WorldWideScience

Sample records for replica exchange method

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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

  15. 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.

  16. 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...

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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)].

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  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. 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.

  17. 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.

  18. 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.

  19. 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,...

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  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. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  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. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Method for nanomodulation of metallic thin films following the replica-antireplica process based on porous alumina membranes

    Science.gov (United States)

    Palma, J. L.; Denardin, J. C.; Escrig, J.

    2017-03-01

    In this paper we have introduced a method for modulation of metallic thin films by sputtering of metals on anodized aluminum templates. Using a high deposition rate during deposition of the non-magnetic metal on the Al pattern, we have separated the two metallic surfaces and, thus, imprinted a pattern of nanohills on a non-magnetic metallic film, such as Au, Ag or Cu. The morphology of the nanostructured metallic films was determined by scanning electron microscopy. Thus, we have confirmed that the ordering degree of the Al template remained after the replication process. Additionally, and as an example of use of these films, we have prepared Supermalloy thin films deposited by sputtering onto these nanostructured non-magnetic metals. The room temperature magnetic behavior of these thin films is also studied. Interestingly, we have found that when the external magnetic field is applied out of plane of the substrate, the coercivity increases linearly as we increase the radius of the nanohills. These soft magnetic films can open new opportunities for magnetic field sensor applications.

  1. 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

  2. The path exchange method for hybrid LCA.

    Science.gov (United States)

    Lenzen, Manfred; Crawford, Robert

    2009-11-01

    Hybrid techniques for Life-Cycle Assessment (LCA) provide a way of combining the accuracy of process analysis and the completeness of input-output analysis. A number of methods have been suggested to implement a hybrid LCA in practice, with the main challenge being the integration of specific process data with an overarching input-output system. In this work we present a new hybrid LCA method which works at the finest input-output level of detail: structural paths. This new Path Exchange method avoids double-counting and system disturbance just as previous hybrid LCA methods, but instead of a large LCA database it requires only a minimum of external information on those structural paths that are to be represented by process data.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. Ion exchange materials, method of forming ion exchange materials, and methods of treating liquids

    Science.gov (United States)

    Wertsching, Alan K.; Peterson, Eric S.; Wey, John E.

    2007-12-25

    The invention includes an ion affinity material having an organic component which is sulfonated and which is chemically bonded to an inorganic substrate component. The invention includes a method of forming a metal binding material. A solid support material comprising surface oxide groups is provided and an organic component having at least one alkyl halide is covalently linked to at least some of the surface oxide groups to form a modified support material. The at least one alkyl halide is subsequently converted into an alkyl sulfonate. The invention further includes a method and system for extracting ions from a liquid. An ion exchange material having a sulfonated alkyl silane component covalently bonded to a metal oxide support material is provided and a liquid is exposed to the ion exchange material.

  8. Development and Application of Ligand-Exchange Reaction Method ...

    African Journals Online (AJOL)

    Erah

    Methods: The method is based on ligand-exchange reaction. ... Clonazepam, Ligand-exchange reaction, Kinetic spectrometry, Validation, Pharmaceutical ... sensitive and selective analytical method for ... does not need sophisticated instruments or ..... of clonazepam in human serum ("Lytorol N) by standard addition method.

  9. 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.

  10. 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.

  11. 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.

  12. Porous Aluminas: The bio template method for the synthesis of stable high surface area aluminas; Aluminas porosas: El metodo de bio-replica para la sintesis de aluminas estables de alta superficie especifica

    Energy Technology Data Exchange (ETDEWEB)

    Benitez Guerrero, M.; Perez Maqueda, L.; Pena Castro, P.; Pascual Cosp, J.

    2013-07-01

    Development of porous alumina has been the objective of numerous studies in recent decades, due to the intrinsic properties of aluminium oxide, such as high melting point, low thermal conductivity, chemical inertness and corrosion resistance which, in addition to a high surface area and permeability, make aluminas being used for many different industrial and technical applications. The crystallographic and textural stability of alumina acquires significant importance in those processes involving high temperatures; however, most of the synthesis methods yield metastable oxides of little interest in high-temperature processes due to the transformation to alpha phase, with the consequent reduction in surface area. The present article reviews diverse procedures for obtaining porous alumina with high specific surface area, including methods and strategies for preparing high surface alpha-alumina. Within this framework, the paper analyzes the results obtained through bio replica of lignocellulose materials. This technology allows preparing aluminas with the complex structural hierarchy of the lignocellulose templates. (Author)

  13. 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.

  14. 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

  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. 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.

  17. 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

  18. 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.

  19. Microchannel crossflow fluid heat exchanger and method for its fabrication

    Science.gov (United States)

    Swift, Gregory W.; Migliori, Albert; Wheatley, John C.

    1985-01-01

    A microchannel crossflow fluid heat exchanger and a method for its fabrication are disclosed. The heat exchanger is formed from a stack of thin metal sheets which are bonded together. The stack consists of alternating slotted and unslotted sheets. Each of the slotted sheets includes multiple parallel slots which form fluid flow channels when sandwiched between the unslotted sheets. Successive slotted sheets in the stack are rotated ninety degrees with respect to one another so as to form two sets of orthogonally extending fluid flow channels which are arranged in a crossflow configuration. The heat exchanger has a high surface to volume ratio, a small dead volume, a high heat transfer coefficient, and is suitable for use with fluids under high pressures. The heat exchanger has particular application in a Stirling engine that utilizes a liquid as the working substance.

  20. 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...

  1. 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

  2. Heat exchanger device and method for heat removal or transfer

    Science.gov (United States)

    Koplow, Jeffrey P [San Ramon, CA

    2012-07-24

    Systems and methods for a forced-convection heat exchanger are provided. In one embodiment, heat is transferred to or from a thermal load in thermal contact with a heat conducting structure, across a narrow air gap, to a rotating heat transfer structure immersed in a surrounding medium such as air.

  3. Heat exchanger device and method for heat removal or transfer

    Science.gov (United States)

    Koplow, Jeffrey P

    2013-12-10

    Systems and methods for a forced-convection heat exchanger are provided. In one embodiment, heat is transferred to or from a thermal load in thermal contact with a heat conducting structure, across a narrow air gap, to a rotating heat transfer structure immersed in a surrounding medium such as air.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. Numerical computation of sapphire crystal growth using heat exchanger method

    Science.gov (United States)

    Lu, Chung-Wei; Chen, Jyh-Chen

    2001-05-01

    The finite element software FIDAP is employed to study the temperature and velocity distribution and the interface shape during a large sapphire crystal growth process using a heat exchanger method (HEM). In the present study, the energy input to the crucible by the radiation and convection inside the furnace and the energy output through the heat exchanger is modeled by the convection boundary conditions. The effects of the various growth parameters are studied. It is found that the contact angle is obtuse before the solid-melt interface touches the sidewall of the crucible. Therefore, hot spots always appear in this process. The maximum convexity decreases significantly when the cooling-zone radius (RC) increases. The maximum convexity also decreases significantly as the combined convection coefficient inside the furnace (hI) decreases.

  10. 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.

  11. 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.

  12. The water exchange method for colonoscopy-effect of coaching

    Science.gov (United States)

    Cheung, R; Fan, RS; Fischer, LS; Friedland, S; Ho, SB; Hsieh, YH; Hung, I; Li, MK; Matsui, S; Mcquaid, KR; Ohning, G; Ojuri, A; Sato, T; Shergill, AK; Shoham, MA; Simons, TC; Walter, MH; Yen, A

    2012-01-01

    The growing popularity of water immersion is supported by its long history as an adjunct to air insufflation; after facilitating colonoscope passage, the infused water is conveniently removed during withdrawal. Water exchange, a modification of water immersion to minimize discomfort in scheduled unsedated patients in the U.S. is new. Even though it may be superior in reducing pain and increasing adenoma detection, the paradigm shift to complete exclusion of air during insertion necessitates removal of infused water containing residual feces, a step often perceived as laborious and time-consuming. The nuances are the efficient steps to remove infused water predominantly during insertion to maintain minimal distension and deliver salvage cleansing. Mastery of the novel maneuvers with practice returns insertion time towards baseline. In this observational study the impact of direct verbal coaching on the primary outcome of intention-to-treat cecal intubation was assessed. The results showed that 14 of 19 (74%) experienced colonoscopists achieved 100% intention-to-treat cecal intubation. Initiation of the examination with water exchange did not preclude completion when conversion to the more familiar air insufflation method was deemed necessary to achieve cecal intubation (total 98%). The overall intention-to-treat cecal intubation rate was 88%, 90% in male and 87% in female. Only 2.7% of bowel preparation was rated as poor during withdrawal. The mean volume of water infused and cecal intubation time was 1558 ml and 18 min, respectively. Direct coaching appears to facilitate understanding of the nuances of the water exchange method. Studies of individual learning curves are necessary. PMID:23805391

  13. 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.

  14. 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...

  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. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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 ...

  1. Cation Exchange Capacity of Biochar: An urgent method modification

    Science.gov (United States)

    Munera, Jose; Martinsen, Vegard; Mulder, Jan; Tau Strand, Line; Cornelissen, Gerard

    2017-04-01

    A better understanding of the cation exchange capacity (CEC) values of biochar and its acid neutralizing capacity (ANC) is crucial when tailoring a single biochar for a particular soil and crop. Literature values for the CEC of biochar are surprisingly variable, commonly ranging from 5 to 50 cmol+/Kg even as high as 69 to 204 cmol+/Kg and often poorly reproducible, suggesting methodological problems. Ashes and very fine pores in biochar may complicate the analysis and thus compromise the results. Here, we modify and critically assess different steps in a common method for CEC determination in biochar and investigate how the measured CEC may be affected by slow cation diffusion from micro-pores. We modified the existing ammonium acetate (NH4-OAc) method (buffered at pH 7), based on displaced ammonium (NH4+) in potassium chloride (KCl) extracts after removing excess NH4-OAc with alcohol in batch mode. We used pigeon pea biochar (produced at 350 ˚C; particle size 0.5mm to 2mm) to develop the method and we tested its reproducibility in biochars with different ANC. The biochar sample (1.00g) was pH-adjusted to 7 after 2 days of equilibration, using hydrochloric acid (HCl), and washed with water until the conductivity of the water was removed the soluble ash component, while simultaneously allowing the NH4-OAc to buffer at pH 7. To assess the importance of diffusion limitation of replacing cations (NH4+ and K+) in micro-pores, we equilibrated the biochar with NH4-OAc for 1 and 7 days, and after washing with alcohol, for 1, 3 and 7 days with KCl. The effects of the washing volume of alcohol (15, 30 and 45 ml) and of the biochar to NH4OAc solution ratio (1:15, 1:30 and 1:45) were also tested. The CEC values were corrected for dry matter content and mass losses during the process. Results indicate that the measured CEC values of the modified method were highly reproducible and that 1 day shaking with NH4OAc and KCl is enough to saturate the exchange sites with NH4+ and

  2. Auxiliary Density Matrix Methods for Hartree-Fock Exchange Calculations.

    Science.gov (United States)

    Guidon, Manuel; Hutter, Jürg; VandeVondele, Joost

    2010-08-10

    The calculation of Hartree-Fock exchange (HFX) is computationally demanding for large systems described with high-quality basis sets. In this work, we show that excellent performance and good accuracy can nevertheless be obtained if an auxiliary density matrix is employed for the HFX calculation. Several schemes to derive an auxiliary density matrix from a high-quality density matrix are discussed. Key to the accuracy of the auxiliary density matrix methods (ADMM) is the use of a correction based on standard generalized gradient approximations for HFX. ADMM integrates seamlessly in existing HFX codes and, in particular, can be employed in linear scaling implementations. Demonstrating the performance of the method, the effect of HFX on the structure of liquid water is investigated in detail using Born-Oppenheimer molecular dynamics simulations (300 ps) of a system of 64 molecules. Representative for large systems are calculations on a solvated protein (Rubredoxin), for which ADMM outperforms the corresponding standard HFX implementation by approximately a factor 20.

