferred over spot sampling to integrate all pollution events over a given exposure time. In this work, we propose to compare the conventional pharmaceutical polar organic chemical integrative sampler (POCIS) with modified POCISs containing two different receiving phases: a standard polystyrene divinylbenzene polymer with a higher specific surface area (Chromabond HR-X) and a mixed-mode anion exchange sorbent providing additional strong anion exchange interaction sites (Oasis MAX). Due to its hydrophobic character, Chromabond HR-X had little interaction with water (no sampling of acidic herbicides); whereas Oasis MAX provided acceptable sampling parameters (longer kinetic regime together with higher sampling rates). Additional experiments with POCIS-MAX showed no influence of nitrates on analyte uptakes, and linear isotherms reaching 10 μg L⁻¹, supporting the applicability of this device for the sampling of organic acids in continental water. The performance and reference compound (PRC) approach would be then applicable for POCIS-MAX if no competition is observed with other anions, especially organic acids (e.g., humic acids).

  12. Application of Replica Technique and SEM in Accuracy Measurement of Ceramic Crowns

    Science.gov (United States)

    Trifkovic, B.; Budak, I.; Todorovic, A.; Hodolic, J.; Puskar, T.; Jevremovic, D.; Vukelic, D.

    2012-01-01

    The paper presents a comparative study of the measuring values of the marginal gap related to the ceramic crowns made by dental CAD/CAM system using the replica technique and SEM. The study was conducted using three experimental groups, which consisted of ceramic crowns manufactured by the Cerec CAD/CAM system. The scanning procedure was carried out using three specialized dental 3D digitization systems from the Cerec family - two types of extraoral optical scanning systems and an intraoral optical scanner. Measurements of the marginal gap were carried out using the replica technique and SEM. The comparison of aggregate values of the marginal gap using the replica technique showed a statistically significant difference between the systems. The measured values of marginal gaps of ceramic crowns using the replica technique were significantly lower compared to those measured by SEM. The results indicate that the choice of technique for measuring the accuracy of ceramic crowns influences the final results of investigation.

  13. Automated magnification calibration in transmission electron microscopy using Fourier analysis of replica images.

    NARCIS (Netherlands)

    Laak, J.A.W.M. van der; Dijkman, H.B.P.M.; Pahlplatz, M.M.M.

    2006-01-01

    The magnification factor in transmission electron microscopy is not very precise, hampering for instance quantitative analysis of specimens. Calibration of the magnification is usually performed interactively using replica specimens, containing line or grating patterns with known spacing. In the pre

  14. Rapid prototyping of replica knee implants for in vitro testing

    Directory of Open Access Journals (Sweden)

    Verjans Mark

    2016-09-01

    Full Text Available The understanding of the complex biomechanics of the knee is a key for an optimal implant design. To easily investigate the influence of prosthetic designs on knee biomechanics a rapid prototyping workflow for knee implants has been developed and evaluated. Therefore, different manufacturing technologies and post-treatment methods have been examined and overall seven different replica knee implants were manufactured. For evaluation, the manufacturing properties such as surface accuracy and roughness were determined and kinematic behaviour was investigated in a novel knee testing rig. It was carried out that PolyJet-Modelling with a sanded surface resulted in changed kinematic patterns compared to a usual CoCr-UHMWPE implant. However, fused deposition modelling using ABS and subsequent surface smoothening with acetone vapor showed the lowest roughness of the manufactured implants and only minor kinematic differences. For this reason this method constitutes a promising approach towards an optimal implant design for improved patient-satisfaction and long lifetime of the implant. Finally the workflow is not only limited to the knee.

  15. Critiques, replicas and proposals for the New Urbanism Vision

    Directory of Open Access Journals (Sweden)

    Alaide Retana

    2014-03-01

    Full Text Available The new urbanism (NU is a vision of planning and urban design emerged in 1993, which finds its basis in the design of traditional communities. This trend has had various criticisms and replicas, which were reviewed in relation to urban sprawl, transportation, re-densifying, mix of uses of land, design, gentrification, pedestrianization and safety, which were analyzed in the neighborhood of Santa Barbara in Toluca, Mexico. This area was chosen for being traditional and forming part of the historical center of the city, which even though it was not designed under the guidelines of the NU, it has the quality of traditional, from which the NU would theoretically has taken its essence. The objective of this analysis is to establish whether the NU has the essence of a traditional Mexican neighborhood, as well as to check if the criticisms of the NU are informed when applied to a space belonging to a Mexican historic center that has been abandoned by problems of insecurity and degradation. The general conclusion is that the traditional neighborhoods have provided design elements to the NU, which will refute some of the criticisms, however, proposals for NU in neighborhoods of his-toric centers have to be based on the community, the architecture and existing urbanism, since these elements are those that give the identity.

  16. Evidence for intercontinental parasite exchange through molecular detection and characterization of haematozoa in northern pintails (Anas acuta) sampled throughout the North Pacific Basin

    Science.gov (United States)

    Ramey, Andy M.; Schmutz, Joel A.; Reed, John A.; Fujita, Go; Scotton, Bradley D.; Casler, Bruce; Fleskes, Joseph P.; Konishi, Kan; Uchida, Kiyoshi; Yabsley, Michael J.

    2015-01-01

    Empirical evidence supports wild birds as playing a role in the interhemispheric exchange of bacteria and viruses; however, data supporting the redistribution of parasites among continents are limited. In this study, the hypothesis that migratory birds contribute to the redistribution of parasites between continents was tested by sampling northern pintails (Anas acuta) at locations throughout the North Pacific Basin in North America and East Asia for haemosporidian infections and assessing the genetic evidence for parasite exchange. Of 878 samples collected from birds in Alaska (USA), California (USA), and Hokkaido (Japan) during August 2011 - May 2012 and screened for parasitic infections using molecular techniques, Leucocytozoon, Haemoproteus, and Plasmodium parasites were detected in 555 (63%), 44 (5%), and 52 (6%) samples, respectively. Using an occupancy modeling approach, the probability of detecting parasites via replicate genetic tests was estimated to be high (p ≥ 0.95). Multi-model inference supported variation of Leucocytozoon parasite prevalence by northern pintail age class and geographic location of sampling in contrast to Haemoproteus and Plasmodium parasites for which there was only support for variation in parasite prevalence by sampling location. Thirty-one unique mitochondrial DNA haplotypes were detected among haematozoa infecting northern pintails including seven lineages shared between samples from North America and Japan. The finding of identical parasite haplotypes at widely distributed geographic locations and general lack of genetic structuring by continent in phylogenies for Leucocytozoon and Plasmodium provides evidence for intercontinental genetic exchange of haemosporidian parasites. Results suggest that migratory birds, including waterfowl, could therefore facilitate the introduction of avian malaria and other haemosporidia to novel hosts and spatially distant regions.

  17. Computing Relative Free Energies of Solvation Using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange

    Science.gov (United States)

    2010-10-21

    transfor- mation, the hybrid potential VAB remains well-defined. Therefore, the associated reversible work can be computed. This reversible work formally...corresponds to changing the potential of the system VAB from the state that represents the original molecule A to the state that corresponds to molecule...constructed. Typically, the hybrid Hamiltonian of the system (HAB) that includes the potential VAB is linearly interpolated between the end points, molecules

  18. Replica exchange Monte Carlo simulations of the ising spin glass: Static and dynamic properties

    Science.gov (United States)

    Yucesoy, Burcu

    Spin glasses have been the subject of intense study and considerable controversy for decades, and the low-temperature phase of short-range spin glasses is still poorly understood. Our main goal is to improve our understanding in this area and find an answer to the following question: Are there only a single pair or a countable infinity of pure states in the low temperature phase of the EA spin glass? To that aim we first start by introducing spin glasses and provide a brief history of their research, then proceed to describe our method of simulation, the parallel tempering Monte Carlo algorithm. Next, we present the results of a large-scale numerical study of the equilibrium three-dimensional Edwards-Anderson Ising spin glass with Gaussian disorder. In order to understand how the parallel tempering algorithm works, we measure various static, as well as dynamical quantities, such as the autocorrelation times and round-trip times for the parallel tempering Monte Carlo method. We examine the correlation between static and dynamic observables for ˜ 5000 disorder realizations and up to 1000 spins down to temperatures at 20% of the critical temperature, and our results show that autocorrelation times are directly correlated with the roughness of the free-energy landscape. In the following chapters, the three- and four-dimensional Edwards-Anderson and mean-field Sherrington-Kirkpatrick Ising spin glasses are studied again via large scale Monte Carlo simulations at low temperatures, deep within the spin glass phase. Performing a careful statistical analysis of several thousand independent disorder realizations and using an observable that detects peaks in the overlap distribution, we show that the Sherrington-Kirkpatrick and Edwards-Anderson models have a distinctly different low-temperature behavior. We arrive to the following conclusion: The structure of the spin-glass overlap distribution for the Edwards-Anderson model suggests that its low-temperature phase has only a single pair of pure states. Finally we present results for several new observables, along with a few preliminary studies and suggestions for future research.

  19. Sample to sample fluctuations in the random energy model

    Energy Technology Data Exchange (ETDEWEB)

    Derrida, B. (Service de Physique Theorique, CEN Saclay, 91 - Gif-sur-Yvette (France)); Toulouse, G. (E.S.P.C.I., 75 - Paris (France))

    1985-03-15

    In the spin glass phase, mean field theory says that the weights of the valleys vary from sample to sample. Exact expressions for the probability laws of these fluctuations are derived, from the random energy model, without recourse to the replica method.

  20. Design of replica bit line control circuit to optimize power for SRAM

    Science.gov (United States)

    Pengjun, Wang; Keji, Zhou; Huihong, Zhang; Daohui, Gong

    2016-12-01

    A design of a replica bit line control circuit to optimize power for SRAM is proposed. The proposed design overcomes the limitations of the traditional replica bit line control circuit, which cannot shut off the word line in time. In the novel design, the delay of word line enable and disable paths are balanced. Thus, the word line can be opened and shut off in time. Moreover, the chip select signal is decomposed, which prevents feedback oscillations caused by the replica bit line and the replica word line. As a result, the switch power caused by unnecessary discharging of the bit line is reduced. A 2-kb SRAM is fully custom designed in an SMIC 65-nm CMOS process. The traditional replica bit line control circuit and the new replica bit line control circuit are used in the designed SRAM, and their performances are compared with each other. The experimental results show that at a supply voltage of 1.2 V, the switch power consumption of the memory array can be reduced by 53.7%. Project supported by the Zhejiang Provincial Natural Science Foundation of China (No. LQ14F040001), the National Natural Science Foundation of China (Nos. 61274132, 61234002, 61474068), and the K. C. Wong Magna Fund in Ningbo University.

  1. Determination of traces of Pt and Rh in soil and quartz samples contaminated by automobile exhaust after an ion-exchange matrix separation.

    Science.gov (United States)

    Kowalska, Joanna; Kińska, Katarzyna; Pałdyna, Joanna; Czyżewska, Monika; Boder, Kamila; Krasnodębska-Ostręga, Beata

    2014-09-01

    Monitoring of PGEs content in the natural samples is a crucial point in the environment science since catalytic car converters have been introduced. In the presented paper application of a very sensitive voltammetric method for determination of traces of Pt and Rh in the environmental samples contaminated by automobile exhausts is discussed. Voltammetric measurements were carried out in the supporting electrolyte containing formaldehyde and semicarbazide. PGEs were separated from the digested solutions of soils or quartz samples, collected from monitoring plots-by applying an ion-exchange resin Cellex-T. Pt was very effectively separated from the matrix approaching nearly 100% recovery after its elution by hydrochloric acid. Moreover the conditions of soil and quartz samples digestion were discussed. To validate the obtained result an independent analytical method-ICP MS was applied and analysis of certified reference material road dust 723-was completed.

  2. A 10-bit 250 MSPS charge-domain pipelined ADC with replica controlled PVT insensitive BCT circuit

    Science.gov (United States)

    Songren, Huang; Hong, Zhang; Zhenhai, Chen; Shuang, Zhu; Zongguang, Yu; Hongwen, Qian; Yue, Hao

    2015-05-01

    A low power 10-bit 250 MSPS charge-domain (CD) pipelined analog-to-digital converter (ADC) is introduced. The ADC is implemented in MOS bucket-brigade devices (BBDs) based CD pipelined architecture. A replica controlled boosted charge transfer (BCT) circuit is introduced to reject the influence of PVT variations on the charge transfer process. Based on replica controlled BCT, the CD pipelined ADC is designed and realized in a 1P6M 0.18 μm CMOS process. The ADC achieves an SFDR of 64.4 dB, an SNDR of 56.9 dB and an ENOB of 9.2 for a 9.9 MHz input; and an SFDR of 63.1 dB, an SNR of 55.2 dB, an SNDR of 54.5 dB and an ENOB of 8.7 for a 220.5 MHz input at full sampling rate. The DNL is +0.5/ -0.55 LSB and INL is +0.8/ -0.85 LSB. The power consumption of the prototype ADC is only 45 mW at 1.8 V supply and it occupies an active die area of 1.56 mm2. Project supported by the National Natural Science Foundation of China (No. 61106027).

  3. An ingenious replica templated from the light trapping structure in butterfly wing scales

    Science.gov (United States)

    Han, Zhiwu; Niu, Shichao; Yang, Meng; Zhang, Junqiu; Yin, Wei; Ren, Luquan

    2013-08-01

    Although the physical mechanism of light trapping property of butterfly wings is well understood, it remains a challenge to create artificial replicas of these natural functional structures. Here, we synthesized a SiO2 inverse replica of a light trapping structure in butterfly wing scales using a method combining a sol-gel process and subsequent selective etching. First, the reflectance spectrum was taken to measure the reflectivity. Then, FESEM and TEM were used to observe the coupling structure of scales and the replicas. Afterwards, assisted by SEM and TEM data, 3D optimized models of the structures and fabrication process were generated by software. Finally, the parametric comparisons of the morphologies and structures between the original template and the inverse SiO2 replica were carefully conducted, and it was found that the original structures of bio-templates were well inherited by the structures of the inverse replica. This work would open up possibilities for an extensive study of mimicking novel bio-inspired functional materials, and the reported biomimetic technique confirms the feasibility of extending the functional structures in butterfly wings to particular optical devices in the field of space exploration, space equipment, photoelectrical devices and photo-induced sensors.Although the physical mechanism of light trapping property of butterfly wings is well understood, it remains a challenge to create artificial replicas of these natural functional structures. Here, we synthesized a SiO2 inverse replica of a light trapping structure in butterfly wing scales using a method combining a sol-gel process and subsequent selective etching. First, the reflectance spectrum was taken to measure the reflectivity. Then, FESEM and TEM were used to observe the coupling structure of scales and the replicas. Afterwards, assisted by SEM and TEM data, 3D optimized models of the structures and fabrication process were generated by software. Finally, the parametric

  4. Magnetic graphene - polystyrene sulfonic acid nano composite: A dispersive cation exchange sorbent for the enrichment of aminoalcohols and ethanolamines from environmental aqueous samples.

    Science.gov (United States)

    Chinthakindi, Sridhar; Purohit, Ajay; Singh, Varoon; Tak, Vijay; Dubey, D K; Pardasani, Deepak

    2015-12-04

    Present study aimed at graphene surface modification to achieve selective analyte binding in dispersive solid phase extraction. Magnetic graphene - polystyrene sulfonic acid (MG-PSS) cation exchange nano-composite was prepared by non-covalent wrapping method. Composite was characterized by FT-IR and zeta potential. Material exhibited good dispersion in water and high exchange capacity of 1.97±0.16mMg(-1). Prepared nano-sorbent was then exploited for the cation exchange extraction and gas chromatography mass spectrometric analysis of Chemical Weapons Convention relevant aminoalcohols and ethanolamines from aqueous samples. Extraction parameters such as sorbent amount, extraction time, desorption conditions and sample pH were optimized and effect of common matrix interferences such as polyethylene glycol and metal salts was also studied. Three milligram of sorbent per mL of sample with 20min of extraction time at room temperature afforded 70-81% recoveries of the selected analytes spiked at concentration level of 1μgmL(-1). Method showed good linearity in the studied range with r(2)≥0.993. The limits of detection and limits of quantification ranged from 23 to 54ngmL(-1) and 72 to 147ngmL(-1), respectively. The relative standard deviation for intra- and inter-day precision ranged from 4.6 to 10.2% and 7.4 to 14.8% respectively. Applicability of the method to different environmental samples as well as the proficiency tests conducted by the Organization for the Prohibition of Chemical Weapons (OPCW) was also ascertained.

  5. Sulphonic acid strong cation-exchange restricted access columns in sample cleanup for profiling of endogenous peptides in multidimensional liquid chromatography. Structure and function of strong cation-exchange restricted access materials.

    Science.gov (United States)

    Machtejevas, E; Denoyel, R; Meneses, J M; Kudirkaite, V; Grimes, B A; Lubda, D; Unger, K K

    2006-08-04

    In this work, the pore structural parameters and size exclusion properties of LiChrospher strong cation-exchange and reverse phase restricted access materials (RAM) are analysed. The molecular weight size exclusion limit for polystyrenes was found to be about 17.7 kDa, while for standard proteins, the molecular weight size exclusion limit was higher, at approximately 25 kDa. The average pore diameter on a volume basis calculated from the pore network model changes from 8.5 nm (native LiChrospher) to 8.6 nm (diol derivative) to 8.2 nm (sulphonic acid derivative) to 6.9 nm (n-octadecyl derivative). Additional characterisations were performed on restricted access materials with nitrogen sorption at 77 K, water adsorption at 25 degrees C, intrusion-extrusion of water (in order to evaluate the hydrophobic properties of the pores of the hydrophobic RAM), and zeta potential measurements by microelectrophoresis. For peptide analysis out of the biofluids, the strong cation-exchange functionality seems to be particularly suitable mainly because of the high loadability of the strong cation-exchange restricted access material (SCX-RAM) and the fact that one can work under non-denaturing conditions to perform effective chromatographic separations. For bacitracin, the dynamic capacity of the SCX-RAM columns does not reach its maximum value in the analysed range. For lysozyme, the dynamic capacity reaches a value of 0.08 mg/ml of column volume before column is overloaded. Additionally, the proper column operating conditions that lead to the total effective working time of the RAM column to be equal to approximately 500 injections (depending on the type of sample), is comprehensively described. The SCX-RAM column was used in the same system analysing urine samples for the period of 1 month (approximately 150 injections) with run-to-run reproducibility below 5% RSD and below 10% RSD for the relative fractions.

  6. Replica analysis of overfitting in regression models for time-to-event data

    Science.gov (United States)

    Coolen, A. C. C.; Barrett, J. E.; Paga, P.; Perez-Vicente, C. J.

    2017-09-01

    Overfitting, which happens when the number of parameters in a model is too large compared to the number of data points available for determining these parameters, is a serious and growing problem in survival analysis. While modern medicine presents us with data of unprecedented dimensionality, these data cannot yet be used effectively for clinical outcome prediction. Standard error measures in maximum likelihood regression, such as p-values and z-scores, are blind to overfitting, and even for Cox’s proportional hazards model (the main tool of medical statisticians), one finds in literature only rules of thumb on the number of samples required to avoid overfitting. In this paper we present a mathematical theory of overfitting in regression models for time-to-event data, which aims to increase our quantitative understanding of the problem and provide practical tools with which to correct regression outcomes for the impact of overfitting. It is based on the replica method, a statistical mechanical technique for the analysis of heterogeneous many-variable systems that has been used successfully for several decades in physics, biology, and computer science, but not yet in medical statistics. We develop the theory initially for arbitrary regression models for time-to-event data, and verify its predictions in detail for the popular Cox model.

  7. Communication: Multiple atomistic force fields in a single enhanced sampling simulation

    Energy Technology Data Exchange (ETDEWEB)

    Hoang Viet, Man [Department of Physics, North Carolina State University, Raleigh, North Carolina 27695-8202 (United States); Derreumaux, Philippe, E-mail: philippe.derreumaux@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France); Institut Universitaire de France, 103 Bvd Saint-Germain, 75005 Paris (France); Nguyen, Phuong H., E-mail: phuong.nguyen@ibpc.fr [Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris (France)

    2015-07-14

    The main concerns of biomolecular dynamics simulations are the convergence of the conformational sampling and the dependence of the results on the force fields. While the first issue can be addressed by employing enhanced sampling techniques such as simulated tempering or replica exchange molecular dynamics, repeating these simulations with different force fields is very time consuming. Here, we propose an automatic method that includes different force fields into a single advanced sampling simulation. Conformational sampling using three all-atom force fields is enhanced by simulated tempering and by formulating the weight parameters of the simulated tempering method in terms of the energy fluctuations, the system is able to perform random walk in both temperature and force field spaces. The method is first demonstrated on a 1D system and then validated by the folding of the 10-residue chignolin peptide in explicit water.

  8. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    Science.gov (United States)

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.

  9. A distinct group of CpG islands shows differential DNA methylation between replicas of the same cell line in vitro.

    Science.gov (United States)

    Cocozza, Sergio; Scala, Giovanni; Miele, Gennaro; Castaldo, Imma; Monticelli, Antonella

    2013-10-10

    CpG dinucleotide-rich genomic DNA regions, known as CpG islands (CGIs), can be methylated at their cytosine residues as an epigenetic mark that is stably inherited during cell mitosis. Differentially methylated regions (DMRs) are genomic regions showing different degrees of DNA methylation in multiple samples. In this study, we focused our attention on CGIs showing different DNA methylation between two culture replicas of the same cell line. We used methylation data of 35 cell lines from the Encyclopedia of DNA Elements (ENCODE) consortium to identify CpG islands that were differentially methylated between replicas of the same cell line and denoted them Inter Replicas Differentially Methylated CpG islands (IRDM-CGIs). We identified a group of IRDM-CGIs that was consistently shared by different cell lines, and denoted it common IRDM-CGIs. X chromosome CGIs were overrepresented among common IRDM-CGIs. Autosomal IRDM-CGIs were preferentially located in gene bodies and intergenic regions had a lower G + C content, a smaller mean length, and a reduced CpG percentage. Functional analysis of the genes associated with autosomal IRDM-CGIs showed that many of them are involved in DNA binding and development. Our results show that several specific functional and structural features characterize common IRDM-CGIs. They may represent a specific subset of CGIs that are more prone to being differentially methylated for their intrinsic characteristics.

  10. Monitoring of sulphites levels in shrimps samples collected in Puglia (Italy) by ion-exchange chromatography with conductivity detection.

    Science.gov (United States)

    Iammarino, Marco; Di Taranto, Aurelia; Ientile, Anna Rita

    2014-01-01

    In shrimps the treatment with sulphiting agents is currently the best option for controlling Melanosis, which is a visual defect of the products that compromises marketability. However, sulphites may cause pseudo-allergic reactions in humans. In this study, 210 samples of shrimps were analysed in order to assess the residual levels of sulphiting agents. A quantifiable sulphites concentration was detected in 76 samples, and these concentrations were higher than the legal limits in eight samples. Considering the important pseudo-allergenic effects caused by these food additives, the non-negligible percentage of 3.8% and the high levels registered in non-compliant samples (up to 1174.1 mg kg(-1)), a strong contrast action based on permanent controls is necessary. Moreover, the levels measured in whole samples were up to four times higher than in the edible parts. These results suggest to consider the introduction of legal limits, related to sulphurous anhydride in the whole product.

  11. Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling.

    Science.gov (United States)

    Mori, Toshifumi; Hamers, Robert J; Pedersen, Joel A; Cui, Qiang

    2014-07-17

    Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.

  12. A rapid sample-exchange mechanism for cryogen-free dilution refrigerators compatible with multiple high-frequency signal connections

    Science.gov (United States)

    Batey, G.; Chappell, S.; Cuthbert, M. N.; Erfani, M.; Matthews, A. J.; Teleberg, G.

    2014-03-01

    Researchers attempting to study quantum effects in the solid-state have a need to characterise samples at very low-temperatures, and frequently in high magnetic fields. Often coupled with this extreme environment is the requirement for high-frequency signalling to the sample for electrical control or measurements. Cryogen-free dilution refrigerators allow the necessary wiring to be installed to the sample more easily than their wet counterparts, but the limited cooling power of the closed cycle coolers used in these systems means that the experimental turn-around time can be longer. Here we shall describe a sample loading arrangement that can be coupled with a cryogen-free refrigerator and that allows samples to be loaded from room temperature in a matter of minutes. The loaded sample is then cooled to temperatures ∼10 mK in ∼7 h. This apparatus is compatible with systems incorporating superconducting magnets and allows multiple high-frequency lines to be connected to the cold sample.

  13. Assessment of hydro/oleophobicity for shark skin replica with riblets.

    Science.gov (United States)

    Kim, Tae Wan

    2014-10-01

    The shark skin has a unique skin structure which enables the shark to swim faster and more efficiently due to an intriguing three-dimensional rib pattern. Shark skin has also known as having functional performances such as self cleaning and anti-fouling as well as excellent drag reduction due to a hierarchical structure built up by micro grooves and nano-long chain mucus drag reduction interface around the shark body. In this study, the wetting properties for the biomimetic surfaces that replicate shark skin are assessed. First of all, the shark skin replicas are obtained using the micro molding technique directly from a shark skin template. The quantitative replication precision of the shark skin replicas is evaluated comparing with the geometry of shark skin template using 3D and 2D surface profiles are measured. Then contact angles in the conditions of solid-air-water, solid-air-oil and solid-water-oil interfaces are evaluated for shark skin replicas. The effect of Teflon coating on the wetting properties of shark skin replicas is also observed. The results show the shark skin replica by the micro molding technique gives better effect on the wetting performance, and the micro riblets on shark skin improve the wettability feature.

  14. The Construction and Validation of All-Atom Bulk-Phase Models of Amorphous Polymers Using the TIGER2/TIGER3 Empirical Sampling Method.

    Science.gov (United States)

    Li, Xianfeng; Murthy, Sanjeeva; Latour, Robert A

    2011-07-12

    A new empirical sampling method termed "temperature intervals with global exchange of replicas and reduced radii" (TIGER3) is presented and demonstrated to efficiently equilibrate entangled long-chain molecular systems such as amorphous polymers. The TIGER3 algorithm is a replica exchange method in which simulations are run in parallel over a range of temperature levels at and above a designated baseline temperature. The replicas sampled at temperature levels above the baseline are run through a series of cycles with each cycle containing four stages - heating, sampling, quenching, and temperature level reassignment. The method allows chain segments to pass through one another at elevated temperature levels during the sampling stage by reducing the van der Waals radii of the atoms, thus eliminating chain entanglement problems. Atomic radii are then returned to their regular values and re-equilibrated at elevated temperature prior to quenching to the baseline temperature. Following quenching, replicas are compared using a Metropolis Monte Carlo exchange process for the construction of an approximate Boltzmann-weighted ensemble of states and then reassigned to the elevated temperature levels for additional sampling. Further system equilibration is performed by periodic implementation of the previously developed TIGER2 algorithm between cycles of TIGER3, which applies thermal cycling without radii reduction. When coupled with a coarse-grained modeling approach, the combined TIGER2/TIGER3 algorithm yields fast equilibration of bulk-phase models of amorphous polymer, even for polymers with complex, highly branched structures. The developed method was tested by modeling the polyethylene melt. The calculated properties of chain conformation and chain segment packing agreed well with published data. The method was also applied to generate equilibrated structural models of three increasingly complex amorphous polymer systems: poly(methyl methacrylate), poly

  15. Dialysis is superior to anion exchange for removal of dissolved inorganic nitrogen from freshwater samples prior to dissolved organic nitrogen determination

    DEFF Research Database (Denmark)

    Graeber, Daniel; Gücker, Björn; Zwirnmann, Elke;

    2012-01-01

    Dissolved organic nitrogen (DON) is usually determined as the difference between total dissolved nitrogen (TDN) and dissolved inorganic nitrogen (DIN). When applying this approach to samples with high DIN concentrations, there is a risk, that small relative errors in TDN and DIN measurements may...... propagate into high absolute errors of the determined DON concentration. To reduce such errors, two pretreatment methods have been suggested for the removal of DIN prior to the determination of DON: anion-exchange pretreatment (AEP) and dialysis pretreatment (DP). In this study, we tested the suitability...... of AEP and DP for DIN removal in order to increase DON determination accuracy of freshwater samples. The AEP pretreatment performed well for standard compounds, yielding high dissolved organic carbon (DOC) recovery rates and > 99% removal of nitrate, whereas DON recovery rates varied and no removal...

  16. Multiscale enhanced path sampling based on the Onsager-Machlup action: Application to a model polymer

    CERN Document Server

    Fujisaki, Hiroshi; Moritsugu, Kei; Kidera, Akinori

    2013-01-01

    We propose a novel path sampling method based on the Onsager-Machlup (OM) action by generalizing the multiscale enhanced sampling (MSES) technique suggested by Moritsugu and coworkers (J. Chem. Phys. 133, 224105 (2010)). The basic idea of this method is that the system we want to study (for example, some molecular system described by molecular mechanics) is coupled to a coarse-grained (CG) system, which can move more quickly and computed more efficiently than the original system. We simulate this combined system (original + CG system) using (underdamped) Langevin dynamics where different heat baths are coupled to the two systems. When the coupling is strong enough, the original system is guided by the CG system, and able to sample the configuration and path space more efficiency. We need to correct the bias caused by the coupling, however, by employing the Hamiltonian replica exchange where we prepare many path replica with different coupling strengths. As a result, an unbiased path ensemble for the original ...

  17. Sulfur geochemistry of hydrothermal waters in Yellowstone National Park, Wyoming, USA. III. An anion-exchange resin technique for sampling and preservation of sulfoxyanions in natural waters

    Science.gov (United States)

    Druschel, G.K.; Schoonen, M.A.A.; Nordstorm, D.K.; Ball, J.W.; Xu, Y.; Cohn, C.A.

    2003-01-01

    A sampling protocol for the retention, extraction, and analysis of sulfoxyanions in hydrothermal waters has been developed in the laboratory and tested at Yellowstone National Park and Green Lake, NY. Initial laboratory testing of the anion-exchange resin Bio-Rad??? AG1-X8 indicated that the resin was well suited for the sampling, preservation, and extraction of sulfate and thiosulfate. Synthetic solutions containing sulfate and thiosulfate were passed through AG1-X8 resin columns and eluted with 1 and 3 M KCl, respectively. Recovery ranged from 89 to 100%. Comparison of results for water samples collected from five pools in Yellowstone National Park between on-site IC analysis (U.S. Geological Survey mobile lab) and IC analysis of resin-stored sample at SUNY-Stony Brook indicates 96 to 100% agreement for three pools (Cinder, Cistern, and an unnamed pool near Cistern) and 76 and 63% agreement for two pools (Sulfur Dust and Frying Pan). Attempts to extract polythionates from the AG1-X8 resin were made using HCl solutions, but were unsuccessful. Bio-Rad??? AG2-X8, an anion-exchange resin with weaker binding sites than the AG1-X8 resin, is better suited for polythionate extraction. Sulfate and thiosulfate extraction with this resin has been accomplished with KCl solutions of 0.1 and 0.5 M, respectively. Trithionate and tetrathionate can be extracted with 4 M KCl. Higher polythionates can be extracted with 9 M hydrochloric acid. Polythionate concentrations can then be determined directly using ion chromatographic methods, and laboratory results indicate recovery of up to 90% for synthetic polythionate solutions using AG2-X8 resin columns. ?? The Royal Society of Chemistry and the Division of Geochemistry of the American Chemical Society 2003.

  18. Sulfur geochemistry of hydrothermal waters in Yellowstone National Park, Wyoming, USA. III. An anion-exchange resin technique for sampling and preservation of sulfoxyanions in natural waters

    Directory of Open Access Journals (Sweden)

    Ball James W

    2003-06-01

    Full Text Available A sampling protocol for the retention, extraction, and analysis of sulfoxyanions in hydrothermal waters has been developed in the laboratory and tested at Yellowstone National Park and Green Lake, NY. Initial laboratory testing of the anion-exchange resin Bio-Rad™ AG1-X8 indicated that the resin was well suited for the sampling, preservation, and extraction of sulfate and thiosulfate. Synthetic solutions containing sulfate and thiosulfate were passed through AG1-X8 resin columns and eluted with 1 and 3 M KCl, respectively. Recovery ranged from 89 to 100%. Comparison of results for water samples collected from five pools in Yellowstone National Park between on-site IC analysis (U.S. Geological Survey mobile lab and IC analysis of resin-stored sample at SUNY-Stony Brook indicates 96 to 100% agreement for three pools (Cinder, Cistern, and an unnamed pool near Cistern and 76 and 63% agreement for two pools (Sulfur Dust and Frying Pan. Attempts to extract polythionates from the AG1-X8 resin were made using HCl solutions, but were unsuccessful. Bio-Rad™ AG2-X8, an anion-exchange resin with weaker binding sites than the AG1-X8 resin, is better suited for polythionate extraction. Sulfate and thiosulfate extraction with this resin has been accomplished with KCl solutions of 0.1 and 0.5 M, respectively. Trithionate and tetrathionate can be extracted with 4 M KCl. Higher polythionates can be extracted with 9 M hydrochloric acid. Polythionate concentrations can then be determined directly using ion chromatographic methods, and laboratory results indicate recovery of up to 90% for synthetic polythionate solutions using AG2-X8 resin columns.

  19. Nickel replicas as calibration reference standards for industrial surface texture instruments

    DEFF Research Database (Denmark)

    Sammatini-Malberg, Maria-Pia

    The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale.......The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale....

  20. Sampling conformational space of intrinsically disordered proteins in explicit solvent: Comparison between well-tempered ensemble approach and solute tempering method.

    Science.gov (United States)

    Han, Mengzhi; Xu, Ji; Ren, Ying

    2017-03-01

    Intrinsically disordered proteins (IDPs) are a class of proteins that expected to be largely unstructured under physiological conditions. Due to their heterogeneous nature, experimental characterization of IDP is challenging. Temperature replica exchange molecular dynamics (T-REMD) is a widely used enhanced sampling method to probe structural characteristics of these proteins. However, its application has been hindered due to its tremendous computational cost, especially when simulating large systems in explicit solvent. Two methods, parallel tempering well-tempered ensemble (PT-WTE) and replica exchange with solute tempering (REST), have been proposed to alleviate the computational expense of T-REMD. In this work, we select three different IDP systems to compare the sampling characteristics and efficiencies of the two methods Both the two methods could efficiently sample the conformational space of IDP and yield highly consistent results for all the three IDPs. The efficiencies of the two methods: are compatible, with about 5-6 times better than the plain T-REMD. Besides, the advantages and disadvantages of each method are also discussed. Specially, the PT-WTE method could provide temperature dependent data of the system which could not be achieved by REST, while the REST method could readily be used to a part of the system, which is quite efficient to simulate some biological processes. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. On the Application of Replica Molding Technology for the Indirect Measurement of Surface and Geometry of Micromilled Components

    DEFF Research Database (Denmark)

    Baruffi, Federico; Parenti, Paolo; Cacciatore, Francesco

    2017-01-01

    the replica molding technology. The method consists of obtaining a replica of the feature that is inaccessible for standard measurement devices and performing its indirect measurement. This paper examines the performance of a commercial replication media applied to the indirect measurement of micromilled...

  2. FTIR study of ageing of fast drying oil colour (FDOC) alkyd paint replicas

    Science.gov (United States)

    Duce, Celia; Della Porta, Valentina; Tiné, Maria Rosaria; Spepi, Alessio; Ghezzi, Lisa; Colombini, Maria Perla; Bramanti, Emilia

    2014-09-01

    We propose ATR-FTIR spectroscopy for the characterization of the spectral changes in alkyd resin from the Griffin Alkyd Fast Drying Oil Colour range (Winsor & Newton), occurring over 550 days (∼18 months) of natural ageing and over six months of artificial ageing under an acetic acid atmosphere. Acetic acid is one of the atmospheric pollutants found inside museums in concentrations that can have a significant effect on the works exhibited. During natural ageing we observed an increase and broadening of the OH group band around 3300 cm-1 and an increase in bands in the region 1730-1680 cm-1 due to carbonyl stretching. We found a broad band around 1635 cm-1 likely due to Cdbnd O stretching vibrations of β dichetons. These spectral changes are the result of autooxidation reactions during natural ageing and crosslinking, which then form f alcohols and carbonyl species. The increase in absorbance at 1635 cm-1 was selected as a parameter to monitor the ageing process of paintings prepared with FDOC, without the need for any extractive procedure. FTIR spectra of paint replicas kept under an acetic acid atmosphere indicated the chemical groups involved in the reaction with acid, thus suggesting which spectral FTIR regions could be investigated in order to follow any degradation in real paintings. A red paint sample from a hyper-realistic artwork (“Racconta storie”, 2003) by the Italian painter Patrizia Zara was investigated by FTIR in order to evaluate the effects of 10 years natural ageing on alkyd colours. The results obtained suggested that after the end of chemical drying (autooxidation), alkyd colours are very stable.

  3. Stability study of As(III), As(V), MMA and DMA by anion exchange chromatography and HG-AFS in wastewater samples

    Energy Technology Data Exchange (ETDEWEB)

    Segura, Marta; Munoz, Juan; Madrid, Yolanda; Camara, Carmen [Departamento de Quimica Analitica, Facultad de Ciencias Quimicas, Universidad Complutense, 28040 Madrid (Spain)

    2002-10-01

    The stability of arsenic species {l_brace}arsenate [As(V)], monomethylarsonate [MMA], dimethylarsinate [DMA] and arsenite [As(III)]{r_brace} in two types of urban wastewater samples (raw and treated) was evaluated. Water samples containing a mixture of the different arsenic species were stored in the absence of light at three different temperatures: +4 C, +20 C and +40 C. At regular time intervals, arsenic species were determined by high performance liquid chromatography (HPLC)-hydride generation (HG)-atomic fluorescence spectrometry (AFS). The experimental conditions for the separation of arsenic species by HPLC and their determination by AFS were directly optimised from wastewater samples. As(III), As(V), MMA and DMA were separated on an anion exchange column using phosphate buffer (pH 6.0) as the mobile phase. Under these conditions the four arsenic species were separated in less than 10 min. The detection limits were 0.6, 0.9, 0.9 and 1.8 {mu}g L{sup -1} for As(III), DMA, MMA and As(V), respectively. As(V), MMA and DMA were found stable in the two types of urban wastewater samples over the 4-month period at the three different temperatures tested, while the concentration of As(III) in raw wastewater sample decreased after 2 weeks of storage. A greater stability of As(III) was found in the treated urban wastewater sample. As(III) remained unaltered in this matrix at pH 7.27 over the period studied, while at lower pH (1.6) losses of As(III) were detected after 1 month of storage. The results show that the decrease in As(III) concentration with time was accompanied by an increase in As(V) concentration. (orig.)

  4. Nickel replicas as calibration reference standards for industrial surface texture instruments

    DEFF Research Database (Denmark)

    Sammatini-Malberg, Maria-Pia

    The present report is a documentation of measurements carried out at DTU on Nickel replicas. The research is performed in the frame of the project with contract SMT4-CT97-2176 with title: Calibration Standards for Surface Topography Measuring Systems down to Nanometric Scale....

  5. Investigation of the Airflow inside Realistic and Semi-Realistic Replicas of Human Airways

    Directory of Open Access Journals (Sweden)

    Lizal Frantisek

    2015-01-01

    Full Text Available Measurement of velocity in human lungs during breathing cycle is a challenging task for researchers, since the measuring location is accessible only with significant difficulties. A special measuring rig consisting of optically transparent replica of human lungs, breathing simulator, particle generator and Laser-Doppler anemometer was developed and used for investigation of the velocity in specific locations of lungs during simulated breathing cycle. Experiments were performed on two different replicas of human lungs in corresponding measuring points to facilitate the analysis of the influence of the geometry and its simplification on the flow. The analysis of velocity course and turbulence intensity revealed that special attention should be devoted to the modelling of vocal cords position during breathing, as the position of laryngeal jet created by vocal cords significantly influences velocity profiles in trachea. The shapes of velocity courses during expiration proved to be consistent for both replicas; however magnitudes of peak expiratory velocity differ between the corresponding measuring points in both the replicas.

  6. Fast Optimal Replica Placement with Exhaustive Search Using Dynamically Reconfigurable Processor

    Directory of Open Access Journals (Sweden)

    Hidetoshi Takeshita

    2011-01-01

    Full Text Available This paper proposes a new replica placement algorithm that expands the exhaustive search limit with reasonable calculation time. It combines a new type of parallel data-flow processor with an architecture tuned for fast calculation. The replica placement problem is to find a replica-server set satisfying service constraints in a content delivery network (CDN. It is derived from the set cover problem which is known to be NP-hard. It is impractical to use exhaustive search to obtain optimal replica placement in large-scale networks, because calculation time increases with the number of combinations. To reduce calculation time, heuristic algorithms have been proposed, but it is known that no heuristic algorithm is assured of finding the optimal solution. The proposed algorithm suits parallel processing and pipeline execution and is implemented on DAPDNA-2, a dynamically reconfigurable processor. Experiments show that the proposed algorithm expands the exhaustive search limit by the factor of 18.8 compared to the conventional algorithm search limit running on a Neumann-type processor.

  7. Use of the femoral vein ('groin injecting' by a sample of needle exchange clients in Bristol, UK

    Directory of Open Access Journals (Sweden)

    Maliphant John

    2005-04-01

    Full Text Available Abstract Background Use of the femoral vein for intravenous access by injecting drug users (IDUs (commonly called 'groin injecting' is a practice that is often observed but on which little is written in the literature. The purpose of this study was to describe self-reported data from a sample of groin injectors on the natural history and rationale regarding their groin injecting, to inform future research and the development of appropriate harm reduction strategies. Methods A convenience sample of groin injectors willing to participate in a semi-structured interview were recruited through the Bristol Drugs Project Harm Reduction Service. The interviews were conducted over the period of one week. Data on transition to groin injecting, rationale for use and incidence of problems were collected. Results Forty seven IDUs currently injecting in their femoral vein ('groin' were interviewed, 66% (n = 31 male and 34% (n = 16 female. Their mean age was 31 yrs (range 17 to 50 yrs; SD = 7.7. The mean length of time since first injecting episode was 9.6 yrs (range 6 mths to 30 yrs; SD = 7.0. The mean length of time since use of the groin began was 2.6 years (range 1 mth to 15 yrs; SD = 3.3. The mean length of time between first injection and first use of the groin was 7.0 yrs (SD = 7.0. One person had used no other area for venous access prior to using the groin, nine people had used one, nine people had used two, 10 people had used three, five people had used four and 13 people had used more than four areas. The main reason given for starting to inject in the groin was that 'no other sites were left'. However further discussion identified this meant no other convenient sites were accessible. Practises such as the rotation of injecting sites, as advocated in many harm reduction leaflets, were reported to be difficult and unreliable. The risk of missing the vein and subsequently losing the 'hit' was considered high. Use of the non-dominant hand to administer

  8. MC ICP-MS δ(34)S(VCDT) measurement of dissolved sulfate in environmental aqueous samples after matrix separation by means of an anion exchange membrane.

    Science.gov (United States)

    Hanousek, Ondrej; Berger, Torsten W; Prohaska, Thomas

    2016-01-01

    Analysis of (34)S/(32)S of sulfate in rainwater and soil solutions can be seen as a powerful tool for the study of the sulfur cycle. Therefore, it is considered as a useful means, e.g., for amelioration and calibration of ecological or biogeochemical models. Due to several analytical limitations, mainly caused by low sulfate concentration in rainwater, complex matrix of soil solutions, limited sample volume, and high number of samples in ecosystem studies, a straightforward analytical protocol is required to provide accurate S isotopic data on a large set of diverse samples. Therefore, sulfate separation by anion exchange membrane was combined with precise isotopic measurement by multicollector inductively coupled plasma mass spectrometry (MC ICP-MS). The separation method proved to be able to remove quantitatively sulfate from matrix cations (Ca, K, Na, or Li) which is a precondition in order to avoid a matrix-induced analytical bias in the mass spectrometer. Moreover, sulfate exchange on the resin is capable of preconcentrating sulfate from low concentrated solutions (to factor 3 in our protocol). No significant sulfur isotope fractionation was observed during separation and preconcentration. MC ICP-MS operated at edge mass resolution has enabled the direct (34)S/(32)S analysis of sulfate eluted from the membrane, with an expanded uncertainty U (k = 2) down to 0.3 ‰ (a single measurement). The protocol was optimized and validated using different sulfate solutions and different matrix compositions. The optimized method was applied in a study on solute samples retrieved in a beech (Fagus sylvatica) forest in the Vienna Woods. Both rainwater (precipitation and tree throughfall) and soil solution δ (34)SVCDT ranged between 4 and 6 ‰, the ratio in soil solution being slightly lower. The lower ratio indicates that a considerable portion of the atmospherically deposited sulfate is cycled through the organic S pool before being released to the soil solution

  9. Coupling on-line preconcentration by ion-exchange with ETAAS. A novel flow injection approach based on the use of a renewable microcolumn as demonstrated for the determination of nickel in environmental and biological samples

    DEFF Research Database (Denmark)

    Wang, Jianhua; Hansen, Elo Harald

    2000-01-01

    A novel way of exploiting flow injection/sequential injection (FIA/SIA) on-line ion-exchange preconcentration with detection by electrothermal atomic absorption spectrometry (ETAAS) is described and demonstrated for the determination of trace-levels of nickel. Based on the use of a renewable...... microcolumn incorporated within an integrated micro FI-system, the column is loaded with a defined volume of small beads of an SP Sephadex C-25 cation-exchange resin and subsequently exposed to a metered amount of sample solution. However, instead of eluting the retained analyte from the organic ion-exchange...

  10. Chiral resolution of salbutamol in plasma sample by a new chiral ligand-exchange chromatography method after its extraction with nano-sized imprinted polymer.

    Science.gov (United States)

    Alizadeh, Taher; Shamkhali, Amir Naser

    2016-01-15

    A new chromatographic procedure, based upon chiral ligand-exchange principal, was developed for the resolution of salbutamol enantiomers. The separation was carried out on a C18 column. (l)-Alanine and Cu(2+) were applied as chiral resolving agent and complexing ion, respectively. The kind of copper salt had definitive effect on the enantioseparation. Density functional theory (DFT) was used to substantiate the effect of various anions, accompanying Cu(2+), on the formation of ternary complexes, assumed to be created during separation process. The DFT results showed that the anion kind had huge effect on the stability difference between two corresponding diastereomeric complexes and their chemical structures. It was shown that the extent of participation of the chiral selector in the ternary diastereomeric complexes formation was managed by the anion kind, affecting thus the enantioseparation efficiency of the developed method. Water/methanol (70:30) mixture containing (l)-alanine-Cu(2+) (4:1) was found to be the best mobile phase for salbutamol enantioseparation. In order to analyze sulbutamol enantiomers in plasma samples, racemic salbutamol was first extracted from the samples via nano-sized salbutamol-imprinted polymer and then enantioseparated by the developed method.

  11. Techniques of replica symmetry breaking and the storage problem of the McCulloch-Pitts neuron

    Science.gov (United States)

    Györgyi, G.

    2001-02-01

    In this article we review the framework for spontaneous replica symmetry breaking. Subsequently that is applied to the example of the statistical mechanical description of the storage properties of a McCulloch-Pitts neuron, i.e., simple perceptron. It is shown that in the neuron problem, the general formula that is at the core of all problems admitting Parisi's replica symmetry breaking ansatz with a one-component order parameter appears. The details of Parisi's method are reviewed extensively, with regard to the wide range of systems where the method may be applied. Parisi's partial differential equation and related differential equations are discussed, and the Green function technique is introduced for the calculation of replica averages, the key to determining the averages of physical quantities. The Green function of the Fokker-Planck equation due to Sompolinsky turns out to play the role of the statistical mechanical Green function in the graph rules for replica correlators. The subsequently obtained graph rules involve only tree graphs, as appropriate for a mean-field-like model. The lowest order Ward-Takahashi identity is recovered analytically and shown to lead to the Goldstone modes in continuous replica symmetry breaking phases. The need for a replica symmetry breaking theory in the storage problem of the neuron has arisen due to the thermodynamical instability of formerly given solutions. Variational forms for the neuron's free energy are derived in terms of the order parameter function x( q), for different prior distribution of synapses. Analytically in the high temperature limit and numerically in generic cases various phases are identified, among them is one similar to the Parisi phase in long-range interaction spin glasses. Extensive quantities like the error per pattern change slightly with respect to the known unstable solutions, but there is a significant difference in the distribution of non-extensive quantities like the synaptic overlaps and the

  12. How could the replica method improve accuracy of performance assessment of channel coding?

    Science.gov (United States)

    Kabashima, Yoshiyuki

    2009-12-01

    We explore the relation between the techniques of statistical mechanics and information theory for assessing the performance of channel coding. We base our study on a framework developed by Gallager in IEEE Trans. Inform. Theory IT-11, 3 (1965), where the minimum decoding error probability is upper-bounded by an average of a generalized Chernoff's bound over a code ensemble. We show that the resulting bound in the framework can be directly assessed by the replica method, which has been developed in statistical mechanics of disordered systems, whereas in Gallager's original methodology further replacement by another bound utilizing Jensen's inequality is necessary. Our approach associates a seemingly ad hoc restriction with respect to an adjustable parameter for optimizing the bound with a phase transition between two replica symmetric solutions, and can improve the accuracy of performance assessments of general code ensembles including low density parity check codes, although its mathematical justification is still open.

  13. Beyond Storage Capacity in a Single Model Neuron: Continuous Replica Symmetry Breaking

    Science.gov (United States)

    Györgyi, G.; Reimann, P.

    2000-10-01

    A single McCulloch-Pitts neuron, that is, the simple perceptron is studied, with focus on the region beyond storage capacity. It is shown that Parisi's hierarchical ansatz for the overlap matrix of the synaptic couplings with so called continuous replica symmetry breaking is a solution, and as we propose it is the exact one, to the equilibrium problem. We describe some of the most salient features of the theory and give results about the low temperature region. In particular, the basics of the Parisi technique and the way to calculate thermodynamical expectation values is explained. We have numerically extremized the replica free energy functional for some parameter settings, and thus obtained the order parameter function, i.e., the probability distribution of overlaps. That enabled us to evaluate the probability density of the local stability parameter. We also performed a simulation and found a local stability density closer to the theoretical curve than previous numerical results were.

  14. Evaluation of generalized degrees of freedom for sparse estimation by replica method

    Science.gov (United States)

    Sakata, A.

    2016-12-01

    We develop a method to evaluate the generalized degrees of freedom (GDF) for linear regression with sparse regularization. The GDF is a key factor in model selection, and thus its evaluation is useful in many modelling applications. An analytical expression for the GDF is derived using the replica method in the large-system-size limit with random Gaussian predictors. The resulting formula has a universal form that is independent of the type of regularization, providing us with a simple interpretation. Within the framework of replica symmetric (RS) analysis, GDF has a physical meaning as the effective fraction of non-zero components. The validity of our method in the RS phase is supported by the consistency of our results with previous mathematical results. The analytical results in the RS phase are calculated numerically using the belief propagation algorithm.

  15. Virtual Replica of Matter in Bivacuum & Possible Mechanism of Distant Mind - Matter and Mind - Mind Interaction

    CERN Document Server

    Kaivarainen, A

    2001-01-01

    The original mechanism of bivacuum mediated Mind-Matter and Mind-Mind interaction, proposed here, is based on the following stages of long term efforts: New dynamic models of bivacuum, sub-elementary particles and corpuscle-wave [C-W] duality, as a background of Superunification; New Hierarchic theory of liquids and solids; New Hierarchic model of elementary act of consciousness; Virtual Replica (VR)of matter, including living organisms, in bivacuum; The distant resonant [Mind-Bivacuum-Matter] and [Mind-Bivacuum-Mind] interaction, mediated by Bivacuum oscillation (BvO, accompanied by virtual particles/antiparticles pressure oscillation. The latter factor is related to oscillation of vacuum permittivity and permeability. The virtual replica (VR) of condensed matter (living organisms in private case), may influence the properties of virtual pressure of bivacuum in following manner: 1) changing the amplitude of virtual pressure waves (VPW) in-phase with Bivacuum oscillations (BvO). This factor is dependent on fr...

  16. Your Laptop to the Rescue: Using the Child Language Data Exchange System Archive and CLAN Utilities to Improve Child Language Sample Analysis.

    Science.gov (United States)

    Ratner, Nan Bernstein; MacWhinney, Brian

    2016-05-01

    In this article, we review the advantages of language sample analysis (LSA) and explain how clinicians can make the process of LSA faster, easier, more accurate, and more insightful than LSA done "by hand" by using free, available software programs such as Computerized Language Analysis (CLAN). We demonstrate the utility of CLAN analysis in studying the expressive language of a very large cohort of 24-month-old toddlers tracked in a recent longitudinal study; toddlers in particular are the most likely group to receive LSA by clinicians, but existing reference "norms" for this population are based on fairly small cohorts of children. Finally, we demonstrate how a CLAN utility such as KidEval can now extract potential normative data from the very large number of corpora now available for English and other languages at the Child Language Data Exchange System project site. Most of the LSA measures that we studied appear to show developmental profiles suggesting that they may be of specifically higher value for children at certain ages, because they do not show an even developmental trajectory from 2 to 7 years of age.

  17. PHYSICAL DISABILITY, STIGMA, AND PHYSICAL ACTIVITY IN CHILDREN: A REPLICA STUDY

    OpenAIRE

    Gebhardt, Markus; MORA Julio G.; SCHWAB Susanne

    2016-01-01

    Introduction: Stereotypes can be reduced through positive descriptions. A stigma that able-bodied adults have towards children with physical disability can be reduced when the child is portrayed as being active. The study found out that a sporty active child, who uses a wheelchair, is perceived as more competent than the sporty active able-bodied child. Objective: This study is a replica study to support the hypotheses and to examine the stereotypes of able-bodied adults towards children w...

  18. Impact of Channel Estimation Errors on Multiuser Detection via the Replica Method

    Directory of Open Access Journals (Sweden)

    Li Husheng

    2005-01-01

    Full Text Available For practical wireless DS-CDMA systems, channel estimation is imperfect due to noise and interference. In this paper, the impact of channel estimation errors on multiuser detection (MUD is analyzed under the framework of the replica method. System performance is obtained in the large system limit for optimal MUD, linear MUD, and turbo MUD, and is validated by numerical results for finite systems.

  19. Short-range Ising spin glasses: The metastate interpretation of replica symmetry breaking

    Science.gov (United States)

    Read, N.

    2014-09-01

    Parisi's formal replica-symmetry-breaking (RSB) scheme for mean-field spin glasses has long been interpreted in terms of many pure states organized ultrametrically. However, the early version of this interpretation, as applied to the short-range Edwards-Anderson model, runs into problems because as shown by Newman and Stein (NS) it does not allow for chaotic size dependence, and predicts non-self-averaging that cannot occur. NS proposed the concept of the metastate (a probability distribution over infinite-size Gibbs states in a given sample that captures the effects of chaotic size dependence) and a nonstandard interpretation of the RSB results in which the metastate is nontrivial and is responsible for what was called non-self-averaging. In this picture, each state drawn from the metastate has the ultrametric properties of the old theory, but when the state is averaged using the metastate, the resulting mixed state has little structure. This picture was constructed so as to agree both with the earlier RSB results and with rigorous results. Here we use the effective field theory of RSB, in conjunction with the rigorous definitions of pure states and the metastate in infinite-size systems, to show that the nonstandard picture follows directly from the RSB mean-field theory. In addition, the metastate-averaged state possesses power-law correlations throughout the low-temperature phase; the corresponding exponent ζ takes the value 4 according to the field theory in high dimensions d, and describes the effective fractal dimension of clusters of spins. Further, the logarithm of the number of pure states in the decomposition of the metastate-averaged state that can be distinguished if only correlations in a window of size W can be observed is of order Wd -ζ. These results extend the nonstandard picture quantitatively; we show that arguments against this scenario are inconclusive. More generally, in terms of Parisi's function q (x), if q(0)≠∫01dxq(x ), then the

  20. Evaluation of internal adaptation in ceramic and composite resin inlays by silicon replica technique.

    Science.gov (United States)

    Karakaya, S; Sengun, A; Ozer, F

    2005-06-01

    This study was aimed at investigating the internal adaptation of a ceramic (Ceramco II) and two composite resin inlay materials (SureFil and 3M Filtek Z 250) using silicon replica technique as an indicator. Forty-five standard mesial-occlusal-distal (MOD) cavities were prepared into brass moulds by using computer numerically controlled system. Inlays were prepared according to manufacturers' instructions with indirect methods. Replicas of the prepared cavities and inlays were produced with a polyvinyl siloxane material (Elite H-D). The spaces between inlays and cavities were filled by different coloured light-body polyvinyl siloxane material. Two parallel slices (mesio-distally) were obtained from the replicas with a sharp blade. Different coloured polyvinyl siloxane material thickness between cavity and inlay was measured at seven points (mesial, occlusal and distal). The data were evaluated with anova and Tukey's honestly significantly different (HSD) statistical tests. In the SureFil and Ceramco II groups, the sizes of the contraction gaps at mesial and distal gingival floors were greater than that of the occlusal marginal walls. In comparison of gap formation at occlusal regions, while the 3M composite group showed highest gap values (204.33 +/- 75.45 microm), the Ceramco II group revealed the lowest (141.17 +/- 23.66 microm) (P 0.05). In conclusion, our results showed that ceramic inlays did not confer any big advantage for internal adaptation over the composite inlays.

  1. Recent advances in fabrication of monolayer colloidal crystals and their inverse replicas

    Institute of Scientific and Technical Information of China (English)

    YE XiaoZhou; QI LiMin

    2014-01-01

    Monolayer colloidal crystals(MCCs)are two-dimensional(2D)colloidal crystals consisting of a monolayer of monodisperse colloidal particles arrayed with a 2D periodic order.In recent years,MCCs have attracted intensive interest because they can act as 2D photonic crystals and be used as versatile templates for fabrication of various 2D nanostructure arrays.In this review,we provide an overview of the recent progress in the controllable fabrication of MCCs and their inverse replicas.First,some newly-developed methods for the self-assembly of MCCs based on different strategies including interfacial assembly and convective assembly are introduced.Second,some representative novel methods regarding the fabrication of various functional2D inverse replicas of MCCs,such as 2D arrays of nanobowls,nanocaps,and hollow spheres,as well as 2D monolayer inverse opals(MIOs),are described.In addition,the potential applications of MCCs and their inverse replicas are discussed.

  2. Characterization of Nb SRF cavity materials by white light interferometry and replica techniques

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Chen [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States); Reece, Charles [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); Kelley, Michael, E-mail: mkelley@jlab.org [Thomas Jefferson National Accelerator Facility, Newport News, VA 23606 (United States); The Applied Science Department, The College of William and Mary, Williamsburg, VA 23185 (United States)

    2013-06-01

    Much work has shown that the topography of the interior surface is an important contributor to the performance of Nb superconducting radiofrequency (SRF) accelerator cavities. Micron-scale topography is implicated in non-linear loss mechanisms that limit the useful accelerating gradient range and impact cryogenic cost. Aggressive final chemical treatments in cavity production seek to reliably obtain “smoothest” surfaces with superior performance. Process development suffers because the cavity interior surface cannot be viewed directly without cutting out pieces, rendering the cavities unavailable for further study. Here we explore replica techniques as an alternative, providing imprints of cavity internal surface that can be readily examined. A second matter is the topography measurement technique used. Atomic force microscopy (AFM) has proven successful, but too time intensive for routine use in this application. We therefore introduce white light interferometry (WLI) as an alternative approach. We examined real surfaces and their replicas, using AFM and WLI. We find that the replica/WLI is promising to provide the large majority of the desired information, recognizing that a trade-off is being made between best lateral resolution (AFM) and the opportunity to examine much more surface area (WLI).

  3. Biosynthesis of cathodoluminescent zinc oxide replicas using butterfly (Papilio paris) wing scales as templates

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Wang [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Zhang Di [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China)], E-mail: zhangdi@sjtu.edu.cn; Fan Tongxiang; Ding Jian; Gu Jiajun [State Key Lab of Metal Matrix Composites, Shanghai Jiao Tong University, 200240, Shanghai (China); Guo Qixin; Ogawa, Hiroshi [Department of Electrical and Electronic Engineering, Saga University, Saga 840-8502 (Japan)

    2009-01-01

    Papilio paris butterflies have an iridescent blue color patch on their hind wings which is visible over a wide viewing angle. Optical and scanning electron microscopy observations of scales from the wings show that the blue color scales have very different microstructure to the matt black ones which also populate the wings. Scanning electron micrographs of the blue scales show that their surfaces comprise a regular two-dimensional array of concavities. By contrast the matt black scales have fine, sponge-like structure, between the ridges and the cross ribs in the scales. Using both types of scale as bio-templates, we obtain zinc oxide (ZnO) replicas of the microstructures of the original scales. Room temperature (T = 300 K) cathodoluminescence spectra of these ZnO replicas have also been studied. Both spectra show a similar sharp near-band-edge emission, but have different green emission, which we associate with the different microstructures of the ZnO replicas.

  4. Photovoltaic performance of nanoporous TiO2 replicas synthesized from mesoporous materials for dye-sensitized solar cells.

    Science.gov (United States)

    Hwang, Kyung-Jun; Yoo, Seung-Joon; Kim, Sung-Soo; Kim, Ji-Man; Shim, Wang-Geun; Kim, Sun-Il; Lee, Jae-Wook

    2008-10-01

    For dye-sensitized solar cell (DSSC), highly ordered nanoporous TiO2 materials with crystalline frameworks were successfully synthesized from different silica templates including SBA-15, KIT-6 and MSU-H. A photoelectrode in DSSC was fabricated by adsorbing cis-bis(isothiocyanato)bis(2,2'-bipyridyl-4,4'-dicarboxylato)-ruthenium(II)bis-tetrabutylammonium dye (N719) onto the prepared TiO2 nanoparticles. The samples were characterized by XRD, TEM, FE-SEM, AFM and Brunauer-Emmett-Teller (BET), and FT-IR analysis. An investigation of the influence of the bonding structure of N719 dye and nanoporous TiO2 on the photovoltaic performance of DSSC revealed that the bonding structure of N719 on TiO2 films is caused by the unidentate and bidentate linkage. Based on the overall conversion efficiency (eta), fill factor (FF), open-circuit voltage (V(oc)) and short-circuit current (/sc) from the I-V curves measured, it was observed that the photoelectric performance is strongly dependent on the dispersion properties of the nanoporous TiO2 replicas from mesoporous silica templates.

  5. Recommendations for replica testing of high temperature components in power plant; Rekommendationer foer replikprovning av hoegtemperaturkomponenter i kraftanlaeggningar

    Energy Technology Data Exchange (ETDEWEB)

    Storesund, Jan [Det Norske Veritas AB, Stockholm (Sweden)

    2000-08-01

    Replica testing is a non-destructive testing method where the microstructure of the surface of a component is replicated. This involves careful metallographical preparation which in some points also should be adapted to the aims of the investigation. There are published guidelines for replica testing of high temperature components in power plant, for instance by Nordtest, but these may be considered to be insufficient to assure the required quality and reproducibility of the replicas. There are no certification systems for the replica method in Sweden as well as abroad and the experience has shown that differences in the performance that existing praxis can involve may give significant influence on the results when the replicas are evaluated. In the present project recommendations have been compiled for replica testing with regard to creep damage on occurring heat resistant steel types in Swedish power plants. The recommendations consist of guidelines for metallographical replication in the field and cover: - Test positions at weldments and pipe bends; - Equipment; - Rough and fine grinding; - Macro-etching; - Electrolytic and mechanical polishing; - Etching; - Replication; - Documentation and storage; - Personnel. They describe differences in the testing of the different materials and the purpose is to assure replica testing of the highest quality and reproducibility. The recommendations have been compiled by use of guidelines and company standards as a starting point. Some points in the recommendations refer to trials for verification which have been carried out within the frame of the project. The trials have been focused on the appearance of creep damage and microstructure in different established methods for polishing and etching. Comments and closer descriptions for some points of the test procedures are given in an appendix to the recommendations.

  6. Inferring predator behavior from attack rates on prey-replicas that differ in conspicuousness.

    Directory of Open Access Journals (Sweden)

    Yoel E Stuart

    Full Text Available Behavioral ecologists and evolutionary biologists have long studied how predators respond to prey items novel in color and pattern. Because a predatory response is influenced by both the predator's ability to detect the prey and a post-detection behavioral response, variation among prey types in conspicuousness may confound inference about post-prey-detection predator behavior. That is, a relatively high attack rate on a given prey type may result primarily from enhanced conspicuousness and not predators' direct preference for that prey. Few studies, however, account for such variation in conspicuousness. In a field experiment, we measured predation rates on clay replicas of two aposematic forms of the poison dart frog Dendrobates pumilio, one novel and one familiar, and two cryptic controls. To ask whether predators prefer or avoid a novel aposematic prey form independently of conspicuousness differences among replicas, we first modeled the visual system of a typical avian predator. Then, we used this model to estimate replica contrast against a leaf litter background to test whether variation in contrast alone could explain variation in predator attack rate. We found that absolute predation rates did not differ among color forms. Predation rates relative to conspicuousness did, however, deviate significantly from expectation, suggesting that predators do make post-detection decisions to avoid or attack a given prey type. The direction of this deviation from expectation, though, depended on assumptions we made about how avian predators discriminate objects from the visual background. Our results show that it is important to account for prey conspicuousness when investigating predator behavior and also that existing models of predator visual systems need to be refined.

  7. Time-reversal focusing of an expanding soliton gas in disordered replicas

    KAUST Repository

    Fratalocchi, Andrea

    2011-05-31

    We investigate the properties of time reversibility of a soliton gas, originating from a dispersive regularization of a shock wave, as it propagates in a strongly disordered environment. An original approach combining information measures and spin glass theory shows that time-reversal focusing occurs for different replicas of the disorder in forward and backward propagation, provided the disorder varies on a length scale much shorter than the width of the soliton constituents. The analysis is performed by starting from a new class of reflectionless potentials, which describe the most general form of an expanding soliton gas of the defocusing nonlinear Schrödinger equation.

  8. Chiral-glass transition and replica symmetry breaking of a three-dimensional heisenberg spin glass

    Science.gov (United States)

    Hukushima; Kawamura

    2000-02-01

    Extensive equilibrium Monte Carlo simulations are performed for a three-dimensional Heisenberg spin glass with the nearest-neighbor Gaussian coupling to investigate its spin-glass and chiral-glass orderings. The occurrence of a finite-temperature chiral-glass transition without the conventional spin-glass order is established. Critical exponents characterizing the transition are different from those of the standard Ising spin glass. The calculated overlap distribution suggests the appearance of a peculiar type of replica-symmetry breaking in the chiral-glass ordered state.

  9. Replica symmetry breaking transition of the weakly anisotropic Heisenberg spin glass in magnetic fields.

    Science.gov (United States)

    Imagawa, Daisuke; Kawamura, Hikaru

    2004-02-20

    The spin and the chirality orderings of the three-dimensional Heisenberg spin glass with the weak random anisotropy are studied under applied magnetic fields by equilibrium Monte Carlo simulations. A replica symmetry breaking transition occurs in the chiral sector accompanied by the simultaneous spin-glass order. The ordering behavior differs significantly from that of the Ising spin glass, despite the similarity in the global symmetry. Our observation is consistent with the spin-chirality decoupling-recoupling scenario of a spin-glass transition.

  10. Investigation on a replica step gauge for optical 3D scanning of micro parts

    DEFF Research Database (Denmark)

    Cantatore, Angela; De Chiffre, Leonardo; Carmignato, S.

    2010-01-01

    . The stability over time of the step gauge was evaluated by repetitive measurement campaigns over a period of eight months, using measurements taken with a tactile CMM and with an optical scanner. Surface cooperativeness was investigated by measuring artefact grooves and pitch and comparing results with tactile......This work deals with investigation of the stability over time and surface cooperativeness of a calibration artefact intended for optical scanner verification. A replica step gauge with 11 grooves, made of bisacryl material for dental applications (luxabite) and previously fabricated was studied...

  11. Anti-stiction coating of PDMS moulds for rapid microchannel fabrication by double replica moulding

    DEFF Research Database (Denmark)

    Zhuang, Guisheng; Kutter, Jörg Peter

    2011-01-01

    ), which resulted in an anti-stiction layer for the improved release after PDMS casting. The deposition of FDTS on an O2 plasma-activated surface of PDMS produced a reproducible and well-performing anti-stiction monolayer of fluorocarbon, and we used the FDTS-coated moulds as micro-masters for rapid......In this paper, we report a simple and precise method to rapidly replicate master structures for fast microchannel fabrication by double replica moulding of polydimethylsiloxane (PDMS). A PDMS mould was surface-treated by vapour phase deposition of 1H,1H,2H,2H-perfluorodecyltrichlorosilane (FDTS...

  12. Photonic ferromagnetic-like spontaneous mode-locking phase transition with replica symmetry breaking in multimode Nd:YAG laser

    CERN Document Server

    Moura, André L; Raposo, Ernesto P; Gomes, Anderson S L; de Araújo, Cid B

    2016-01-01

    The recent reports of the replica symmetry breaking (RSB) phenomenon in photonic experiments [1-5] boosted the understanding of the role of disorder in multimode lasers, as well as helped to settle enlightening connections [6-13] with the statistical physics of complex systems. RSB manifests when identically-prepared system replicas reach distinct states, yielding different measures of observable quantities [14]. Here we demonstrate the RSB in the spontaneous mode-locking regime of a conventional multimode Nd:YAG laser in a closed cavity. The underlying mechanism is quite distinct from that of the RSB spinglass phase in cavityless random lasers with incoherently-oscillating modes. Here, a specific nonuniform distribution of the gain takes place in each pulse, and frustration is induced since the coherent oscillation of a given subset of longitudinal modes dominates and simultaneously inhibits the others. Nevertheless, when high losses are introduced only the replica-symmetric amplified stimulation emission is...