  3. Development of optimization method for plate heat exchanger with undulation

    Directory of Open Access Journals (Sweden)

    Dvořák Václav

    2016-01-01

    Full Text Available The article deals with optimization of undulated heat transfer surface of plate heat exchanger. The goal of optimization is not only to increase effectiveness of heat transfer but also to reduce the pressure drop. A combined pattern of undulation which combines herringbone pattern and wavy pattern was optimized and best values of four parameters were found; angle of herringbone pattern, number, phase and amplitude of longitudinal waves of wavy pattern. The optimization procedure looked for maximum of objective function which was a linear combination of effectiveness and pressure drop. We used simple Monte Carlo method and the optimum was searched for four values of reference pressure drop. Four different optimization were run and we investigated the effect of various definition of objective function and parameters of undulation. It was found that during optimization of combined pattern, the herringbone pattern is more favoured than wavy pattern. It is caused by the fact that herringbone pattern was described by the only one free parameter, which was the angle of undulation, and therefore it is more likely to be found by a stochastic method. This assumption was confirmed when simple wavy pattern was optimized and higher values of objective function and effectiveness were found.

  4. Microchannel laminated mass exchanger and method of making

    Science.gov (United States)

    Martin, Peter M.; Bennett, Wendy D.; Matson, Dean W.; Stewart, Donald C.; Drost, Monte K.; Wegeng, Robert S.; Perez, Joseph M.; Feng, Xiangdong; Liu, Jun

    2000-01-01

    The present invention is a microchannel mass exchanger having a first plurality of inner thin sheets and a second plurality of outer thin sheets. The inner thin sheets each have a solid margin around a circumference, the solid margin defining a slot through the inner thin sheet thickness. The outer thin sheets each have at least two header holes on opposite ends and when sandwiching an inner thin sheet. The outer thin sheets further have a mass exchange medium. The assembly forms a closed flow channel assembly wherein fluid enters through one of the header holes into the slot and exits through another of the header holes after contacting the mass exchange medium.

  5. Various methods to improve heat transfer in exchangers

    Directory of Open Access Journals (Sweden)

    Pavel Zitek

    2015-01-01

    Full Text Available The University of West Bohemia in Pilsen (Department of Power System Engineering is working on the selection of effective heat exchangers. Conventional shell and tube heat exchangers use simple segmental baffles. It can be replaced by helical baffles, which increase the heat transfer efficiency and reduce pressure losses. Their usage is demonstrated in the primary circuit of IV. generation MSR (Molten Salt Reactors. For high-temperature reactors we consider the use of compact desk heat exchangers, which are small, which allows the integral configuration of reactor. We design them from graphite composites, which allow up to 1000°C and are usable as exchangers: salt-salt or salt-acid (e.g. for the hydrogen production. In the paper there are shown thermo-physical properties of salts, material properties and principles of calculations.

  6. Various methods to improve heat transfer in exchangers

    Science.gov (United States)

    Pavel, Zitek; Vaclav, Valenta

    2015-05-01

    The University of West Bohemia in Pilsen (Department of Power System Engineering) is working on the selection of effective heat exchangers. Conventional shell and tube heat exchangers use simple segmental baffles. It can be replaced by helical baffles, which increase the heat transfer efficiency and reduce pressure losses. Their usage is demonstrated in the primary circuit of IV. generation MSR (Molten Salt Reactors). For high-temperature reactors we consider the use of compact desk heat exchangers, which are small, which allows the integral configuration of reactor. We design them from graphite composites, which allow up to 1000°C and are usable as exchangers: salt-salt or salt-acid (e.g. for the hydrogen production). In the paper there are shown thermo-physical properties of salts, material properties and principles of calculations.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. STUDIES ON INOSINE EXTRACTION BY ION EXCHANGE METHOD

    Institute of Scientific and Technical Information of China (English)

    HuangXiwen; ShiFang; 等

    1998-01-01

    The adsorption characteristics of inosine from fermentation solution on anion exchange resin under the condition of different pH,resin type are investigated.Besides,the desorption conditions are studied under different temperature.The adsorption and desorption mechanism are described to obtain the optimum technological condition of inosine extraction.

  12. 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.

  13. MODELING THE CURRENCY EXCHANGE RATE. METHODS AND PRINCIPLES

    OpenAIRE

    Suslov, Mark; Tregub, Ilona

    2015-01-01

    Since currency market is strongly and rapidly developing then it becomes more attractive area for investments, but, also, economic conditions force almost everyone be more financially educated and ready for changes in economic conditions. Currency is the money we pay for the goods and services in our country, but some of them are importing to our country or expressed in foreign currency values. Unfortunately, nobody can predict exact exchange rate, but there is a possibility to get ready for ...

  14. 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.

  15. 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 ...

  16. 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.

  17. A novel method to improve the performance of heat exchanger--Temperature fields coordination of fluids

    Institute of Scientific and Technical Information of China (English)

    GUO Zengyuan; WEI Shu; CHENG Xinguang

    2004-01-01

    The methods to enhance the heat transfer in heat exchanger may be classified into two levels: one is to improve the heat transfer coefficient; the other is to upgrade the whole arrangement of the heat exchangers. For the second level, the performance of heat exchanger can be upgraded by increasing the coordination degree between the temperature fields of cold and hot fluids. When the temperature distributions are similar to each other, the temperature difference field (TDF) is more uniform, which means that the temperature fields are more coordinated with each other. For the cross-flow heat exchanger, rearrangement of the heat exchange surface area should improve the heat transfer effectiveness, which is even equal to that of the counter-flow heat exchanger when the surface area is reassigned optimally. For the multi-stream heat exchanger, the thermal performance is also dependent on the uniformity of the TDF, and the parallel-flow arrangement may achieve higher heat exchange effectiveness than the counter-flow arrangement, which indicates that the performance of heat exchanger depends on the coordination degree of temperature fields instead of the flow arrangement.

  18. 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

  19. 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.

  20. Modeling Multi-commodity Trade Information Exchange Methods

    CERN Document Server

    Traczyk, Tomasz

    2012-01-01

    Market mechanisms are entering into new fields of economy, in which some constraints of physical world, e.g. Kirchoffs Law in power grid, must be taken into account during trading. On such markets, some of commodities, like telecommunication bandwidth or electrical energy, appear to be non-storable, and must be exchanged in real-time. On the other hand, the markets tend to react at shortest possible time, so an idea to delegate some competency to autonomous software agents is very attractive. Multi-commodity mechanism addresses the aforementioned requirements. Modeling the relationships between the commodities allows to formulate new, more sophisticated models and mechanisms, which reflect decision situations in a better manner. Application of multi-commodity approach requires solving several issues related to data modeling, communication, semantics aspects of communication, reliability, etc. This book answers some of the questions and points out promising paths for implementation and development. Presented s...

  1. A Simple and Efficient Method for Purification of Egg White Major Proteins Using Ion Exchange Chromatography

    OpenAIRE

    Sh. Veisi; A. Mostafaie; Z. Mohammad Hasan

    2008-01-01

    Introduction & Objective: Egg white contains four high-quantity proteins which have numerous applications. In this research, a simple and efficient method for the purification of those proteins was designed and performed based on ion exchange chromatography.Materials & Methods: In this experimental study egg white was initially separated from insoluble substances by acidic pH. The resulting extract was isolated after two steps of ion exchange chromatography using CM-Sepharose and DEAE-Sepharo...

  2. Momentum-exchange method in lattice Boltzmann simulations of particle-fluid interactions.

    Science.gov (United States)

    Chen, Yu; Cai, Qingdong; Xia, Zhenhua; Wang, Moran; Chen, Shiyi

    2013-07-01

    The momentum exchange method has been widely used in lattice Boltzmann simulations for particle-fluid interactions. Although proved accurate for still walls, it will result in inaccurate particle dynamics without corrections. In this work, we reveal the physical cause of this problem and find that the initial momentum of the net mass transfer through boundaries in the moving-boundary treatment is not counted in the conventional momentum exchange method. A corrected momentum exchange method is then proposed by taking into account the initial momentum of the net mass transfer at each time step. The method is easy to implement with negligible extra computation cost. Direct numerical simulations of a single elliptical particle sedimentation are carried out to evaluate the accuracy for our method as well as other lattice Boltzmann-based methods by comparisons with the results of the finite element method. A shear flow test shows that our method is Galilean invariant.

  3. 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.

  4. LMFBR type reactor core and its fuel exchange method

    Energy Technology Data Exchange (ETDEWEB)

    Ishibashi, Yoko; Koyama, Jun-ichi; Aoyama, Motoo; Haikawa, Katsumasa; Yamanaka, Akihiro

    1996-08-20

    Upon initial loading, two kinds of fuel assemblies including first fuel assemblies having a highest enrichment degree and second fuel assemblies having a lowest enrichment degree are loaded. The average fuel enrichment degree of an upper region of the first fuel assembly is made greater than that of the lower region. The reactivity of the lower region of the first fuel assembly is made lower than that of the upper portion to reduce power peak. Upon transfer from a first cycle to a second cycle, at least one of the second fuel assemblies is exchanged by the same number of the third fuel assemblies. In this case, an average fuel enrichment degree of the upper region of the third fuel assembly is made greater than that of the lower region to suppress the reactivity in the lower region of the third fuel assembly lower than the reactivity in the upper region thereby reducing the power peak. Thus, the upper power peak over the entire reactor core is moderated thereby capable of ensuring the reactor shut down margin without deteriorating the same. (N.H.)

  5. Wave function method to forecast foreign currencies exchange rates at ultra high frequency electronic trading in foreign currencies exchange markets

    OpenAIRE

    Ledenyov, Dimitri O.; Ledenyov, Viktor O.

    2015-01-01

    The accurate forecast of the foreign currencies exchange rates at the ultra high frequency electronic trading in the foreign currencies exchange markets is a main topic of our research: 1) the present state of the foreign currencies exchange markets in Asia, Europe and North America; 2) the research review on the classic forecast techniques of the foreign currencies exchange rates dynamics in the foreign currencies exchange markets in the classic finances theory; 3) the description on the qua...

  6. 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.

  7. 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.

  8. Commentary: An Exchange of Views on IRA and Reading Methods.

    Science.gov (United States)

    Groff, Patrick; And Others

    1980-01-01

    Groff argues against an IRA (International Reading Association) position statement assertion that no single method is the best for teaching reading, claiming that the phonics method results in the greatest reading achievement. The IRA Board of Directors replies that the position statement appropriately reflects the diverse views about reading held…

  9. A Simple Halide-to-Anion Exchange Method for Heteroaromatic Salts and Ionic Liquids

    Directory of Open Access Journals (Sweden)

    Neus Mesquida

    2012-04-01

    Full Text Available A broad and simple method permitted halide ions in quaternary heteroaromatic and ammonium salts to be exchanged for a variety of anions using an anion exchange resin (A− form in non-aqueous media. The anion loading of the AER (OH− form was examined using two different anion sources, acids or ammonium salts, and changing the polarity of the solvents. The AER (A− form method in organic solvents was then applied to several quaternary heteroaromatic salts and ILs, and the anion exchange proceeded in excellent to quantitative yields, concomitantly removing halide impurities. Relying on the hydrophobicity of the targeted ion pair for the counteranion swap, organic solvents with variable polarity were used, such as CH3OH, CH3CN and the dipolar nonhydroxylic solvent mixture CH3CN:CH2Cl2 (3:7 and the anion exchange was equally successful with both lipophilic cations and anions.

  10. 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.

  11. 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.

  12. Cross-institutional document exchange system using clinical document architecture (CDA) with virtual printing method.

    Science.gov (United States)

    Mihara, Naoki; Ueda, Kanayo; Manabe, Shirou; Takeda, Toshihiro; Shimai, Yoshie; Horishima, Hiroyuki; Murata, Taizo; Fujii, Ayumi; Matsumura, Yasushi

    2015-01-01

    Recently one patient received care from several hospitals at around the same time. When the patient visited a new hospital, the new hospital's physician tried to get patient information the previous hospital. Thus, patient information is frequently exchanged between them. Many types of healthcare facilities have implemented an electronic medical record system, but in Japan, healthcare information exchange is often done by paper. In other words, after a clinical doctor prints a referral document and sends it to another hospital's physician, another hospital's doctor receives it and scans to store the EMR in his own hospital's system. It is a wasteful way to exchange healthcare information about a patient. In order to solve this problem, we have developed a cross-institutional document exchange system using clinical document architecture (CDA) with a virtual printing method.

  13. A method for the production of weakly acidic cation exchange resins

    Science.gov (United States)

    Heller, H.; Werner, F.; Mitschker, A.; Diehl, H. V.; Schaefer, A.

    1991-12-01

    The invention relates to a nonpolluting method for the production of weakly acidic cation exchange resins by saponification of cross-linked acrylonitrile bead polymers, with an alkaline saponification agent at elevated temperature, according to which method the bead polymer and alkaline saponification agent are jointly added only at elevated temperature.

  14. 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...

  15. A general method for the analysis of compact multifluid heat exchangers.

    Science.gov (United States)

    Demetri, E. P.; Platt, M.

    1972-01-01

    An analytical method of treating the complex heat-transfer processes involved in compact multifluid heat exchangers is described. The method is based on representing the heat transfer by means of the analogy between heat-transfer paths and electrical circuits. For plate-fin configurations, it includes the effects of heat exchange among nonadjacent fluids due to conduction through the fins of intervening passages. The application of the developed solution procedures to the design and analysis of multifluid heat exchangers is also discussed. Results obtained in using the electrical-analog method to examine the effects of conduction on performance are presented graphically in parametric form for a number of three-fluid plate-fin configurations. The discussion of the data presented includes a comparison with results given by alternative analytical procedures which neglect direct transfer between nonadjacent fluids.

  16. 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...

  17. Asymptotically adjusted self-consistent multiplicative parameter exchange-energy-functional method: Application to diatomic molecules

    Science.gov (United States)

    Karasiev, Valentin V.; Ludeña, Eduardo V.

    2002-03-01

    An asymptotically adjusted self-consistent α (AASCα) method is advanced for the purpose of constructing an accurate orbital-dependent local exchange potential with correct asymptotic behavior. This local potential is made up of the Slater potential plus an additional term containing a multiplicative parameter αx (a self-consistently determined orbital functional) times a local response potential that is approximated using standard exchange-energy functionals. Applications of the AASCα functionals to diatomic molecules yield significantly improved total, exchange, and atomization energies that compare quite well, but at a much lower computational cost, with those obtained by the exact orbital-dependent exchange energy treatment [S. Ivanov, S. Hirata, and R. J. Bartlett, Phys. Rev. Lett. 83, 5455 (1999); A. Görling, Phys. Rev. Lett. 83, 5459 (1999)] (in fact, the present results are very close to the Hartree-Fock ones). Moreover, because in the AASCα method the exchange potential tends toward the correct (-1/r) asymptotic behavior, the ionization potentials approximated by the negative of the highest-occupied-orbital energy have a closer agreement with experimental values than those resulting from current approximate density functionals. Finally, we show that in the context of the present method it is possible to introduce some generalizations to the Gritsenko-van Leeuwen-van Lenthe-Baerends model [O. Gritsenko, R. van Leeuwen, E. van Lenthe, and E. J. Baerends, Phys. Rev. A 51, 1944 (1995)].

  18. A Numerical Algorithm and a Graphical Method to Size a Heat Exchanger

    DEFF Research Database (Denmark)

    Berning, Torsten

    2011-01-01

    This paper describes the development of a numerical algorithm and a graphical method that can be employed in order to determine the overall heat transfer coefficient inside heat exchangers. The method is based on an energy balance and utilizes the spreadsheet application software Microsoft Excel......TM. The application is demonstrated in an example for designing a single pass shell and tube heat exchanger that was developed in the Department of Materials Technology of the Norwegian University of Science and Technology (NTNU) where water vapor is superheated by a secondary oil cycle. This approach can be used...

  19. 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.

  20. 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.

  1. 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,...

  2. A screening method for the optimal selection of plate heat exchanger configurations

    Directory of Open Access Journals (Sweden)

    Pinto J.M.

    2002-01-01

    Full Text Available An optimization method for determining the best configuration(s of gasketed plate heat exchangers is presented. The objective is to select the configuration(s with the minimum heat transfer area that still satisfies constraints on the number of channels, the pressure drop of both fluids, the channel flow velocities and the exchanger thermal effectiveness. The configuration of the exchanger is defined by six parameters, which are as follows: the number of channels, the numbers of passes on each side, the fluid locations, the feed positions and the type of flow in the channels. The resulting configuration optimization problem is formulated as the minimization of the exchanger heat transfer area and a screening procedure is proposed for its solution. In this procedure, subsets of constraints are successively applied to eliminate infeasible and nonoptimal solutions. Examples show that the optimization method is able to successfully determine a set of optimal configurations with a minimum number of exchanger evaluations. Approximately 5 % of the pressure drop and channel velocity calculations and 1 % of the thermal simulations are required for the solution.

  3. Researching Online Foreign Language Interaction and Exchange: Theories, Methods and Challenges. Telecollaboration in Education. Volume 3

    Science.gov (United States)

    Dooly, Melinda; O'Dowd, Robert

    2012-01-01

    This book provides an accessible introduction to some of the methods and theoretical approaches for investigating foreign language (FL) interaction and exchange in online environments. Research approaches which can be applied to Computer-Mediated Communication (CMC) are outlined, followed by discussion of the way in which tools and techniques for…

  4. Distant exchange interactions in Cd1-xMnxS from magnetization steps method

    Science.gov (United States)

    Gratens, X.; Chitta, V.

    2017-07-01

    Three new distant neighbor (DN) antiferromagnetic exchange constants have been measured in wurtzite Cd1-xMnxS (x = 0.0087 and x = 0.0278) using the magnetization steps method in the millikelvin regime. The second (J(2)), third (J(3)), and fourth (J(4)) largest exchange constants (after the two first neighbor exchange interactions J1 and J1' ) have been measured. The results are J(2) = 300 ± 10 mK, J(3) = 173 ± 10 mK, and J(4) = 55 ± 10 mK. No significant change of the exchange constant values has been observed as a function of the Mn concentration. The mapping of the DN exchange interactions has been investigated within a sphere of radius 2 times the nearest neighbors distance. The only way to identify the J constants was using the number coordination Zn of the different DN classes: J(2) is associated to DN classes with Zn = 6, J(3) with Zn = 12, and J(4) is ascribed to a group of three DN classes with J values around J(4). The magnitude of the J constants is not in agreement with theoretical predictions of the monotonic decrease of the exchange constant with increasing distance. The present results are similar to those obtained for Cd1-xMnxSe but are different from the ones obtained for Zn1-xMnxO. The present work confirms the long-range character of the DN exchange interactions in the wurtzite type Mn-based II-VI diluted magnetic semiconductors.

  5. 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.

  6. Axial flow heat exchanger devices and methods for heat transfer using axial flow devices

    Energy Technology Data Exchange (ETDEWEB)

    Koplow, Jeffrey P.

    2016-02-16

    Systems and methods described herein are directed to rotary heat exchangers configured to transfer heat to a heat transfer medium flowing in substantially axial direction within the heat exchangers. Exemplary heat exchangers include a heat conducting structure which is configured to be in thermal contact with a thermal load or a thermal sink, and a heat transfer structure rotatably coupled to the heat conducting structure to form a gap region between the heat conducting structure and the heat transfer structure, the heat transfer structure being configured to rotate during operation of the device. In example devices heat may be transferred across the gap region from a heated axial flow of the heat transfer medium to a cool stationary heat conducting structure, or from a heated stationary conducting structure to a cool axial flow of the heat transfer medium.

  7. ELECTRIC REGENERATION METHOD OF ION EXCHANGE RESIN IN THE MIXED BED

    Institute of Scientific and Technical Information of China (English)

    WangFang

    1998-01-01

    In this paper,the self-regeneration process of the mixed resins consisting of cation and anion ion exchangers in the electrolialyser of the packed bed is analyzed,and an electric regeneration method is put forward to supply the desalinated water by mixed bed.The electric regeneration technology is a new one used for regeneration of the exhausted ion exchangers in the mixed bed,instead of the traditional regenerating process by using acid and alkali liquor.Electric energy is consumed to regenerate the ion exchangers loaded by salts from water treatment without any chemicals-acid and alkali.The advantage of the electric regeneration process exhibited convenient operation,no discharge any waste,and therefore no pollution to the receiving water body and the environmental ground.

  8. One-pot preparation of unsaturated polyester nanocomposites containing functionalized graphene sheets via a novel solvent-exchange method

    Science.gov (United States)

    This paper reports a convenient one-pot method integrating a novel solvent-exchange method into in situ melt polycondensation to fabricate unsaturated polyester nanocomposites containing functionalized graphene sheets (FGS). A novel solvent-exchange method was first developed to prepare graphene oxi...

  9. An analytical method of estimating Value-at-Risk on the Belgrade Stock Exchange

    Directory of Open Access Journals (Sweden)

    Obadović Milica D.

    2009-01-01

    Full Text Available This paper presents market risk evaluation for a portfolio consisting of shares that are continuously traded on the Belgrade Stock Exchange, by applying the Value-at-Risk model - the analytical method. It describes the manner of analytical method application and compares the results obtained by implementing this method at different confidence levels. Method verification was carried out on the basis of the failure rate that demonstrated the confidence level for which this method was acceptable in view of the given conditions.

  10. 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...

  11. A Pole Assignment Design Method of Process Control System for Tubular Heat Exchanger

    Institute of Scientific and Technical Information of China (English)

    周清泉

    1992-01-01

    This Paper has first studied the simplified model of tubular heat exchanger which is widely used in the industry and other field.On the basis of reference 2,a new pole assignment design method of pro-cess control system with derivative control action is found.For the above system,the method and the for-mation which calculate the feedback matrix K and gain matrix L is given,and the simulation of the system is made.