  13. Flow field analysis in a compliant acinus replica model using particle image velocimetry (PIV).

    Science.gov (United States)

    Berg, Emily J; Weisman, Jessica L; Oldham, Michael J; Robinson, Risa J

    2010-04-19

    Inhaled particles reaching the alveolar walls have the potential to cross the blood-gas barrier and enter the blood stream. Experimental evidence of pulmonary dosimetry, however, cannot be explained by current whole lung dosimetry models. Numerical and experimental studies shed some light on the mechanisms of particle transport, but realistic geometries have not been investigated. In this study, a three dimensional expanding model including two generations of respiratory bronchioles and five terminal alveolar sacs was created from a replica human lung cast. Flow visualization techniques were employed to quantify the fluid flow while utilizing streamlines to evaluate recirculation. Pathlines were plotted to track the fluid motion and estimate penetration depth of inhaled air. This study provides evidence that the two generations immediately proximal to the terminal alveolar sacs do not have recirculating eddies, even for intense breathing. Results of Peclet number calculations indicate that substantial convective motion is present in vivo for the case of deep breathing, which significantly increases particle penetration into the alveoli. However, particle diffusion remains the dominant mechanism of particle transport over convection, even for intense breathing because inhaled particles do not reach the alveolar wall in a single breath by convection alone. Examination of the velocity fields revealed significant uneven ventilation of the alveoli during a single breath, likely due to variations in size and location. This flow field data, obtained from replica model geometry with realistic breathing conditions, provides information to better understand fluid and particle behavior in the acinus region of the lung.

  14. Manufacture of patient-specific vascular replicas for endovascular simulation using fast, low-cost method

    Science.gov (United States)

    Kaneko, Naoki; Mashiko, Toshihiro; Ohnishi, Taihei; Ohta, Makoto; Namba, Katsunari; Watanabe, Eiju; Kawai, Kensuke

    2016-12-01

    Patient-specific vascular replicas are essential to the simulation of endovascular treatment or for vascular research. The inside of silicone replica is required to be smooth for manipulating interventional devices without resistance. In this report, we demonstrate the fabrication of patient-specific silicone vessels with a low-cost desktop 3D printer. We show that the surface of an acrylonitrile butadiene styrene (ABS) model printed by the 3D printer can be smoothed by a single dipping in ABS solvent in a time-dependent manner, where a short dip has less effect on the shape of the model. The vascular mold is coated with transparent silicone and then the ABS mold is dissolved after the silicone is cured. Interventional devices can pass through the inside of the smoothed silicone vessel with lower pushing force compared to the vessel without smoothing. The material cost and time required to fabricate the silicone vessel is about USD $2 and 24 h, which is much lower than the current fabrication methods. This fast and low-cost method offers the possibility of testing strategies before attempting particularly difficult cases, while improving the training of endovascular therapy, enabling the trialing of new devices, and broadening the scope of vascular research.

  15. PHYSICAL DISABILITY, STIGMA, AND PHYSICAL ACTIVITY IN CHILDREN: A REPLICA STUDY

    Directory of Open Access Journals (Sweden)

    Markus GEBHARDT

    2016-04-01

    Full Text Available Introduction: Stereotypes can be reduced through positive descriptions. A stigma that able-bodied adults have towards children with physical disability can be reduced when the child is portrayed as being active. The study found out that a sporty active child, who uses a wheelchair, is perceived as more competent than the sporty active able-bodied child. Objective: This study is a replica study to support the hypotheses and to examine the stereotypes of able-bodied adults towards children with and without (physical disabilities. Methods: This study presents two experimental replica studies using a 2 (physical activity x 2 (sporty activities. The dependent variables were the perception of competencies and warmth according to Stereotype Content Model (SCM. Study 1 is an online experiment with 355 students of the Open University of Hagen. Study 2 surveys 1176 participants (from Munich and Graz with a paper-pencil-questionnaire. Results: The significant interaction effect was not supported by our studies. The sporty able-bodied child was rated higher in competences than the sporty child, who use a wheelchair. Sporting activity only reduces the stigma towards children with a physical disability slightly. Conclusion: The stigma towards children with physical disability can be reduced when the child is portrayed as being active, but the effect was not strong enough to chance the original classification by the SCM.

  16. In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands.

    Directory of Open Access Journals (Sweden)

    Anna Russo

    Full Text Available Short peptides can be designed in silico and synthesized through automated techniques, making them advantageous and versatile protein binders. A number of docking-based algorithms allow for a computational screening of peptides as binders. Here we developed ex-novo peptides targeting the maltose site of the Maltose Binding Protein, the prototypical system for the study of protein ligand recognition. We used a Monte Carlo based protocol, to computationally evolve a set of octapeptides starting from a polialanine sequence. We screened in silico the candidate peptides and characterized their binding abilities by surface plasmon resonance, fluorescence and electrospray ionization mass spectrometry assays. These experiments showed the designed binders to recognize their target with micromolar affinity. We finally discuss the obtained results in the light of further improvement in the ex-novo optimization of peptide based binders.

  17. Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle.

    Science.gov (United States)

    Cavalli, Andrea; Camilloni, Carlo; Vendruscolo, Michele

    2013-03-07

    In order to characterise the dynamics of proteins, a well-established method is to incorporate experimental parameters as replica-averaged structural restraints into molecular dynamics simulations. Here, we justify this approach in the case of interproton distance information provided by nuclear Overhauser effects by showing that it generates ensembles of conformations according to the maximum entropy principle. These results indicate that the use of replica-averaged structural restraints in molecular dynamics simulations, given a force field and a set of experimental data, can provide an accurate approximation of the unknown Boltzmann distribution of a system.

  18. Research on the Effect of Exchange Rate on Outward Foreign Direct Investment: Based on China's Sample%对外直接投资中的汇率影响因素:中国样本

    Institute of Scientific and Technical Information of China (English)

    陶士贵; 相瑞

    2012-01-01

    With the huge increase of FDI ( Foreign exchange reserves), China begins to accelerate the development strategy of "going out", and foreign direct investment grows rapidly. According to the Ministry of Commerce of the People's Republic of China statistics, Chinese domestic investors, direct investment total of 129 countries and regions around the world 3125 foreign enterprises in 2010, total non-financial direct investment of $ 59 billion, an increase of 36.3% in 2010. China's total non-financial foreign direct investment had reached $ 258.8 billion until the end of 2010. Turnover of overseas contracted projects reached $ 92. 2 billion in 2010 which has an increase of 18.7 percent compared with last year. From the existing research, many foreign scholars attempt to connect exchange rate with FDI, but most articles study the developed countries, the conclusions also vary widely. Most of the domestic papers research the influence of fluctuations in the RMB exchange rate for China attracting FDI, the studies of reverse direct investment in China are less, and research priorities focus on location choice of FDI. The research to connect RMB exchange rate with FDI are also less, and more emphasis on theoretical study and simple mathematical model. Exchange rate movements from changes in investment costs and financing costs, changes in exports, changes in relative wealth, as well as the capitalization rate of change in four aspects affect a country's foreign direct investment. We use panel data model to estimate the data before and after the RMB exchange rate in 2005 (Sample spacing: 2002 - 2009) for the influence of RMB real exchange rate on Chinese foreign direct investment. The result demonstrates to us that, along with the appreciation of the RMB, outward direct investment flow of china is increasing, which is positively correlated with RMB real exchange rate. After the second reform of RMB exchange rate in 2005, Chinese foreign direct investment

  19. Analysis and optimization of weighted ensemble sampling

    CERN Document Server

    Aristoff, David

    2016-01-01

    We give a mathematical framework for weighted ensemble (WE) sampling, a binning and resampling technique for efficiently computing probabilities in molecular dynamics. We prove that WE sampling is unbiased in a very general setting that includes adaptive binning. We show that when WE is used for stationary calculations in tandem with a Markov state model (MSM), the MSM can be used to optimize the allocation of replicas in the bins.

  20. Generic, hierarchical framework for massively parallel Wang-Landau sampling.

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P

    2013-05-24

    We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models including spin glasses, the Ising model, and the Potts model, lattice protein adsorption, and the self-assembly process in amphiphilic solutions. Without loss of accuracy, the method gives significant speed-up and potentially scales up to petaflop machines.

  1. Generic, Hierarchical Framework for Massively Parallel Wang-Landau Sampling

    Science.gov (United States)

    Vogel, Thomas; Li, Ying Wai; Wüst, Thomas; Landau, David P.

    2013-05-01

    We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models including spin glasses, the Ising model, and the Potts model, lattice protein adsorption, and the self-assembly process in amphiphilic solutions. Without loss of accuracy, the method gives significant speed-up and potentially scales up to petaflop machines.

  2. A generic, hierarchical framework for massively parallel Wang Landau sampling

    Energy Technology Data Exchange (ETDEWEB)

    Vogel, Thomas [University of Georgia, Athens, GA; Li, Ying Wai [ORNL; Wuest, Thomas [Swiss Federal Research Institute, Switzerland; Landau, David P [University of Georgia, Athens, GA

    2013-01-01

    We introduce a parallel Wang Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of com- plex systems, we apply it to the self-assembly process in amphiphilic solutions and to lattice protein adsorption. Without loss of accuracy, the method gives significant speed-up on small architectures like multi-core processors, and should be beneficial for petaflop machines.

  3. Partitioning net ecosystem carbon exchange into net assimilation and respiration using 13CO2 measurements: A cost-effective sampling strategy

    Science.gov (United States)

    OgéE, J.; Peylin, P.; Ciais, P.; Bariac, T.; Brunet, Y.; Berbigier, P.; Roche, C.; Richard, P.; Bardoux, G.; Bonnefond, J.-M.

    2003-06-01

    The current emphasis on global climate studies has led the scientific community to set up a number of sites for measuring the long-term biosphere-atmosphere net CO2 exchange (net ecosystem exchange, NEE). Partitioning this flux into its elementary components, net assimilation (FA), and respiration (FR), remains necessary in order to get a better understanding of biosphere functioning and design better surface exchange models. Noting that FR and FA have different isotopic signatures, we evaluate the potential of isotopic 13CO2 measurements in the air (combined with CO2 flux and concentration measurements) to partition NEE into FR and FA on a routine basis. The study is conducted at a temperate coniferous forest where intensive isotopic measurements in air, soil, and biomass were performed in summer 1997. The multilayer soil-vegetation-atmosphere transfer model MuSICA is adapted to compute 13CO2 flux and concentration profiles. Using MuSICA as a "perfect" simulator and taking advantage of the very dense spatiotemporal resolution of the isotopic data set (341 flasks over a 24-hour period) enable us to test each hypothesis and estimate the performance of the method. The partitioning works better in midafternoon when isotopic disequilibrium is strong. With only 15 flasks, i.e., two 13CO2 nighttime profiles (to estimate the isotopic signature of FR) and five daytime measurements (to perform the partitioning) we get mean daily estimates of FR and FA that agree with the model within 15-20%. However, knowledge of the mesophyll conductance seems crucial and may be a limitation to the method.

  4. Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

    Science.gov (United States)

    Miao, Yinglong; McCammon, J Andrew

    Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

  5. Instituto de Fisica, UFRGS, CP 15051, 91501-970, Porto Alegre RS, Brazil: Replica theory of granular media

    Science.gov (United States)

    Arenzon, Jeferson J.

    1999-03-01

    An infinite range spin-glass-like model for granular systems is introduced and studied through the replica mean-field formalism. Equilibrium, density-dependent properties under vibration and gravity are obtained that qualitatively resemble the results from real and numerical experiments.

  6. Validation of airway resistance models for predicting pressure loss through anatomically realistic conducting airway replicas of adults and children.

    Science.gov (United States)

    Borojeni, Azadeh A T; Noga, Michelle L; Martin, Andrew R; Finlay, Warren H

    2015-07-16

    This work describes in vitro measurement of the total pressure loss at varying flow rate through anatomically realistic conducting airway replicas of 10 children, 4 to 8 years old, and 5 adults. Experimental results were compared with analytical predictions made using published airway resistance models. For the adult replicas, the model proposed by van Ertbruggen et al. (2005. J. Appl. Physiol. 98, 970-980) most accurately predicted central conducting airway resistance for inspiratory flow rates ranging from 15 to 90 L/min. Models proposed by Pedley et al. (1970. J. Respir. Physiol. 9, 371-386) and by Katz et al. (2011. J. Biomech. 44, 1137-1143) also provided reasonable estimates, but with a tendency to over predict measured pressure loss for both models. For child replicas, the Pedley and Katz models both provided good estimation of measured pressure loss at flow rates representative of resting tidal breathing, but under predicted measured values at high inspiratory flow rate (60 L/min). The van Ertbruggen model, developed based on flow simulations performed in an adult airway model, tended to under predict measured pressure loss through the child replicas across the range of flow rates studied (2 to 60 L/min). These results are intended to provide guidance for selection of analytical pressure loss models for use in predicting airway resistance and ventilation distribution in adults and children. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Sealant retention is better assessed through colour photographs than through the replica and the visual examination methods

    NARCIS (Netherlands)

    Hu, X.; Fan, M.; Rong, W.; Lo, E.C.; Bronkhorst, E.M.; Frencken, J.E.F.M.

    2014-01-01

    The aim of this study was to test the hypothesis that the colour photograph method has a higher level of validity for assessing sealant retention than the visual clinical examination and replica methods. Sealed molars were assessed by two evaluators. The scores for the three methods were compared ag

  8. Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge

    Science.gov (United States)

    Ding, Chao; Yang, Lijun; Wu, Meng

    2017-01-01

    Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies. PMID:28098846

  9. Localization-Free Detection of Replica Node Attacks in Wireless Sensor Networks Using Similarity Estimation with Group Deployment Knowledge.

    Science.gov (United States)

    Ding, Chao; Yang, Lijun; Wu, Meng

    2017-01-15

    Due to the unattended nature and poor security guarantee of the wireless sensor networks (WSNs), adversaries can easily make replicas of compromised nodes, and place them throughout the network to launch various types of attacks. Such an attack is dangerous because it enables the adversaries to control large numbers of nodes and extend the damage of attacks to most of the network with quite limited cost. To stop the node replica attack, we propose a location similarity-based detection scheme using deployment knowledge. Compared with prior solutions, our scheme provides extra functionalities that prevent replicas from generating false location claims without deploying resource-consuming localization techniques on the resource-constraint sensor nodes. We evaluate the security performance of our proposal under different attack strategies through heuristic analysis, and show that our scheme achieves secure and robust replica detection by increasing the cost of node replication. Additionally, we evaluate the impact of network environment on the proposed scheme through theoretic analysis and simulation experiments, and indicate that our scheme achieves effectiveness and efficiency with substantially lower communication, computational, and storage overhead than prior works under different situations and attack strategies.

  10. The 2003 Goddard Rocket Replica Project: A Reconstruction of the World's First Functional Liquid Rocket System

    Science.gov (United States)

    Farr, R. A.; Elam, S. K.; Hicks, G. D.; Sanders, T. M.; London, J. R.; Mayne, A. W.; Christensen, D. L.

    2003-01-01

    As a part of NASA s 2003 Centennial of Flight celebration, engineers and technicians at Marshall Space Flight Center (MSFC), Huntsville, Alabama, in cooperation with the Alabama-Mississippi AIAA Section, have reconstructed historically accurate, functional replicas of Dr. Robert H. Goddard s 1926 first liquid- fuel rocket. The purposes of this project were to clearly understand, recreate, and document the mechanisms and workings of the 1926 rocket for exhibit and educational use, creating a vital resource for researchers studying the evolution of liquid rocketry for years to come. The MSFC team s reverse engineering activity has created detailed engineering-quality drawings and specifications describing the original rocket and how it was built, tested, and operated. Static hot-fire tests, as well as flight demonstrations, have further defined and quantified the actual performance and engineering actual performance and engineering challenges of this major segment in early aerospace history.

  11. Statistical mechanics of the denatured state of a protein using replica-averaged metadynamics.

    Science.gov (United States)

    Camilloni, Carlo; Vendruscolo, Michele

    2014-06-25

    The characterization of denatured states of proteins is challenging because the lack of permanent structure in these states makes it difficult to apply to them standard methods of structural biology. In this work we use all-atom replica-averaged metadynamics (RAM) simulations with NMR chemical shift restraints to determine an ensemble of structures representing an acid-denatured state of the 86-residue protein ACBP. This approach has enabled us to reach convergence in the free energy landscape calculations, obtaining an ensemble of structures in relatively accurate agreement with independent experimental data used for validation. By observing at atomistic resolution the transient formation of native and non-native structures in this acid-denatured state of ACBP, we rationalize the effects of single-point mutations on the folding rate, stability, and transition-state structures of this protein, thus characterizing the role of the unfolded state in determining the folding process.

  12. Shear modulus of glasses: results from the full replica-symmetry-breaking solution.

    Science.gov (United States)

    Yoshino, Hajime; Zamponi, Francesco

    2014-08-01

    We compute the shear modulus of amorphous hard and soft spheres, using the exact solution in infinite spatial dimensions that has been developed recently. We characterize the behavior of this observable in the whole phase diagram, and in particular around the glass and jamming transitions. Our results are consistent with other theoretical approaches, which are unified within this general picture, and they are also consistent with numerical and experimental results. Furthermore, we discuss some properties of the out-of-equilibrium dynamics after a deep quench close to the jamming transition, and we show that a combined measure of the shear modulus and of the mean square displacement allows one to probe experimentally the complex structure of phase space predicted by the full replica-symmetry-breaking solution.

  13. Coexistence of Replica Bands and Superconductivity in FeSe Monolayer Films

    Science.gov (United States)

    Rebec, S. N.; Jia, T.; Zhang, C.; Hashimoto, M.; Lu, D.-H.; Moore, R. G.; Shen, Z.-X.

    2017-02-01

    To elucidate the mechanisms behind the enhanced Tc in monolayer (1 ML) FeSe on SrTiO3 (STO), we grew highly strained 1 ML FeSe on the rectangular (100) face of rutile TiO2 , and observed the coexistence of replica bands and superconductivity with a Tc of 63 K. From the similar Tc between this system and 1ML FeSe on STO (001), we conclude that strain and dielectric constant are likely unimportant to the enhanced Tc in these systems. A systematic comparison of 1 ML FeSe on TiO2 with other systems in the FeSe family shows that while charge transfer alone can enhance Tc, it is only with the addition of interfacial electron-phonon coupling that Tc can be increased to the level seen in 1 ML FeSe on STO.

  14. Orientational glass: Full replica symmetry breaking in generalized spin glass-like models without reflection symmetry

    Energy Technology Data Exchange (ETDEWEB)

    Tareyeva, E.E. [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); Schelkacheva, T.I., E-mail: tanschelk@gmail.com [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); Chtchelkatchev, N.M. [Institute for High Pressure Physics, Russian Academy of Sciences, 142190 Troitsk (Russian Federation); L.D. Landau Institute for Theoretical Physics, Russian Academy of Sciences, 117940 Moscow (Russian Federation); Department of Theoretical Physics, Moscow Institute of Physics and Technology, 141700 Moscow (Russian Federation)

    2013-02-15

    We investigate near the point of glass transition the expansion of the free energy corresponding to the generalized Sherrington–Kirkpatrick model with arbitrary diagonal operators U{sup -hat} standing instead of Ising spins. We focus on the case when U{sup -hat} is an operator with broken reflection symmetry. Such a consideration is important for understanding the behavior of spin glass-like phases in a number of real physical systems, mainly in orientational glasses in mixed molecular crystals which present just the case. We build explicitly a full replica symmetry breaking (FRSB) solution of the equations for the orientational glass order parameters when the nonsymmetric part of U{sup -hat} is small. This particular result presents a counterexample in the context of usually adopted conjecture of the absence of FRSB solution in systems with no reflection symmetry.

  15. Behavioural responses of dogs to asymmetrical tail wagging of a robotic dog replica.

    Science.gov (United States)

    Artelle, K A; Dumoulin, L K; Reimchen, T E

    2011-03-01

    Recent evidence suggests that bilateral asymmetry in the amplitude of tail wagging of domestic dogs (Canis familiaris) is associated with approach (right wag) versus withdrawal (left wag) motivation and may be the by-product of hemispheric dominance. We consider whether such asymmetry in motion of the tail, a crucial appendage in intra-specific communication in all canids, provides visual information to a conspecific leading to differential behaviour. To evaluate this, we experimentally investigated the approach behaviour of free-ranging dogs to the asymmetric tail wagging of a life-size robotic dog replica. Our data, involving 452 separate interactions, showed a significantly greater proportion of dogs approaching the model continuously without stopping when the tail wagged to the left, compared with a right wag, which was more likely to yield stops. While the results indicate that laterality of a wagging tail provides behavioural information to conspecifics, the responses are not readily integrated into the predicted behaviour based on hemispheric dominance.

  16. Orientational glass: Full replica symmetry breaking in generalized spin glass-like models without reflection symmetry

    Science.gov (United States)

    Tareyeva, E. E.; Schelkacheva, T. I.; Chtchelkatchev, N. M.

    2013-02-01

    We investigate near the point of glass transition the expansion of the free energy corresponding to the generalized Sherrington-Kirkpatrick model with arbitrary diagonal operators Uˆ standing instead of Ising spins. We focus on the case when Uˆ is an operator with broken reflection symmetry. Such a consideration is important for understanding the behavior of spin glass-like phases in a number of real physical systems, mainly in orientational glasses in mixed molecular crystals which present just the case. We build explicitly a full replica symmetry breaking (FRSB) solution of the equations for the orientational glass order parameters when the nonsymmetric part of Uˆ is small. This particular result presents a counterexample in the context of usually adopted conjecture of the absence of FRSB solution in systems with no reflection symmetry.

  17. Pion emission from the T2K replica target: method, results and application

    CERN Document Server

    Abgrall, N; Anticic, T; Antoniou, N; Argyriades, J; Baatar, B; Blondel, A; Blumer, J; Bogomilov, M; Bravar, A; Brooks, W; Brzychczyk, J; Bubak, A; Bunyatov, S A; Busygina, O; Christakoglou, P; Chung, P; Czopowicz, T; Davis, N; Debieux, S; Di Luise, S; Dominik, W; Dumarchez, J; Dynowski, K; Engel, R; Ereditato, A; Esposito, L S; Feofilov, G A; Fodor, Z; Ferrero, A; Fulop, A; Gazdzicki, M; Golubeva, M; Grabez, B; Grebieszkow, K; Grzeszczuk, A; Guber, F; Haesler, A; Hakobyan, H; Hasegawa, T; Idczak, R; Igolkin, S; Ivanov, Y; Ivashkin, A; Kadija, K; Kapoyannis, A; Katrynska, N; Kielczewska, D; Kikola, D; Kirejczyk, M; Kisiel, J; Kiss, T; Kleinfelder, S; Kobayashi, T; Kochebina, O; Kolesnikov, V I; Kolev, D; Kondratiev, V P; Korzenev, A; Kowalski, S; Krasnoperov, A; Kuleshov, S; Kurepin, A; Lacey, R; Larsen, D; Laszlo, A; Lyubushkin, V V; Mackowiak-Pawlowska, M; Majka, Z; Maksiak, B; Malakhov, A I; Maletic, D; Marchionni, A; Marcinek, A; Maris, I; Marin, V; Marton, K; Matulewicz, T; Matveev, V; Melkumov, G L; Messina, M; Mrowczynski, St; Murphy, S; Nakadaira, T; Nishikawa, K; Palczewski, T; Palla, G; Panagiotou, A D; Paul, T; Peryt, W; Petukhov, O; Planeta, R; Pluta, J; Popov, B A; Posiadala, M; Pulawski, S; Puzovic, J; Rauch, W; Ravonel, M; Renfordt, R; Robert, A; Rohrich, D; Rondio, E; Rossi, B; Roth, M; Rubbia, A; Rustamov, A; Rybczynski, M; Sadovsky, A; Sakashita, K; Savic, M; Sekiguchi, T; Seyboth, P; Shibata, M; Sipos, M; Skrzypczak, E; Slodkowski, M; Staszel, P; Stefanek, G; Stepaniak, J; Strabel, C; Strobele, H; Susa, T; Szuba, M; Tada, M; Taranenko, A; Tereshchenko, V; Tolyhi, T; Tsenov, R; Turko, L; Ulrich, R; Unger, M; Vassiliou, M; Veberic, D; Vechernin, V V; Vesztergombi, G; Wilczek, A; Wlodarczyk, Z; Wojtaszek-Szwarc, A; Wyszynski, O; Zambelli, L; Zipper, W; Hartz, M; Ichikawa, A K; Kubo, H; Marino, A D; Matsuoka, K; Murakami, A; Nakaya, T; Suzuki, K; Yuan, T; Zimmerman, E D

    2013-01-01

    The T2K long-baseline neutrino oscillation experiment in Japan needs precise predictions of the initial neutrino flux. The highest precision can be reached based on detailed measurements of hadron emission from the same target as used by T2K exposed to a proton beam of the same kinetic energy of 30 GeV. The corresponding data were recorded in 2007-2010 by the NA61/SHINE experiment at the CERN SPS using a replica of the T2K graphite target. In this paper details of the experiment, data taking, data analysis method and results from the 2007 pilot run are presented. Furthermore, the application of the NA61/SHINE measurements to the predictions of the T2K initial neutrino flux is described and discussed.

  18. The replica symmetric solution for orthogonally constrained Heisenberg model on Bethe lattice

    Science.gov (United States)

    Concetti, Francesco

    2017-02-01

    In this paper, we study the thermodynamic properties of a system of D-components classical Heisenberg spins lying on the vertices of a random regular graph, with an unconventional first neighbor non-random interaction J{{≤ft({{\\mathbf{S}}i}\\centerdot {{\\mathbf{S}}k}\\right)}2} . We can consider this model as a continuum version of anti-ferromagnetic D-states Potts model. We compute the paramagnetic free energy, using a new approach, presented in this paper for the first time, based on the replica method. Through the linear stability analysis, we obtain an instability line on the temperature-connectivity plane that provides a bound to the appearance of a phase transition. We also argue about the character of the instability observed.

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

    Science.gov (United States)

    Perez, Danny

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

  20. Analysis of non-contact and contact probe-to-sample thermal exchange for quantitative measurements of thin film and nanostructure thermal conductivity by the scanning hot probe method

    Science.gov (United States)

    Wilson, Adam A.

    The ability to measure thermal properties of thin films and nanostructured materials is an important aspect of many fields of academic study. A strategy especially well-suited for nanoscale investigations of these properties is the scanning hot probe technique, which is unique in its ability to non-destructively interrogate the thermal properties with high resolution, both laterally as well as through the thickness of the material. Strategies to quantitatively determine sample thermal conductivity depend on probe calibration. State of the art calibration strategies assume that the area of thermal exchange between probe and sample does not vary with sample thermal conductivity. However, little investigation has gone into determining whether or not that assumption is valid. This dissertation provides a rigorous study into the probe-to-sample heat transfer through the air gap at diffusive distances for a variety of values of sample thermal conductivity. It is demonstrated that the thermal exchange radius and gap/contact thermal resistance varies with sample thermal conductivity as well as tip-to-sample clearance in non-contact mode. In contact mode, it is demonstrated that higher thermal conductivity samples lead to a reduction in thermal exchange radius for Wollaston probe tips. Conversely, in non-contact mode and in contact mode for sharper probe tips where air contributes the most to probe-to-sample heat transfer, the opposite trend occurs. This may be attributed to the relatively strong solid-to-solid conduction occurring between probe and sample for the Wollaston probes. A three-dimensional finite element (3DFE) model was developed to investigate how the calibrated thermal exchange parameters vary with sample thermal conductivity when calibrating the probe via the intersection method in non-contact mode at diffusive distances. The 3DFE model was then used to explore the limits of sensitivity of the experiment for a range of simulated experimental conditions. It

  1. Pico-force optical exchange (pico-FOX): utilizing optical forces applied to an orthogonal electroosmotic flow for particulate enrichment from mixed sample streams.

    Science.gov (United States)

    Staton, Sarah J R; Kim, Soo Y; Hart, Sean J; Collins, Greg E; Terray, Alex

    2013-09-17

    Results are reported from a combined optical force and electrokinetic microfluidic device that separates individual particulates from molecular components in a mixed sample stream. A pico-Newton optical force was applied to an orthogonal electroosmotic flow carrying a hydrodynamically pinched, mixed sample, resulting in the separation of the various particles from the sample stream. Different combinations of polystyrene, PMMA, and silica particles with a commercially available dye were utilized to test the different separation modes available, from purely optical force to combined optical and electrophoretic forces. The impact of various particle properties on particle separation and separation efficiency were explored, including size (2, 6, 10 μm), refractive index, and electrophoretic mobility. Particle addressability was achieved by moving particles to different outlets on the basis of particle size, refractive index, and electrophoretic differences. Separations of 6 and 10 μm polystyrene particles led to only 3% particle contamination in the original sample stream and interparticle type enrichment levels >80%. The unique addressability of three different particle materials (polystyrene, PMMA, and silica) of the same size (2 μm) led to each being separated into a unique outlet without measurable contamination of the other particle types using optical force and electrophoretic mobility. In addition to particle separation, the device was able to minimize dye diffusion, leading to >95% dye recovery. This combined platform would have applications for noninvasive sample preparation of mixed molecular/particulate systems for mating with traditional analytics as well as efficient removal of harmful, degrading components from complex mixtures.

  2. Determination of water-extractable nonstructural carbohydrates, including inulin, in grass samples with high-performance anion exchange chromatography and pulsed amperometric detection.

    Science.gov (United States)

    Raessler, Michael; Wissuwa, Bianka; Breul, Alexander; Unger, Wolfgang; Grimm, Torsten

    2008-09-10

    The exact and reliable determination of carbohydrates in plant samples of different origin is of great importance with respect to plant physiology. Additionally, the identification and quantification of carbohydrates are necessary for the evaluation of the impact of these compounds on the biogeochemistry of carbon. To attain this goal, it is necessary to analyze a great number of samples with both high sensitivity and selectivity within a limited time frame. This paper presents a rugged and easy method that allows the isocratic chromatographic determination of 12 carbohydrates and sugar alcohols from one sample within 30 min. The method was successfully applied to a variety of plant materials with particular emphasis on perennial ryegrass samples of the species Lolium perenne. The method was easily extended to the analysis of the polysaccharide inulin after its acidic hydrolysis into the corresponding monomers without the need for substantial change of chromatographic conditions or even the use of enzymes. It therefore offers a fundamental advantage for the analysis of the complex mixture of nonstructural carbohydrates often found in plant samples.

  3. Heat exchanger

    Energy Technology Data Exchange (ETDEWEB)

    Craig, L.B.; Farma, A.J.

    1987-01-06

    This invention concerns a heat exchanger as used in a space heater, of the type in which hot exhaust gases transfer heat to water or the like flowing through a helical heat exchange coil. A significant improvement to the efficiency of the heat exchange occurring between the air and water is achieved by using a conduit for the water having external helical fluting such that the hot gases circulate along two paths, rather than only one. A preferred embodiment of such a heat exchanger includes a porous combustion element for producing radiant heat from a combustible gas, surrounded by a helical coil for effectively transferring the heat in the exhaust gas, flowing radially from the combustion element, to the water flowing through the coil. 4 figs.

  4. Use of a polystyrene-divinylbenzene-based weakly acidic cation-exchange resin column and propionic acid as an eluent in ion-exclusion/adsorption chromatography of aliphatic carboxylic acids and ethanol in food samples.

    Science.gov (United States)

    Mori, Masanobu; Hironaga, Takahiro; Kajiwara, Hiroe; Nakatani, Nobutake; Kozaki, Daisuke; Itabashi, Hideyuki; Tanaka, Kazuhiko

    2011-01-01

    We developed an ion-exclusion/adsorption chromatography (IEAC) method employing a polystyrene-divinylbenzene-based weakly acidic cation-exchange resin (PS-WCX) column with propionic acid as the eluent for the simultaneous determination of multivalent aliphatic carboxylic acids and ethanol in food samples. The PS-WCX column well resolved mono-, di-, and trivalent carboxylic acids in the acidic eluent. Propionic acid as the eluent gave a higher signal-to-noise ratio, and enabled sensitive conductimetric detection of analyte acids. We found the optimal separation condition to be the combination of a PS-WCX column and 20-mM propionic acid. Practical applicability of the developed method was confirmed by using a short precolumn with a strongly acidic cation-exchange resin in the H(+)-form connected before the separation column; this was to remove cations from food samples by converting them to hydrogen ions. Consequently, common carboxylic acids and ethanol in beer, wine, and soy sauce were successfully separated by the developed method.

  5. Dialysis is superior to anion exchange for removal of dissolved inorganic nitrogen from freshwater samples prior to dissolved organic nitrogen determination

    DEFF Research Database (Denmark)

    Graeber, Daniel; Gücker, Björn; Zwirnmann, Elke

    2012-01-01

    Dissolved organic nitrogen (DON) is usually determined as the difference between total dissolved nitrogen (TDN) and dissolved inorganic nitrogen (DIN). When applying this approach to samples with high DIN concentrations, there is a risk, that small relative errors in TDN and DIN measurements may...... of AEP and DP for DIN removal in order to increase DON determination accuracy of freshwater samples. The AEP pretreatment performed well for standard compounds, yielding high dissolved organic carbon (DOC) recovery rates and > 99% removal of nitrate, whereas DON recovery rates varied and no removal...

  6. Rapid isolation of plutonium in environmental solid samples using sequential injection anion exchange chromatography followed by detection with inductively coupled plasma mass spectrometry

    DEFF Research Database (Denmark)

    Qiao, Jixin; Hou, Xiaolin; Roos, Per

    2011-01-01

    size effect upon the separation efficiency revealed that small-sized (2 mL) columns sufficed to handle up to 50 g of environmental soil samples. Under the optimum conditions, chemical yields of plutonium exceeded 90% and the decontamination factors for uranium, thorium and lead ranged from 103 to 104...

  7. Observation of Replica Symmetry Breaking in the 1D Anderson Localization Regime in an Erbium-Doped Random Fiber Laser

    CERN Document Server

    Gomes, Anderson S L; Pincheira, Pablo I R; Moura, André L; Gagné, Mathieu; Kashyap, Raman; Raposo, Ernesto P; de Araújo, Cid B

    2016-01-01

    The analogue of the paramagnetic to spin-glass phase transition in disordered magnetic systems, leading to the phenomenon of replica symmetry breaking, has been recently demonstrated in a two-dimensional random laser consisting of an organic-based amorphous solid-state thin film. We report here the first demonstration of replica symmetry breaking in a one-dimensional photonic system consisting of an erbium-doped random fiber laser operating in the continuous-wave regime based on a unique random fiber grating system, which plays the role of the random scatterers and operates in the Anderson localization regime. The clear transition from a photonic paramagnetic to a photonic spin glass phase, characterized by the probability distribution function of the Parisi overlap, was verified and characterized. In this unique system, the radiation field interacts only with the gain medium, and the fiber grating, which provides the disordered feedback mechanism, does not interfere with the pump.

  8. Synthetic fossilization of soft biological tissues and their shape-preserving transformation into silica or electron-conductive replicas.