  12. Evaluation and comparison of diffusion MR methods for measuring apparent transcytolemmal water exchange rate constant

    Science.gov (United States)

    Tian, Xin; Li, Hua; Jiang, Xiaoyu; Xie, Jingping; Gore, John C.; Xu, Junzhong

    2017-02-01

    Two diffusion-based approaches, CG (constant gradient) and FEXI (filtered exchange imaging) methods, have been previously proposed for measuring transcytolemmal water exchange rate constant kin, but their accuracy and feasibility have not been comprehensively evaluated and compared. In this work, both computer simulations and cell experiments in vitro were performed to evaluate these two methods. Simulations were done with different cell diameters (5, 10, 20 μm), a broad range of kin values (0.02-30 s-1) and different SNR's, and simulated kin's were directly compared with the ground truth values. Human leukemia K562 cells were cultured and treated with saponin to selectively change cell transmembrane permeability. The agreement between measured kin's of both methods was also evaluated. The results suggest that, without noise, the CG method provides reasonably accurate estimation of kin especially when it is smaller than 10 s-1, which is in the typical physiological range of many biological tissues. However, although the FEXI method overestimates kin even with corrections for the effects of extracellular water fraction, it provides reasonable estimates with practical SNR's and more importantly, the fitted apparent exchange rate AXR showed approximately linear dependence on the ground truth kin. In conclusion, either CG or FEXI method provides a sensitive means to characterize the variations in transcytolemmal water exchange rate constant kin, although the accuracy and specificity is usually compromised. The non-imaging CG method provides more accurate estimation of kin, but limited to large volume-of-interest. Although the accuracy of FEXI is compromised with extracellular volume fraction, it is capable of spatially mapping kin in practice.

  13. 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...

  14. 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...

  15. 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.

  16. Mercury Exchange at the Air-Water-Soil Interface: An Overview of Methods

    Directory of Open Access Journals (Sweden)

    Fengman Fang

    2002-01-01

    Full Text Available An attempt is made to assess the present knowledge about the methods of determining mercury (Hg exchange at the air-water-soil interface during the past 20 years. Methods determining processes of wet and dry removal/deposition of atmospheric Hg to aquatic and terrestrial ecosystems, as well as methods determining Hg emission fluxes to the atmosphere from natural surfaces (soil and water are discussed. On the basis of the impressive advances that have been made in the areas relating to Hg exchange among air-soil-water interfaces, we analyzed existing problems and shortcomings in our current knowledge. In addition, some important fields worth further research are discussed and proposed.

  17. A Simple and Efficient Method for Purification of Egg White Major Proteins Using Ion Exchange Chromatography

    Directory of Open Access Journals (Sweden)

    Sh. Veisi

    2008-04-01

    Full Text Available Introduction & Objective: Egg white contains four high-quantity proteins which have numerous applications. In this research, a simple and efficient method for the purification of those proteins was designed and performed based on ion exchange chromatography.Materials & Methods: In this experimental study egg white was initially separated from insoluble substances by acidic pH. The resulting extract was isolated after two steps of ion exchange chromatography using CM-Sepharose and DEAE-Sepharose columns, respectively. Purification degree and yield of each fraction were analyzed by electrophoresis densitometry.Results: The results showed that purification degrees of ovalbumin, ovotransferrin, ovomucoid and lysozyme were 97, 98, 85 and 99 percent and their yields were 98, 98 95 and 99 percent, respectively.Conclusion: High yields, reproducibility and feasibility on low or high scales are considered as the strengths of this method.

  18. 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.

  19. Performance of adsorbent-embedded heat exchangers using binder-coating method

    KAUST Repository

    Li, Ang

    2016-01-01

    The performance of adsorption (AD) chillers or desalination cycles is dictated by the rates of heat and mass transfer of adsorbate in adsorbent-packed beds. Conventional granular-adsorbent, packed in fin-tube heat exchangers, suffered from poor heat transfer in heating (desorption) or cooling (adsorption) processes of the batch-operated cycles, with undesirable performance parameters such as higher footprint of plants, low coefficient of performance (COP) of AD cycles and higher capital cost of the machines. The motivation of present work is to mitigate the heat and mass "bottlenecks" of fin-tube heat exchangers by using a powdered-adsorbent cum binder coated onto the fin surfaces of exchangers. Suitable adsorbent-binder pairs have been identified for the silica gel adsorbent with pore surface areas up to 680 m2/g and pore diameters less than 6 nm. The parent silica gel remains largely unaffected despite being pulverized into fine particles of 100 μm, and yet maintaining its water uptake characteristics. The paper presents an experimental study on the selection and testing processes to achieve high efficacy of adsorbent-binder coated exchangers. The test results indicate 3.4-4.6 folds improvement in heat transfer rates over the conventional granular-packed method, resulting a faster rate of water uptake by 1.5-2 times on the suitable silica gel type. © 2015 Elsevier Ltd. All rights reserved.

  20. Temperature and thermal stress evolutions in sapphire crystal during the cooling process by heat exchanger method

    Science.gov (United States)

    Ma, Wencheng; Zhao, Wenhan; Wu, Ming; Ding, Guoqiang; Liu, Lijun

    2017-09-01

    Transient numerical calculations were carried out to predict the evolutions of temperature and thermal stress in sapphire single crystal during the cooling process by heat exchanger method (HEM). Internal radiation in the semitransparent sapphire crystal was taken into account using the finite volume method (FVM) in the global heat transfer model. The numerical results seem to indicate that the narrow bottom region of the sapphire crystal is subjected to high thermal stress during the cooling process, which could be responsible for the seed cracking of the as-grown crystal, while the thermal stress is relatively small in the central main body of the crystal, and is less than 10 MPa during the whole cooling process. The fast decrease of the thermal stress in the bottom region of the crystal during the initial stage of cooling process is dominated by the reduction of the cooling helium gas in the heat exchanger shaft, and is not significantly affected by the heating power reduction rate.

  1. Electronic properties of antiferromagnetic UBi2 metal by exact exchange for correlated electrons method

    Directory of Open Access Journals (Sweden)

    E Ghasemikhah

    2012-03-01

    Full Text Available This study investigated the electronic properties of antiferromagnetic UBi2 metal by using ab initio calculations based on the density functional theory (DFT, employing the augmented plane waves plus local orbital method. We used the exact exchange for correlated electrons (EECE method to calculate the exchange-correlation energy under a variety of hybrid functionals. Electric field gradients (EFGs at the uranium site in UBi2 compound were calculated and compared with the experiment. The EFGs were predicted experimentally at the U site to be very small in this compound. The EFG calculated by the EECE functional are in agreement with the experiment. The densities of states (DOSs show that 5f U orbital is hybrided with the other orbitals. The plotted Fermi surfaces show that there are two kinds of charges on Fermi surface of this compound.

  2. 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.

  3. A new method for analyzing heat exchangers-matching of temperature field

    Science.gov (United States)

    Wang, HuanGuang; Huai, XiuLan

    2012-10-01

    In heat exchangers, the magnitude of Nu of each duct is influenced by the temperature field, since the ratio of heat capacity rate will influence the matching status of the temperature field between contacting ducts, the total heat transfer coefficient is related with the ratio of heat capacity rate. Considering this relationship, a new method for analyzing heat exchanger is proposed — matching of temperature field. First, for a single duct with the temperature field varying exponentially along the flow direction, its Nu is calculated. Then under the hypothesis that the thermal resistance of the wall is negligible, the matching condition was set like this: both the temperature and heat flux are equal for the hot and cold fluids at the wall, so the matching relationship of parameter that describes the temperature field of the hot and cold fluids, was obtained. Finally the relationship between the total Nu and the ratio of heat capacity rate along with the ratio of inherent thermal resistance is obtained. Compared with traditional analyzing methods, the temperature matching method can be used to get the total heat transfer coefficient directly, and also be used for optimization of heat exchanger design. For a parallel flow, the optimal ratio of heat capacity rate is reciprocal to the ratio of inherent thermal resistance, and for a counter flow, the optimal ratio of heat capacity rate is zero or infinity.

  4. Ion exchange liquid chromatography method for the direct determination of small ribonucleic acids.

    Science.gov (United States)

    McGinnis, A Cary; Cummings, Brian S; Bartlett, Michael G

    2013-10-17

    Bioanalysis of siRNAs is challenging due to their size (5-14 kDa) and negative charge across the backbone, which complicates both sample preparation and chromatography. We present here a one step sample preparation combined with non-denaturing anion exchange chromatography with UV detection for the quantitation of siRNA and its chain shortened metabolites. The sample preparation uses a novel lysis buffer with proteinase K to effectively isolate siRNA from cells and formulated media with greater than 95% recovery. The ion exchange chromatography allows for a lower limit of quantitation of 6 ng mL(-1) in cells and media equivalent to 6 ng/200,000 cells. This method is applied to study the uptake of siRNA in prostate cancer cells and the disappearance in the media and siRNA metabolism. siRNA metabolites are identified by matching the retention time of standards to metabolite peaks. Identification is further confirmed by mass spectrometry. To our knowledge this is the first ion exchange method reported for the quantitation of siRNA from a biological matrix. It is also the first non-denaturing chromatographic method reported for siRNA quantitation.

  5. Diluted melt proton exchange slab waveguides in LiNbO3: A new fabrication and characterization method

    DEFF Research Database (Denmark)

    Veng, Torben; Skettrup, Torben

    1997-01-01

    A method of dilute-melt proton exchange employing a mixture of glycerol and KHSO4 with lithium benzoate added is used to fabricate planar waveguides in c-cut LiNbO3. With this exchange melt system the waveguide refractive index profiles can be fabricated with a high degree of reproducibility. In ...... refractive index change and composition of this glycerol, KHSO4 and lithium benzoate exchange melt system....

  6. Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer

    Directory of Open Access Journals (Sweden)

    Michael eHines

    2011-11-01

    Full Text Available The performance of several spike exchange methods using a Blue Gene/P supercomputerhas been tested with 8K to 128K cores using randomly connected networks of up to 32M cells with 1k connections per cell and 4M cells with 10k connections per cell. The spike exchange methods used are the standard Message Passing Interface collective, MPI_Allgather, and several variants of the non-blocking multisend method either implemented via non-blocking MPI_Isend, or exploiting the possibility of very low overhead direct memory access communication available on the Blue Gene/P. In all cases the worst performing method was that using MPI_Isend due to the high overhead of initiating a spike communication. The two best performing methods --- the persistent multisend method using the Record-Replay feature of the Deep Computing Messaging Framework DCMF_Multicast;and a two phase multisend in which a DCMF_Multicast is used to first send to a subset of phase 1 destination cores which then pass it on to their subset of phase 2 destination cores --- had similar performance with very low overhead for the initiation of spike communication. Departure from ideal scaling for the multisend methods is almost completely due to load imbalance caused by the largevariation in number of cells that fire on each processor in the interval between synchronization. Spike exchange time itself is negligible since transmission overlaps with computation and is handled by a direct memory access controller. We conclude that ideal performance scaling will be ultimately limited by imbalance between incoming processor spikes between synchronization intervals. Thus, counterintuitively, maximization of load balance requires that the distribution of cells on processors should not reflect neural net architecture but be randomly distributed so that sets of cells which are burst firing together should be on different processors with their targets on as large a set of processors as possible.