    Science.gov (United States)

    Townson, Jason L; Lin, Yu-Shen; Chou, Stanley S; Awad, Yasmine H; Coker, Eric N; Brinker, C Jeffrey; Kaehr, Bryan

    2014-12-08

    Structural preservation of complex biological systems from the subcellular to whole organism level in robust forms, enabling dissection and imaging while preserving 3D context, represents an enduring grand challenge in biology. Here we report a simple immersion method for structurally preserving intact organisms via conformal stabilization within silica. This self-limiting process, which we refer to as silica bioreplication, occurs by condensation of water-soluble silicic acid proximally to biomolecular interfaces throughout the organism. Conformal nanoscopic silicification of all biomolecular features imparts structural rigidity enabling the preservation of shape and nano-to-macroscale dimensional features upon drying to form a biocomposite and further high temperature oxidative calcination to form silica replicas or reductive pyrolysis to form electrically conductive carbon replicas of complete organisms. The simplicity and generalizability of this approach should facilitate efforts in biological preservation and analysis and could enable the development of new classes of biomimetic composite materials.

  9. Comparing 2D pictures with 3D replicas for the digital preservation and analysis of tangible heritage.

    OpenAIRE

    Galeazzi, Fabrizio; Di Giuseppantonio Di Franco, Paola; Matthews, Justin L.

    2015-01-01

    This is the author accepted manuscript. The final version is available from Taylor & Francis via http://dx.doi.org/10.1080/09647775.2015.1042515 In this paper, we present two experiments designed to compare 2D digital pictures and 3D digital replicas of artefacts, to understand how differently these media facilitate the perception and understanding of our past. Archaeologists and museum experts have commonly used 2D digital pictures to preserve and study artefacts. Recently these scholars ...

  10. The out-of-sample forecasting performance of non-linear models of real exchange rate behaviour: The case of the South African Rand

    Directory of Open Access Journals (Sweden)

    Aye, Goodness C.

    2013-04-01

    Full Text Available This paper analyses the out-of-sample forecasting performance of non-linear vs. linear models for the South African rand against the United States dollar and the British pound, in real terms. We compare the forecasting performance of point, interval and density forecasts for non-linear Band-TAR and ESTAR models to linear autoregressive models. Our data spans from 1970:01 to 2012:07, and we found that there are no significant gains from using either the Band-TAR or ESTAR non-linear models, compared to the linear AR model in terms of out-of-sample forecasting performance, especially at short horizons. We draw similar conclusions to other literature, and find that for the South African rand against the United States dollar and British pound, non-linearities are too weak for Band-TAR and ESTAR models to estimate.

  11. Multiple Replicas of Block Copolymer Thin Films from a Brushless Organosilicate Substrate

    Science.gov (United States)

    Suh, Hyo Seon; Yoon, Hyunsik; Char, Kookheon

    2011-03-01

    The chain end-grafted polymer brushes or cross-linked polymer mats have typically been utilized as the surface modification layers to induce the perpendicular orientation of block copolymer (BCP) thin films. Instead of such polymer-based approaches, we have recently introduced a new concept to control the BCP orientation using the brushless organosilicate (OS) substrates, whose surface energy can be finely tuned with thermal treatment. In this brushless case, the BCP chains do not penetrate into the underlying hard OS substrates during thermal annealing of BCP films, therefore, the BCP chains at the interface have no entangled structure with fairly weak adhesion of BCP films against the substrate. Owing to such weak adhesion of BCP films against the OS substrate, the perpendicularly oriented BCP film on a neutral OS substrate could be easily peeled off and transferred to a UV-curable resin applied onto the BCP film. The OS substrate after the peel-off process of a BCP film could regenerate the perpendicularly oriented BCP films since the surface energy of the OS substrate remains intact during the peel-off process. Furthermore, the direct-assembled BCP films on chemically patterned OS substrates could also be peeled off and transferred on to a UV-curable resin, allowing us to produce multiple replicas of direct-assembled BCP thin films from a single chemically patterned OS substrate.

  12. Optimization of the replica molding process of PDMS using pennate diatoms

    Science.gov (United States)

    Hlúbiková, D.; Luís, A. T.; Vaché, V.; Ector, L.; Hoffmann, L.; Choquet, P.

    2012-11-01

    Biomimetic fabrication of nanostructured materials has recently attracted the attention of researchers as a cost-effective and easily applicable method of nanotexturing. Different techniques and materials have been used in order to replicate natural patterns, among which polydimethylsiloxane (PDMS Sylgard 184®) was recently used to replicate the micro- and nanoscale patterns from centric diatoms. In this paper, we test the reproducibility and precision of this approach using various morphologically different diatom species trying to optimize the molding parameters. The optimization process is focused on immobilization of diatoms on the glass support, which serves as a master for templating, as well as on the parameters of PDMS fabrication such as the ratio of the curing agent and elastomer, use of vacuum, curing time and temperature. The results indicate that higher ratios of curing agent and elastomer, longer curing time and lower temperature are the most favorable conditions to obtain negative diatom replicas of good quality with features of 50 nm. Although this method can give very precise results producing high-resolution molds with all micro- and nanostructures replicated, we revealed some limitations regarding the size and morphology of the species used. These results indicate that large round and flat diatom species seem to be more suitable for the cast molding.

  13. Replica-moulded polydimethylsiloxane culture vessel lids attenuate osmotic drift in long-term cell cultures

    Indian Academy of Sciences (India)

    Axel Blau; Tanja Neumann; Christiane Ziegler; Fabio Benfenati

    2009-03-01

    An imbalance in medium osmolarity is a determinant that affects cell culture longevity. Even in humidified incubators, evaporation of water leads to a gradual increase in osmolarity overtime. We present a simple replica-moulding strategy for producing self-sealing lids adaptable to standard, small-size cell-culture vessels. They are made of polydimethylsiloxane (PDMS), a flexible, transparent and biocompatible material, which is gas-permeable but largely impermeable to water. Keeping cell cultures in a humidified 5% CO2 incubator at 37°C, medium osmolarity increased by +6.86 mosmol/kg/day in standard 35 mm Petri dishes, while PDMS lids attenuated its rise by a factor of four to changes of +1.72 mosmol/kg/ day. Depending on the lid membrane thickness, pH drifts at ambient CO2 levels were attenuated by a factor of 4 to 9. Comparative evaporation studies at temperatures below 60°C yielded a 10-fold reduced water vapour flux of 1.75 g/day/dm2 through PDMS lids as compared with 18.69 g/day/dm2 with conventional Petri dishes. Using such PDMS lids, about 2/3 of the cell cultures grew longer than 30 days in vitro. Among these, the average survival time was 69 days with the longest survival being 284 days under otherwise conventional cell culture conditions.

  14. Replica Ornstein-Zernike self-consistent theory for mixtures in random pores.

    Science.gov (United States)

    Pellicane, G; Caccamo, C; Wilson, D S; Lee, L L

    2004-06-01

    We present a self-consistent integral equation theory for a binary liquid in equilibrium with a disordered medium, based on the formalism of the replica Ornstein-Zernike (ROZ) equations. Specifically, we derive direct formulas for the chemical potentials and the zero-separation theorems (the latter provide a connection between the chemical potentials and the fluid cavity distribution functions). Next we solve a modified-Verlet closure to ROZ equations, which has built-in parameters that can be adjusted to satisfy the zero-separation theorems. The degree of thermodynamic consistency of the theory is also kept under control. We model the binary fluid in random pores as a symmetrical binary mixture of nonadditive hard spheres in a disordered hard-sphere matrix and consider two different values of the nonadditivity parameter and of the quenched matrix packing fraction, at different mixture concentrations. We compare the theoretical structural properties as obtained through the present approach with Percus-Yevick and Martinov-Sarkisov integral equation theories, and assess both structural and thermodynamic properties by performing canonical standard and biased grand canonical Monte Carlo simulations. Our theory appears superior to the other integral equation schemes here examined and provides reliable estimates of the chemical potentials. This feature should be useful in studying the fluid phase behavior of model adsorbates in random pores in general.

  15. Enhancing dry adhesives and replica molding with ethyl cyano-acrylate

    Science.gov (United States)

    Bovero, E.; Menon, C.

    2014-08-01

    The use of cyano-acrylate to improve the performance of dry adhesives and their method of fabrication is investigated. Specifically, the contributions of this work are: (1) a new adhesion method to adhere to a large variety of surfaces, (2) a strategy to increase the compliance of dry adhesives, and (3) an improved fabrication process for micro-structured dry adhesives based on replica molding. For the first contribution, the adhesion method consists of anchoring a micro-structured dry adhesive to a surface through a layer of hardened ethyl cyano-acrylate (ECA). This method increases the adhesion of the orders of magnitude at the expense of leaving residue after detachment. However, this method preserves reusability. For the second contribution, a double-sided dry adhesive is obtained by introducing a substrate with a millimeter-sized pillar structure, which enabled further increasing adhesion. For the third contribution, an ECA layer is used as a mold for the fabrication of new adhesives. These new types of molds proved able to produce dry adhesives with high reproducibility and low degradation.

  16. Diamond Opal-Replica Photonic Crystals and Graphitic Metallic Photonic Band Gap Structures: Fabrication and Properties

    Science.gov (United States)

    Zakhidov, A. A.; Baughman, R. H.; Iqbal, Z.; Khayrullin, I. I.; Ralchenko, V. G.

    1998-03-01

    We demonstrate a new method for the formation of photonic bandgap crystals that operate at optical wavelengths. This method involves the templating of a self-assempled SiO2 lattice with diamond, graphite, or amorphous forms of carbon, followed by the removal of the original SiO2 lattice matrix by chemical means. Such carbon opal replicas are the "air type" of photonic crystal (where air replaces silica spheres) that are most favourable for photonic bandgap formation. Surprisingly, the structure of the original opal lattice having a typical cubic lattice dimension of 250 nm) is reliably replicated down to the nanometer scale using either a diamond, graphite, or amorphous carbon templated material. The optical properties of these photonic bandgap crystals are reported and compared with both theory and experimental results on other types of opal-derived lattices that we have investigated. The graphitic reverse opal is the first example of a network type metallic photonic crystal for the optical domain, for which a large photonic bandgap have been predicted.

  17. From Dalek half balls to Daft Punk helmets: Mimetic fandom and the crafting of replicas

    Directory of Open Access Journals (Sweden)

    Matt Hills

    2014-06-01

    Full Text Available Mimetic fandom is a surprisingly understudied mode of (culturally masculinized fan activity in which fans research and craft replica props. Mimetic fandom can be considered as (inauthentic and (immaterial, combining noncommercial status with grassroots marketing or brand reinforcement as well as fusing an emphasis on material artifacts with Web 2.0 collective intelligence. Simply analyzing mimetic fandom as part of fannish material culture fails to adequately assess the nonmaterial aspects of this collaborative creativity. Two fan cultures are taken as case studies: Dalek building groups and Daft Punk helmet constructors. These diverse cases indicate that mimetic fandom has a presence and significance that moves across media fandoms and is not restricted to the science fiction, fantasy, and horror followings with which it is most often associated. Mimetic fandom may be theorized as an oscillatory activity that confuses binaries and constructions of (academic/fan authenticity. This fan practice desires and pursues a kind of ontological bridging or unity—from text to reality—that is either absent or less dominant in many other fan activities such as cosplay, screen-used prop collecting, and geographical pilgrimage. Fan studies may benefit from reassessing the place of mimesis, especially in order to theorize fan practices that are less clearly transformative in character.

  18. Replica of human dentin treated with different desensitizing agents: a methodological SEM study in vitro

    Directory of Open Access Journals (Sweden)

    Pereira Jose Carlos

    2002-01-01

    Full Text Available This is a preliminary study to determine a methodological sequence in vitro which may allow the reproduction of dentin for SEM analysis, after the use of different desensitizing agents. Dentin discs obtained from extracted human third molars were etched with 6% citric acid, an artificial smear layer was created and the surface dentin discs were divided into four quadrants. Quadrants 2, 3 and 4 of each disc were conditioned with 6% citric acid. The desensitizing agents (Oxa-Gel®, Gluma Desensitizer and an experimental agent were applied to quadrants 3 and 4. To evaluate the acid resistance of the treatment, quadrant 4 was etched again with 6% citric acid. An impression was then taken with Aquasil ULV. After a setting period of 6 min, each disc was removed from the impression and stored in a moist-free environment for 24 h at 37ºC. After that time, a low-viscosity epoxy resin (Araltec GY 1109 BR was poured into the impression and cured for 24 h. All specimens were metal-coated for SEM analysis. Comparison of the photomicrographs of dentin discs with their respective impressions and resin replicas showed that this technique can reproduce the characteristics of the dentin surface treated with desensitizing agents.

  19. Hydrogel Inverse Replicas of Breath Figures Exhibit Superoleophobicity Due to Patterned Surface Roughness.

    Science.gov (United States)

    Arora, Jaspreet Singh; Cremaldi, Joseph C; Holleran, Mary Kathleen; Ponnusamy, Thiruselvam; He, Jibao; Pesika, Noshir S; John, Vijay T

    2016-02-02

    The wetting behavior of a surface depends on both its surface chemistry and the characteristics of surface morphology and topography. Adding structure to a flat hydrophobic or oleophobic surface increases the effective contact angle and thus the hydrophobicity or oleophobicity of the surface, as exemplified by the lotus leaf analogy. We describe a simple strategy to introduce micropatterned roughness on surfaces of soft materials, utilizing the template of hexagonally packed pores of breath figures as molds. The generated inverse replicas represent micron scale patterned beadlike protrusions on hydrogel surfaces. This added roughness imparts superoleophobic properties (contact angle of the order of 150° and greater) to an inherently oleophobic flat hydrogel surface, when submerged. The introduced pattern on the hydrogel surface changes morphology as it swells in water to resemble morphologies remarkably analogous to the compound eye. Analysis of the wetting behavior using the Cassie-Baxter approximation leads to estimation of the contact angle in the superoleophobic regime and in agreement with the experimental value.

  20. Solid volume fraction estimation of bone:marrow replica models using ultrasound transit time spectroscopy.

    Science.gov (United States)

    Wille, Marie-Luise; Langton, Christian M

    2016-02-01

    The acceptance of broadband ultrasound attenuation (BUA) for the assessment of osteoporosis suffers from a limited understanding of both ultrasound wave propagation through cancellous bone and its exact dependence upon the material and structural properties. It has recently been proposed that ultrasound wave propagation in cancellous bone may be described by a concept of parallel sonic rays; the transit time of each ray defined by the proportion of bone and marrow propagated. A Transit Time Spectrum (TTS) describes the proportion of sonic rays having a particular transit time, effectively describing the lateral inhomogeneity of transit times over the surface aperture of the receive ultrasound transducer. The aim of this study was to test the hypothesis that the solid volume fraction (SVF) of simplified bone:marrow replica models may be reliably estimated from the corresponding ultrasound transit time spectrum. Transit time spectra were derived via digital deconvolution of the experimentally measured input and output ultrasonic signals, and compared to predicted TTS based on the parallel sonic ray concept, demonstrating agreement in both position and amplitude of spectral peaks. Solid volume fraction was calculated from the TTS; agreement between true (geometric calculation) with predicted (computer simulation) and experimentally-derived values were R(2)=99.9% and R(2)=97.3% respectively. It is therefore envisaged that ultrasound transit time spectroscopy (UTTS) offers the potential to reliably estimate bone mineral density and hence the established T-score parameter for clinical osteoporosis assessment.

  1. Exchangeable lower previsions

    CERN Document Server

    de Cooman, Gert; Miranda, Enrique; 10.3150/09-BEJ182

    2009-01-01

    We extend de Finetti's [Ann. Inst. H. Poincar\\'{e} 7 (1937) 1--68] notion of exchangeability to finite and countable sequences of variables, when a subject's beliefs about them are modelled using coherent lower previsions rather than (linear) previsions. We derive representation theorems in both the finite and countable cases, in terms of sampling without and with replacement, respectively.

  2. Heat exchanger restart evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-02-28

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4kA was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summarized herein.

  3. Towards a Standardised Method to Acquire and Store Liver Samples and Guidelines to Improve Quality Control and Exchange of Relative Expression Data

    Directory of Open Access Journals (Sweden)

    Frank M. Riemers

    2013-12-01

    Full Text Available The current ‘state-of-the-art’ molecular techniques are extremely sensitive and consequently prone to false results. Even more so than in the past, today’s hepatology research depends on high quality samples, especially for the molecular analyses. In all steps, starting with specimen sampling, fixation, storage, molecular processing and finally data calculation, variations in procedures between research laboratories may have a profound effect on the final conclusions. At the end of the day, this is an enormous drawback once data from different research institutes need to be reproduced, compared and/or combined. To improve standardisation, the so-called MIQE guidelines (Minimum Information for Publication of Quantitative Real- Time PCR Experiments were presented for quantitative PCR (qPCR studies.1,2 Furthermore, around the same time, recommendations were presented regarding human biospecimen collection, storage and processing, the so-called BRISQ-guidelines (Biospecimen Reporting for Improved Study Quality.3 Finally, the editors of The Journal of Pathology as well as Histopathology required in the December 2012 issue of The Journal of Pathology that researchers needed to follow the BRISQ guidelines in their papers in order to improve the sample quality in biomedical research.4 These initiatives hold great promise to improve the comparison and independent reproduction of data acquired in different research centres. Pancreas, gall bladder and liver research will especially benefit from the standardisation protocols since these organ systems are highly vulnerable to post-biopsy autolytic degradation. This comment illustrates that standardisation in molecular liver research is not yet at the point where experiments can be easily replicated, and data can be compared and combined.

  4. Hydrogen exchange

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Rand, Kasper Dyrberg

    2016-01-01

    Hydrogen exchange (HX) monitored by mass spectrometry (MS) is a powerful analytical method for investigation of protein conformation and dynamics. HX-MS monitors isotopic exchange of hydrogen in protein backbone amides and thus serves as a sensitive method for probing protein conformation...... and dynamics along the entire protein backbone. This chapter describes the exchange of backbone amide hydrogen which is highly quenchable as it is strongly dependent on the pH and temperature. The HX rates of backbone amide hydrogen are sensitive and very useful probes of protein conformation......, as they are distributed along the polypeptide backbone and form the fundamental hydrogen-bonding networks of basic secondary structure. The effect of pressure on HX in unstructured polypeptides (poly-dl-lysine and oxidatively unfolded ribonuclease A) and native folded proteins (lysozyme and ribonuclease A) was evaluated...

  5. Il contributo dell'Ecu alla stabilità dei cambi: un'ulteriore replica

    Directory of Open Access Journals (Sweden)

    H. JAGER

    2013-10-01

    Full Text Available The work is a response to Fornari’s contribution to the discussion of the ECU’s potential effects on exchange-rate stability. In it the authors explain some aspects of their previous study, which in their view are misunderstood by Fornari. They then defend the role of arbitrage and coverage of exchange-rate risk by banks, a point of criticism for Fornari which occupies a prominent place in their article.  JEL Codes: F15, F36, E42Keywords: ECU, exchange rate stability

  6. Il contributo dell'Ecu alla stabilità dei cambi: un'ulteriore replica

    OpenAIRE

    Jager, H; E. DE JONG

    2013-01-01

    The work is a response to Fornari’s contribution to the discussion of the ECU’s potential effects on exchange-rate stability. In it the authors explain some aspects of their previous study, which in their view are misunderstood by Fornari. They then defend the role of arbitrage and coverage of exchange-rate risk by banks, a point of criticism for Fornari which occupies a prominent place in their article.  JEL Codes: F15, F36, E42Keywords: ECU, exchange rate stability

  7. 40 CFR 63.1409 - Heat exchange system provisions.

    Science.gov (United States)

    2010-07-01

    ... locations where the cooling water enters and exits each heat exchanger or any combination of heat exchangers.... (iii) For samples taken at the entrance and exit of each heat exchanger or any combination of heat exchangers, the entrance is the point at which the cooling water enters the individual heat exchanger...

  8. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms.

    Science.gov (United States)

    Mori, Takaharu; Miyashita, Naoyuki; Im, Wonpil; Feig, Michael; Sugita, Yuji

    2016-07-01

    This paper reviews various enhanced conformational sampling methods and explicit/implicit solvent/membrane models, as well as their recent applications to the exploration of the structure and dynamics of membranes and membrane proteins. Molecular dynamics simulations have become an essential tool to investigate biological problems, and their success relies on proper molecular models together with efficient conformational sampling methods. The implicit representation of solvent/membrane environments is reasonable approximation to the explicit all-atom models, considering the balance between computational cost and simulation accuracy. Implicit models can be easily combined with replica-exchange molecular dynamics methods to explore a wider conformational space of a protein. Other molecular models and enhanced conformational sampling methods are also briefly discussed. As application examples, we introduce recent simulation studies of glycophorin A, phospholamban, amyloid precursor protein, and mixed lipid bilayers and discuss the accuracy and efficiency of each simulation model and method. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.

  9. Adaptive Multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

    CERN Document Server

    Navarro, C A; Deng, Youjin

    2015-01-01

    The study of disordered spin systems through Monte Carlo simulations has proven to be a hard task due to the adverse energy landscape present at the low temperature regime, making it difficult for the simulation to escape from a local minimum. Replica based algorithms such as the Exchange Monte Carlo (also known as parallel tempering) are effective at overcoming this problem, reaching equilibrium on disordered spin systems such as the Spin Glass or Random Field models, by exchanging information between replicas of neighbor temperatures. In this work we present a multi-GPU Exchange Monte Carlo method designed for the simulation of the 3D Random Field Model. The implementation is based on a two-level parallelization scheme that allows the method to scale its performance in the presence of faster and GPUs as well as multiple GPUs. In addition, we modified the original algorithm by adapting the set of temperatures according to the exchange rate observed from short trial runs, leading to an increased exchange rate...

  10. Exchange Options

    NARCIS (Netherlands)

    Jamshidian, Farshid

    2007-01-01

    The contract is described and market examples given. Essential theoretical developments are introduced and cited chronologically. The principles and techniques of hedging and unique pricing are illustrated for the two simplest nontrivial examples: the classical Black-Scholes/Merton/Margrabe exchange

  11. International Exchanges

    Institute of Scientific and Technical Information of China (English)

    2014-01-01

    <正>On April 1st,2014,CPAPD Deputy Secretary General Ms.Chen Huaifan met with Mr.Djudjuk Juyoto Suntani,President of the World Peace Committee,Indonesia,who headed the delegation,in the CPAPD office.The two sides exchanged views on issues of common concern including cooperation between the two organizations and the inheritance of Chinese culture.

  12. Exchange Options

    NARCIS (Netherlands)

    Jamshidian, F.

    2007-01-01

    The contract is described and market examples given. Essential theoretical developments are introduced and cited chronologically. The principles and techniques of hedging and unique pricing are illustrated for the two simplest nontrivial examples: the classical Black-Scholes/Merton/Margrabe exchange

  13. On the origin of the shallow and "replica" bands in FeSe monolayer superconductors

    Science.gov (United States)

    Nekrasov, I. A.; Pavlov, N. S.; Sadovskii, M. V.

    2017-03-01

    We compare the electronic structures of single FeSe layer films on SrTiO3 substrate (FeSe/STO) and K x Fe2- y Se2 superconductors obtained from extensive LDA and LDA + DMFT calculations with the results of ARPES experiments. It is demonstrated that correlation effects on Fe-3d states are sufficient in principle to explain the formation of the shallow electron-like bands at the M(X)-point. However, in FeSe/STO these effects alone are apparently insufficient for the simultaneous elimination of the hole-like Fermi surface around the Γ-point which is not observed in ARPES experiments. Detailed comparison of ARPES detected and calculated quasiparticle bands shows reasonable agreement between theory and experiment. Analysis of the bands with respect to their origin and orbital composition shows, that for FeSe/STO system the experimentally observed "replica" quasiparticle band at the M-point (usually attributed to forward scattering interactions with optical phonons in SrTiO3 substrate) can be reasonably understood just as the LDA calculated Fe-3d xy band, renormalized by electronic correlations. The only manifestation of the substrate reduces to lifting the degeneracy between Fe-3d xz and Fe-3d yz bands near M-point. For the case of K x Fe2- y Se2 most bands observed in ARPES can also be understood as correlation renormalized Fe-3d LDA calculated bands, with overall semi-quantitative agreement with LDA + DMFT calculations.

  14. Determination of Cr (Ⅵ) in Water Sample After Preconcentration by On-line Ion Exchange FLAAS%在线离子交换预富集-FLAAS测定环境水样中的铬(Ⅵ)

    Institute of Scientific and Technical Information of China (English)

    李丹; 俞晓峰; 寿淼钧; 叶华俊; 韩双来

    2013-01-01

    采用在线离子交换预富集-火焰原子吸收光谱法(FLAAS)测定环境水样中痕量铬(Ⅵ).通过试验考察样品溶液pH、洗脱剂浓度、离子交换树脂用量及共存离子对离子交换树脂富集效果的影响.结果表明,当交换树脂用量为0.50 g,样品溶液pH值为6.0时,用0.60 mol/L盐酸-10%抗坏血酸进行洗脱具有良好效果.铬(Ⅵ)的质量浓度在0~20.0μg/L之间与吸光度呈良好的线性关系,线性相关系数大于0.9998.该方法用于在线分离和富集环境水样中的铬(Ⅵ),灵敏度提高了100倍,加标回收率为96%~104%.%Trace amount of Cr( VI) was determined by using on-line ion-exchange column preconcentration flame atomic absorption spectroscopy system (IE-FLAAS). The effects of experimental variables such as the pH of sample, the concentration of eluent, the content of ion-exchange resin and coexisting ions on the recovery of Cr( VI) were inspected. The optimum operation conditions were as follows:the content of ion-exchange resin was 0.50 g, the pH of solution was 6.0, the eluent was 0.60 mol/L HCl-10% ascorbic acid. The mass concentration of Cr( VI) was linear with absorbance in the range of 0-20.0 μl g/L, the correlation coefficient was more than 0.999. The proposed method was used for on-line separation and preconcentration of Cr( VI) in water sample, the sensitivity of IE-FLAAS was 100 times higher than that of FLAAS and recovery was in the range of 96%-104%.

  15. 40 CFR 63.104 - Heat exchange system requirements.

    Science.gov (United States)

    2010-07-01

    ... heat exchange system or at locations where the cooling water enters and exits each heat exchanger or any combination of heat exchangers. (i) For samples taken at the entrance and exit of recirculating... manufacturing process units. (iii) For samples taken at the entrance and exit of each heat exchanger or...

  16. Ion exchange equilibrium constants

    CERN Document Server

    Marcus, Y

    2013-01-01

    Ion Exchange Equilibrium Constants focuses on the test-compilation of equilibrium constants for ion exchange reactions. The book first underscores the scope of the compilation, equilibrium constants, symbols used, and arrangement of the table. The manuscript then presents the table of equilibrium constants, including polystyrene sulfonate cation exchanger, polyacrylate cation exchanger, polymethacrylate cation exchanger, polysterene phosphate cation exchanger, and zirconium phosphate cation exchanger. The text highlights zirconium oxide anion exchanger, zeolite type 13Y cation exchanger, and

  17. A generic, hierarchical framework for massively parallel Wang-Landau sampling

    CERN Document Server

    Vogel, Thomas; Wüst, Thomas; Landau, David P

    2013-01-01

    We introduce a parallel Wang-Landau method based on the replica-exchange framework for Monte Carlo simulations. To demonstrate its advantages and general applicability for simulations of complex systems, we apply it to different spin models including spin glasses, the Ising model and the Potts model, lattice protein adsorption, and the self-assembly process in amphiphilic solutions. Without loss of accuracy, the method gives significant speed-up and potentially scales up to petaflop machines.

  18. Replicon modes and stability of critical behaviour of disordered systems with respect to the continuous replica symmetry breaking

    Science.gov (United States)

    Fedorenko, A. A.

    2003-02-01

    A field-theory approach is used to investigate the 'spin-glass effects' on the critical behaviour of systems with weak temperature-like quenched disorder. The renormalization group (RG) analysis of the effective Hamiltonian of a model with replica symmetry breaking (RSB) potentials of a general type is carried out in the two-loop approximation. The fixed point (FP) stability, recently found within the one-step RSB RG treatment, is further explored in terms of replicon eigenvalues. We find that the traditional FPs, which are usually considered to describe the disorder-induced universal critical behaviour, remain stable when the continuous RSB modes are taken into account.

  19. Prediction of localized aerosol deposition in a realistic replica of human airways using experimental data and numerical simulation

    Science.gov (United States)

    Lizal, Frantisek; Elcner, Jakub; Belka, Miloslav; Jedelsky, Jan; Jicha, Miroslav

    2016-11-01

    The presence of aerosol deposition hot-spots in human airways presumably contributes to development of various diseases. The overall aerosol deposition in human lungs can be predicted with sufficient accuracy nowadays. However, the prediction of localized aerosol deposition poses arduous challenge, namely in diseased lungs. Numerical simulation is considered to be a promising tool for the successful prediction. Yet, the validation of such simulations is difficult to perform, as not enough experimental data acquired using realistic airway replicas is available. This paper presents a first comparison of localized deposition measurement and simulation performed on the identical realistic geometry. The analysis indicates that both approaches yield similar results for low Reynolds number flows.

  20. Evidence of a one-step replica symmetry breaking in a three-dimensional Potts glass model.

    Science.gov (United States)

    Takahashi, Takashi; Hukushima, Koji

    2015-02-01

    We study a seven-state Potts glass model in three dimensions with first-, second-, and third-nearest-neighbor interactions with a bimodal distribution of couplings by Monte Carlo simulations. Our results show the existence of a spin-glass transition at a finite temperature T(c), a discontinuous jump of an order parameter at T(c) without latent heat, and a nontrivial structure in the order parameter distribution below T(c). They are compatible with one-step replica symmetry breaking.

  1. International Exchanges

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    On October 12,2015,Mr.Zhu Rui,CPAPD Secretary General,chaired informal discussions with U.S.young experts and scholars on arms control and non-proliferation.The two sides exchanged views on international arms control,disarmament,non-proliferation and nuclear security,etc.During October 12 to 16,2015,at the invitation of the CPAPD,a four-member delegation from the Vietnam Peace Committee headed by its Vice-President Ms.Nguyen Thi Hoang Van

  2. Replica Plating and Gene Screening Combined to Separate AHBA Synthase Gene Positive Actinomycetes%平板影印与AHBA合成酶基因筛选用于安莎类抗生素产生菌的分离

    Institute of Scientific and Technical Information of China (English)

    徐祯; 徐庆妍; 胡志钰; 郑忠辉; 黄耀坚

    2012-01-01

    基因筛选是筛选具有抗生素产生潜力微生物的新方法.针对筛选中单菌落分离纯化不仅工作量大,而且耗费时间,采用一种将平板影印技术与PCR扩增技术相结合从土壤中快速获得具有安莎类抗生素产生潜力的放线菌的方法.根据安莎类抗生素合成途径中的3-氨基-5-羟基苯甲酸合成酶(AH BAs)基因的保守性,通过放线菌的培养、影印、AH-BAs基因的PCR扩增,已从33份土样中获得8株AHBAs阳性菌株.结果表明:该方法是一种非常有效的能够快速获得AHBAs基因阳性菌株的方法,并且该方法可扩展用于从土壤中分离其他有价值的抗生素产生菌.%Gene mining is a new strategy to discover microbial natural products. However,it is laborious to inoculate and purify tested strains before gene amplification,so gene mining can not be applied to large amounts of samples. Herein,a high throughput method for the gene mining of soil actinomycetes, combining the replica plating technique and PCR amplification was recommended. In the present work,3-amino-5-hydroxybenxoic acid synthase (AHBAs) were used as amplicated gene. Through soil actinomyctes culture, colony replica planting,PCR amplification of AHBAs genes,isolation of positive strains and characterization of fermentation extracts, eight AHBAs positive strains were selected from 33 plants rhizosphere soil samples. The results showed that the replica plating-gene screening combined technique was useful for the rapid selection of ansamycin-producing actinomycetes, and it could be applied to search for producers of other antibiotics in natural soils.

  3. Relationship between Rheological Behaviour and Final Structure of Al2O3 and YSZ Foams Produced by Replica

    Directory of Open Access Journals (Sweden)

    S. Y. Gómez

    2012-01-01

    Full Text Available Using rheological parameters of ceramic suspensions, it is possible to taylor the structure of the ceramic foams produced by replica. This method consists in the impregnation of a polymeric flexible template (polyurethane foam with a ceramic suspension (slurry containing the appropriate additives, followed by burning out organic compounds and additives and sintering the ceramic structure. In this work, ceramic foams were produced by the replica method from Al2O3 and 3% Y2O3-ZrO2. Rheological parameters of the ceramic suspensions were investigated to improve the mechanical performance of final structures. Different types and quantities of raw materials were combined in order to select the formulations for ceramic foams. The parameters that have a significant influence on the process are the binder type and the amount of solids. Significant changes on the hysteresis area of the suspensions resulted in a lower density of macrodefects in the material. Likewise, when the shear rate viscosity is enhanced, the thickness of the struts increased proportionally. Lastly, when the hysteresis area magnitude and the ceramic thickness increased, the material with higher uniformity was internally densified, and the stress concentration of the internal defects was smoothed

  4. Free-energy calculations of residue mutations in a tripeptide using various methods to overcome inefficient sampling.

    Science.gov (United States)

    Graf, Michael M H; Maurer, Manuela; Oostenbrink, Chris

    2016-11-01

    Previous free-energy calculations have shown that the seemingly simple transformation of the tripeptide KXK to KGK in water holds some unobvious challenges concerning the convergence of the forward and backward thermodynamic integration processes (i.e., hysteresis). In the current study, the central residue X was either alanine, serine, glutamic acid, lysine, phenylalanine, or tyrosine. Interestingly, the transformation from alanine to glycine yielded the highest hysteresis in relation to the extent of the chemical change of the side chain. The reason for that could be attributed to poor sampling of φ2 /ψ2 dihedral angles along the transformation. Altering the nature of alanine's Cβ atom drastically improved the sampling and at the same time led to the identification of high energy barriers as cause for it. Consequently, simple strategies to overcome these barriers are to increase simulation time (computationally expensive) or to use enhanced sampling techniques such as Hamiltonian replica exchange molecular dynamics and one-step perturbation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  5. Modelling the ion-exchange equilibrium in nanoporous materials

    Directory of Open Access Journals (Sweden)

    M. Lukšič

    2012-06-01

    Full Text Available Distribution of a two component electrolyte mixture between the model adsorbent and a bulk aqueous electrolyte solution was studied using the replica Ornstein-Zernike theory and the grand canonical Monte Carlo method. The electrolyte components were modelled to mimic the HCl/NaCl and HCl/CaCl2 mixtures, respectively. The matrix, invaded by the primitive model electrolyte mixture, was formed from monovalent negatively charged spherical obstacles. The solution was treated as a continuous dielectric with the properties of pure water. Comparison of the pair distribution functions (obtained by the two methods between the various ionic species indicated a good agreement between the replica Ornstein-Zernike results and machine calculations. Among thermodynamic properties, the mean activity coefficient of the invaded electrolyte components was calculated. Simple model for the ion-exchange resin was proposed. The selectivity calculations yielded qualitative agreement with the following experimental observations: (i selectivity increases with the increasing capacity of the adsorbent (matrix concentration, (ii the adsorbent is more selective for the ion having higher charge density if its fraction in mixture is smaller.