  7. A Hydrogen Exchange Method Using Tritium and Sephadex: Its Application to Ribonuclease*

    Science.gov (United States)

    Englander, S. Walter

    2012-01-01

    A new method for measuring the hydrogen exchange of macromolecules in solution is described. The method uses tritium to trace the movement of hydrogen, and utilizes Sephadex columns to effect, in about 2 minutes, a separation between tritiated macromolecule and tritiated solvent great enough to allow the measurement of bound tritium. High sensitivity and freedom from artifact is demonstrated and the possible value of the technique for investigation of other kinds of colloid-small molecule interaction is indicated. Competition experiments involving tritium, hydrogen, and deuterium indicate the absence of any equilibrium isotope effect in the ribonuclease-hydrogen isotope system, though a secondary kinetic isotope effect is apparent when ribonuclease is largely deuterated. Ribonuclease shows four clearly distinguishable kinetic classes of exchangeable hydrogens. Evidence is marshaled to suggest the independently measurable classes II, III, and IV (in order of decreasing rate of exchange) to represent “random-chain” peptides, peptides involved in α-helix, and otherwise shielded side-chain and peptide hydrogens, respectively. PMID:14075117

  8. A novel protein refolding method integrating ion exchange chromatography with artificial molecular chaperone

    Institute of Scientific and Technical Information of China (English)

    Qin Ming Zhang; Chao Zhan Wang; Jiang Feng Liu; Li Li Wang

    2008-01-01

    Artificial molecular chaperone (AMC) and ion exchange chromatography (IEC) were integrated, thus a new refolding method,artificial molecular chaperone-ion exchange chromatography (AMC-IEC) was developed. Compared with AMC and IEC, theactivity recovery of lysozyme obtained by AMC-IEC was much higher in the investigated range of initial protein concentrations,and the results show that AMC-IEC is very efficient for protein refolding at high concentrations. When the initial concentration oflysozyme is 180 mg/mL, its activity recovery obtained by AMC-IEC is still as high as 76.6%, while the activity recoveries obtainedby AMC and IEC are 45.6% and 42.4%, respectively.2008 Chao Zhan Wang. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.

  9. A simple method for estimating cation exchange capacity from water vapor sorption

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Tuller, Markus

    2016-01-01

    Knowledge of soil cation exchange capacity (CEC) is crucial for soil fertility considerations, sorption and release of polar and non-polar compounds, engineering applications, and other biogeochemical processes. Standard procedures such as the ammonium acetate or the BaCl2 compulsive exchange...... methods are expensive and laborious, and in previous studies the CEC has been predicted from parameters such as particle size distribution and organic matter content, specific surface area, clay content, and from Atterberg limits. In this study, relative humidity (RH)-dependent pedotransfer functions...... (PTFs) for estimating CEC from soil water content considering hysteresis have been developed based on 203 differently-textured soils. Furthermore, we compared the performance of the new PTFs with existing PTFs that predict CEC from clay content, organic carbon, soil pH and specific surface area. The new...

  10. Exchange bias effect in CoCr2O4/NiO system prepared by two-step method

    Science.gov (United States)

    Wang, L. G.; Zhu, C. M.; Chen, L.; Yuan, S. L.

    2017-02-01

    CoCr2O4/NiO has been successfully synthesized through two-step method. X-ray diffraction results present the coexistence of CoCr2O4 and NiO with pure formation. Micrographs measured with scanning electron microscope and transmission electron microscope display the homogeneous and dense morphology with two kinds of nanoparticles. Exchange bias effect is observed in the sample. The exchange bias field is about 872 Oe at 10 K. As measuring temperature increases, exchange bias effect is weakened with decreasing coercive field. In addition, exchange bias field and the shift of magnetization show the linear relationship with increasing cooling field. The exchange bias behavior can be attributed to the exchange coupling at the disordered interfaces in the sample.

  11. 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.

  12. 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.

  13. 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.

  14. TCP-based window-size delegation method for TXOP Exchange in wireless local area networks

    Directory of Open Access Journals (Sweden)

    Hasegawa Go

    2011-01-01

    Full Text Available Abstract We propose a TCP window-size delegation method for downlink TXOP (transmission opportunity Exchange in wireless local area networks (WLANs. In our method, the 'compliant' stations (STAs cooperatively use their available bandwidth in accordance with their throughput demand. We realize our method only with minimal modifications of the TCP functions of a proxy server, which lets one station (the TXOP provider delegate TCP window size to another station (the TXOP client so that the provider delegates its TXOPs in WLANs to the client. Our method enables an STA to flexibly delegate TXOPs to another STA without adversely affecting the legacy STAs, which is confirmed by computer simulations. We also confirmed that our method requires no modification to legacy access points and STAs.

  15. Improved durability of proton exchange membrane fuel cells by introducing Sn (IV) oxide into electrodes using an ion exchange method

    Science.gov (United States)

    Poulsen, M. G.; Larsen, M. J.; Andersen, S. M.

    2017-03-01

    Electrodes of Proton Exchange Membrane Fuel Cells (PEMFCs), consisting of catalyst-coated gas diffusion layers, were subjected to an optimized ion exchange procedure, in which tin (IV) oxide (SnO2) nanoparticles were introduced into them. Both methanol and sulfuric acid were tested as ion exchange solvents. SnO2 has previously been shown to exhibit radical scavenging abilities towards radicals inside the electrocatalyst layers. Its presence inside the electrodes was confirmed using X-ray photoelectron spectroscopy and X-ray fluorescence. After exposure to an accelerated stress test in a three-electrode setup, the electrodes containing SnO2 were found to have retained approximately 73.0% of their original Pt, while only 53.2% was retained in electrodes treated identically, but without Sn. Similarly, the SnO2-treated electrodes also experienced a smaller loss in electrochemical surface area in comparison to before the accelerated stress test. A membrane electrode assembly (MEA) constructed with a SnO2-containing anode was evaluated over 500 h. The results showed remarkably reduced OCV decay rate and end of test hydrogen crossover compared to the control MEA, indicating that SnO2 aids in impeding membrane thinning and pinhole formation. The results point toward a positive effect of SnO2 on fuel cell durability, by reducing the degradation of the membrane as well as of the ionomer in the electrocatalyst layer.

  16. 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.

  17. Computational methods and challenges in hydrogen/deuterium exchange mass spectrometry.

    Science.gov (United States)

    Claesen, Jürgen; Burzykowski, Tomasz

    2017-09-01

    Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvements and the increased use of protein-HDXMS, large amounts of complex data are generated, which require appropriate analysis. Computational analysis of HDXMS requires several steps. A typical workflow for proteins consists of identification of (non-)deuterated peptides or fragments of the protein under study (local analysis), or identification of the deuterated protein as a whole (global analysis); determination of the deuteration level; estimation of the protection extent or exchange rates of the labile backbone amide hydrogen atoms; and a statistically sound interpretation of the estimated protection extent or exchange rates. Several algorithms, specifically designed for HDX analysis, have been proposed. They range from procedures that focus on one specific step in the analysis of HDX data to complete HDX workflow analysis tools. In this review, we provide an overview of the computational methods and discuss outstanding challenges. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:649-667, 2017. © 2016 Wiley Periodicals, Inc.

  18. Understanding perovskite formation through the intramolecular exchange method in ambient conditions

    Science.gov (United States)

    Szostak, Rodrigo; Castro, Jhon A. P.; Marques, Adriano S.; Nogueira, Ana F.

    2017-04-01

    Among the methods to prepare hybrid organic-inorganic perovskite films, the intramolecular exchange method was the first one that made possible to prepare perovskite solar cells with efficiencies higher than 20%. However, perovskite formation by this method is not completely understood, especially in ambient conditions. In this work, perovskite films were prepared by the intramolecular exchange method in ambient conditions. The spin coating speed and the frequency of the MAI solution dripping onto PbI2(DMSO) were varied during the deposition steps. With the combination of these two parameters, a rigid control of the solvent drying was possible. Thus, depending on the chosen conditions, the intermediate MAPb3I8·2DMSO was formed with residual PbI2. Otherwise, direct formation of perovskite film was attained. A mechanism for the direct formation of bulk perovskite was proposed. We also investigated how the posterior thermal annealing affects the crystallinity and defects in perovskite films. With prolonged thermal annealing, the excess of MAI can be avoided, increasing the efficiency and decreasing the hysteresis of the solar cells. The best perovskite solar cell achieved a stabilized power output of 12.9%. The findings of this work pave the way for realizing the fabrication of efficient perovskite solar cells in ambient atmosphere, a very desirable condition for cost-efficient large scale manufacturing of this technology.

  19. Stratosphere-troposphere exchange from the Lagrangian perspective: a case study and method sensitivities

    Directory of Open Access Journals (Sweden)

    M. S. Bourqui

    2004-06-01

    Full Text Available An important part of extra-tropical stratosphere-to-troposphere transport occurs in association with baroclinic wave breaking and cut-off decay at the tropopause. In the last decade many studies have attempted to estimate stratosphere-troposphere exchange (STE in such synoptic events with various methods, and more recently efforts have been put on inter-comparing these methods. However, large uncertainties remain on the sensitivities to methods intrinsic parameters, and on the best measure for STE with regard to end effects on chemistry.

    The goal of the present study is to address these two fundamental issues in the context of the application of a trajectory-based Lagrangian method, which has been applied in the past to climatological studies and has also been involved in inter-comparison studies, to a typical baroclinic wave breaking event.

    The analysis sheds light on (i the fine mesoscale temporal and spatial structures that are associated with episodic, rapid inflows of stratospheric air into the troposphere; (ii the spatial resolution of 1°×1° required to reasonably capture STE fluxes in such a wave breaking event; (iii the effective removal of spurious exchange events using a threshold residence time; (iv the relevance of residence time distributions for capturing the effective chemical forcing of STE; (v the large differences in the temporal evolution and geographical distribution of STE fluxes across the 2 and the 4 potential vorticity unit iso-surface definitions of the tropopause.

  20. 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/).

  1. Study on occlusal morphology after CAD/CAM zirconia restoration using silicone replica method%氧化锆单冠制作过程中使用硅橡胶复制法对咬合面形态的影响

    Institute of Scientific and Technical Information of China (English)

    王金平; 赵彬; 曹婷婷; 王华

    2013-01-01

    Objective To establish an individualized CAD/CAM zirconia restoration method using silicon replica and investigate its effect on occlusal morphology.Methods Eight super-hard plaster models were created from a set of standardized dental resin model produced by Nissin as controls.A standard all-ceramic FDP of left maxillary first molar was accommodated on the set of standardized dental resin model,and then forty-eight super-hard plaster models were created and divided into two groups.Twenty-four of them were selected randomly to evaluate the occlusal morphology.And the other twenty-four were used to fabricate CAD/CAM zirconia restorations,and divided into three groups:individualized group,one-molding-processing group,two-molding-processing group.The distribution and area of occlusal contact were investigated using three-dimensional analysis method for digital dental casts and compared with control group.Results The areas of occlusal contact showed no significant difference between individualized group and control group at maximum intermaxillary distance of 16 μm and 40 μm (P > 0.05).The areas of occlusal contact in individualized group at maximum intermaxillary distance of 100 μm were less than that in control group (P < 0.05).Statistically significant difference was found in areas of occlusal contact between the other two groups and control group (P < 0.001).The distribution and areas of occlusal contact in individualized group (occlusal stabilization 87.5%) and control group (occlusal stabilization 100%) were mostly consistent.Conclusion CAD/CAM technique combined with silicone replica method enables a closer reconstruction of teeth than traditional one-molding-processing and two-molding-processing method.%目的 应用硅橡胶复制法建立一种个性化氧化锆单冠的设计制作方法,评价该方法对其咬合面形态的影响. 方法 用超硬石膏翻制日进标准树脂模型8副作为对照组.将左侧上颌第一磨牙对应的标

  2. Layered double hydroxides as the next generation inorganic anion exchangers: Synthetic methods versus applicability.

    Science.gov (United States)

    Chubar, Natalia; Gilmour, Robert; Gerda, Vasyl; Mičušík, Matej; Omastova, Maria; Heister, Katja; Man, Pascal; Fraissard, Jacques; Zaitsev, Vladimir

    2017-07-01

    This work is the first report that critically reviews the properties of layered double hydroxides (LDHs) on the level of speciation in the context of water treatment application and dynamic adsorption conditions, as well as the first report to associate these properties with the synthetic methods used for LDH preparation. Increasingly stronger maximum allowable concentrations (MAC) of various contaminants in drinking water and liquid foodstuffs require regular upgrades of purification technologies, which might also be useful in the extraction of valuable substances for reuse in accordance with modern sustainability strategies. Adsorption is the main separation technology that allows the selective extraction of target substances from multicomponent solutions. Inorganic anion exchangers arrived in the water business relatively recently to achieve the newly approved standards for arsenic levels in drinking water. LDHs (or hydrotalcites, HTs) are theoretically the best anion exchangers due to their potential to host anions in their interlayer space, which increases their anion removal capacity considerably. This potential of the interlayer space to host additional amounts of target aqueous anions makes the LDHs superior to bulk anion exchanger. The other unique advantage of these layered materials is the flexibility of the chemical composition of the metal oxide-based layers and the interlayer anions. However, until now, this group of "classical" anion exchangers has not found its industrial application in adsorption and catalysis at the industrial scale. To accelerate application of LDHs in water treatment on the industrial scale, the authors critically reviewed recent scientific and technological knowledge on the properties and adsorptive removal of LDHs from water on the fundamental science level. This also includes review of the research tools useful to reveal the adsorption mechanism and the material properties beyond the nanoscale. Further, these properties are

  3. The role of the exchange in the embedding electrostatic potential for the fragment molecular orbital method.

    Science.gov (United States)

    Fedorov, Dmitri G; Kitaura, Kazuo

    2009-11-01

    We have examined the role of the exchange in describing the electrostatic potential in the fragment molecular orbital method and showed that it should be included in the total Fock matrix to obtain an accurate one-electron spectrum; however, adding it to the Fock matrices of individual fragments and pairs leads to very large errors. For the error analysis we have used the virial theorem; numerical tests have been performed for solvated phenol at the Hartree-Fock level with the 6-31G( *) and 6-311G( * *) basis sets.