  6. Número de replicações de inquéritos dietéticos para estimativa da ingestão de nutrientes em gestantes brasileiras

    Directory of Open Access Journals (Sweden)

    Daniela Saes Sartorelli

    2014-12-01

    Full Text Available Objetivos: determinar o número de replicações de inquéritos dietéticos necessários para estimar a ingestão usual de nutrientes e em categorias de consumo de gestantes no Brasil. Métodos: estudo prospectivo conduzido entre 82 gestantes, no qual as informações sobre energia e 18 nutrientes foram obtidas em três inquéritos recordatórios de 24 horas, sendo um em cada trimestre gestacional. Empregaram-se diferentes fórmulas para o cálculo do número de replicações do método necessárias para classificar as gestantes em categorias de ingestão, que considera a razão das variâncias intrapessoal/interpessoal, e para a estimativa da ingestão usual, baseado na variância intrapessoal. Resultados: para classificar as gestantes em categorias são necessárias entre 11 e 51 replicações do método, considerando-se coeficiente de correlação de 0,9. Admitindo coeficiente de correlação de 0,7, o número de replicações do método variou entre quatro e 19. Para a estimativa da ingestão usual são necessárias entre duas e 33 replicações, admitindo-se um erro de 10%. Considerando-se um erro de 20%, são necessárias entre uma e sete replicações de inquéritos dietéticos. Conclusões: é necessário um elevado número de replicações de inquéritos dietéticos na estimativa da ingestão de nutrientes na gestação e o emprego de um número reduzido de replicações poderá atenuar as associações entre a dieta e desfechos de saúde maternos e fetais.

  7. Determination of S-2-(N,N-diisopropylaminoethyl)- and S-2-(N,N-diethylaminoethyl) methylphosphonothiolate, nerve agent markers, in water samples using strong anion-exchange disk extraction, in vial trimethylsilylation, and gas chromatography-mass spectrometry analysis.

    Science.gov (United States)

    Subramaniam, Raja; Åstot, Crister; Juhlin, Lars; Nilsson, Calle; Östin, Anders

    2012-03-16

    Since the establishment of the Chemical Weapons Convention in 1997, the development of analytical methods for unambiguous identification of large numbers of chemicals related to chemical warfare agents has attracted increased interest. The analytically challenging, zwitterionic S-2-(N,N-diisopropylaminoethyl) methylphosphonothiolate (EA-2192), a highly toxic degradation marker of the nerve agent VX, has been reported to resist trimethylsilylation or to result in an unacceptably high limit of detection in GC-MS analysis. In the present study, the problem is demonstrated to be associated with the presence of salt, which hinders trimethysilylation. EA-2192 was extracted from aqueous samples by use of a strong anion-exchange disk, derivatized as a trimethylsilyl derivative via in vial solid-phase trimethylsilylation and identified by GC-MS. The limits of detection were 10 ng/mL and 100 ng/mL (in a water sample) for SIM and SCAN mode respectively. The analytical method was found to be repeatable with relative standard deviation VX and Russian VX, namely S-2-(N,N-diethylaminoethyl) methylphosphonothiolate, ethyl methylphosphonic acid, methylphosphonic acid, and isobutyl methylphosphonic acid. For the synthesis of reference compounds, EA-2192 and its analog from degradation of the Russian VX isomer, the present methods were improved by using a polymer-bound base, resulting in >90% purity based on (1)H NMR. Based on the current results and earlier work on alkylphosphonic acids using the same method, we conclude that the method is a viable choice for the simultaneous determination of a wide range of degradation products of nerve agents - zwitterionic, monoacid, diacid, and monothioacid chemicals - with excellent performance.

  8. Segmented heat exchanger

    Science.gov (United States)

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  9. Lipid exchange by ultracentrifugation

    DEFF Research Database (Denmark)

    Drachmann, Nikolaj Düring; Olesen, Claus

    2014-01-01

    Lipids play an important role in maintaining P-type ATPase structure and function, and often they are crucial for ATPase activity. When the P-type ATPases are in the membrane, they are surrounded by a mix of different lipids species with varying aliphatic chain lengths and saturation......, and the complex interplay between the lipids and the P-type ATPases are still not well understood. We here describe a robust method to exchange the majority of the lipids surrounding the ATPase after solubilisation and/or purification with a target lipid of interest. The method is based on an ultracentrifugation...... step, where the protein sample is spun through a dense buffer containing large excess of the target lipid, which results in an approximately 80-85 % lipid exchange. The method is a very gently technique that maintains protein folding during the process, hence allowing further characterization...

  10. Adaptive multi-GPU Exchange Monte Carlo for the 3D Random Field Ising Model

    Science.gov (United States)

    Navarro, Cristóbal A.; Huang, Wei; Deng, Youjin

    2016-08-01

    This work presents an adaptive multi-GPU Exchange Monte Carlo approach for the simulation of the 3D Random Field Ising Model (RFIM). The design is based on a two-level parallelization. The first level, spin-level parallelism, maps the parallel computation as optimal 3D thread-blocks that simulate blocks of spins in shared memory with minimal halo surface, assuming a constant block volume. The second level, replica-level parallelism, uses multi-GPU computation to handle the simulation of an ensemble of replicas. CUDA's concurrent kernel execution feature is used in order to fill the occupancy of each GPU with many replicas, providing a performance boost that is more notorious at the smallest values of L. In addition to the two-level parallel design, the work proposes an adaptive multi-GPU approach that dynamically builds a proper temperature set free of exchange bottlenecks. The strategy is based on mid-point insertions at the temperature gaps where the exchange rate is most compromised. The extra work generated by the insertions is balanced across the GPUs independently of where the mid-point insertions were performed. Performance results show that spin-level performance is approximately two orders of magnitude faster than a single-core CPU version and one order of magnitude faster than a parallel multi-core CPU version running on 16-cores. Multi-GPU performance is highly convenient under a weak scaling setting, reaching up to 99 % efficiency as long as the number of GPUs and L increase together. The combination of the adaptive approach with the parallel multi-GPU design has extended our possibilities of simulation to sizes of L = 32 , 64 for a workstation with two GPUs. Sizes beyond L = 64 can eventually be studied using larger multi-GPU systems.

  11. Absolute binding free energies for octa-acids and guests in SAMPL5

    Science.gov (United States)

    Tofoleanu, Florentina; Lee, Juyong; Pickard, Frank C., IV; König, Gerhard; Huang, Jing; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

    2017-01-01

    As part of the SAMPL5 blind prediction challenge, we calculate the absolute binding free energies of six guest molecules to an octa-acid (OAH) and to a methylated octa-acid (OAMe). We use the double decoupling method via thermodynamic integration (TI) or Hamiltonian replica exchange in connection with the Bennett acceptance ratio (HREM-BAR). We produce the binding poses either through manual docking or by using GalaxyDock-HG, a docking software developed specifically for this study. The root mean square deviations for our most accurate predictions are 1.4 kcal mol-1 for OAH with TI and 1.9 kcal mol-1 for OAMe with HREM-BAR. Our best results for OAMe were obtained for systems with ionic concentrations corresponding to the ionic strength of the experimental solution. The most problematic system contains a halogenated guest. Our attempt to model the σ-hole of the bromine using a constrained off-site point charge, does not improve results. We use results from molecular dynamics simulations to argue that the distinct binding affinities of this guest to OAH and OAMe are due to a difference in the flexibility of the host. We believe that the results of this extensive analysis of host-guest complexes will help improve the protocol used in predicting binding affinities for larger systems, such as protein-substrate compounds.

  12. Evaluating benchmarks for Norwegian exchange rate forecasting

    OpenAIRE

    Adrik, Samir

    2016-01-01

    In this thesis, we compare the out-of-sample forecasting abilities of three fundamental exchange rate models (EqCM) against the random walk (without drift), RW. The objective of the thesis is to see how well the RW model preforms against fundamental exchange rate models that in the literature have proven to be better at forecasting the Norwegian exchange rate. These models were tested on an out-of-sample period (2009:1-2015:4) that include two characteristic exchange rate regimes. The models ...

  13. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.

    Science.gov (United States)

    Huang, Xuhui; Bowman, Gregory R; Pande, Vijay S

    2008-05-28

    We have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in a global distributed computing environment. Here we examine the helix-coil transition of a 21 residue alpha-helical peptide in explicit solvent. For ST, we demonstrate the efficacy of a new method for determining initial weights allowing the system to perform a random walk in temperature space based on short trial simulations. These weights are updated throughout the production simulation by an adaptive weighting method. We give a detailed comparison of SREM, ST, as well as standard MD and find that SREM and ST give equivalent results in reasonable agreement with experimental data. In addition, we find that both enhanced sampling methods are much more efficient than standard MD simulations. The melting temperature of the Fs peptide with the AMBER99phi potential was calculated to be about 310 K, which is in reasonable agreement with the experimental value of 334 K. We also discuss other temperature dependent properties of the helix-coil transition. Although ST has certain advantages over SREM, both SREM and ST are shown to be powerful methods via distributed computing and will be applied extensively in future studies of complex bimolecular systems.

  14. Non-invasive Florentine Renaissance Panel Painting Replica Structures Investigation by Using Terahertz Time-Domain Imaging (THz-TDI) Technique

    DEFF Research Database (Denmark)

    Dandolo, Corinna Ludovica Koch; Picollo, Marcello; Cucci, Costanza

    2016-01-01

    The potentials of the Terahertz Time-Domain Imaging (THz-TDI) technique for a non-invasive inspection of panel paintings have been considered in detail. The THz-TD data acquired on a replica of a panel painting made in imitation of Italian Renaissance panel paintings were processed in order to pr...

  15. Quantum Exchangeable Sequences of Algebras

    CERN Document Server

    Curran, Stephen

    2008-01-01

    We extend the notion of quantum exchangeability, introduced by K\\"ostler and Speicher in arXiv:0807.0677, to sequences (\\rho_1,\\rho_2,...c) of homomorphisms from an algebra C into a noncommutative probability space (A,\\phi), and prove a free de Finetti theorem: an infinite quantum exchangeable sequence (\\rho_1,\\rho_2,...c) is freely independent and identically distributed with respect to a conditional expectation. As a corollary we obtain a free analogue of the Hewitt Savage zero-one law. As in the classical case, the theorem fails for finite sequences. We give a characterization of finite quantum exchangeable sequences, which can be viewed as a noncommutative analogue of sampling without replacement. We then give an approximation to how far a finite quantum exchangeable sequence is from being freely independent with amalgamation.

  16. Pu Anion Exchange Process Intensification

    Energy Technology Data Exchange (ETDEWEB)

    Taylor-Pashow, K. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-10-08

    This project seeks to improve the efficiency of the plutonium anion-exchange process for purifying Pu through the development of alternate ion-exchange media. The objective of the project in FY15 was to develop and test a porous foam monolith material that could serve as a replacement for the current anion-exchange resin, Reillex® HPQ, used at the Savannah River Site (SRS) for purifying Pu. The new material provides advantages in efficiency over the current resin by the elimination of diffusive mass transport through large granular resin beads. By replacing the large resin beads with a porous foam there is much more efficient contact between the Pu solution and the anion-exchange sites present on the material. Several samples of a polystyrene based foam grafted with poly(4-vinylpyridine) were prepared and the Pu sorption was tested in batch contact tests.

  17. Replica symmetry breaking in specially designed TiO$_{2}$ nanoparticles-based dye-colloidal random laser

    CERN Document Server

    Pincheira, Pablo I R; Carreño, Sandra J M; Fewo, Serge I; Moura, André L; Raposo, Ernesto P; Gomes, Anderson S L; de Araújo, Cid B

    2015-01-01

    Replica symmetry breaking (RSB) is a concept inherent to the theory of spin glasses and complex systems, which describes how identical systems prepared under identical initial conditions can reach different states. RSB was predicted and demonstrated, for the first time in any physical system, using random lasers (RLs) operating in the coherent feedback regime. However, attempts to show RSB in RLs operating in the incoherent feedback regime based on colloidal solution of dye and scatterer particles failed. In the present letter, by using specially designed nanoparticles scatterers which prevents photodegradation of the dye, we present clear evidence of RSB in a RL operating in the incoherent feedback regime based on ethanol solution of Rhodamine 6G and amorphous TiO$_{2}$ nanoparticles.

  18. Fabrication of uniform DNA-conjugated hydrogel microparticles via replica molding for facile nucleic acid hybridization assays.

    Science.gov (United States)

    Lewis, Christina L; Choi, Chang-Hyung; Lin, Yan; Lee, Chang-Soo; Yi, Hyunmin

    2010-07-01

    We identify and investigate several critical parameters in the fabrication of single-stranded DNA conjugated poly(ethylene glycol) (PEG) microparticles based on replica molding (RM) for highly uniform and robust nucleic acid hybridization assays. The effects of PEG-diacrylate, probe DNA, and photoinitiator concentrations on the overall fluorescence and target DNA penetration depth upon hybridization are examined. Fluorescence and confocal microscopy results illustrate high conjugation capacity of the probe and target DNA, femtomole sensitivity, and sequence specificity. Combined, these findings demonstrate a significant step toward simple, robust, and scalable procedures to manufacture highly uniform and high-capacity hybridization assay particles in a well-controlled manner by exploiting many advantages that the batch processing-based RM technique offers. We envision that the results presented here may be readily applied to rapid and high-throughput hybridization assays for a wide variety of applications in bioprocess monitoring, food safety, and biological threat detection.

  19. Entropy generation in Gaussian quantum transformations: applying the replica method to continuous-variable quantum information theory

    Science.gov (United States)

    Gagatsos, Christos N.; Karanikas, Alexandros I.; Kordas, Georgios; Cerf, Nicolas J.

    2016-02-01

    In spite of their simple description in terms of rotations or symplectic transformations in phase space, quadratic Hamiltonians such as those modelling the most common Gaussian operations on bosonic modes remain poorly understood in terms of entropy production. For instance, determining the quantum entropy generated by a Bogoliubov transformation is notably a hard problem, with generally no known analytical solution, while it is vital to the characterisation of quantum communication via bosonic channels. Here we overcome this difficulty by adapting the replica method, a tool borrowed from statistical physics and quantum field theory. We exhibit a first application of this method to continuous-variable quantum information theory, where it enables accessing entropies in an optical parametric amplifier. As an illustration, we determine the entropy generated by amplifying a binary superposition of the vacuum and a Fock state, which yields a surprisingly simple, yet unknown analytical expression.

  20. Timing Foreign Exchange Markets

    Directory of Open Access Journals (Sweden)

    Samuel W. Malone

    2016-03-01

    Full Text Available To improve short-horizon exchange rate forecasts, we employ foreign exchange market risk factors as fundamentals, and Bayesian treed Gaussian process (BTGP models to handle non-linear, time-varying relationships between these fundamentals and exchange rates. Forecasts from the BTGP model conditional on the carry and dollar factors dominate random walk forecasts on accuracy and economic criteria in the Meese-Rogoff setting. Superior market timing ability for large moves, more than directional accuracy, drives the BTGP’s success. We explain how, through a model averaging Monte Carlo scheme, the BTGP is able to simultaneously exploit smoothness and rough breaks in between-variable dynamics. Either feature in isolation is unable to consistently outperform benchmarks throughout the full span of time in our forecasting exercises. Trading strategies based on ex ante BTGP forecasts deliver the highest out-of-sample risk-adjusted returns for the median currency, as well as for both predictable, traded risk factors.

  1. Efficiently computing pathway free energies: New approaches based on chain-of-replica and Non-Boltzmann Bennett reweighting schemes.

    Science.gov (United States)

    Hudson, Phillip S; White, Justin K; Kearns, Fiona L; Hodoscek, Milan; Boresch, Stefan; Lee Woodcock, H

    2015-05-01

    Accurately modeling condensed phase processes is one of computation's most difficult challenges. Include the possibility that conformational dynamics may be coupled to chemical reactions, where multiscale (i.e., QM/MM) methods are needed, and this task becomes even more daunting. Free energy simulations (i.e., molecular dynamics), multiscale modeling, and reweighting schemes. Herein, we present two new approaches for mitigating the aforementioned challenges. The first is a new chain-of-replica method (off-path simulations, OPS) for computing potentials of mean force (PMFs) along an easily defined reaction coordinate. This development is coupled with a new distributed, highly-parallel replica framework (REPDstr) within the CHARMM package. Validation of these new schemes is carried out on two processes that undergo conformational changes. First is the simple torsional rotation of butane, while a much more challenging glycosidic rotation (in vacuo and solvated) is the second. Additionally, a new approach that greatly improves (i.e., possibly an order of magnitude) the efficiency of computing QM/MM PMFs is introduced and compared to standard schemes. Our efforts are grounded in the recently developed method for efficiently computing QM-based free energies (i.e., QM-Non-Boltzmann Bennett, QM-NBB). Again, we validate this new technique by computing the QM/MM PMF of butane's torsional rotation. The OPS-REPDstr method is a promising new approach that overcomes many limitations of standard pathway simulations in CHARMM. The combination of QM-NBB with pathway techniques is very promising as it offers significant advantages over current procedures. Efficiently computing potentials of mean force is a major, unresolved, area of interest. This article is part of a Special Issue entitled Recent developments of molecular dynamics. Copyright © 2014. Published by Elsevier B.V.

  2. Novel approach to the fabrication of an artificial small bone using a combination of sponge replica and electrospinning methods

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Yang-Hee; Lee, Byong-Taek, E-mail: lbt@sch.ac.kr [Department of Biomedical Engineering and Materials, School of Medicine, Soonchunhyang University 366-1, Ssangyong-dong, Cheonan, Chungnam 330-090 (Korea, Republic of)

    2011-06-15

    In this study, a novel artificial small bone consisting of ZrO{sub 2}-biphasic calcium phosphate/polymethylmethacrylate-polycaprolactone-hydroxyapatite (ZrO{sub 2}-BCP/PMMA-PCL-HAp) was fabricated using a combination of sponge replica and electrospinning methods. To mimic the cancellous bone, the ZrO{sub 2}/BCP scaffold was composed of three layers, ZrO{sub 2}, ZrO{sub 2}/BCP and BCP, fabricated by the sponge replica method. The PMMA-PCL fibers loaded with HAp powder were wrapped around the ZrO{sub 2}/BCP scaffold using the electrospinning process. To imitate the Haversian canal region of the bone, HAp-loaded PMMA-PCL fibers were wrapped around a steel wire of 0.3 mm diameter. As a result, the bundles of fiber wrapped around the wires imitated the osteon structure of the cortical bone. Finally, the ZrO{sub 2}/BCP scaffold was surrounded by HAp-loaded PMMA-PCL composite bundles. After removal of the steel wires, the ZrO{sub 2}/BCP scaffold and bundles of HAp-loaded PMMA-PCL formed an interconnected structure resembling the human bone. Its diameter, compressive strength and porosity were approximately 12 mm, 5 MPa and 70%, respectively, and the viability of MG-63 osteoblast-like cells was determined to be over 90% by the MTT (3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) assay. This artificial bone shows excellent cytocompatibility and is a promising bone regeneration material.

  3. 云计算环境下的动态数据副本管理策略%Dynamic data replica management strategy in cloud computing environment

    Institute of Scientific and Technical Information of China (English)

    邓见光; 赵跃龙; 袁华强

    2015-01-01

    Focusing on the frequent single point of failure in cloud computer system ,a dynamic data replica management strategy was proposed in cloud computer environment .The replica placement de-cision of the proposed replica management strategy was made by specifically analyzing the state param-eters of target node ,including the current load condition ,the size of the current available storage ca-pacity ,the communication bandwidth ,the historical access record and its historical failure record . And at the same time ,a higher priority was provided to the bigger file replica in the decision-making of replica replacement .Experimental results illustrate that the proposed dynamic replica management strategy is stable in the criterion of average data access distance ,and w hich outperforms other several classic replica strategy in the measurements of the system load balance level and the average task exe-cution time .%针对云计算系统中的单点失效问题 ,提出一种云计算环境下的动态数据副本管理策略 .该管理策略通过综合考虑目标放置节点的当前负载状况、可用存储空间大小、通信带宽以及其历史访问记录和历史失效记录等状态参数来进行数据文件的副本放置决策 ,并在进行副本置换操作时给予大尺寸数据文件副本更高的优先权 .测试结果表明 :该管理策略具有较为稳定的平均数据访问距离 ,且在云计算系统的负载均衡水平和平均任务执行时间指标上优于另外几种经典的副本策略 .

  4. Handbook on heat exchangers

    Science.gov (United States)

    Bazhan, Pavel I.; Kanevets, Georgii E.; Seliverstov, Vladimir M.

    Essential data on heat exchange equipment used in ship, locomotive, automotive, and aircraft powerplants are presented in a systematic manner. The data cover the principal types and technical and performance characteristics of heat exchangers, fundamentals of the theory of heat exchange, calculation of heat transfer coefficients for different types of heat exchange apparatus, optimization of heat exchangers, computer-aided design of heat exchange equipment, testing techniques, and test result processing.

  5. Totalization Data Exchange (TDEX)

    Data.gov (United States)

    Social Security Administration — The Totalization Data Exchange (TDEX) process is an exchange between SSA and its foreign country partners to identify deaths of beneficiaries residing abroad. The...

  6. Model Uncertainty and Exchange Rate Forecasting

    OpenAIRE

    Kouwenberg, Roy; Markiewicz, Agnieszka; Verhoeks, Ralph; Zwinkels, Remco

    2013-01-01

    textabstractWe propose a theoretical framework of exchange rate behavior where investors focus on a subset of economic fundamentals. We find that any adjustment in the set of predictors used by investors leads to changes in the relation between the exchange rate and fundamentals. We test the validity of this framework via a backward elimination rule which captures the current set of fundamentals that best predicts the exchange rate. Out-of-sample forecasting tests show that the backward elimi...

  7. Insights into the folding and unfolding processes of wild-type and mutated SH3 domain by molecular dynamics and replica exchange molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Wen-Ting Chu

    Full Text Available Src-homology regions 3 (SH3 domain is essential for the down-regulation of tyrosine kinase activity. Mutation A39V/N53P/V55L of SH3 is found to be relative to the urgent misfolding diseases. To gain insight, the human and gallus SH3 domains (PDB ID: 1NYG and 2LP5, including 58 amino acids in each protein, were selected for MD simulations (Amber11, ff99SB force field and cluster analysis to investigate the influence of mutations on the spatial structure of the SH3 domain. It is found that the large conformational change of mutations mainly exists in three areas in the vicinity of protein core: RT loop, N-src loop, distal β-hairpin to 310 helix. The C-terminus of the mutated gallus SH3 is disordered after simulation, which represents the intermediate state of aggregation. The disappeared strong Hbond net in the mutated human and gallus systems will make these mutated proteins looser than the wild-type proteins. Additionally, by performing the REMD simulations on the gallus SH3 domain, the mutated domain is found to have an obvious effect on the unfolding process. These studies will be helpful for further aggregation mechanisms investigations on SH3 family.

  8. Sampling impairments influence over stealthy fiber-optic signal decryption

    Science.gov (United States)

    Yeminy, Tomer; Sadot, Dan; Zalevsky, Zeev

    2013-03-01

    Recently we have proposed a method for temporal and spectral stealthy fiber-optic communications. In this technique the signal is spread in the time domain below the noise level and the power spectral density of the signal is spread beneath the noise level in the frequency domain. The power spectral density of the signal is reconstructed by means of sampling which results in coherent addition of the encrypted signal spectral replicas. Hence, the sampling quality plays a major role in the ability to successfully decrypt the received covert signal. In this paper, we mathematically and numerically analyze the effect of sampling impairments over the decryption performance.

  9. 云存储智能多数据副本放置机制��%Intelligent Multiple Data Replica Placement Scheme for Cloud Storage

    Institute of Scientific and Technical Information of China (English)

    张榜; 王兴伟; 黄敏

    2014-01-01

    The data replica management scheme is a critical component of cloud storage system. In order to improve its scalability and reliability at the same time shorten user access time, the multiple data replica scheme should be adopted and the proper placement for each replica should be determined. Thus, this paper proposes an intelligent multiple data replica placement scheme for cloud storage. This scheme is based on p-center model with minimizing user access cost as its optimization objective. It uses genetic algorithm (GA) to find the optimal data replica placement solution and uses biogeography-based optimization (BBO) algorithm to optimally assign user access request to the specific data replica. The proposed scheme has been implemented based on CloudSim and performance evaluation has been done. The simulation results show that it is both feasible and effective.%数据副本管理机制是云存储系统的重要组成部分。为了提高云存储系统的可伸缩性、可靠性,同时改善用户访问时间,通常采用多数据副本机制,并且需要解决数据副本放置问题。为此,提出了一种用于云存储系统的智能多数据副本放置机制。该机制基于p-中心模型,以最小化访问代价为优化目标,基于遗传算法(genetic algorithm,GA)确定优化的数据副本放置方案,基于生物地理学优化(biogeography-based optimization,BBO)算法确定用户访问请求对数据副本的优化分配。基于CloudSim进行了仿真实现和性能评价,结果表明,云存储智能多数据副本放置机制是可行和有效的。

  10. Inorganic ion exchangers for nuclear waste remediation

    Energy Technology Data Exchange (ETDEWEB)

    Clearfield, A.; Bortun, A.; Bortun, L.; Behrens, E. [Texas A& M Univ., College Station, TX (United States)

    1997-10-01

    The objective of this work is to provide a broad spectrum of inorganic ion exchangers that can be used for a range of applications and separations involving remediation of groundwater and tank wastes. The authors intend to scale-up the most promising exchangers, through partnership with AlliedSignal Inc., to provide samples for testing at various DOE sites. While much of the focus is on exchangers for removal of Cs{sup +} and Sr{sup 2+} from highly alkaline tank wastes, especially at Hanford, the authors have also synthesized exchangers for acid wastes, alkaline wastes, groundwater, and mercury, cobalt, and chromium removal. These exchangers are now available for use at DOE sites. Many of the ion exchangers described here are new, and others are improved versions of previously known exchangers. They are generally one of three types: (1) layered compounds, (2) framework or tunnel compounds, and (3) amorphous exchangers in which a gel exchanger is used to bind a fine powder into a bead for column use. Most of these exchangers can be regenerated and used again.

  11. Actin-myosin interactions visualized by the quick-freeze, deep-etch replica technique.

    Science.gov (United States)

    Heuser, J E; Cooke, R

    1983-09-05

    A new method of preparing biological samples for electron microscopy has been used to re-examine the structure of actin filaments, actin filaments decorated by myosin subfragment-1 (S1), and insect flight muscles. Samples were quick-frozen by contact with a block of copper cooled to approximately 4 K; then were freeze-fractured, deep-etched, rotary-replicated with platinum, and viewed in a transmission electron microscope. By this approach, actin filaments display prominent transverse bands whose repeat (approximately 5.5 nm) and pitch (approximately 15 to 20 degrees) fit with the expected left-handed "genetic" helix. Freeze-etched actin filaments do not, however, display the usual two-start helix as prominently as is seen after negative staining, and they also appear substantially thicker than after negative staining (9 to 10 nm versus 8 nm). The latter two-start helix appears very clearly after S1 decoration. Nevertheless, freeze-etched acto-S1 does not display the "arrowheads" that are seen after negative staining. Instead it displays the outer envelope of the helically deployed S1, and as would be expected from current models derived from optical reconstruction of negatively stained samples, this surface view looks only slightly polarized. Finally, the quick-freeze, deep-etch approach provides particularly distinct images of the crossbridges in insect flight muscles. These are plentiful and regularly arranged in rigor muscles, but rare in muscles relaxed with ATP before freezing. In rigor muscles fixed with aldehydes, these crossbridges assume a broad distribution of inclination, ranging from 45 degrees to 90 degrees with a mean of approximately 80 degrees, which is less tilt than has been seen before in thin-sectioned muscles. However, when aldehyde fixation is followed by exposure to tannic acid with or without uranyl acetate block-staining, crossbridges assume a more acute angle with respect to the fiber axis, centering around 45 degrees. This is associated

  12. A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge

    Science.gov (United States)

    Pal, Rajat Kumar; Haider, Kamran; Kaur, Divya; Flynn, William; Xia, Junchao; Levy, Ronald M.; Taran, Tetiana; Wickstrom, Lauren; Kurtzman, Tom; Gallicchio, Emilio

    2017-01-01

    As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.

  13. Involvement of microbial mats in early fossilization by decay delay and formation of impressions and replicas of vertebrates and invertebrates

    Science.gov (United States)

    Iniesto, Miguel; Buscalioni, Ángela D.; Carmen Guerrero, M.; Benzerara, Karim; Moreira, David; López-Archilla, Ana I.

    2016-05-01

    Microbial mats have been hypothesized to improve the persistence and the preservation of organic remains during fossilization processes. We test this hypothesis with long-term experiments (up to 5.5 years) using invertebrate and vertebrate corpses. Once placed on mats, the microbial community coats the corpses and forms a three-dimensional sarcophagus composed of microbial cells and exopolymeric substances (EPS). This coverage provides a template for i) moulding superficial features, resulting in negative impressions, and ii) generating replicas. The impressions of fly setulae, fish scales and frog skin verrucae are shaped mainly by small cells in an EPS matrix. Microbes also replicate delicate structures such as the three successive layers that compose a fish eye. The sarcophagus protects the body integrity, allowing the persistence of inner organs such as the ovaries and digestive apparatus in flies, the swim bladder and muscles in fish, and the bone marrow in frog legs. This study brings strong experimental evidence to the idea that mats favour metazoan fossilization by moulding, replicating and delaying decay. Rapid burial has classically been invoked as a mechanism to explain exceptional preservation. However, mats may play a similar role during early fossilization as they can preserve complex features for a long time.

  14. Adsorption of a Hard Sphere Fluid in a Disordered Polymerized Matrix: Application of the Replica Ornstein-Zernike Equations

    Science.gov (United States)

    Pizio; Trokhymchuk; Henderson; Labik

    1997-07-01

    A model of hard spheres adsorbed in disordered porous media is studied using the associative replica Ornstein-Zernike (ROZ) equations. Extending previous studies of adsorption in a hard sphere matrices, we investigate a polymerized matrix. We consider an associating fluid of hard spheres with two intracore attractive sites per particle; consequently chains consisting of overlapping hard spheres can be formed due to the chemical association. This is the generalization of the model with sites on the surface of Wertheim that has been studied in the bulk by Chang and Sandler. The matrix structure is obtained in the polymer Percus-Yevick approximation. We solve the ROZ equations in the associative hypernetted chain approximation. The pair distribution functions, the fluid compressibility, the equation of state and chemical potential of the adsorbed fluid are obtained and discussed. It is shown that the adsorption of a hard sphere fluid in a matrix at given density, but consisting of longer chains of overlapping hard spheres, is higher than the adsorption of this fluid in a hard sphere matrix.

  15. A replica technique for extracting precipitates from neutron-irradiated or thermal-aged vanadium alloys for TEM analysis

    Energy Technology Data Exchange (ETDEWEB)

    Fukumoto, K., E-mail: fukumoto@u-fukui.ac.jp; Iwasaki, M.

    2014-06-01

    A carbon replica technique has been developed to extract precipitates from vanadium alloys. Using this technique, precipitation phases can be extracted from neutron-irradiated or thermal-aged V–4Cr–4Ti alloys. Precipitate identification using EDS X-ray analysis and electron diffraction was facilitated. Only NaCl type of Ti(OCN) precipitate was formed in the thermal-aged V–4Cr–4Ti alloys at 600 °C for 20 h and cation sub-lattice was only occupied by Ti atoms. However, the thin plate of precipitates with NaCl type of crystallographic structure could be seen in the V–4Cr–4Ti alloys irradiated at 593 °C in the JOYO fast reactor. The precipitate contained chromium and vanadium atoms on the cation sub-lattice as well as titanium atoms. It is considered that the phase of MX type (M = Ti, V, Cr and X = O, N, C) is a metastable phase under neutron irradiation.

  16. A replica technique for extracting precipitates from neutron-irradiated or thermal-aged vanadium alloys for TEM analysis

    Science.gov (United States)

    Fukumoto, K.; Iwasaki, M.

    2014-06-01

    A carbon replica technique has been developed to extract precipitates from vanadium alloys. Using this technique, precipitation phases can be extracted from neutron-irradiated or thermal-aged V-4Cr-4Ti alloys. Precipitate identification using EDS X-ray analysis and electron diffraction was facilitated. Only NaCl type of Ti(OCN) precipitate was formed in the thermal-aged V-4Cr-4Ti alloys at 600 °C for 20 h and cation sub-lattice was only occupied by Ti atoms. However, the thin plate of precipitates with NaCl type of crystallographic structure could be seen in the V-4Cr-4Ti alloys irradiated at 593 °C in the JOYO fast reactor. The precipitate contained chromium and vanadium atoms on the cation sub-lattice as well as titanium atoms. It is considered that the phase of MX type (M = Ti, V, Cr and X = O, N, C) is a metastable phase under neutron irradiation.

  17. A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Kimori, Yoshitaka [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan); Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502 (Japan); Oguchi, Yosuke [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Ichise, Norihiko [Department of Visual Communication, Komazawa Women' s University, Inagi, Tokyo 206-8511 (Japan); Baba, Norio [Department of Electric Engineering, Kogakuin University, Hachioji, Tokyo 192-0015 (Japan); Katayama, Eisaku [Division of Biomolecular Imaging, Institute of Medical Science, The University of Tokyo, Minato-ku, Tokyo 108-8639 (Japan)]. E-mail: ekatayam@ims.u-tokyo.ac.jp

    2007-01-15

    Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the 'Structural analysis of single molecules', we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.

  18. A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy.

    Science.gov (United States)

    Kimori, Yoshitaka; Oguchi, Yosuke; Ichise, Norihiko; Baba, Norio; Katayama, Eisaku

    2007-01-01

    Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the "Structural analysis of single molecules", we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.

  19. The use of rapid prototyped implants to simulate knee joint abnormalities for in vitro testing: a validation study with replica implants of the native trochlea.

    Science.gov (United States)

    Van Haver, Annemieke; De Roo, Karel; De Beule, Matthieu; Van Cauter, Sofie; Labey, Luc; De Baets, Patrick; Claessens, Tom; Verdonk, Peter

    2014-08-01

    To investigate the biomechanical effect of skeletal knee joint abnormalities, the authors propose to implant pathologically shaped rapid prototyped implants in cadaver knee specimens. This new method was validated by replacing the native trochlea by a replica implant on four cadaver knees with the aid of cadaver-specific guiding instruments. The accuracy of the guiding instruments was assessed by measuring the rotational errors of the cutting planes (on average 3.01° in extension and 1.18° in external/internal rotation). During a squat and open chain simulation, the patella showed small differences in its articulation with the native trochlea and the replica trochlea, which could partially be explained by the rotational errors of the implants. This study concludes that this method is valid to investigate the effect of knee joint abnormalities with a replica implant as a control condition to account for the influence of material properties and rotational errors of the implant. © IMechE 2014.