  4. Amide-Exchange-Rate-Edited NMR (AERE-NMR) Experiment:A Novel Method for Resolving Overlapping Resonances

    Institute of Scientific and Technical Information of China (English)

    LIU Xue-Hui; LIN Dong-Hai

    2007-01-01

    This paper describes an amide-exchange-rate-edited (AERE) NMR method that can effectively alleviate the problem of resonance overlap for proteins and peptides. This method exploits the diversity of amide proton exchange rates and consists of two complementary experiments: (1) SEA (solvent exposed amide)-type NMR experiments to map exchangeable surface residues whose amides are not involved in hydrogen bonding, and (2) presat-type NMR experiments to map solvent inaccessibly buried residues or nonexchangeable residues located in hydrogen-bonded secondary structures with properly controlled saturation transfer via amide proton exchanges with the solvent. This method separates overlapping resonances in a spectrum into two complementary spectra. The AERE-NMR method was demonstrated with a sample of 15N/13C/2H(70%) labeled ribosome-inactivating protein trichosanthin of 247 residues.

  5. Ultrafiltration technique in conjunction with competing ligand exchange method for Ni–humics speciation in aquatic environment

    Digital Repository Service at National Institute of Oceanography (India)

    Chakraborty, P.; Boissel, M.; Reuillon, A.; Babu, P.V.R.; Parthiban, G.

    The combination of ultrafiltration technique with competing ligand exchange method provides a better understanding of interactions between Ni and different molecular weight fractions of humic acid (HA) at varying pH in aquatic environment...

  6. 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.

  7. Input data preprocessing method for exchange rate forecasting via neural network

    Directory of Open Access Journals (Sweden)

    Antić Dragan S.

    2014-01-01

    Full Text Available The aim of this paper is to present a method for neural network input parameters selection and preprocessing. The purpose of this network is to forecast foreign exchange rates using artificial intelligence. Two data sets are formed for two different economic systems. Each system is represented by six categories with 70 economic parameters which are used in the analysis. Reduction of these parameters within each category was performed by using the principal component analysis method. Component interdependencies are established and relations between them are formed. Newly formed relations were used to create input vectors of a neural network. The multilayer feed forward neural network is formed and trained using batch training. Finally, simulation results are presented and it is concluded that input data preparation method is an effective way for preprocessing neural network data. [Projekat Ministarstva nauke Republike Srbije, br.TR 35005, br. III 43007 i br. III 44006

  8. A fast determination method for transverse relaxation of spin-exchange-relaxation-free magnetometer.

    Science.gov (United States)

    Lu, Jixi; Qian, Zheng; Fang, Jiancheng

    2015-04-01

    We propose a fast and accurate determination method for transverse relaxation of the spin-exchange-relaxation-free (SERF) magnetometer. This method is based on the measurement of magnetic resonance linewidth via a chirped magnetic field excitation and the amplitude spectrum analysis. Compared with the frequency sweeping via separate sinusoidal excitation, our method can realize linewidth determination within only few seconds and meanwhile obtain good frequency resolution. Therefore, it can avoid the drift error in long term measurement and improve the accuracy of the determination. As the magnetic resonance frequency of the SERF magnetometer is very low, we include the effect of the negative resonance frequency caused by the chirp and achieve the coefficient of determination of the fitting results better than 0.998 with 95% confidence bounds to the theoretical equation. The experimental results are in good agreement with our theoretical analysis.

  9. A method for detector description exchange among ROOT GEANT4 and GEANT3

    Institute of Scientific and Technical Information of China (English)

    YOU Zheng-Yun; LIANG Yu-Tie; MAO Ya-Jun

    2008-01-01

    GEANT3 and GEANT4 are the detector simulation software programs that are widely used in most nuclear and particle physics experiments. ROOT is a program for framework, data analysis, online and offline software. Detector description is an important function in all these programs. Due to different detector construction methods and respective detector data representative, it is difficult to exchange the detector data among them. A new method based on GDML is developed to automatically convert the detector data among ROOT, GEANT4 and GEANT3. Any existing detector geometry in one program can be mapped to the geometry in the other two programs. In the software development of an experiment, different applications can share and reuse the same detector description. The application of this method in the PHENIX experiment upgrade and PHENIX Forward Vertex Silicon detector design is introduced.

  10. An empirical analysis to study the cyclical trends on stock exchange using wavelet methods

    Directory of Open Access Journals (Sweden)

    Shapour Mohammadi

    2011-01-01

    Full Text Available During the past few decades, there have been many evidences to believe that the stock markets around the world follow cyclical trends. In this paper, we study the cyclical trends using wavelet function based on various time windows on some major stock market indices. We use two methods of Daubechies and reverse bi-orthogonal wavelet methods and determine the optimal values of both methods. The results are used for Tehran stock exchange using the most recent ten years daily information as an empirical study. The details of our analysis on TEDPIX index for the last decade indicate that there are, at least, four trends of weekly, monthly, quarterly and yearly and the cycles would be expected to be repeated in future.

  11. Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer.

    Science.gov (United States)

    Hines, Michael; Kumar, Sameer; Schürmann, Felix

    2011-01-01

    For neural network simulations on parallel machines, interprocessor spike communication can be a significant portion of the total simulation time. The performance of several spike exchange methods using a Blue Gene/P (BG/P) supercomputer has been tested with 8-128 K cores using randomly connected networks of up to 32 M cells with 1 k connections per cell and 4 M cells with 10 k connections per cell, i.e., on the order of 4·10(10) connections (K is 1024, M is 1024(2), and k is 1000). The spike exchange methods used are the standard Message Passing Interface (MPI) collective, MPI_Allgather, and several variants of the non-blocking Multisend method either implemented via non-blocking MPI_Isend, or exploiting the possibility of very low overhead direct memory access (DMA) communication available on the BG/P. In all cases, the worst performing method was that using MPI_Isend due to the high overhead of initiating a spike communication. The two best performing methods-the persistent Multisend method using the Record-Replay feature of the Deep Computing Messaging Framework DCMF_Multicast; and a two-phase multisend in which a DCMF_Multicast is used to first send to a subset of phase one destination cores, which then pass it on to their subset of phase two destination cores-had similar performance with very low overhead for the initiation of spike communication. Departure from ideal scaling for the Multisend methods is almost completely due to load imbalance caused by the large variation in number of cells that fire on each processor in the interval between synchronization. Spike exchange time itself is negligible since transmission overlaps with computation and is handled by a DMA controller. We conclude that ideal performance scaling will be ultimately limited by imbalance between incoming processor spikes between synchronization intervals. Thus, counterintuitively, maximization of load balance requires that the distribution of cells on processors should not reflect

  12. Method for Incorporation of Controllability in Heat Exchanger Network Synthesis by Integrating Mathematical Programming and Knowledge Engineering

    Institute of Scientific and Technical Information of China (English)

    李志红

    2002-01-01

    A method for incorporation of controlling the heat exchanger networks with or without splits is proposed by integrating mathematical programming and knowledge engineering.The simultaneous optimal mathematical model is established.This method can be practically used in the integration of large-scale heat exchanger networks,not only to synthesize automatically but also to satisfy the requirement of structural controllability with more nobjective human intervention.

  13. Optical methods to study the gas exchange processes in large diesel engines

    Energy Technology Data Exchange (ETDEWEB)

    Gros, S.; Hattar, C. [Wartsila Diesel International Oy, Vaasa (Finland); Hernberg, R.; Vattulainen, J. [Tampere Univ. of Technology, Tampere (Finland). Plasma Technology Lab.

    1996-12-01

    To be able to study the gas exchange processes in realistic conditions for a single cylinder of a large production-line-type diesel engine, a fast optical absorption spectroscopic method was developed. With this method line-of-sight UV-absorption of SO{sub 2} contained in the exhaust gas was measured as a function of time in the exhaust port area in a continuously fired medium speed diesel engine type Waertsilae 6L20. SO{sub 2} formed during the combustion from the fuel contained sulphur was used as a tracer to study the gas exchange as a function of time in the exhaust channel. In this case of a 4-stroke diesel engine by assuming a known concentration of SO{sub 2} in the exhaust gas after exhaust valve opening and before inlet and exhaust valve overlap period, the measured optical absorption was used to determine the gas density and further the instantaneous exhaust gas temperature during the exhaust cycle. (author)

  14. COMPARISON OF THE INITIAL PUBLIC OFFERING METHODS IN THE ISTANBUL STOCK EXCHANGE

    Directory of Open Access Journals (Sweden)

    GÜRAY KÜÇÜKKOCAOĞLU

    2013-06-01

    Full Text Available The Turkish IPO market gives issuers and underwriters a choice of different IPO selling mechanisms. Accordingly, firms may offer their shares to the public through one of the following two methods of sale; Collection of Bids (Fixed-Price Offering and Book Building Method and Sale through the Stock Exchange. In this paper we try to answer the question of “What kind of selling and underwriting procedure might be preferred for controlling the amount and volatility of underpricing in the Istanbul Stock Exchange (ISE”. Using 1993-2005 firm and issue data, we compare the book building mechanism and the fixed price offer available in the ISE. The empirical analysis reveals significant first day underpricing of 7.13% in fixed price offers and 10.61% in book building mechanism. We also show that market returns prior to IPOs, a proxy for the overall market’s price momentum in the 3 months prior to an offering, is a significant ex ante predictor of the level of underpricing. Our findings confirm that firms prefer to go public in “hot markets” and the Market Return variable, calculated as the weighted average of the returns of the market index for the 3 months before the IPO pricing date, has a significant impact on the underpricing of the issues.

  15. A new cation-exchange method for accurate field speciation of hexavalent chromium

    Science.gov (United States)

    Ball, J.W.; McCleskey, R.B.