  20. Demonstration of characteristic skin surface contours of extramammary Paget's disease and parapsoriasis en plaque by image analysis of negative impression replicas.

    Science.gov (United States)

    Kikuchi, Katsuko; Aiba, Setsuya; O'Goshi, Ken-ichiro; Yanai, Motohiro; Takahashi, Motoji; Kasai, Hidefumi; Tagami, Hachiro

    2002-10-01

    The surface contours of lesional skin of certain skin diseases, such as parapsoriasis en plaque (PEP) and extramammary Paget's disease (EMPD), in which there is a massive infiltration by non-epidermal cells, looks somewhat different from that of the adjacent normal skin, needless to state that they are apparently different from that of ordinary chronic inflammatory dermatoses where we found acanthotic epidermis accompanied by hyperkeratosis. We attempted to objectively characterize these unique skin surface changes qualitatively and quantitatively using non-invasive methods. Negative impression replicas were taken from the lesional skin of patients with EMPD or PEP as well as from the adjacent uninvolved skin. The findings were confirmed histologically. The replicas were examined by using computerized image analysis. Several parameters were analyzed that correlate with the changes in the anisotropy of the skin furrows (VC1), average skin roughness (KSD), average length of skin furrows (LEN), and number of skin furrows (NUM). There were significant decreases in KSD and NUM in EMPD, indicating a smoother skin surface in the lesional skin than in the adjacent normal skin. In contrast, the PEP lesion had an increase in VC1 and LEN and a decrease in NUM, which suggests larger skin ridges in the lesional skin than in the uninvolved skin. Thus the unique skin surface of the cutaneous disorders accompanied by epidermal invasion by non-epidermal cells, such as EMPD and PEP, was characterized both qualitatively and quantitatively using computerized image analysis of negative impression replicas.

  1. VT Telephone Exchange Boundaries

    Data.gov (United States)

    Vermont Center for Geographic Information — (Link to Metadata) The UtilityTelecom_EXCHANGE represents Vermont Telephone Exchange boundaries as defined by the VT Public Service Board. The original data was...

  2. Indiana Health Information Exchange

    Science.gov (United States)

    The Indiana Health Information Exchange is comprised of various Indiana health care institutions, established to help improve patient safety and is recognized as a best practice for health information exchange.

  3. Forecasting Exchange Rate Volatility in the Presence of Jumps

    OpenAIRE

    Busch, Thomas; Christensen, Bent Jesper; Nielsen, Morten Ørregaard

    2005-01-01

    We study measures of foreign exchange rate volatility based on high-frequency (5-minute) $/DM exchange rate returns using recent nonparametric statistical techniques to compute realized return volatility and its separate continuous sample path and jump components, and measures based on prices of exchange rate futures options, allowing calculation of option implied volatility. We find that implied volatility is an informationally efficient but biased forecast of future realized exchange rate v...

  4. Report of the pollack (Pollachius pollachius) Exchange 2016

    OpenAIRE

    Mahe, Kelig; Dufour, Jean-Louis; Mccausland, Ian; Sainza, Maria; Leal, Ana; Gonzalez, Cristina; Elleboode, Romain

    2016-01-01

    In September 2015, the Working Group on Biological Parameters (WGBIOP) recommended the first otolith exchange for Pollachius pollachius in 2016 (Otolith Exchanges proposals for 2016/2017; ICES, 2015). Kélig Mahe (IFREMER, France) was decided to be the responsible to organise this otolith exchange. A total of 5 readers from 2 countries (France & Spain) participated at the exchange of 2016. The otoliths of 314 individuals sampled from 2011 to 2015 in Southern stock (ICES area: IXa; n=99) and in...

  5. Approximate strip exchanging.

    Science.gov (United States)

    Roy, Swapnoneel; Thakur, Ashok Kumar

    2008-01-01

    Genome rearrangements have been modelled by a variety of primitives such as reversals, transpositions, block moves and block interchanges. We consider such a genome rearrangement primitive Strip Exchanges. Given a permutation, the challenge is to sort it by using minimum number of strip exchanges. A strip exchanging move interchanges the positions of two chosen strips so that they merge with other strips. The strip exchange problem is to sort a permutation using minimum number of strip exchanges. We present here the first non-trivial 2-approximation algorithm to this problem. We also observe that sorting by strip-exchanges is fixed-parameter-tractable. Lastly we discuss the application of strip exchanges in a different area Optical Character Recognition (OCR) with an example.

  6. The Radioecology Exchange

    Energy Technology Data Exchange (ETDEWEB)

    Barnett, Catherine L.; Beresford, Nicholas A.; Patel, Sabera; Wells, Claire; Howard, Brenda J. [NERC Centre for Ecology and Hydrology, CEH Lancaster, Lancaster Environment Centre, Library Av., Bailrigg, Lancaster, LA1 4AP (United Kingdom); Mora, Juan Carlos; Real, Almudena [Centro de Investigaciones Energeticas, Medioambientales y Tecnologicas (CIEMAT), Avenida complutense 22, Madrid, 28040 (Spain); Beaugelin-Seiller, Karine; Gilbin, Rodolphe; Hinton, Thomas [IRSN-Institut de Radioprotection et de Surete Nucleaire, 31, Avenue de la Division Leclerc, 92260 Fontenay-Aux-Roses (France); Vesterbacka, Pia; Muikku, Maarit; Outola, Iisa [Radiation and Nuclear Safety Authority, P.O. Box 14, FI-00881 Helsinki (Finland); Skuterud, Lavrans; AlbumYtre-Eide, Martin [Norwegian Radiation Protection Authority, Grini Naeringspark 13, Oesteraas, 1332 (Norway); Bradshaw, Clare; Stark, Karolina; Jaeschke, Ben [Stockholms Universitet, Universitetsvaegen 10, Stockholm, 10691 (Sweden); Oughton, Deborah; Skipperud, Lindis [NMBU Norwegian University of Life Science P.O. Box 5003N-1432 Aas, Oslo (Norway); Vandenhove, Hildegarde; Vanhoudt, Nathalie [SCK.CEN, Studiecentrum voor Kernenergie/Centre d' Etude de l' Energie Nucleaire, Avenue Herrmann-Debroux 40, BE-1160 Brussels (Belgium); Willrodt, Christine; Steiner, Martin [Bundesamt fuer Strahlenschutz, Willy-Brandt-Strasse 5, 38226 Salzgitter (Germany)

    2014-07-01

    The Radioecology Exchange (www.radioecology-exchange.org) was created in 2011 under the EU FP7 STAR (Strategy for Allied Radioecology) network of excellence. The project aims to integrate the research efforts on radioecology of nine European organisations into a sustainable network. The web site (together with associated Twitter feeds and Facebook page) currently provides the gateway to project outputs and other on-line radiation protection and radioecological resources. In 2013, the EU FP7 COMET (Coordination and implementation of a pan-European instrument for radioecology) project commenced; it aims to strengthen research on the impact of radiation on man and the environment. COMET includes the STAR partners with the addition of one Japanese and two Ukrainian research institutes. As STAR and COMET interact closely together and with the European Radioecology Alliance (www.er-alliance.org/), the Radioecology Exchange will be modified to become an international 'hub' for information related to radioecology. Project specific information will be hosted on separate web sites www.star-radioecology.org and www.comet-radioecology.org. This paper will present an overview of the resources hosted on the Radioecology Exchange inviting other scientists to contribute. Highlighted aspects of the site include: Social media (News blog, Twitter, Facebook) - Items announcing project outputs, training courses, jobs, studentships etc. Virtual laboratory - Information which encourages integration through joint research and integrated use of data and sample materials. These pages will focus on three categories: (1) Methodological: descriptions and video clips of commonly used analytical methods and protocols and the procedures used in STAR and COMET; (2) Informative: databases made available by STAR/COMET partners together with details of sample archives held. Fact-sheets on radio-ecologically important radionuclides and 'topical descriptions' which show absorbed

  7. Edge exchangeable models for network data

    CERN Document Server

    Crane, Harry

    2016-01-01

    Exchangeable models for vertex labeled graphs cannot replicate the large sample behaviors of sparsity and power law degree distributions observed in many network datasets. Out of this mathematical impossibility emerges the question of how network data can be modeled in a way that reflects known empirical behaviors and respects basic statistical principles. We address this question by observing that edges, not vertices, act as the statistical units in most network datasets, making a theory of edge labeled networks more natural for most applications. Within this context we introduce the new invariance principle of {\\em edge exchangeability}, which unlike its vertex exchangeable counterpart can produce networks with sparse and/or power law structure. We characterize the class of all edge exchangeable network models and identify a particular two parameter family of models with suitable theoretical properties for statistical inference. We discuss issues of estimation from edge exchangeable models and compare our a...

  8. Adaptively Compressed Exchange Operator

    CERN Document Server

    Lin, Lin

    2016-01-01

    The Fock exchange operator plays a central role in modern quantum chemistry. The large computational cost associated with the Fock exchange operator hinders Hartree-Fock calculations and Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, even for systems consisting of hundreds of atoms. We develop the adaptively compressed exchange operator (ACE) formulation, which greatly reduces the computational cost associated with the Fock exchange operator without loss of accuracy. The ACE formulation does not depend on the size of the band gap, and thus can be applied to insulating, semiconducting as well as metallic systems. In an iterative framework for solving Hartree-Fock-like systems, the ACE formulation only requires moderate modification of the code, and can be potentially beneficial for all electronic structure software packages involving exchange calculations. Numerical results indicate that the ACE formulation can become advantageous even for small systems with tens...

  9. Laser Processed Heat Exchangers

    Science.gov (United States)

    Hansen, Scott

    2017-01-01

    The Laser Processed Heat Exchanger project will investigate the use of laser processed surfaces to reduce mass and volume in liquid/liquid heat exchangers as well as the replacement of the harmful and problematic coatings of the Condensing Heat Exchangers (CHX). For this project, two scale unit test articles will be designed, manufactured, and tested. These two units are a high efficiency liquid/liquid HX and a high reliability CHX.

  10. Microsoft Exchange 2013 cookbook

    CERN Document Server

    Van Horenbeeck, Michael

    2013-01-01

    This book is a practical, hands-on guide that provides the reader with a number of clear, step-by-step exercises.""Microsoft Exchange 2013 Cookbook"" is targeted at network administrators who deal with the Exchange server in their day-to-day jobs. It assumes you have some practical experience with previous versions of Exchange (although this is not a requirement), without being a subject matter expert.

  11. Rapid Replica Copy Algorithm Based on Popularity in Hadoop%基于热度的Hadoop快速副本复制算法

    Institute of Scientific and Technical Information of China (English)

    张倩; 郑烇; 王嵩

    2015-01-01

    In cloud storage centers, replica of file may be lost because of the failure of nodes, which will affect the reliability of system, as well as the efficiency of file concurrent access. There are some deficiencies in the default replica copy algorithm in Hadoop, such as a concentration of data transfer process on a few DataNodes, load imbalance, low disk I/O throughput. To address this issue, this paper proposes a rapid replica copy algorithm based on popularity in Hadoop. It handles the popular block firstly, and chooses source and destination DataNodes properly. The simulation results show that the proposed algorithm improves the disk I/O throughput, load balance, and reduces average service response time significantly.%在云存储中心,由于节点失效带来的文件数据块副本丢失不仅会影响系统的可靠性,还会影响文件的并发访问效率。针对 Hadoop 中默认的副本复制方法存在的问题,即副本复制过程某些节点数据传输过于集中,负载不均衡,磁盘 I/O 吞吐率低,提出一种基于热度的快速副本复制算法。该算法优先复制热度高的数据块,合理选择数据块复制的源节点和目的节点。仿真结果表明,该算法平衡了系统的工作负载,提高了磁盘 I/O 吞吐率,显著降低用户请求平均响应时间。

  12. A novel approach to evaluating the reproducibility of a replication technique for the manufacture of electroconductive replicas for use in quantitative clinical dental wear studies.

    Science.gov (United States)

    Chadwick, R G; Mitchell, H L; Ward, S

    2004-04-01

    The assessment of the progression of tooth surface loss has until recently been limited to either the application of subjective ranking scales or visual comparison of sequential study casts. The development of quantitative measuring techniques offers the potential of greater accuracy and sensitivity. As direct intra-oral measurement is problematical such approaches often utilize impressions of the teeth, recorded at different epochs, to construct replicas for mapping and comparison. This in vitro investigation sought to determine the reproducibility of such an approach taking into account the total process chain. Two inlay cavities (one large, one small) were prepared in the palatal aspect of a plastic maxillary central incisor and restored with two flush fitting inlays. A series of impressions of this tooth were recorded, using a special tray and an addition cured light bodied silicone impression material (President, Coltene, Switzerland), with (a) both inlays in (b) both inlays out (c) large inlay out and small inlay in (d) large inlay in and small inlay out - a total of 16 impressions. Electroconductive replicas were fabricated from these and mapped using a computer controlled probe. Each series simulated wear of the tooth. A surface matching and difference detection algorithm was then used to compare each series of replicas and calculate the proportion of the surface undergoing simulated wear by a direct comparison of (a) matched to (b) or, indirectly as the summation of the results of matches of (a) with (c) and (a) with (d). The mean proportion of the surface with wear calculated directly was 26.6% (s.d.=0.6) and indirectly 26.1% (s.d. = 0.5). A one-way anova revealed no significant difference (P > 0.05). It is concluded that determining wear by this method is highly reproducible.

  13. Usable optimistic fair exchange

    OpenAIRE

    Küpçü, Alptekin; Lysyanskaya, A.

    2012-01-01

    Fairly exchanging digital content is an everyday problem. It has been shown that fair exchange cannot be achieved without a trusted third party (called the Arbiter). Yet, even with a trusted party, it is still non-trivial to come up with an efficient solution, especially one that can be used in a p2p file sharing system with a high volume of data exchanged. We provide an efficient optimistic fair exchange mechanism for bartering digital files, where receiving a payment in return for a file (b...

  14. Exchange rate regime choice

    Directory of Open Access Journals (Sweden)

    Beker Emilija

    2006-01-01

    Full Text Available The choice of an adequate exchange rate regime proves to be a highly sensitive field within which the economic authorities present and confirm themselves. The advantages and disadvantages of fixed and flexible exchange rate regimes, which have been quite relativized from the conventional point of view, together with simultaneous, but not synchronized effects of structural and external factors, remain permanently questioned throughout a complex process of exchange rate regime decision making. The paper reflects the attempt of critical identification of the key exchange rate performances with emphasis on continuous non-uniformity and (uncertainty of shelf life of a relevant choice.

  15. Non-invasive Florentine Renaissance Panel Painting Replica Structures Investigation by Using Terahertz Time-Domain Imaging (THz-TDI) Technique

    Science.gov (United States)

    Koch Dandolo, Corinna L.; Picollo, Marcello; Cucci, Costanza; Jepsen, Peter Uhd

    2016-11-01

    The potentials of the Terahertz Time-Domain Imaging (THz-TDI) technique for a non-invasive inspection of panel paintings have been considered in detail. The THz-TD data acquired on a replica of a panel painting made in imitation of Italian Renaissance panel paintings were processed in order to provide insights as to the limits and potentials of the technique in detecting different kinds of underdrawings and paint layers. Constituent layers, construction techniques, and anomalies were identified and localized by interpreting the extracted THz dielectric stratigraphy.

  16. Conductive polymer-mediated 2D and 3D arrays of Mn3O4 nanoblocks and mesoporous conductive polymers as their replicas.

    Science.gov (United States)

    Nakagawa, Yoshitaka; Kageyama, Hiroyuki; Matsumoto, Riho; Oaki, Yuya; Imai, Hiroaki

    2015-11-28

    Orientation-controlled 2D and 3D microarrays of Mn3O4 nanocuboids that were mediated by a conductive polymer were fabricated by evaporation-induced self-assembly of the oxide nanoblocks and subsequent polymerization of pyrrole in the interparticle spaces. Free-standing mesoporous polypyrroles (PPy) having chain- and square-grid-like nanovoid arrays were obtained as replicas of the composite assemblies by dissolving the oxide nanoblocks. The PPy-mediated manganese oxide arrays exhibited stable electrochemical performance as an ultrathin anode of a lithium-ion secondary battery.

  17. Expression and biological activity of double replica retrovirus carrier-mediated neurotrophin-3 in olfactory ensheathing cells

    Institute of Scientific and Technical Information of China (English)

    Shougang Guo; Yifeng Du; Feng Jin; Minzhong Wang

    2009-01-01

    : Recombinant double replica retrovirus NT-3 gene was stably and effectivelyexpressed in OECs, and the expressed NT-3 possessed biological activity that promoted neuronalsurvival.

  18. Source and replica calculations

    Energy Technology Data Exchange (ETDEWEB)

    Whalen, P.P.

    1994-02-01

    The starting point of the Hiroshima-Nagasaki Dose Reevaluation Program is the energy and directional distributions of the prompt neutron and gamma-ray radiation emitted from the exploding bombs. A brief introduction to the neutron source calculations is presented. The development of our current understanding of the source problem is outlined. It is recommended that adjoint calculations be used to modify source spectra to resolve the neutron discrepancy problem.

  19. Intervento di replica

    Directory of Open Access Journals (Sweden)

    Gianluigi Rossini

    2013-12-01

    Full Text Available Già dalla discussione che si sta sviluppando su questa rivista intorno al libro di Antonello credo si veda bene una contrapposizione che mi capita spesso di rilevare nel dibattito nostrano: da un lato la sacrosanta irritazione verso un certo conservatorismo di sinistra e verso la lamentosa condanna “crisologica” della contemporaneità, atteggiamenti tanto diffusi quanto sterili; dall’altro una condivisibile preoccupazione: non diventeremo, per dirla con Milan Kundera, gli «allegri alleati dei nostri stessi becchini»? Nell’affrancarci da posizioni che sembrano obsolete, cosa ci rimane da contrapporre al dominio dell’ideologia mercantile e brutalmente quantitativa del neoliberismo?

  20. Optimization of Heat Exchangers

    Energy Technology Data Exchange (ETDEWEB)

    Ivan Catton

    2010-10-01

    The objective of this research is to develop tools to design and optimize heat exchangers (HE) and compact heat exchangers (CHE) for intermediate loop heat transport systems found in the very high temperature reator (VHTR) and other Generation IV designs by addressing heat transfer surface augmentation and conjugate modeling. To optimize heat exchanger, a fast running model must be created that will allow for multiple designs to be compared quickly. To model a heat exchanger, volume averaging theory, VAT, is used. VAT allows for the conservation of mass, momentum and energy to be solved for point by point in a 3 dimensional computer model of a heat exchanger. The end product of this project is a computer code that can predict an optimal configuration for a heat exchanger given only a few constraints (input fluids, size, cost, etc.). As VAT computer code can be used to model characteristics )pumping power, temperatures, and cost) of heat exchangers more quickly than traditional CFD or experiment, optimization of every geometric parameter simultaneously can be made. Using design of experiment, DOE and genetric algorithms, GE, to optimize the results of the computer code will improve heat exchanger disign.

  1. Building Relationships through Exchange

    Science.gov (United States)

    Primavera, Angi; Hall, Ellen

    2011-01-01

    From the moment of birth, children form and develop relationships with others in their world based on exchange. Children recognize that engaging in such encounters offers them the opportunity to enter into a relationship with another individual and to nurture that relationship through the exchange of messages and gifts, items and ideas. At Boulder…

  2. Aberration Corrected Emittance Exchange

    CERN Document Server

    Nanni, Emilio A

    2015-01-01

    Full exploitation of emittance exchange (EEX) requires aberration-free performance of a complex imaging system including active radio-frequency (RF) elements which can add temporal distortions. We investigate the performance of an EEX line where the exchange occurs between two dimensions with normalized emittances which differ by orders of magnitude. The transverse emittance is exchanged into the longitudinal dimension using a double dog-leg emittance exchange setup with a 5 cell RF deflector cavity. Aberration correction is performed on the four most dominant aberrations. These include temporal aberrations that are corrected with higher order magnetic optical elements located where longitudinal and transverse emittance are coupled. We demonstrate aberration-free performance of emittances differing by 4 orders of magnitude, i.e. an initial transverse emittance of $\\epsilon_x=1$ pm-rad is exchanged with a longitudinal emittance of $\\epsilon_z=10$ nm-rad.

  3. DOES CURRENCY SUBSTITUTION AFFECT EXCHANGE RATE VOLATILITY?

    Directory of Open Access Journals (Sweden)

    Hisao Kumamoto

    2014-10-01

    Full Text Available This study investigates the impacts of the degree of currency substitution on nominal exchange rate volatility in seven countries (Indonesia, the Philippines, the Czech Republic, Hungary, Poland, Argentina, and Peru. We use the Threshold ARCH model to consider the ratchet effect of currency substitution and sample periods in the 2000s, during which time the economies of the sample countries stabilized, while the U.S. dollar and euro depreciated against other major currencies following the recent global financial crisis. The presented empirical analyses show that the degree of currency substitution has significant positive effects on the conditional variance of the depreciation rate of the nominal exchange rate in most sample countries. Moreover, a shock to the depreciation rate of the nominal exchange rate has asymmetric effects on the conditional variance, depending on the sign. One possible explanation for these differential effects is the existence of the ratchet effect of currency substitution.

  4. Evaluation of the marginal and internal gaps of three different dental prostheses: comparison of the silicone replica technique and three-dimensional superimposition analysis.

    Science.gov (United States)

    Park, Jin-Young; Bae, So-Yeon; Lee, Jae-Jun; Kim, Ji-Hwan; Kim, Hae-Young; Kim, Woong-Chul

    2017-06-01

    The purposes of this study were to evaluate the marginal and internal gaps, and the potential clinical applications of three different methods of dental prostheses fabrication, and to compare the prostheses prepared using the silicone replica technique (SRT) and those prepared using the three-dimensional superimposition analysis (3DSA). Five Pekkton, lithium disilicate, and zirconia crowns were each manufactured and tested using both the SRT and the two-dimensional section of the 3DSA. The data were analyzed with the nonparametric version of a two-way analysis of variance using rank-transformed values and the Tukey's post-hoc test (α = .05). Significant differences were observed between the fabrication methods in the marginal gap (P .350), deep chamfer (P > .719), and axial wall (P > .150). As the 3DSA method is three-dimensional, it allows for the measurement of arbitrary points. All of the three fabrication methods are valid for measuring clinical objectives because they produced prostheses within the clinically acceptable range. Furthermore, a three-dimensional superimposition analysis verification method such as the silicone replica technique is also applicable in clinical settings.

  5. Optimizing the performance of bias-exchange metadynamics: folding a 48-residue LysM domain using a coarse-grained model.

    Science.gov (United States)

    Cossio, Pilar; Marinelli, Fabrizio; Laio, Alessandro; Pietrucci, Fabio

    2010-03-11

    Computer simulation of complex conformational transitions in biomolecules, such as protein folding, is considered one of the main goals of computational chemistry. A recently developed methodology, bias-exchange metadynamics, was successfully used to reversibly fold some small globular proteins. The objective of this work is to further improve this promising technique. This is accomplished by searching for the optimal set of parameters that enable folding a 48 amino acid protein, 1E0G , in the shortest possible time, using a coarse-grained force field UNRES. It is shown that bias-exchange metadynamics, if appropriately optimized, allows finding the folded state of 1E0G significantly faster than normal replica exchange.

  6. 基于 Shamir 秘密共享的云端多副本审计%Multiple-replica auditing in clouds using Shamir secret sharing

    Institute of Scientific and Technical Information of China (English)

    田晖; 陈羽翔; 黄永峰

    2016-01-01

    For auditing the integrity of multiple-replica in clouds,a public auditing scheme based on Shamir secret sharing was presented.The scheme can generate diverse data tags for different replicas of a given file using Shamir-secret-sharing algorithm,which is helpful for avoiding possible attacks from cloud service provider (CSP)and locating errors while the CSP does not exactly store all required replicas.Further,the scheme support batch auditing for multiple-replicas using Boneh-Lynn-Shacham (BLS)signature and bilinear maps,which can cut down times of interactions between the CSP and the auditor,and reduce communication costs.Moreover,random masks were introduced in user′s data preprocessing and auditing process to avert conspiracy attack of the CSP and prevent privacy leakage. The security of the presented scheme was proved in theory,and the auditing performance was experi-mentally compared with that of the previous work.The experimental results demonstrate that the pro-posed scheme can effectively achieve secure auditing for multiple-replica in clouds,and outperforms the existing methods on both time and space costs.%针对云端多副本审计问题,提出了一种基于 Shamir 秘密共享的审计方案。该方案利用 Shamir 秘密共享算法为同一数据文件的所有副本生成不同的数据标签,以防范云服务提供商的多种攻击,且根据该算法特性生成的聚合标签能有助于实现云服务提供商未完全持有全部副本数据时的出错定位;利用 BLS (Boneh-Lynn-Shacham)签名和双线性映射技术实现了多副本的批量审计,避免了云服务提供商与审计者之间的多次交互,从而降低了审计过程中的通信开销;通过在用户数据预处理阶段引入随机掩码实现了对合谋攻击的防范,并在审计过程中应用随机掩码避免了用户隐私的泄漏。对提出方案的安全性进行了理论证明,并与已有方法在性能方面进行了比较和实

  7. A Bayesian Justification for Random Sampling in Sample Survey

    Directory of Open Access Journals (Sweden)

    Glen Meeden

    2012-07-01

    Full Text Available In the usual Bayesian approach to survey sampling the sampling design, plays a minimal role, at best. Although a close relationship between exchangeable prior distributions and simple random sampling has been noted; how to formally integrate simple random sampling into the Bayesian paradigm is not clear. Recently it has been argued that the sampling design can be thought of as part of a Bayesian's prior distribution. We will show here that under this scenario simple random sample can be given a Bayesian justification in survey sampling.

  8. Exchange rate regimes and external financial stability

    Directory of Open Access Journals (Sweden)

    Stoica Ovidiu

    2016-01-01

    Full Text Available Financial stability within the framework of the global financial crisis has become a common topic for researchers and practitioners. In order to analyse the impact of exchange rate regimes on financial stability we use both the de jure and de facto exchange rate classifications. We apply the model to a 1999-2010 annual data sample for 135 countries and territories, grouped by the level of economic development. Our second focus is the investigation of the effects of the exchange rate regimes in three economic integration areas (member countries of the European Union 27, the Southern Common Market, and the Association of Southeast Asian Nations on financial stability. Our results generally support the central banks’ concerns that the flexibility of exchange rate regimes should be reduced in order to sustain financial stability; however, the findings are not robust when using alternative regime classifications.

  9. Anion exchange membrane

    Science.gov (United States)

    Verkade, John G; Wadhwa, Kuldeep; Kong, Xueqian; Schmidt-Rohr, Klaus

    2013-05-07

    An anion exchange membrane and fuel cell incorporating the anion exchange membrane are detailed in which proazaphosphatrane and azaphosphatrane cations are covalently bonded to a sulfonated fluoropolymer support along with anionic counterions. A positive charge is dispersed in the aforementioned cations which are buried in the support to reduce the cation-anion interactions and increase the mobility of hydroxide ions, for example, across the membrane. The anion exchange membrane has the ability to operate at high temperatures and in highly alkaline environments with high conductivity and low resistance.

  10. Heat exchanger design handbook

    CERN Document Server

    Thulukkanam, Kuppan

    2013-01-01

    Completely revised and updated to reflect current advances in heat exchanger technology, Heat Exchanger Design Handbook, Second Edition includes enhanced figures and thermal effectiveness charts, tables, new chapter, and additional topics--all while keeping the qualities that made the first edition a centerpiece of information for practicing engineers, research, engineers, academicians, designers, and manufacturers involved in heat exchange between two or more fluids.See What's New in the Second Edition: Updated information on pressure vessel codes, manufacturer's association standards A new c

  11. Exchange Rate in Focus

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    China announced the reform of its decade-old RMB exchange rate regime last July, linking the RMB to a basket of currencies rather than the U.S. dollar alone, and allowing the RMB to appreciate 2 percent against the U.S. currency. Since then, different viewpoints on the new regime have been voiced. The People's Bank of China, the central bank, said in a statement in late March that it would further improve the system, broadening the foreign exchange market, increasing the flexibility of the RMB exchange r...

  12. Radiotoxicological analyses of {sup 239+240}Pu and {sup 241}Am in biological samples by anion-exchange and extraction chromatography: a preliminary study for internal contamination evaluations

    Energy Technology Data Exchange (ETDEWEB)

    Ridone, S.; Arginelli, D.; Bortoluzzi, S.; Canuto, G.; Montalto, M.; Nocente, M.; Vegro, M. [Italian National Agency for New Technologies, Energy and the Environment (ENEA), Research Centre of Saluggia, Radiation Protection Institute, Saluggia, VC (Italy)

    2006-07-01

    Many biological samples (urines and faeces) have been analysed by means of chromatographic extraction columns, utilising two different resins (AG 1-X2 resin chloride and T.R.U.), in order to detect the possible internal contamination of {sup 239{sup +}}{sup 240}Pu and {sup 241}Am, for some workers of a reprocessing nuclear plant in the decommissioning phase. The results obtained show on one hand the great suitability of the first resin for the determination of plutonium, and on the other the great selectivity of the second one for the determination of americium.

  13. Data Exchange Inventory System (DEXI)

    Data.gov (United States)

    Social Security Administration — Enterprise tool used to identify data exchanges occurring between SSA and our trading partners. DEXI contains information on both incoming and outgoing exchanges and...

  14. Exchange Risk Management Policy

    CERN Document Server

    2005-01-01

    At the Finance Committee of March 2005, following a comment by the CERN Audit Committee, the Chairman invited the Management to prepare a document on exchange risk management policy. The Finance Committee is invited to take note of this document.

  15. NASA Earth Exchange (NEX)

    Data.gov (United States)

    National Aeronautics and Space Administration — The NASA Earth Exchange (NEX) represents a new platform for the Earth science community that provides a mechanism for scientific collaboration and knowledge sharing....

  16. Active microchannel heat exchanger

    Science.gov (United States)

    Tonkovich, Anna Lee Y [Pasco, WA; Roberts, Gary L [West Richland, WA; Call, Charles J [Pasco, WA; Wegeng, Robert S [Richland, WA; Wang, Yong [Richland, WA

    2001-01-01

    The present invention is an active microchannel heat exchanger with an active heat source and with microchannel architecture. The microchannel heat exchanger has (a) an exothermic reaction chamber; (b) an exhaust chamber; and (c) a heat exchanger chamber in thermal contact with the exhaust chamber, wherein (d) heat from the exothermic reaction chamber is convected by an exothermic reaction exhaust through the exhaust chamber and by conduction through a containment wall to the working fluid in the heat exchanger chamber thereby raising a temperature of the working fluid. The invention is particularly useful as a liquid fuel vaporizer and/or a steam generator for fuel cell power systems, and as a heat source for sustaining endothermic chemical reactions and initiating exothermic reactions.

  17. Emittance exchange results

    Energy Technology Data Exchange (ETDEWEB)

    Fliller, R.P., III; /Brookhaven; Koeth, T.; /Rutgers U., Piscataway

    2009-09-01

    The promise of next-generation light sources depends on the availability of ultra-low emittance electron sources. One method of producing low transverse emittance beams is to generate a low longitudinal emittance beam and exchange it with a large transverse emittance. Experiments are underway at Fermilab's A0 Photoinjector and ANL's Argonne Wakefield Accelerator using the exchange scheme of Kim and Sessler. The experiment at the A0 Photoinjector exchanges a large longitudinal emittance with a small transverse emittance. AWA expects to exchange a large transverse emittance with a small longitudinal emittance. In this paper we discuss recent results at A0 and AWA and future plans for these experiments.

  18. Emittance Exchange Results

    Energy Technology Data Exchange (ETDEWEB)

    Fliller III,R.; Koeth, T.

    2009-05-04

    The promise of next-generation light sources depends on the availability of ultra-low emittance electron sources. One method of producing low transverse emittance beams is to generate a low longitudinal emittance beam and exchange it with a large transverse emittance. Experiments are underway at Fermilab's A0 Photoinjector and ANL's Argonne Wakefield Accelerator using the exchange scheme of Kim and Sessler. The experiment at the A0 Photoinjector exchanges a large longitudinal emittance with a small transverse emittance. AWA expects to exchange a large transverse emittance with a small longitudinal emittance. In this paper we discuss recent results at A0 and AWA and future plans for these experiments.

  19. Microplate Heat Exchanger Project

    Data.gov (United States)

    National Aeronautics and Space Administration — We propose a microplate heat exchanger for cryogenic cooling systems used for continuous flow distributed cooling systems, large focal plane arrays, multiple cooling...

  20. HUD Exchange Grantee Database

    Data.gov (United States)

    Department of Housing and Urban Development — The About Grantees section of the HUD Exchange brings up contact information, reports, award, jurisdiction, and location data for organizations that receive HUD...

  1. Compact, super heat exchanger

    Science.gov (United States)

    Fortini, A.; Kazaroff, J. M.

    1980-01-01

    Heat exchanger uses porous media to enhance heat transfer through walls of cooling channels, thereby lowering wall temperature. Porous media within cooling channel increases internal surface area from which heat can be transferred to coolant. Comparison data shows wall has lower temperature and coolant has higher temperature when porous medium is used within heat exchanger. Media can be sintered powedered metal, metal fibers, woven wire layers, or any porous metal having desired permeability and porosity.

  2. The impact of exchange rate uncertainty on exports: the case of Turkey

    OpenAIRE

    Orhan KARACA; Saatcioğlu, Cem

    2004-01-01

    In this paper we examined the relationship between exchange rate uncertainty and exports in Turkey. Sample period of the study is 1981, May 1, the date Turkey introduced flexible exchange rate system after quiting fixed exchange rate system, and 2001, February 22 when exchange rates were left floating. The results of this study, in which quarterly data are used, indicate that exchange rate uncertainty affects exports negatively in Turkey. This finding is valid both for long-run and short-run.