    2003-01-01

    A new method for field speciation of Cr(VI) has been developed to meet present stringent regulatory standards and to overcome the limitations of existing methods. The method consists of passing a water sample through strong acid cation-exchange resin at the field site, where Cr(III) is retained while Cr(VI) passes into the effluent and is preserved for later determination. The method is simple, rapid, portable, and accurate, and makes use of readily available, inexpensive materials. Cr(VI) concentrations are determined later in the laboratory using any elemental analysis instrument sufficiently sensitive to measure the Cr(VI) concentrations of interest. The new method allows measurement of Cr(VI) concentrations as low as 0.05 ??g 1-1, storage of samples for at least several weeks prior to analysis, and use of readily available analytical instrumentation. Cr(VI) can be separated from Cr(III) between pH 2 and 11 at Cr(III)/Cr(VI) concentration ratios as high as 1000. The new method has demonstrated excellent comparability with two commonly used methods, the Hach Company direct colorimetric method and USEPA method 218.6. The new method is superior to the Hach direct colorimetric method owing to its relative sensitivity and simplicity. The new method is superior to USEPA method 218.6 in the presence of Fe(II) concentrations up to 1 mg 1-1 and Fe(III) concentrations up to 10 mg 1-1. Time stability of preserved samples is a significant advantage over the 24-h time constraint specified for USEPA method 218.6.

  16. 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.

  17. 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...

  18. 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…

  19. 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…

  20. 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.

  1. An extended stochastic reconstruction method for catalyst layers in proton exchange membrane fuel cells

    Science.gov (United States)

    Kang, Jinfen; Moriyama, Koji; Kim, Seung Hyun

    2016-09-01

    This paper presents an extended, stochastic reconstruction method for catalyst layers (CLs) of Proton Exchange Membrane Fuel Cells (PEMFCs). The focus is placed on the reconstruction of customized, low platinum (Pt) loading CLs where the microstructure of CLs can substantially influence the performance. The sphere-based simulated annealing (SSA) method is extended to generate the CL microstructures with specified and controllable structural properties for agglomerates, ionomer, and Pt catalysts. In the present method, the agglomerate structures are controlled by employing a trial two-point correlation function used in the simulated annealing process. An off-set method is proposed to generate more realistic ionomer structures. The variations of ionomer structures at different humidity conditions are considered to mimic the swelling effects. A method to control Pt loading, distribution, and utilization is presented. The extension of the method to consider heterogeneity in structural properties, which can be found in manufactured CL samples, is presented. Various reconstructed CLs are generated to demonstrate the capability of the proposed method. Proton transport properties of the reconstructed CLs are calculated and validated with experimental data.

  2. Estimating groundwater exchange with lakes: 1. The stable isotope mass balance method

    Science.gov (United States)

    Krabbenhoft, David P.; Bowser, Carl J.; Anderson, Mary P.; Valley, John W.

    1990-01-01

    Groundwater inflow and outflow contributions to the hydrologic budget of lakes can be determined using a stable isotope (18O/16O) mass balance method. The stable isotope method provides a way of integrating the spatial and temporal complexities of the flow field around a lake, thereby offering an appealing alternative to the traditional time and labor intensive methods using seepage meters and an extensive piezometer network. In this paper the method is applied to a lake in northern Wisconsin, demonstrating that it can be successfully applied to lakes in the upper midwest where thousands of similar lakes exist. Inflow and outflow rates calculated for the Wisconsin lake using the isotope mass balance method are 29 and 54 cm/yr, respectively, which compare well to estimates, derived independently using a three-dimensional groundwater flow and solute transport model, of 20 and 50 cm/yr. Such a favorable comparison lends confidence to the use of the stable isotope method to estimate groundwater exchange with lakes. In addition, utilization of stable isotopes in studies of groundwater-lake systems lends insight into mixing processes occurring in the unsaturated zone and in the aquifer surrounding the lake and verifies assumed flow paths based on head measurements in piezometers.

  3. 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.

  4. 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.

  5. The long-run dynamic relationship between exchange rate and its attention index: Based on DCCA and TOP method

    Science.gov (United States)

    Wang, Xuan; Guo, Kun; Lu, Xiaolin

    2016-07-01

    The behavior information of financial market plays a more and more important role in modern economic system. The behavior information reflected in INTERNET search data has already been used in short-term prediction for exchange rate, stock market return, house price and so on. However, the long-run relationship between behavior information and financial market fluctuation has not been studied systematically. Further, most traditional statistic methods and econometric models could not catch the dynamic and non-linear relationship. An attention index of CNY/USD exchange rate is constructed based on search data from 360 search engine of China in this paper. Then the DCCA and Thermal Optimal Path methods are used to explore the long-run dynamic relationship between CNY/USD exchange rate and the corresponding attention index. The results show that the significant interdependency exists and the change of exchange rate is 1-2 days lag behind the attention index.

  6. 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

  7. 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.

  8. 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.

  9. A Throughfall Collection Method Using Mixed Bed Ion Exchange Resin Columns

    Directory of Open Access Journals (Sweden)

    Mark E. Fenn

    2002-01-01

    Full Text Available Measurement of ionic deposition in throughfall is a widely used method for measuring deposition inputs to the forest floor. Many studies have been published, providing a large database of throughfall deposition inputs to forests. However, throughfall collection and analysis is labor intensive and expensive because of the large number of replicate collectors needed and because sample collection and chemical analyses are required on a stochastic precipitation event-based schedule. Therefore we developed and tested a throughfall collector system using a mixed bed ion exchange resin column. We anticipate that this method will typically require only one to three samplings per year. With this method, bulk deposition and bulk throughfall are collected by a funnel or snow tube and ions are retained as the solution percolates through the resin column. Ions retained by the resin are then extracted in the same column with 2N KCl and analyzed for nitrate and ammonium. Deposition values in throughfall from conventional throughfall solution collectors and colocated ion exchange samplers were not significantly different during consecutive 3- and 4-month exposure periods at a high (Camp Paivika; >35 kg N ha-1 year-1 and a low deposition (Barton Flats; 5–9 kg N ha-1 year-1 site in the San Bernardino Mountains in southern California. N deposition in throughfall under mature pine trees at Camp Paivika after 7 months of exposure was extremely high (87 and 92 kg ha-1 based on the two collector types compared to Barton Flats (11 and 13 kg ha-1. A large proportion of the N deposited in throughfall at Camp Paivika occurred as fog drip, demonstrating the importance of fog deposition as an input source of N at this site. By comparison, bulk deposition rates in open areas were 5.1 and 5.4 kg ha-1 at Camp Paivika based on the two collector types, and 1.9 and 3.0 kg ha-1 at Barton Flats.

  10. A Review of Metallic Bipolar Plates for Proton Exchange Membrane Fuel Cells: Materials and Fabrication Methods

    Directory of Open Access Journals (Sweden)

    Shahram Karimi

    2012-01-01

    Full Text Available The proton exchange membrane fuel cell offers an exceptional potential for a clean, efficient, and reliable power source. The bipolar plate is a key component in this device, as it connects each cell electrically, supplies reactant gases to both anode and cathode, and removes reaction products from the cell. Bipolar plates have been fabricated primarily from high-density graphite, but in recent years, much attention has been paid to developing cost-effective and feasible alternative materials. Two different classes of materials have attracted attention: metals and composites. This paper offers a comprehensive review of the current research being carried out on metallic bipolar plates, covering materials and fabrication methods.

  11. A sugar-template manufacturing method for microsystem ion-exchange membranes

    Science.gov (United States)

    Festarini, Rio V.; Pham, Minh-Hao; Liu, Xinyue; Barz, Dominik P. J.

    2017-07-01

    In this work, we report on a novel method for producing ion-exchange membranes that can be integrated directly into polydimethylsiloxane-based micro devices. Ionomers such as NafionTM, a copolymer with high conductivity and selectivity to small cations, are generally incompatible with common micro device materials due to the chemical inertness of the tetrafluoroethylene-based skeleton and the swelling in aqueous solutions. Hence, we introduce a microfabrication concept where we use consolidated sugar granules as a template to produce a porous polydimethylsiloxane scaffold. Ionomer and scaffold are combined to a composite membrane where the cohesion of these incompatible materials is of rather mechanical nature; i.e. the ionomer is physically entrapped in the scaffold. Electrochemical impedance spectroscopy measurements reveal the excellent membrane conductivity for the upper electrolyte concentrations tested in this work.

  12. Proton exchange membrane fuel cell system diagnosis based on the signed directed graph method

    Science.gov (United States)

    Hua, Jianfeng; Lu, Languang; Ouyang, Minggao; Li, Jianqiu; Xu, Liangfei

    The fuel-cell powered bus is becoming the favored choice for electric vehicles because of its extended driving range, zero emissions, and high energy conversion efficiency when compared with battery-operated electric vehicles. In China, a demonstration program for the fuel cell bus fleet operated at the Beijing Olympics in 2008 and the Shanghai Expo in 2010. It is necessary to develop comprehensive proton exchange membrane fuel cell (PEMFC) diagnostic tools to increase the reliability of these systems. It is especially critical for fuel-cell city buses serving large numbers of passengers using public transportation. This paper presents a diagnostic analysis and implementation study based on the signed directed graph (SDG) method for the fuel-cell system. This diagnostic system was successfully implemented in the fuel-cell bus fleet at the Shanghai Expo in 2010.

  13. A general method for tritium labelling of benzimidazole carbamates by catalytic exchange in dioxane solutions

    Energy Technology Data Exchange (ETDEWEB)

    Lacey, E. (Commonwealth Scientific and Industrial Research Organization, Glebe, NSW (Australia). Div. of Animal Health, McMaster Lab.); Dawson, M. (Sydney Univ. (Australia). Dept. of Pharmacy); Long, M.A.; Than, C. (New South Wales Univ., Kensington (Australia). School of Chemistry)

    1989-12-01

    Benzimidazole carbamates (BZCs) act as inhibitors of the tubulin-microtubule equilibria in eukaryotic organisms. Recently drug resistance to this class of compounds in helminth parasites has been shown to be due to a reduced ability of resistant tubulin to bind BZCs. In order to quantitate the nature of the tubulin-BZC interaction a general method for the specific tritium labelling of BZCs has been developed. The BZCs: mebendazole, oxfendazole, parbendazole, oxibendazole, albendazole and fenbendazole were labelled by catalytic exchange using palladium on calcium carbonate in pure dioxane at 60{sup 0}C under tritium gas. The position of label incorporation for tritiated albendazole was determined by tritium-NMR as the 4-position of benzimadazole nucleus. The yields for individual BZCs varied from 8 to 68% for a range of specific activity of 0.44 to 13.4 Ci/mmole. (author).

  14. Creation of recognition sites for organophosphate esters based on charge transfer and ligand exchange imprinting methods.

    Science.gov (United States)

    Say, Ridvan

    2006-10-01

    This manuscript describes a method for the selective binding behavior of paraoxan and parathion compounds on surface imprinted polymers which were prepared using both charge transfer (CT) (methacryloyl-antipyrine, MAAP) and ligand-exchange (LE) (methacryloyl-antipyrine-gadalonium, MAAP-Gd) monomers. These polymers were prepared in the presence of azobisisobutyronitrile (AIBN) as an initiator and crosslinking EDMA and were imprinted with organophosphate esters. Influence of CT and LE imprinting on the creation of recognition sites toward paraoxan and parathion was determined applying adsorption isotherms. The effect of initial concentration of paraoxan and parathion, adsorption time and imprinting efficiency on adsorption selectivity for MIP-CT and MIP-LE was investigated. Association constant (K(ass)), number of accessible sites (Q(max)), relative selectivity coefficient (k') and binding ability were also evaluated.

  15. 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.