  3. Private Health Insurance Exchanges

    Science.gov (United States)

    Buttorff, Christine; Nowak, Sarah; Syme, James; Eibner, Christine

    2017-01-01

    Abstract Private health insurance exchanges offer employer health insurance, combining online shopping, increased plan choice, benefit administration, and cost-containment strategies. This article examines how private exchanges function, how they may affect employers and employees, and the possible implications for the Affordable Care Act's (ACA's) Small Business Health Options Program (SHOP) Marketplaces. The authors found that private exchanges could encourage employees to select less-generous plans. This could expose employees to higher out-of-pocket costs, but premium contributions would drop substantially, so net spending would decrease. On the other hand, employee spending may increase if, in moving to private exchanges, employers decrease their health insurance contributions. Most employers can avoid the ACA's “Cadillac tax” by reducing the generosity of the plans they offer, regardless of whether they move to a private exchange. There is not yet enough evidence to determine whether the private exchanges will become prominent in the insurance market and how they will affect employers and their employees. PMID:28845340

  4. 教育资源网格模型及副本创建策略%Education Resource Grid Model and Replica Creation Strategies

    Institute of Scientific and Technical Information of China (English)

    邢长明; 刘方爱; 杨林; 厉文

    2009-01-01

    教育资源网格是解决目前分布式教育资源共享问题的有效手段.针对中小学教育资源共享问题,提出了层次式的教育资源网格模型,定义了各层节点的功能.通过与欧洲数据网格对比,分析了教育资源网格的特点.基于层次式的教育资源网格,对影响副本创建策略性能的因素进行了分析,然后引入网络带宽和文件大小两个参数,提出了一种动态副本创建策略(dynamic replica creation strategy,简称EDRS).利用数据网格模拟工具OptorSim构建了教育资源网格虚拟环境,分析比较了EDRS策略与Caching-LRU策略、Caching-LFU策略和基于经济模型的副本创建策略的性能.最后,综合各项指标分析了不同策略对教育资源网格系统性能的影响.结果表明,EDRS策略在教育资源网格应用中有着更好的系统性能.%The education resource grid is an effective measure to solve the problem of sharing distributed education resources at present. First, with regard to the education resource sharing in secondary and elementary schools, a hierarchy model of education resource grid is proposed and the functions of nodes in each layer are defined in this paper. By comparing with the European Data Grid, the education resource grid is analyzed with its characteristics. Then based on the hierarchy grid model, some factors, which influence the performance of replica creation strategy, are analyzed and a dynamic replica creation strategy (EDRS) is proposed by introducing two parameters, i.e., the network bandwidth and file size. With the data grid simulation tool OptorSim, the performances of EDRS with Caching-LRU, Caching-LFU and the economic model strategy are compared respectively. At last, the influence of different strategies on the performance of the education resource grid system is analyzed by synthesizing each parameter. The result indicates that the EDRS has a better system performance in applications of the education resource

  5. Nanotechnology for forensic sciences: analysis of PDMS replica of the case head of spent cartridges by optical microscopy, SEM and AFM for the ballistic identification of individual characteristic features of firearms.

    Science.gov (United States)

    Valle, Francesco; Bianchi, Michele; Tortorella, Silvia; Pierini, Giovanni; Biscarini, Fabio; D'Elia, Marcello

    2012-10-10

    A novel application of replica molding to a forensic problem, viz. the accurate reproduction of the case head of gun and rifle cartridges, prior and after been shot, is presented. The fabrication of an arbitrary number of identical copies of the region hit by the firing pin and by the breech face is described. The replicas can be (i) handled without damaging the original evidence, (ii) distributed to different law enforcement agencies for comparison against other evidences found on crime scenes or ballistic tests of seized firearms, (iii) maintained on a file by the laboratories. A detailed analysis of the morphological features of the replicas has been carried out by standard microscopy techniques as well as by advanced microscopy such as scanning probe and scanning electron leading to a quantitative morphological characterization of the case heads down to the nanometer scale. The assignment of the cartridge replicas to the shooting weapon is demonstrated to hold below the micron scale, while it is hindered at the nanometer level both by the manufacturing differences and by eventual modifications occurring on the firing pin.

  6. SEM/EDX and vis spectrophotometry study of the stability of resin-bound mortars used for casting replicas and filling missing parts of historic stone fountains.

    Science.gov (United States)

    Roig-Salom, José-Luis; Doménech-Carbó, María-Teresa; de la Cruz-Cañizares, Juana; Bolívar-Galiano, Fernando; Pelufo-Carbonell, María-José; Peraza-Zurita, Yaiza

    2003-04-01

    A study by SEM/EDX and spectrophotometry in the visible region attempting to assess the stability of new resin-bound mortars used for casting replicas of marble historic fountains is presented in this paper. Different accelerating tests such as thermal ageing, UV light ageing, ageing in an SO(2) pollutant chamber, freezing cycles ageing, salt crystallisation ageing, natural ageing and biological attack have been applied to a series of test specimens prepared with polyester-, epoxy- and gel-coat-bound mortars. Examination of morphology, measurement of chemical composition and chromatic coordinates before and after ageing treatments establish the higher stability and resistance properties of these resin-bound mortars by comparison to those from the natural marbles.

  7. Oligomer Formation of Amyloid-β(29-42) from Its Monomers Using the Hamiltonian Replica-Permutation Molecular Dynamics Simulation.

    Science.gov (United States)

    Itoh, Satoru G; Okumura, Hisashi

    2016-07-14

    Oligomers of amyloid-β peptides (Aβ) are formed during the early stage of the amyloidogenesis process and exhibit neurotoxicity. The oligomer formation process of Aβ and even that of Aβ fragments are still poorly understood, though understanding of these processes is essential for remedying Alzheimer's disease. In order to better understand the oligomerization process of the C-terminal Aβ fragment Aβ(29-42) at the atomic level, we performed the Hamiltonian replica-permutation molecular dynamics simulation with Aβ(29-42) molecules using the explicit water solvent model. We observed that oligomers increased in size through the sequential addition of monomers to the oligomer, rather than through the assembly of small oligomers. Moreover, solvent effects played an important role in this oligomerization process.

  8. Skylab 3600 groove/mm replica grating with a scandium-silicon multilayer coating and high normal-incidence efficiency at 38-nm wavelength.

    Science.gov (United States)

    Seely, John F; Uspenskii, Yu A; Pershin, Yu P; Kondratenko, V V; Vinogradov, A V

    2002-04-01

    A Sc-Si multilayer coating was applied to a replica of the 3600 groove/mm grating, developed for the SO82A spectroheliograph that flew on the Skylab mission, for the purpose of enhancing the normal-incidence efficiency in the extreme-ultraviolet region. The efficiency, measured at an angle of incidence of 6 degrees with synchrotron radiation, had a maximum value of 7.2% at a wavelength of 38 nm and was a factor of 3 higher than the efficiency of the gold-coated Skylab grating. The measured efficiency of the Sc-Si grating was in good agreement with the efficiency calculated by use of the modified integral method.

  9. Replica symmetry breaking in the critical behavior in the m-component ferromagnetic spin systems with a short-range disorder

    Science.gov (United States)

    Wu, Xin-tian

    We investigate the replica symmetry breaking (RSB) in m-component ferromagnetic spin systems with a short-range disorder. Using ε-expansion the Landau-Ginzburg Hamiltonian with a RSB quartic interaction term is studied, where ε=4- d, d is the spatial dimension. The differential recursion relations of renormalization group (RG) are derived to the second order of ε. The replicon eigenvalue, which is a simple way to investigate the stability with respect to the continuous RSB modes, is defined. The fixed points and their eigenvalues are obtained. For m mc, we find a stable fixed point, which is not only stable in the one-step RSB subspace but also stable with respect to the continuous RSB. However, it is unphysical. For m> mc only the pure fixed point is physical and stable.

  10. Hierarchical control of porous silica by pH adjustment: Alkyl polyamines as surfactants for bimodal silica synthesis and its carbon replica

    Science.gov (United States)

    Abellán, G.; Carrillo, A. I.; Linares, N.; Serrano, E.; García-Martínez, J.

    2009-08-01

    Bimodal macro-mesoporous silica networks have been prepared in a simple one-pot synthesis using an inexpensive tetramine surfactant and tetraethoxysilane as a silica precursor. These novel materials show high pore volumes and templated mesopores (average pore size 3.0 nm) embedded in 20 nm thick walls forming interparticle large meso/macropores. The judicious control of the pH during the silica formation allows for the precise control of the interparticle condensation, likely due to the change in the interaction between the tetramine surfactant and the silica precursors. Finally, a highly porous carbon replica with bimodal porosity was prepared by using the bimodal silica as a hard sacrificial template. The microstructure of the silica template was accurately transferred to the carbon material obtaining high surface areas (up to 1300 m 2 g -1) and total pore volumes ≥2 cm 3 g -1.

  11. Interface free-energy exponent in the one-dimensional Ising spin glass with long-range interactions in both the droplet and broken replica symmetry regions

    Science.gov (United States)

    Aspelmeier, T.; Wang, Wenlong; Moore, M. A.; Katzgraber, Helmut G.

    2016-08-01

    The one-dimensional Ising spin-glass model with power-law long-range interactions is a useful proxy model for studying spin glasses in higher space dimensions and for finding the dimension at which the spin-glass state changes from having broken replica symmetry to that of droplet behavior. To this end we have calculated the exponent that describes the difference in free energy between periodic and antiperiodic boundary conditions. Numerical work is done to support some of the assumptions made in the calculations and to determine the behavior of the interface free-energy exponent of the power law of the interactions. Our numerical results for the interface free-energy exponent are badly affected by finite-size problems.

  12. The use of 3D laser imaging and a new breast replica cast as a method to optimize autologous breast reconstruction after mastectomy.

    Science.gov (United States)

    Ahcan, Uros; Bracun, Drago; Zivec, Katarina; Pavlic, Rok; Butala, Peter

    2012-04-01

    Aesthetically pleasing and symmetrical breasts are the goal of reconstructive breast surgery. Sometimes, however, multiple procedures are needed to improve a reconstructed breast's symmetry and appearance. In order to avoid additional corrective procedures, we have developed a new method that uses a reverse engineering technique to produce what we call a new breast replica cast (NBRC). The NBRC is a mould of the contralateral healthy breast, designed according to preoperative laser 3D images. During surgery, the mould is used to help shape the new breast. With this method, we are able to achieve breast symmetry in terms of volume, projection, contour, and position on the chest wall more accurately, more quickly, and more safely than before. Copyright © 2011 Elsevier Ltd. All rights reserved.

  13. Exchanging Description Logic Knowledge Bases

    NARCIS (Netherlands)

    Arenas, M.; Botoeva, E.; Calvanese, D.; Ryzhikov, V.; Sherkhonov, E.

    2012-01-01

    In this paper, we study the problem of exchanging knowledge between a source and a target knowledge base (KB), connected through mappings. Differently from the traditional database exchange setting, which considers only the exchange of data, we are interested in exchanging implicit knowledge. As rep

  14. Using Ion Exchange Chromatography to Separate and Quantify Complex Ions

    Science.gov (United States)

    Johnson, Brian J.

    2014-01-01

    Ion exchange chromatography is an important technique in the separation of charged species, particularly in biological, inorganic, and environmental samples. In this experiment, students are supplied with a mixture of two substitution-inert complex ions. They separate the complexes by ion exchange chromatography using a "flash"…

  15. Using Ion Exchange Chromatography to Separate and Quantify Complex Ions

    Science.gov (United States)

    Johnson, Brian J.

    2014-01-01

    Ion exchange chromatography is an important technique in the separation of charged species, particularly in biological, inorganic, and environmental samples. In this experiment, students are supplied with a mixture of two substitution-inert complex ions. They separate the complexes by ion exchange chromatography using a "flash"…

  16. Ion exchange phenomena

    Energy Technology Data Exchange (ETDEWEB)

    Bourg, I.C.; Sposito, G.

    2011-05-01

    Ion exchange phenomena involve the population of readily exchangeable ions, the subset of adsorbed solutes that balance the intrinsic surface charge and can be readily replaced by major background electrolyte ions (Sposito, 2008). These phenomena have occupied a central place in soil chemistry research since Way (1850) first showed that potassium uptake by soils resulted in the release of an equal quantity of moles of charge of calcium and magnesium. Ion exchange phenomena are now routinely modeled in studies of soil formation (White et al., 2005), soil reclamation (Kopittke et al., 2006), soil fertilitization (Agbenin and Yakubu, 2006), colloidal dispersion/flocculation (Charlet and Tournassat, 2005), the mechanics of argillaceous media (Gajo and Loret, 2007), aquitard pore water chemistry (Tournassat et al., 2008), and groundwater (Timms and Hendry, 2007; McNab et al., 2009) and contaminant hydrology (Chatterjee et al., 2008; van Oploo et al., 2008; Serrano et al., 2009).

  17. Microgravity condensing heat exchanger

    Science.gov (United States)

    Thomas, Christopher M. (Inventor); Ma, Yonghui (Inventor); North, Andrew (Inventor); Weislogel, Mark M. (Inventor)

    2011-01-01

    A heat exchanger having a plurality of heat exchanging aluminum fins with hydrophilic condensing surfaces which are stacked and clamped between two cold plates. The cold plates are aligned radially along a plane extending through the axis of a cylindrical duct and hold the stacked and clamped portions of the heat exchanging fins along the axis of the cylindrical duct. The fins extend outwardly from the clamped portions along approximately radial planes. The spacing between fins is symmetric about the cold plates, and are somewhat more closely spaced as the angle they make with the cold plates approaches 90.degree.. Passageways extend through the fins between vertex spaces which provide capillary storage and communicate with passageways formed in the stacked and clamped portions of the fins, which communicate with water drains connected to a pump externally to the duct. Water with no entrained air is drawn from the capillary spaces.

  18. 基于小世界的物联网中副本定位算法%Replica Location Algorithm Approach Based on the Small World in the Internet of Things

    Institute of Scientific and Technical Information of China (English)

    高辉; 张冬悦; 赵俊涛; 吴吉红

    2012-01-01

    Internet of Things has a large amount of data,heterogeneous node,extensive distribution,etc.Replica can improve data access performance.According to the requirements of fast and efficient replica location for the Internet of things,a replica location method based on the class of small world-the class level and the domain level in the Internet of Things is presented.From the local clustering of data access in the Internet of Things,nodes are divided into the class level and domain level.Given the class-domain data access characteristics,two-way circular message diffusion mechanism to achieve replica of the local and global location is proposed to increase the replica location efficiency.%物联网具有数据量大,节点异构且分布广泛等特点。采用副本存储可以提高数据访问性能。针对物联网中对副本定位快速高效要求的问题,提出一种基于小世界的类-域层次的物联网中副本定位方法。从物联网中数据访问的局部聚类性考虑,将节点划分为类层次和域层次,分别采用根据类-域数据访问特点的双向环形消息扩散机制,实现副本的局部和全局定位,从而提高副本定位的效率。

  19. Tuning Exchange Anisotropy of Exchange-Biased System

    Institute of Scientific and Technical Information of China (English)

    XU Yan; HU Jing-Guo; R.L.Stamps

    2008-01-01

    Exchange anisotropy in FM/AFM bilayers has given a lot of static magnetization properties such as enhanced coercivity and magnetization loop shifts.These phenomena are primarily from the effective anisotropies intro-duced into a ferromagnet by exchange coupling with a strongly anisotropic antiferromagnet.These effective anisotropies can also be used to explain the dynamic consequences of exchange-biased bilayers.In this article,the dynamic con-sequences such as exchange-induced susceptibility,exchange-induced permeability,and the corresponding domain wall characteristics in the exchange-biased structures of ferromagnet/antiferromagnetl/antiferromagnet2 are studied.The results show that the second antiferromagnetic layer can largely affect the dynamic consequences of exchange-biased bilayers.Especially in the ease of critical temperature,the effects become more obvious.Practically,the exchange anisotropy of biased bilayer system can be tuned by exchange coupling with the second antiferromagnetic layer.

  20. McCoy cell line as a possible model containing CD4+ receptors for the study of HIV-1 replication Células de linhagem McCoy como um possível modelo contendo receptores CD4+ para estudos da replicação do HIV

    Directory of Open Access Journals (Sweden)

    Yeda L. Nogueira

    2003-08-01

    Full Text Available Several studies have recently shown the use of recombinant rabies virus as potential vector-viral vaccine for HIV-1. The sequence homology between gp 120 and rabies virus glycoprotein has been reported. The McCoy cell line has therefore been used to show CD4+ or CD4+ like receptors. Samples of HIV-1 were isolated, when plasma of HIV-1 positive patients was inoculated in the McCoy cell line. The virus infection was then studied during successive virus passages. The proteins released in the extra cellular medium were checked for protein activity, by exposure to SDS Electrophoresis and blotting to nitro-cellulose filter, then reacting with sera of HIV positive and negative patients. Successive passages were performed, and showed viral replication, membrane permeabilization, the syncytium formation, and the cellular lysis (cytopathic effect. Flow cytometry analysis shows clear evidence that CD4+ receptors are present in this cell line, which enhances the likelihood of easy isolation and replication of HIV. The results observed allow the use of this cell line as a possible model for isolating HIV, as well as for carrying out studies of the dynamics of viral infection in several situations, including exposure to drugs in pharmacological studies, and possibly studies and analyses of the immune response in vaccine therapies.Recentes estudos demonstraram o uso do vírus raiva como modelo vetor para produzir vacinas expressando as glicoproteínas do vírus HIV-1. A homologia na seqüência entre gp120 do vírus HIV-1 e a glicoproteína G do vírus rábico já foi previamente relatada. Devido a estes fatos a linhagem de célula McCoy utilizada com sucesso para a replicação do vírus rábico foi utilizada para demonstrar a replicação do HIV-1. Amostra de HIV-1 foi isolada de plasma de um paciente soro positivo e inoculada em células de linhagem McCoy e então a infecção viral foi estudada em passagens sucessivas do vírus nesta célula. As prote

  1. Bank Liquidity and Exchange Rate Regimes

    OpenAIRE

    Bunda, Irina; Desquilbet, Jean-Baptiste

    2003-01-01

    International audience; Combining panel data on bank liquidity at the individual level and data on their macroeconomic environment, for a sample of commercial banks in emerging countries between 1995 and 2000, we show that their exists a “bank liquidity smile across exchange rate regimes”. In extreme regimes at both ends of the line, i.e. for pure floating exchange rate regimes at one end and currency boards and dollarized economies at the other end, bank assets are more liquid than in interm...

  2. Synthesis, characterization and ion exchange properties of zirconium(IV) tungstoiodophosphate, a new cation exchanger

    Indian Academy of Sciences (India)

    Weqar Ahmad Siddiqui; Shakeel Ahmad Khan

    2007-02-01

    Zirconium(IV) tungstoiodophosphate has been synthesized under a variety of conditions. The most chemically and thermally stable sample is prepared by adding a mixture of aqueous solutions of 0.5 mol L-1 sodium tungstate, potassium iodate and 1 mol L-1 orthophosphoric acid to aqueous solution of 0.1 mol L-1 zirconium(IV) oxychloride. Its ion exchange capacity for Na+ and K+ was found to be 2.20 and 2.35 meq g-1 dry exchanger, respectively. The material has been characterized on the basis of chemical composition, pH titration, Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis. The effect on the exchange capacity of drying the exchanger at different temperatures has been studied. The analytical importance of the material has been established by quantitative separation of Pb2+ from other metal ions.

  3. Dimer Metadynamics

    CERN Document Server

    Nava, Marco; Perego, Claudio; Parrinello, Michele

    2016-01-01

    Sampling complex potential energies is one of the most pressing challenges of contemporary computational science. Inspired by recent efforts that use quantum effects and discretized Feynman's path integrals to overcome large barriers we propose a replica exchange method. In each replica two copies of the same system with halved potential strengths interact via inelastic springs. The strength of the spring is varied in the different replicas so as to bridge the gap between the infinitely strong spring, that corresponds to the Boltzmann replica and the less tight ones. We enhance the spring length fluctuations using Metadynamics. We test the method on simple yet challenging problems.

  4. Sampling algorithms

    CERN Document Server

    Tillé, Yves

    2006-01-01

    Important progresses in the methods of sampling have been achieved. This book draws up an inventory of methods that can be useful for selecting samples. Forty-six sampling methods are described in the framework of general theory. This book is suitable for experienced statisticians who are familiar with the theory of survey sampling.

  5. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  6. Sample Design.

    Science.gov (United States)

    Ross, Kenneth N.

    1987-01-01

    This article considers various kinds of probability and non-probability samples in both experimental and survey studies. Throughout, how a sample is chosen is stressed. Size alone is not the determining consideration in sample selection. Good samples do not occur by accident; they are the result of a careful design. (Author/JAZ)

  7. Balanced sampling

    NARCIS (Netherlands)

    Brus, D.J.

    2015-01-01

    In balanced sampling a linear relation between the soil property of interest and one or more covariates with known means is exploited in selecting the sampling locations. Recent developments make this sampling design attractive for statistical soil surveys. This paper introduces balanced sampling

  8. Slice Sampling

    CERN Document Server

    Neal, R M

    2000-01-01

    Markov chain sampling methods that automatically adapt to characteristics of the distribution being sampled can be constructed by exploiting the principle that one can sample from a distribution by sampling uniformly from the region under the plot of its density function. A Markov chain that converges to this uniform distribution can be constructed by alternating uniform sampling in the vertical direction with uniform sampling from the horizontal `slice' defined by the current vertical position, or more generally, with some update that leaves the uniform distribution over this slice invariant. Variations on such `slice sampling' methods are easily implemented for univariate distributions, and can be used to sample from a multivariate distribution by updating each variable in turn. This approach is often easier to implement than Gibbs sampling, and more efficient than simple Metropolis updates, due to the ability of slice sampling to adaptively choose the magnitude of changes made. It is therefore attractive f...

  9. Baltic Exchange toodi Tallinna

    Index Scriptorium Estoniae

    2007-01-01

    Viimane osa merekonteineritesse kokkupakitud Londoni laevandus- ja merebörsi Baltic Exchange'i endise peakorteri detailidest jõudis 2007. a. juunis Tallinna. Hoone detailid ostnud ärimehed Heiti Hääl ja Eerik-Niiles Kross plaanivad leida hoonele koha Tallinna kesklinnas. E.-N. Krossi kommentaar

  10. Telephone Exchange Maintenance

    CERN Multimedia

    2005-01-01

    Urgent maintenance work on CERN telephone exchanges will be performed on 24 March from 6 a.m. to 8 a.m. Telephone services may be disrupted or even interrupted during this time. For more details, please contact us by email at Standard.Telephone@cern.ch.

  11. Currency Exchange Rates.

    Science.gov (United States)

    Siler, Carl R.

    This curriculum unit of the Muncie (Indiana) Southside High School is to simulate the dynamics of foreign currency exchange rates from the perspectives of: (1) a major U.S. corporation, ABB Power T & D Company, Inc., of Muncie, Indiana, a manufacturer of large power transformers for the domestic and foreign markets; and (2) individual…

  12. Microtube strip heat exchanger

    Science.gov (United States)

    Doty, F. D.

    1991-04-01

    During the last quarter, Doty Scientific, Inc. (DSI) continued to make progress on the microtube strip (MTS) heat exchangers. The team has begun a heat exchanger stress analysis; however, they have been concentrating the bulk of their analytical energies on a computational fluid dynmaics (CFD) model to determine the location and magnitude of shell-side flow maldistribution which decreases heat exchanger effectiveness. DSI received 120 fineblanked tubestrips from Southern Fineblanking (SFB) for manufacturing process development. Both SFB and NIST provided inspection reports of the tubestrips. DSI completed the tooling required to encapsulate a tube array and press tubestrips on the array. Pressing the tubestrips on tube arrays showed design deficiencies both in the tubestrip design and the tooling design. DSI has a number of revisions in process to correct these deficiencies. The research effort has identified a more economical fusible alloy for encapsulating the tube array, and determined the parameters required to successfully encapsulate the tube array with the new alloy. A more compact MTS heat exchanger bank was designed.

  13. Nature's Heat Exchangers.

    Science.gov (United States)

    Barnes, George

    1991-01-01

    Discusses the heat-transfer systems of different animals. Systems include heat conduction into the ground, heat transferred by convection, heat exchange in lizards, fish and polar animals, the carotid rete system, electromagnetic radiation from animals and people, and plant and animal fiber optics. (MDH)

  14. Counterflow Regolith Heat Exchanger

    Science.gov (United States)

    Zubrin, Robert; Jonscher, Peter

    2013-01-01

    A problem exists in reducing the total heating power required to extract oxygen from lunar regolith. All such processes require heating a great deal of soil, and the heat energy is wasted if it cannot be recycled from processed material back into new material. The counterflow regolith heat exchanger (CoRHE) is a device that transfers heat from hot regolith to cold regolith. The CoRHE is essentially a tube-in-tube heat exchanger with internal and external augers attached to the inner rotating tube to move the regolith. Hot regolith in the outer tube is moved in one direction by a right-hand - ed auger, and the cool regolith in the inner tube is moved in the opposite direction by a left-handed auger attached to the inside of the rotating tube. In this counterflow arrangement, a large fraction of the heat from the expended regolith is transferred to the new regolith. The spent regolith leaves the heat exchanger close to the temperature of the cold new regolith, and the new regolith is pre-heated close to the initial temperature of the spent regolith. Using the CoRHE can reduce the heating requirement of a lunar ISRU system by 80%, reducing the total power consumption by a factor of two. The unique feature of this system is that it allows for counterflow heat exchange to occur between solids, instead of liquids or gases, as is commonly done. In addition, in variants of this concept, the hydrogen reduction can be made to occur within the counterflow heat exchanger itself, enabling a simplified lunar ISRU (in situ resource utilization) system with excellent energy economy and continuous nonbatch mode operation.

  15. Analytical applications of ion exchangers

    CERN Document Server

    Inczédy, J

    1966-01-01

    Analytical Applications of Ion Exchangers presents the laboratory use of ion-exchange resins. This book discusses the development in the analytical application of ion exchangers. Organized into 10 chapters, this book begins with an overview of the history and significance of ion exchangers for technical purposes. This text then describes the properties of ion exchangers, which are large molecular water-insoluble polyelectrolytes having a cross-linked structure that contains ionic groups. Other chapters consider the theories concerning the operation of ion-exchange resins and investigate th

  16. Exchange bias mediated by interfacial nanoparticles (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Berkowitz, A. E., E-mail: aberk@ucsd.edu [Department of Physics, University of California, San Diego, La Jolla, California 92093 (United States); Center for Magnetic Recording Research, University of California, California 92093 (United States); Sinha, S. K. [Department of Physics, University of California, San Diego, La Jolla, California 92093 (United States); Fullerton, E. E. [Center for Magnetic Recording Research, University of California, California 92093 (United States); Smith, D. J. [Department of Physics, Arizona State University, Tempe, Arizona 85287 (United States)

    2015-05-07

    The objective of this study on the iconic exchange-bias bilayer Permalloy/CoO has been to identify those elements of the interfacial microstructure and accompanying magnetic properties that are responsible for the exchange-bias and hysteretic properties of this bilayer. Both epitaxial and polycrystalline samples were examined. X-ray and neutron reflectometry established that there existed an interfacial region, of width ∼1 nm, whose magnetic properties differed from those of Py or CoO. A model was developed for the interfacial microstructure that predicts all the relevant properties of this system; namely; the temperature and Permalloy thickness dependence of the exchange-bias, H{sub EX}, and coercivity, H{sub C}; the much smaller measured values of H{sub EX} from what was nominally expected; the different behavior of H{sub EX} and H{sub C} in epitaxial and polycrystalline bilayers. A surprising result is that the exchange-bias does not involve direct exchange-coupling between Permalloy and CoO, but rather is mediated by CoFe{sub 2}O{sub 4} nanoparticles in the interfacial region.

  17. Capillary sample

    Science.gov (United States)

    ... several times a day using capillary blood sampling. Disadvantages to capillary blood sampling include: Only a limited ... do not constitute endorsements of those other sites. Copyright 1997-2017, A.D.A.M., Inc. Duplication ...

  18. EXCHANGE RATE - REGIMES AND POLICIES

    Directory of Open Access Journals (Sweden)

    Novak Lučić

    2014-12-01

    Full Text Available Exchange rate of one currency is the price of the currency expressed in units of other currency. It is formed by the interaction of supply and demand in the foreign exchange market. Given that the exchange rate has a direct impact on the competitiveness of a country in terms of features of its exports and imports, in its balance of payments, and indirectly the overall economic and social development, in addition to acting in market principles - supply and demand in the formation of the equilibrium exchange rate, exchange rate is subject to different, stronger or weaker, more or less, forms of intervention. In the search for the optimal exchange rate policy of the national currency, the monetary authorities are positioned between the two extremes - the complete abandonment of the exchange rate to the market laws of supply and demand, or fixing the exchange rate for any of the selected anchor currency.

  19. Data Exchange Inventory (DEXI) System

    Data.gov (United States)

    Social Security Administration — DEXI is an intranet application used by SSA users to track all incoming and outgoing data exchanges between SSA and our data exchange partners. Information such as...

  20. A Firm-Specific Analysis of the Exchange-Rate Exposure of Dutch Firms

    NARCIS (Netherlands)

    A. de Jong (Abe); J. Ligterink; V. Macrae

    2002-01-01

    textabstractWe examine the relationship between exchange-rate changes and stock returns for a sample of Dutch firms over 1994-1998. We find that over 50% of the firms are significantly exposed to exchange-rate risk. Furthermore, all firms with significant exchange-rate exposure benefit from a

  1. A firm-specific exposure analyis of the exchange-rate exposure of Dutch firms

    NARCIS (Netherlands)

    de Jong, A.; Ligterink, J.; Macrae, V.

    2006-01-01

    We examine the relationship between exchange-rate changes and stock returns for a sample of Dutch firms over 1994-1998. We find that over 50 per cent of the firms are significantly exposed to exchange-rate risk. Furthermore, all firms with significant exchange-rate exposure benefit from a

  2. A firm-specific exposure analyis of the exchange-rate exposure of Dutch firms

    NARCIS (Netherlands)

    de Jong, A.; Ligterink, J.; Macrae, V.

    2006-01-01

    We examine the relationship between exchange-rate changes and stock returns for a sample of Dutch firms over 1994-1998. We find that over 50 per cent of the firms are significantly exposed to exchange-rate risk. Furthermore, all firms with significant exchange-rate exposure benefit from a depreciati

  3. ICP-AES Determination of Rare Earth Elements in Water Sample After Separation and Enrichment by Amphiprotic Ion Exchange Fiber Column%两性离子交换纤维柱富集-电感耦合等离子体原子发射光谱法测定水样中稀土元素

    Institute of Scientific and Technical Information of China (English)

    洪欣; 龚琦

    2011-01-01

    提出了两性离子交换纤维柱吸附富集镧、钕、铕、钆、铒和镱,1.5 mol·L(-1)硝酸溶液作洗脱剂,电感耦合等离子体原子发射光谱法测定水样中上述痕量稀土元素含量的方法.在优化的试验条件下,两性离子交换纤维柱对镧、钕、铕、钆、铒和镱的吸附容量分别为7.32,7.61,8.04,7.95,9.12,8.49 mg·g(-1);镧、钕、铕、钆、铒和镱的检出限(3S/N)分别为0.032,0.068,0.033,0.053,0.045,0.019μg·L(-1).方法用于水样中镧、钕、铕、钆、铒和镱含量的测定,回收率在90.0%-101.0%之间,相对标准偏差(n=5)在1.7%~5.4%之间.%Trace amounts of rare earth (RE) elements, including La, Nd, Eu, Gd, Er and Yb in water sample were adsorbed and enriched by amphiprotic ion exchange fiber column, and desorbed from the column by eluting with 1.5 mol · L-1 HNO3.The solution obtained was used for ICP-AES determination of the RE elements mentioned above.Under the optimum conditions, the adsorption capacity of the amphiprotic ion exchange fiber column toward La, Nd, Eu, Gd, Er and Yb were found to be 7.32, 7.61, 8.04, 7.95, 9.12 and 8.49 mg · g-1 respectively.Values of detection limits (3S/N) of this method were 0.032 , 0.068, 0.033, 0.053, 0.045 and 0.019 μg · L-1 respectively.The proposed method was applied to the determination of trace amounts of the RE's in water samples, giving the values of recovery.in the range of 90.0%-101% and RSD's (n=5) ranged from 1.7% to 5.4%.

  4. The Exchange Rate Forecasting Puzzle

    OpenAIRE

    Francis Vitek

    2005-01-01

    We survey and update the empirical literature concerning the predictability of nominal exchange rates using structural macroeconomic models over the recent floating exchange rate period. In particular, we consider both flexible and sticky price versions of the monetary model of nominal exchange rate determination. In agreement with the existing empirical literature, we find that nominal exchange rate movements are difficult to forecast, with a random walk generally dominating the monetary mod...

  5. Geology Exchange Program

    Science.gov (United States)

    Because geology professors cannot bring ore deposits from around the globe into their classrooms, the next best thing is to take their students to the deposits, according to David Norman, an associate professor of geochemistry at New Mexico Tech and Angus Moore of the Royal School of Mines. They organized a new exchange program between the New Mexico Institute of Mining and Technology in Socorro, N.M., and the Royal School of Mines in London, England. In May, 14 students from England toured deposits in New Mexico, Arizona, Utah, and Colorado; in the photograph, Norman (on the right) describes a rock from a New Mexico ore deposit to some of the visitors from England. In early June a contingency from New Mexico Tech began studying deposits in England, Spain, and Portugal. Norman and Moore say that the exchange program may be expanded next year.

  6. Exchange rate rebounds after foreign exchange market interventions

    Science.gov (United States)

    Hoshikawa, Takeshi

    2017-03-01

    This study examined the rebounds in the exchange rate after foreign exchange intervention. When intervention is strongly effective, the exchange rate rebounds at next day. The effect of intervention is reduced slightly by the rebound after the intervention. The exchange rate might have been 67.12-77.47 yen to a US dollar without yen-selling/dollar-purchasing intervention of 74,691,100 million yen implemented by the Japanese government since 1991, in comparison to the actual exchange rate was 103.19 yen to the US dollar at the end of March 2014.

  7. Heat exchange apparatus

    Science.gov (United States)

    Degtiarenko, Pavel V.

    2003-08-12

    A heat exchange apparatus comprising a coolant conduit or heat sink having attached to its surface a first radial array of spaced-apart parallel plate fins or needles and a second radial array of spaced-apart parallel plate fins or needles thermally coupled to a body to be cooled and meshed with, but not contacting the first radial array of spaced-apart parallel plate fins or needles.

  8. Exchange Rate Predictions

    OpenAIRE

    Yablonskyy, Karen

    2012-01-01

    The aim of this thesis is to analyze the foreign exchange currency forecasting techniques. Moreover the central idea behind the topic is to develop the strategy of forecasting by choosing indicators and techniques to make own forecast on currency pair EUR/USD. This thesis work is a mixture of theory and practice analyses. The goal during the work on this project was to study different types of forecasting techniques and make own forecast, practice forecasting and trading on Forex platform, ba...

  9. Thermoelectric heat exchange element

    Science.gov (United States)

    Callas, James J.; Taher, Mahmoud A.

    2007-08-14

    A thermoelectric heat exchange module includes a first substrate including a heat receptive side and a heat donative side and a series of undulatory pleats. The module may also include a thermoelectric material layer having a ZT value of 1.0 or more disposed on at least one of the heat receptive side and the heat donative side, and an electrical contact may be in electrical communication with the thermoelectric material layer.

  10. Exchange Rate Predictions

    OpenAIRE

    Yablonskyy, Karen

    2012-01-01

    The aim of this thesis is to analyze the foreign exchange currency forecasting techniques. Moreover the central idea behind the topic is to develop the strategy of forecasting by choosing indicators and techniques to make own forecast on currency pair EUR/USD. This thesis work is a mixture of theory and practice analyses. The goal during the work on this project was to study different types of forecasting techniques and make own forecast, practice forecasting and trading on Forex platform, ba...

  11. Hydrogen Exchange Mass Spectrometry.

    Science.gov (United States)

    Mayne, Leland

    2016-01-01

    Hydrogen exchange (HX) methods can reveal much about the structure, energetics, and dynamics of proteins. The addition of mass spectrometry (MS) to an earlier fragmentation-separation HX analysis now extends HX studies to larger proteins at high structural resolution and can provide information not available before. This chapter discusses experimental aspects of HX labeling, especially with respect to the use of MS and the analysis of MS data.

  12. Thermoelectric heat exchange element

    Energy Technology Data Exchange (ETDEWEB)

    Callas, James J. (Peoria, IL); Taher, Mahmoud A. (Peoria, IL)

    2007-08-14

    A thermoelectric heat exchange module includes a first substrate including a heat receptive side and a heat donative side and a series of undulatory pleats. The module may also include a thermoelectric material layer having a ZT value of 1.0 or more disposed on at least one of the heat receptive side and the heat donative side, and an electrical contact may be in electrical communication with the thermoelectric material layer.

  13. On Exchange QB∞-Rings

    Institute of Scientific and Technical Information of China (English)

    Huanyin Chen

    2007-01-01

    In this paper, we introduce a new class of rings, the QB∞-rings. We investigate necessary and sufficient conditions under which an exchange ring is a QB∞-ring. The modules over an exchange QB∞-ring are studied. Also, we prove that every regular square matrix over an exchange QB∞-ring admits a diagonal reduction by pseudo-invertible matrices.

  14. O3 and NOx Exchange

    NARCIS (Netherlands)

    Loubet, B.; Castell, J.F.; Laville, P.; Personne, E.; Tuzet, A.; Ammann, C.; Emberson, L.; Ganzeveld, L.; Kowalski, A.S.; Merbold, L.; Stella, P.; Tuovinen, J.P.

    2015-01-01

    This discussion was based on the background document “Review on modelling atmosphere-biosphere exchange of Ozone and Nitrogen oxides”, which reviews the processes contributing to biosphere-atmosphere exchange of O3 and NOx, including stomatal and non-stomatal exchange of O3 and NO, NO2.

  15. The stability of exchange networks

    NARCIS (Netherlands)

    Doğan, G.; Assen, M. van; Rijt, A. van de; Buskens, V.W.

    2009-01-01

    Economic and sociological exchange theories predict divisions of exchange benefits given an assumed fixed network of exchange relations. Since network structure has been found to have a large impact on actors’ payoffs, actors have strong incentives for network change.Weanswer the question what happe

  16. Scraped surface heat exchangers.

    Science.gov (United States)

    Rao, Chetan S; Hartel, Richard W

    2006-01-01

    Scraped surface heat exchangers (SSHEs) are commonly used in the food, chemical, and pharmaceutical industries for heat transfer, crystallization, and other continuous processes. They are ideally suited for products that are viscous, sticky, that contain particulate matter, or that need some degree of crystallization. Since these characteristics describe a vast majority of processed foods, SSHEs are especially suited for pumpable food products. During operation, the product is brought in contact with a heat transfer surface that is rapidly and continuously scraped, thereby exposing the surface to the passage of untreated product. In addition to maintaining high and uniform heat exchange, the scraper blades also provide simultaneous mixing and agitation. Heat exchange for sticky and viscous foods such as heavy salad dressings, margarine, chocolate, peanut butter, fondant, ice cream, and shortenings is possible only by using SSHEs. High heat transfer coefficients are achieved because the boundary layer is continuously replaced by fresh material. Moreover, the product is in contact with the heating surface for only a few seconds and high temperature gradients can be used without the danger of causing undesirable reactions. SSHEs are versatile in the use of heat transfer medium and the various unit operations that can be carried out simultaneously. This article critically reviews the current understanding of the operations and applications of SSHEs.

  17. The exchangeability of shape

    Directory of Open Access Journals (Sweden)

    Kaba Dramane

    2010-10-01

    Full Text Available Abstract Background Landmark based geometric morphometrics (GM allows the quantitative comparison of organismal shapes. When applied to systematics, it is able to score shape changes which often are undetectable by traditional morphological studies and even by classical morphometric approaches. It has thus become a fast and low cost candidate to identify cryptic species. Due to inherent mathematical properties, shape variables derived from one set of coordinates cannot be compared with shape variables derived from another set. Raw coordinates which produce these shape variables could be used for data exchange, however they contain measurement error. The latter may represent a significant obstacle when the objective is to distinguish very similar species. Results We show here that a single user derived dataset produces much less classification error than a multiple one. The question then becomes how to circumvent the lack of exchangeability of shape variables while preserving a single user dataset. A solution to this question could lead to the creation of a relatively fast and inexpensive systematic tool adapted for the recognition of cryptic species. Conclusions To preserve both exchangeability of shape and a single user derived dataset, our suggestion is to create a free access bank of reference images from which one can produce raw coordinates and use them for comparison with external specimens. Thus, we propose an alternative geometric descriptive system that separates 2-D data gathering and analyzes.

  18. Bacterial Exchange in Household Washing Machines

    Science.gov (United States)

    Callewaert, Chris; Van Nevel, Sam; Kerckhof, Frederiek-Maarten; Granitsiotis, Michael S.; Boon, Nico

    2015-01-01

    Household washing machines (WMs) launder soiled clothes and textiles, but do not sterilize them. We investigated the microbial exchange occurring in five household WMs. Samples from a new cotton T-shirt were laundered together with a normal laundry load. Analyses were performed on the influent water and the ingoing cotton samples, as well as the greywater and the washed cotton samples. The number of living bacteria was generally not lower in the WM effluent water as compared to the influent water. The laundering process caused a microbial exchange of influent water bacteria, skin-, and clothes-related bacteria and biofilm-related bacteria in the WM. A variety of biofilm-producing bacteria were enriched in the effluent after laundering, although their presence in the cotton sample was low. Nearly all bacterial genera detected on the initial cotton sample were still present in the washed cotton samples. A selection for typical skin- and clothes-related microbial species occurred in the cotton samples after laundering. Accordingly, malodour-causing microbial species might be further distributed to other clothes. The bacteria on the ingoing textiles contributed for a large part to the microbiome found in the textiles after laundering. PMID:26696989

  19. Experimental study on heat exchange of several types of exchangers

    Institute of Scientific and Technical Information of China (English)

    周志华; 赵振华; 于洋

    2009-01-01

    Aiming at the ground-coupled source heat pump that possesses the shortcomings of occupying larger land,this article studies the heat exchanged of heat exchanger in piling,and compares it with common heat exchangers buried directly. The result indicates that the heat exchanger makes the best use of structure of building,saves land,reduces the construction cost,and the heat exchanged is obviously more than exchangers buried directly. In winter condition,when W-shape pipe heat exchanger in pile foundation is 50 m deep and diameter is 800 mm,it transfers 1.2-1.3 times as large as the one of single U-shape buried directly at the flow rate of 0.6 m/s,whose borehole diameter is 300 mm. And in summer condition it does about 2.0-2.3 times as that of U-shape one.

  20. Measurements of π{sup ±} differential yields from the surface of the T2K replica target for incoming 31 GeV/c protons with the NA61/SHINE spectrometer at the CERN SPS

    Energy Technology Data Exchange (ETDEWEB)

    Abgrall, N.; Ajaz, M.; Blondel, A.; Bravar, A.; Debieux, S.; Haesler, A.; Korzenev, A.; Ravonel, M. [University of Geneva, Geneva (Switzerland); Aduszkiewicz, A.; Dominik, W.; Kuich, M.; Matulewicz, T.; Posiadala-Zezula, M. [University of Warsaw, Warsaw (Poland); Ali, Y. [Jagiellonian University, Cracow (Poland); COMSATS Institute of Information Technology, Department of Physics, Islamabad (Pakistan); Andronov, E.; Feofilov, G.A.; Igolkin, S.; Kondratiev, V.P.; Seryakov, A.; Vechernin, V.V.; Vinogradov, L. [St. Petersburg State University, Saint Petersburg (Russian Federation); Anticic, T.; Kadija, K.; Susa, T. [Ruder Boskovic Institute, Zagreb (Croatia); Antoniou, N.; Christakoglou, P.; Davis, N.; Diakonos, F.; Kapoyannis, A.; Panagiotou, A.D.; Vassiliou, M. [University of Athens, Athens (Greece); Baatar, B.; Bunyatov, S.A.; Kolesnikov, V.I.; Krasnoperov, A.; Lyubushkin, V.V.; Malakhov, A.I.; Matveev, V.; Melkumov, G.L.; Tereshchenko, V. [Joint Institute for Nuclear Research, Dubna (Russian Federation); Bay, F.; Di Luise, S.; Rubbia, A.; Sgalaberna, D. [ETH Zuerich, Zuerich (Switzerland); Bluemer, J.; Dembinski, H.; Engel, R.; Herve, A.E.; Mathes, H.J.; Roth, M.; Szuba, M.; Ulrich, R.; Unger, M.; Veberic, D. [Karlsruhe Institute of Technology, Karlsruhe (Germany); Bogomilov, M.; Kolev, D.; Tsenov, R. [University of Sofia, Faculty of Physics, Sofia (Bulgaria); Brandin, A.; Selyuzhenkov, I.; Taranenko, A. [National Research Nuclear University ' ' MEPhI' ' (Moscow Engineering Physics Institute), Moscow (Russian Federation); Brzychczyk, J.; Larsen, D.; Planeta, R.; Richter-Was, E.; Staszel, P.; Wyszynski, O. [Jagiellonian University, Cracow (Poland); Busygina, O.; Golubeva, M.; Guber, F.; Ivashkin, A.; Kurepin, A.; Sadovsky, A. [Institute for Nuclear Research, Moscow (Russian Federation); Cirkovic, M.; Manic, D.; Puzovic, J. [University of Belgrade, Belgrade (Serbia); Czopowicz, T.; Dynowski, K.; Grebieszkow, K.; Mackowiak-Pawlowska, M.; Maksiak, B.; Sarnecki, R.; Slodkowski, M.; Tefelska, A.; Tefelski, D. [Warsaw University of Technology, Warsaw (Poland); Deveaux, M.; Koziel, M.; Renfordt, R.; Stroebele, H. [University of Frankfurt, Frankfurt (Germany); Dumarchez, J.; Robert, A. [LPNHE, University of Paris VI and VII, Paris (France); Ereditato, A.; Hierholzer, M.; Nirkko, M.; Pistillo, C.; Redij, A. [University of Bern, Bern (Switzerland); Fodor, Z. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); University of Wroclaw, Wroclaw (Poland); Garibov, A. [National Nuclear Research Center, Baku (Azerbaijan); Gazdzicki, M. [University of Frankfurt, Frankfurt (Germany); Jan Kochanowski University in Kielce, Kielce (Poland); Grzeszczuk, A.; Kaptur, E.; Kisiel, J.; Kowalski, S.; Pulawski, S.; Schmidt, K.; Wilczek, A. [University of Silesia, Katowice (Poland); Hasegawa, T.; Kobayashi, T.; Nakadaira, T.; Nishikawa, K.; Sakashita, K.; Sekiguchi, T.; Shibata, M.; Tada, M.; Friend, M. [Institute for Particle and Nuclear Studies, Tsukuba (Japan); Johnson, S.R.; Marino, A.D.; Rumberger, B.T.; Zimmerman, E.D. [University of Colorado, Boulder (United States); Kowalik, K.; Rondio, E.; Stepaniak, J. [National Centre for Nuclear Research, Warsaw (Poland); Laszlo, A.; Marton, K.; Vesztergombi, G. [Wigner Research Centre for Physics of the Hungarian Academy of Sciences, Budapest (Hungary); Lewicki, M.; Naskret, M.; Turko, L. [University of Wroclaw, Wroclaw (Poland); Marcinek, A. [Jagiellonian University, Cracow (Poland); University of Wroclaw, Wroclaw (PL); Messerly, B.; Nagai, Y.; Paolone, V. [University of Pittsburgh, Pittsburgh (US); Mills, G.B.; Yarritu, K. [Los Alamos National Laboratory, Los Alamos (US); Morozov, S.; Petukhov, O. [Institute for Nuclear Research, Moscow (RU); National Research Nuclear University ' ' MEPhI' ' (Moscow Engineering Physics Institute), Moscow (RU); Mrowczynski, S.; Rybczynski, M.; Seyboth, P.; Stefanek, G.; Wlodarczyk, Z.; Wojtaszek-Szwarc, A. [Jan Kochanowski University in Kielce, Kielce (PL); Pavin, M. [Ruder Boskovic Institute, Zagreb (HR); LPNHE, University of Paris VI and VII, Paris (FR); Popov, B.A. [LPNHE, University of Paris VI and VII, Paris (FR); Joint Institute for Nuclear Research, Dubna (RU); Rauch, W. [Fachhochschule Frankfurt, Frankfurt (DE); Roehrich, D. [University of Bergen, Bergen (NO); Rustamov, A. [National Nuclear Research Center, Baku (AZ); University of Frankfurt, Frankfurt (DE); Zambelli, L. [LPNHE, University of Paris VI and VII, Paris (FR); Institute for Particle and Nuclear Studies, Tsukuba (JP); Galymov, V. [IPNL, University of Lyon, Villeurbanne (FR); Hartz, M. [Kavli Institute for the Physics and Mathematics of the Universe (WPI), The University of Tokyo Institutes for Advanced Study, University of Tokyo, Kashiwa, Chiba (JP); TRIUMF, Vancouver, BC (CA); Hiraki, T.; Ichikawa, A.; Kubo, H.; Matsuoka, K.; Murakami, A.; Nakaya, T.; Suzuki, K. [Kyoto University, Department of Physics, Kyoto (JP); Tzanov, M. [Louisiana State University, Department of Physics and Astronomy, Baton Rouge, LA (US); Yu, M. [York University, Department of Physics and Astronomy, Toronto, ON (CA); Collaboration: NA61/SHINE Collaboration

    2016-11-15

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of π{sup ±}-mesons from the surface of the T2K replica target for incoming 31 GeV/c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed. (orig.)

  1. Measurements of charged pion differential yields from the surface of the T2K replica target for incoming 31 GeV/c protons with the NA61/SHINE spectrometer at the CERN SPS

    CERN Document Server

    Abgrall, N; Ajaz, M; Ali, Y; Andronov, E; Anticic, T; Antoniou, N; Baatar, B; Bay, F; Blondel, A; Blümer, J; Bogomilov, M; Brandin, A; Bravar, A; Brzychczyk, J; Bunyatov, S A; Busygina, O; Christakoglou, P; Cirkovic, M; Czopowicz, T; Davis, N; Debieux, S; Dembinski, H; Deveaux, M; Diakonos, F; Di Luise, S; Dominik, W; Dumarchez, J; Dynowski, K; Engel, R; Ereditato, A; Feofilov, G A; Fodor, Z; Garibov, A; Gazdzicki, M; Golubeva, M; Grebieszkow, K; Grzeszczuk, A; Guber, F; Haesler, A; Hasegawa, T; Hervé, A E; Hierholzer, M; Igolkin, S; Ivashkin, A; Johnson, S R; Kadija, K; Kapoyannis, A; Kaptur, E; Kisiel, J; Kobayashi, T; Kolesnikov, V I; Kolev, D; Kondratiev, V P; Korzenev, A; Kowalik, K; Kowalski, S; Koziel, M; Krasnoperov, A; Kuich, M; Kurepin, A; Larsen, D; László, A; Lewicki, M; Lyubushkin, V V; Mackowiak-Pawłowska, M; Maksiak, B; Malakhov, A I; Manic, D; Marcinek, A; Marino, A D; Marton, K; Mathes, H -J; Matulewicz, T; Matveev, V; Melkumov, G L; Messerly, B; Mills, G B; Morozov, S; Mrówczynski, S; Nagai, Y; Nakadaira, T; Naskret, M; Nirkko, M; Nishikawa, K; Panagiotou, A D; Paolone, V; Pavin, M; Petukhov, O; Pistillo, C; Płaneta, R; Popov, B A; Posiadała-Zezula, M; Puławski, S; Puzovic, J; Rauch, W; Ravonel, M; Redij, A; Renfordt, R; Richter-Was, E; Robert, A; Röhrich, D; Rondio, E; Roth, M; Rubbia, A; Rumberger, B T; Rustamov, A; Rybczynski, M; Sadovsky, A; Sakashita, K; Sarnecki, R; Schmidt, K; Sekiguchi, T; Selyuzhenkov, I; Seryakov, A; Seyboth, P; Sgalaberna, D; Shibata, M; Słodkowski, M; Staszel, P; Stefanek, G; Stepaniak, J; Ströbele, H; Šuša, T; Szuba, M; Tada, M; Taranenko, A; Tefelska, A; Tefelski, D; Tereshchenko, V; Tsenov, R; Turko, L; Ulrich, R; Unger, M; Vassiliou, M; Veberic, D; Vechernin, V V; Vesztergombi, G; Vinogradov, L; Wilczek, A; Włodarczyk, Z; Wojtaszek-Szwarc, A; Wyszynski, O; Yarritu, K; Zambelli, L; Zimmerman, E D; Friend, M; Galymov, V; Hartz, M; Hiraki, T; Ichikawa, A; Kubo, H; Matsuoka, K; Murakami, A; Nakaya, T; Suzuki, K; Tzanov, M; Yu, M

    2016-01-01

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of charged pions from the surface of the T2K replica target for incoming 31 GeV/c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed

  2. Measurements of π ^± differential yields from the surface of the T2K replica target for incoming 31 GeV/ c protons with the NA61/SHINE spectrometer at the CERN SPS

    Science.gov (United States)

    Abgrall, N.; Aduszkiewicz, A.; Ajaz, M.; Ali, Y.; Andronov, E.; Antićić, T.; Antoniou, N.; Baatar, B.; Bay, F.; Blondel, A.; Blümer, J.; Bogomilov, M.; Brandin, A.; Bravar, A.; Brzychczyk, J.; Bunyatov, S. A.; Busygina, O.; Christakoglou, P.; Ćirković, M.; Czopowicz, T.; Davis, N.; Debieux, S.; Dembinski, H.; Deveaux, M.; Diakonos, F.; Di Luise, S.; Dominik, W.; Dumarchez, J.; Dynowski, K.; Engel, R.; Ereditato, A.; Feofilov, G. A.; Fodor, Z.; Garibov, A.; Gaździcki, M.; Golubeva, M.; Grebieszkow, K.; Grzeszczuk, A.; Guber, F.; Haesler, A.; Hasegawa, T.; Hervé, A. E.; Hierholzer, M.; Igolkin, S.; Ivashkin, A.; Johnson, S. R.; Kadija, K.; Kapoyannis, A.; Kaptur, E.; Kisiel, J.; Kobayashi, T.; Kolesnikov, V. I.; Kolev, D.; Kondratiev, V. P.; Korzenev, A.; Kowalik, K.; Kowalski, S.; Koziel, M.; Krasnoperov, A.; Kuich, M.; Kurepin, A.; Larsen, D.; László, A.; Lewicki, M.; Lyubushkin, V. V.; Maćkowiak-Pawłowska, M.; Maksiak, B.; Malakhov, A. I.; Manić, D.; Marcinek, A.; Marino, A. D.; Marton, K.; Mathes, H.-J.; Matulewicz, T.; Matveev, V.; Melkumov, G. L.; Messerly, B.; Mills, G. B.; Morozov, S.; Mrówczyński, S.; Nagai, Y.; Nakadaira, T.; Naskręt, M.; Nirkko, M.; Nishikawa, K.; Panagiotou, A. D.; Paolone, V.; Pavin, M.; Petukhov, O.; Pistillo, C.; Płaneta, R.; Popov, B. A.; Posiadała-Zezula, M.; Puławski, S.; Puzović, J.; Rauch, W.; Ravonel, M.; Redij, A.; Renfordt, R.; Richter-Wąs, E.; Robert, A.; Röhrich, D.; Rondio, E.; Roth, M.; Rubbia, A.; Rumberger, B. T.; Rustamov, A.; Rybczynski, M.; Sadovsky, A.; Sakashita, K.; Sarnecki, R.; Schmidt, K.; Sekiguchi, T.; Selyuzhenkov, I.; Seryakov, A.; Seyboth, P.; Sgalaberna, D.; Shibata, M.; Słodkowski, M.; Staszel, P.; Stefanek, G.; Stepaniak, J.; Ströbele, H.; Šuša, T.; Szuba, M.; Tada, M.; Taranenko, A.; Tefelska, A.; Tefelski, D.; Tereshchenko, V.; Tsenov, R.; Turko, L.; Ulrich, R.; Unger, M.; Vassiliou, M.; Veberič, D.; Vechernin, V. V.; Vesztergombi, G.; Vinogradov, L.; Wilczek, A.; Włodarczyk, Z.; Wojtaszek-Szwarc, A.; Wyszyński, O.; Yarritu, K.; Zambelli, L.; Zimmerman, E. D.; Friend, M.; Galymov, V.; Hartz, M.; Hiraki, T.; Ichikawa, A.; Kubo, H.; Matsuoka, K.; Murakami, A.; Nakaya, T.; Suzuki, K.; Tzanov, M.; Yu, M.

    2016-11-01

    Measurements of particle emission from a replica of the T2K 90 cm-long carbon target were performed in the NA61/SHINE experiment at CERN SPS, using data collected during a high-statistics run in 2009. An efficient use of the long-target measurements for neutrino flux predictions in T2K requires dedicated reconstruction and analysis techniques. Fully-corrected differential yields of π ^± -mesons from the surface of the T2K replica target for incoming 31 GeV/ c protons are presented. A possible strategy to implement these results into the T2K neutrino beam predictions is discussed and the propagation of the uncertainties of these results to the final neutrino flux is performed.

  3. Real Exchange Rate Targets, Nominal Exchange Rate Policies, and Inflation Real Exchange Rate Targets, Nominal Exchange Rate Policies, and Inflation

    Directory of Open Access Journals (Sweden)

    J. Saúl Lizondo

    1991-03-01

    Full Text Available Real Exchange Rate Targets, Nominal Exchange Rate Policies, and Inflation Thh paper examines the implications of some nominal exchange rate policies aimed or attaining a given real exchange rate target. A policy rule that sets the rate of nominal depreciation as a function of the departures of the real exchange rate from its target level is unable to achieve the target. In contrast, a policv rule that sets the change in the rate of depreciation as a function of those departures may lead the economy to the target, under certain conditions. However, this policy could also lead the economy to a process of accelerating inflation.

  4. Mastering Microsoft Exchange Server 2010

    CERN Document Server

    McBee, Jim

    2010-01-01

    A top-selling guide to Exchange Server-now fully updated for Exchange Server 2010. Keep your Microsoft messaging system up to date and protected with the very newest version, Exchange Server 2010, and this comprehensive guide. Whether you're upgrading from Exchange Server 2007 SP1 or earlier, installing for the first time, or migrating from another system, this step-by-step guide provides the hands-on instruction, practical application, and real-world advice you need.: Explains Microsoft Exchange Server 2010, the latest release of Microsoft's messaging system that protects against spam and vir

  5. Integrated Foreign Exchange Risk Management

    DEFF Research Database (Denmark)

    Aabo, Tom; Høg, Esben; Kuhn, Jochen

    Empirical research has focused on export as a proxy for the exchange rate exposure and the use of foreign exchange derivatives as the instrument to deal with this exposure. This empirical study applies an integrated foreign exchange risk management approach with a particular focus on the role...... of import in medium-sized, manufacturing firms in Denmark (a small, open economy). We find a strong, negative relation between import and foreign exchange derivatives usage on the aggregate level. Our findings are consistent with the notion that firms use import to match the foreign exchange exposure...... created by foreign sales activities....

  6. Integrated Foreign Exchange Risk Management

    DEFF Research Database (Denmark)

    Aabo, Tom; Høg, Esben; Kuhn, Jochen

    Empirical research has focused on export as a proxy for the exchange rate exposure and the use of foreign exchange derivatives as the instrument to deal with this exposure. This empirical study applies an integrated foreign exchange risk management approach with a particular focus on the role...... of import in medium-sized, manufacturing firms in Denmark (a small, open economy). We find a strong, negative relation between import and foreign exchange derivatives usage on the aggregate level. Our findings are consistent with the notion that firms use import to match the foreign exchange exposure...

  7. Language sampling

    DEFF Research Database (Denmark)

    Rijkhoff, Jan; Bakker, Dik

    1998-01-01

    This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our ...... sampling method is used with different genetic classifications (Voegelin & Voegelin 1977, Ruhlen 1987, Grimes ed. 1997) and argue that —on the whole— our sampling technique compares favourably with other methods, especially in the case of exploratory research.......This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our...

  8. Language sampling

    DEFF Research Database (Denmark)

    Rijkhoff, Jan; Bakker, Dik

    1998-01-01

    This article has two aims: [1] to present a revised version of the sampling method that was originally proposed in 1993 by Rijkhoff, Bakker, Hengeveld and Kahrel, and [2] to discuss a number of other approaches to language sampling in the light of our own method. We will also demonstrate how our...... sampling method is used with different genetic classifications (Voegelin & Voegelin 1977, Ruhlen 1987, Grimes ed. 1997) and argue that —on the whole— our sampling technique compares favourably with other methods, especially in the case of exploratory research....

  9. Effect of cross sectional geometry on PDMS micro peristaltic pump performance: comparison of SU-8 replica molding vs. micro injection molding.

    Science.gov (United States)

    Graf, Neil J; Bowser, Michael T

    2013-10-07

    Two different fabrication methods were employed to fabricate micropumps with different cross-sectional channel geometries. The first was to fabricate rectangular cross-sectional microchannel geometries using the well known fabrication method of replica molding (REM). The second, and far less utilized fabrication technique, was to create microchannel molds using an in-house fabricated handheld micro injection molding apparatus. The injection mold apparatus was designed for use with elastomeric room temperature vulcanization (RTV) polymers, as opposed to most other injection molding machines, which are designed for use with thermoplastic polymers. The injection mold's bottom plate was used as a microchannel molding template. The molding template was created by threading a small-diameter wire (150 μm or less) through the injection mold's bottom plate, with subsequent adhesion and smoothing of a thin piece of aluminum foil over the wire-raised injection mold template. When molded against, the template produced a rounded/Gaussian-shaped PDMS microchannel. The design of the injection mold will be presented, along with a direct comparison for micropump performance metrics such as flow rate, valving characteristics, and maximum backpressures attainable for each of the respective micropump channel geometries.

  10. Determination of gold,platinum and palladium in geological samples by inductively coupled plasma mass spectrometry after concentration with 717 anion exchange resin%717阴离子交换树脂富集-电感耦合等离子体质谱法测定地质样品中痕量金铂钯

    Institute of Scientific and Technical Information of China (English)

    李丹; 王锝; 李彪

    2011-01-01

    The adsorption property and separation conditions of 717 anion exchange resin to trace gold,platinum and palladium in geological samples were studied. The sample was dissolved with HCl+ aqua regia under heating in water bath. Only Mo in dissolved elements had interference with the determination of Pd, which could be eliminated using mathematical formula correction. When the flow rate of eluent was 2 mL/min, the enrichment effects of gold, platinum and palladium in 5 % HCl medium reached its best, and the recoveries were close to 100 %. After correcting the influence of coexisting ions, the national first-class certified reference materials were determined by inductively coupled plasma mass spectrometry, and the difference between determination results and certified values was satisfactory. The detection limit of method were 0. 6 ng/mL, 0. 5 ng/mL and 0. 7 ng/mL for Pd, Pt and Au, respectively. Five random geological samples were analyzed by this method in comparison with NiS fire assay-ICP-MS method. The determination results were consistent. The results of two methods were checked by double sample's variance F test, and there was no significant difference.%研究了717型阴离子交换树脂对地质样品中痕量金、铂、钯的吸附性能及分离条件.采用水浴加热,HCl+王水的方式溶解样品,溶出的干扰元素只有Mo对Pd的测定造成干扰,采用数学公式校正可消除此干扰.在5%的HCl介质中,洗脱剂流速为2 mL/min时,金、铂、钯的富集效果最佳,回收率接近100%.经对共存离子影响的校正,用电感耦合等离子体质谱法测定国家一级标准物质,其结果较认定值不超差.方法检出限为Pd 0.6 ng/mL,Pt 0.5ng/mL,Au 0.7ng/mL.随机选取5个地质样品用本法进行分析,同时与硫镍试金-ICP-MS法进行比较,结果一致.两组结果经双样本方差F检验,无显著性差异.

  11. State Health Facts - State Decisions on Exchanges

    Data.gov (United States)

    U.S. Department of Health & Human Services — State Decisions For Creating Health Insurance Exchanges, including Exchange Decision, Federal Approval Status, Structure of Exchange, and Type of Exchange.

  12. Forecasting Exchange Rate Volatility in the Presence of Jumps

    DEFF Research Database (Denmark)

    Busch, Thomas; Christensen, Bent Jesper; Nielsen, Morten Ørregaard

    of exchange rate futures options, allowingcalculation of option implied volatility. We find that implied volatility is an informationallyefficient but biased forecast of future realized exchange rate volatility. Furthermore,we show that log-normality is an even better distributional approximation...... for impliedvolatility than for realized volatility in this market. Finally, we show that the jump componentof future realized exchange rate volatility is to some extent predictable, and thatoption implied volatility is the dominant forecast of the future jump component.......We study measures of foreign exchange rate volatility based on high-frequency (5-minute) $/DM exchange rate returns using recent nonparametric statistical techniquesto compute realized return volatility and its separate continuous sample path and jumpcomponents, and measures based on prices...

  13. Sampling Development

    Science.gov (United States)

    Adolph, Karen E.; Robinson, Scott R.

    2011-01-01

    Research in developmental psychology requires sampling at different time points. Accurate depictions of developmental change provide a foundation for further empirical studies and theories about developmental mechanisms. However, overreliance on widely spaced sampling intervals in cross-sectional and longitudinal designs threatens the validity of…

  14. Small particle heat exchangers

    Energy Technology Data Exchange (ETDEWEB)

    Hunt, A.J.

    1978-06-01

    A dispersion of small absorbing particles forms an ideal system to collect radiant energy, transform it to heat, and efficiently transfer the heat to a surrounding fluid. If the heated fluid is a pressurized gas, it can be passed through an expansion turbine to create useful mechanical energy. The most obvious application of this technique is its use in a solar collection system. In this case, the incoming sunlight is used to heat a compressed gas in an engine utilizing a Brayton cycle. The solar collection system may utilize high concentration as provided by a central receiver or parabolic dish, medium concentration from a linear collector, or possibly no concentration using a flat plate collector, if precautions were taken to reduce the heat losses. The same concept may be applied generally to non-solar heat exchangers. These may be of the type used to heat a gas from a combustion source, or in general as a gas to gas heat exchanger. The latter application may be limited to rather high temperature. Each of the above applications is discussed. First, a description of the concept is applied to a solar central-tower system. The general principles are described, including the optical and physical characteristics of the particles, the confinement of the gas-particle mixture, and the system considerations; the latter include the amount and type of particles, the receiver efficiency and the generation of the particles. The same considerations are reviewed for applications to linear trough and flat plate receivers. Finally, the use of small particles in non-solar heat exchangers is considered.

  15. Cryogenic regenerative heat exchangers

    CERN Document Server

    Ackermann, Robert A

    1997-01-01

    An in-depth survey of regenerative heat exchangers, this book chronicles the development and recent commercialization of regenerative devices for cryogenic applications. Chapters cover historical background, concepts, practical applications, design data, and numerical solutions, providing the latest information for engineers to develop advanced cryogenic machines. The discussions include insights into the operation of a regenerator; descriptions of the cyclic and fluid temperature distributions in a regenerator; data for various matrix geometries and materials, including coarse and fine bronze, stainless steel-woven wire mesh screens, and lead spheres; and unique operating features of cryocoolers that produce deviations from ideal regenerator theory.

  16. SPEEDUP{trademark} ion exchange column model

    Energy Technology Data Exchange (ETDEWEB)

    Hang, T.

    2000-03-06

    A transient model to describe the process of loading a solute onto the granular fixed bed in an ion exchange (IX) column has been developed using the SpeedUp{trademark} software package. SpeedUp offers the advantage of smooth integration into other existing SpeedUp flowsheet models. The mathematical algorithm of a porous particle diffusion model was adopted to account for convection, axial dispersion, film mass transfer, and pore diffusion. The method of orthogonal collocation on finite elements was employed to solve the governing transport equations. The model allows the use of a non-linear Langmuir isotherm based on an effective binary ionic exchange process. The SpeedUp column model was tested by comparing to the analytical solutions of three transport problems from the ion exchange literature. In addition, a sample calculation of a train of three crystalline silicotitanate (CST) IX columns in series was made using both the SpeedUp model and Purdue University's VERSE-LC code. All test cases showed excellent agreement between the SpeedUp model results and the test data. The model can be readily used for SuperLig{trademark} ion exchange resins, once the experimental data are complete.

  17. Exchange rate exposure of firms and the demand for foreign exchange derivatives in Brazil: did hedge or speculatiom matter?

    Directory of Open Access Journals (Sweden)

    Fernando Nascimento de Oliveira

    2012-12-01

    Full Text Available This paper examines empirically how the demand of foreign exchange derivatives by Brazilian corporations is related to their exchange rate exposure. With the help of an original database of 74,567 contracts written from 1999 to 2002 between corporations and financial institutions, we were able to identify the corporations that speculated and the ones that hedged with foreign exchange derivatives during this period. Our results show that the exchange rate exposure is positively related to the foreign operational exposures for firms that speculated and negatively related for firms that hedged in 2002. For the other years of the sample period, speculation or hedge did not affect the relationship between the exchange rate exposure and the foreign operational exposure of firms.

  18. Real exchange rate fluctuations, endogenous tradability and exchange rate regime

    OpenAIRE

    Kanda Naknoi

    2005-01-01

    This paper, empirically and theoretically, studies variance decomposition of real exchange rate. We find that deviations from the law of one price for traded goods drive most real exchange rates. However, the relative price of nontraded goods is also important for some countries maintaining stable exchange rate. We propose an explanation based on dynamics of comparative advantage. Our model predicts that comovement of terms of trade and productivity differentials of the nontraded and the expo...

  19. Synthesis of Heat Exchanger Network Considering Multipass Exchangers

    Institute of Scientific and Technical Information of China (English)

    李绍军; 姚平经

    2001-01-01

    Many methods have been proposed for synthesis of heat exchanger networks in recent years, most of which consider single pass exchangers. In this study some evolutionary rules have been proposed for synthesis of multipass exchanger networks. The method is based on the heuristic that optimal networks should feature maximum energy recovery and have the minimum number of shells. The effectiveness of the developed evolutionary rules is demonstrated through some literature examples.

  20. Capital Flows, Exchange Rate Flexibility, and the Real Exchange Rate

    OpenAIRE

    Jean-Louis Combes; Patrick Plane; Tidiane Kinda

    2011-01-01

    This paper analyzes the impact of capital inflows and exchange rate flexibility on the real exchange rate in developing countries based on panel cointegration techniques. The results show that public and private flows are associated with a real exchange rate appreciation. Among private flows, portfolio investment has the highest appreciation effect-almost seven times that of foreign direct investment or bank loans-and private transfers have the lowest effect. Using a de facto measure of excha...