  16. Novel Method for Exchange of Impella Circulatory Assist Catheter: The "Trojan Horse" Technique.

    Science.gov (United States)

    Phillips, Colin T; Tamez, Hector; Tu, Thomas M; Yeh, Robert W; Pinto, Duane S

    2017-07-01

    Patients with an indwelling Impella may require escalation of hemodynamic support or exchange to another circulatory assistance platform. As such, preservation of vascular access is preferable in cases where anticoagulation cannot be discontinued or to facilitate exchange to an alternative catheter or closure device. Challenges exist in avoiding bleeding and loss of wire access in these situations. We describe a single-access "Trojan Horse" technique that minimizes bleeding while maintaining arterial access for rapid exchange of this percutaneous ventricular assist device.

  17. 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.

  18. Synthesis of Giant Unilamellar Vesicles (GUV) from Liposomes Prepared by the Rapid Solvent Exchange (RSE) Method

    Science.gov (United States)

    Baykal-Caglar, Eda

    2010-10-01

    Lipid bilayers, which is an important constituent of cell membranes, has been extensively studied by biophysicists. Cell membranes perform many vital cell functions such as signal transduction and transportation of materials needed for the functioning of the cell organelles. Understanding the organization and dynamics of lipid bilayers is important for understanding the processes taking place in cell membranes. Giant Unilamellar Vesicles (GUVs) are cell-sized model systems that allow direct visualization of membrane-related phenomena using fluorescence microscopy. In this study, we investigated the synthesis of GUVs from much smaller liposomes (less than 0.5 microns) produced by the Rapid Solvent Exchange (RSE) method in aqueous solutions of high and low ionic strength. The GUVs synthesized using RSE liposomes are more uniform in lipid composition than that synthesized by other methods. We made a number of modifications to the original electroformation method, and we are able to prepare GUVs from RSE liposomes both in high ionic strength and low ionic strength buffers. Using our optimized procedure, we are also able to produce high quality multi-component GUVs to study the dynamics of lipid domains.

  19. A simple method for air/sea gas exchange measurement in mesocosms and its application in carbon budgeting

    Directory of Open Access Journals (Sweden)

    J. Czerny

    2012-09-01

    Full Text Available Mesocosms as large experimental vessels principally provide the opportunity of performing elemental budget calculations e.g. to derive net biological turnover rates. However, the system is in most cases not closed at the water surface and gases can exchange with the atmosphere. Previous attempts to budget carbon pools in mesocosms relied on educated guesses concerning the exchange of CO2 with the atmosphere. Nevertheless, net primary production rates derived from these budget calculations were, despite large uncertainties in air/sea gas exchange, often more reasonable than cumulative extrapolations of bioassays. While bioassays have limitations representing the full spectrum of trophic levels and abiotic conditions inside the mesocosms, calculating dissolved inorganic carbon uptake inside the mesocosms has the potential to deliver net community production rates representative of the enclosed system. Here, we present a simple method for precise determination of air/sea gas exchange velocities in mesocosms using N2O as a deliberate tracer. Beside the application for carbon budgeting, exchange velocities can be used to calculate exchange rates of any gas of known concentration, e.g. to calculate aquatic production rates of climate relevant trace gases. Using an arctic (Kiel Off Shore Mesocosms for future Ocean Simulation mesocosm experiment as an exemplary dataset, it is shown that application of the presented method largely improves accuracy of carbon budget estimates. Methodology of manipulation, measurement, data processing and conversion to CO2 fluxes are explained. A theoretical discussion of prerequisites for precise gas exchange measurements provides a guideline for the applicability of the method under various experimental conditions.

  20. Technical Note: A simple method for air–sea gas exchange measurements in mesocosms and its application in carbon budgeting

    Directory of Open Access Journals (Sweden)

    J. Czerny

    2013-03-01

    Full Text Available Mesocosms as large experimental units provide the opportunity to perform elemental mass balance calculations, e.g. to derive net biological turnover rates. However, the system is in most cases not closed at the water surface and gases exchange with the atmosphere. Previous attempts to budget carbon pools in mesocosms relied on educated guesses concerning the exchange of CO2 with the atmosphere. Here, we present a simple method for precise determination of air–sea gas exchange in mesocosms using N2O as a deliberate tracer. Beside the application for carbon budgeting, transfer velocities can be used to calculate exchange rates of any gas of known concentration, e.g. to calculate aquatic production rates of climate relevant trace gases. Using an arctic KOSMOS (Kiel Off Shore Mesocosms for future Ocean Simulation experiment as an exemplary dataset, it is shown that the presented method improves accuracy of carbon budget estimates substantially. Methodology of manipulation, measurement, data processing and conversion to CO2 fluxes are explained. A theoretical discussion of prerequisites for precise gas exchange measurements provides a guideline for the applicability of the method under various experimental conditions.

  1. Role of Internal Radiation in Oxide Crystal Growth by Heat Exchanger Method

    Directory of Open Access Journals (Sweden)

    Wencheng Ma

    2017-01-01

    Full Text Available Internal radiation was investigated using the finite volume method for the heat exchanger method (HEM growth of oxide crystals. Special attention was devoted to the temperature and thermal stress distributions in the bottom region of the grown crystal at the end of the solidification process. The numerical results show that internal radiation strongly strengthens heat transport through the crystal. However, it causes isotherms to intensively concentrate in the crystal bottom region, leading to a significant increase in the temperature gradient and thermal stress in this region. Then, the effect of absorption coefficient on this phenomenon was numerically investigated. It was found that the radiation heat transfer rate at the bottom surface of the crystal monotonically decreases as the absorption coefficient is increased, while the conduction heat transfer rate first increases and then decreases as the absorption coefficient is increased, under the interaction between internal radiation and heat conduction. The variations of the maximum temperature gradient and thermal stress in the crystal bottom show the same tendency as the conduction heat transfer rate. This study indicates that the role of internal radiation on the heat transfer and thermal stress in oxide crystal by HEM process shows some differences from that by Czochralski and Kyropoulos processes.

  2. Response time of indirectly accessed gas exchange depends on measurement method.

    Science.gov (United States)

    Rafl, Jakub; Kulhanek, Filip; Kudrna, Petr; Ort, Vaclav; Roubik, Karel

    2017-08-12

    Noninvasive techniques are routinely used for assessment of tissue effects of lung ventilation. However, comprehensive studies of the response time of the methods are scarce. The aim of this study was to compare the response time of noninvasive methods for monitoring of gas exchange to sudden changes in the composition of the inspired gas. A prospective experimental study with 16 healthy volunteers was conducted. A ventilation circuit was designed that enabled a fast change in the composition of the inspiratory gas mixture while allowing spontaneous breathing. The volunteers inhaled a hypoxic mixture, then a hypercapnic mixture, a hyperoxic mixture and finally a 0.3% CO mixture. The parameters with the fastest response to the sudden change of O2 in inhaled gas were peripheral capillary oxygen saturation (SpO2) and regional tissue oxygenation (rSO2). Transcutaneous oxygen partial pressure (tcpO2) had almost the same time of reaction, but its time of relaxation was 2-3 times longer. End-tidal carbon dioxide (EtCO2) response time to change of CO2 concentration in inhaled gas was less than half in comparison with transcutaneous carbon dioxide partial pressure (tcpCO2). All the examined parameters and devices reacted adequately to changes in gas concentration in the inspiratory gas mixture.

  3. In-service inspection method for low-finned ferritic stainless steel tubes for new heat exchanger

    Energy Technology Data Exchange (ETDEWEB)

    Iwai, O.; Goto, M. [Toshiba Corp., Yokohama (Japan)

    1994-12-31

    Conventional inner eddy current test cannot obtain sufficient evaluation for low finned ferritic stainless steel tube inspection. The authors tried various methods and developed special partial saturation eddy current method. This paper summarizes typical experimental results of fundamental studies and trials, and introduces developed ECT data acquisition and evaluation system. Moisture Separator Heater (MSH) used in ABWR (Advanced Boiling Water Reactor) plant is a new type heat exchanger to increase plant thermal efficiency. There are four single tubesheet heaters in a MSH vessel. Each heater has hundreds of low finned tubes made of ferritic stainless steel. In nuclear power plants, non-magnetic materials (austenitic stainless steel, titanium, aluminum brass, etc.,) are mainly used as heat exchanger tubes such as the tubes of feedwater heater, condenser, evaporator and so on. Conventional ECT (Eddy Current Test) method are easily applied for the inspection of these heat exchanger tubes. In recent years, the authors started using ferritic stainless steel tube for new heat exchangers such as MSH because of its superior heat transfer efficiency. However, high permeability of ferritic stainless steel prevents the inspection of these tubes using conventional ECT method. To inspect MSH tubes periodically is important to confirm and maintain reliability of MSH. They tried applying various inspection methods and have developed special ECT method for low finned ferritic stainless steel tubes.

  4. 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.

  5. 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

  6. 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.

  7. Determining the cation exchange capacity of montmorillonite by simultaneous thermal analysis method

    Science.gov (United States)

    Boeva, N. M.; Bocharnikova, Yu. I.; Belousov, P. E.; Zhigarev, V. V.

    2016-08-01

    A way of determining the cation exchange capacity of montmorillonite by simultaneous thermal analysis is developed using as an example the bentonites of the 10th Khutor deposit (Republic of Khakassia) and the Vodopadnyi area (Sakhalin Island). A correlation is established between the cation exchange capacity of smectite and its weight loss upon heating in the range of dehydration; the enthalpy of dehydration of montmorillonite; and the weight loss and the enthalpy of thermal dissociation of ethylene glycol contained in the interlayer space of the mineral's crystal structure. These data open up new possibilities for determining the cation exchange capacity of montmorillonite, the most important technological indicator of the natural clay nanomineral.

  8. Quantifying exchange coupling in f-ion pairs using the diamagnetic substitution method

    Energy Technology Data Exchange (ETDEWEB)

    Lukens, Wayne W.; Walter, Marc D.

    2010-04-01

    One of the challenges in the chemistry of actinide and lanthanide (f-ion) is quantifying exchange coupling between f-ions. While qualitative information about exchange coupling may be readily obtained using the diamagnetic substitution approach, obtaining quantitative information is much more difficult. This article describes how exchange coupling may be quantified using the susceptibility of a magnetically isolated analog, as in the diamagnetic substitution approach, along with the anisotropy of the ground state as determined by EPR spectroscopy. Several examples are used to illustrate and test this approach.

  9. Titanium microgram weight low to 50 mg and measurement based on exchange weighing method

    Science.gov (United States)

    Ren, Xiaoping; Dong, Lei; Wang, Jian; Wang, Xiaolei

    2017-03-01

    The microgram weights have wide applications in the mechanical testing of nano- and bio-material sensors. They are increasing the requirement of small force and mass below 1 mg among the researchers, industry and bio-pharmaceutical manufacturing. In this paper, the current research status is presented, both from the measurement method and manufacture of microgram weights. The commonly used material for micro-weights is stainless steel and aluminum. Now NIM has developed another kind of microgram weights with titanium alloy. For the reason that it has smaller size than normal material like aluminum, special designed exchange weighing pan was used in measurement, which solved the problems that the weighing hooks cannot carry up and down the wire shape microgram weight. Then this kind of microgram weights was tested in subdivision measurement on an automatic mass comparator. It showed good performance in the experiment, which extends the choice for the industrial and metrological user. The uncertainty evaluation of micro-weight values range from 0.05 mg to 0.5 mg with standard uncertainty between 0.2 g and 0.1 μg.

  10. A new method for antimony speciation in plant biomass and nutrient media using anion exchange cartridge.

    Science.gov (United States)

    Tisarum, Rujira; Ren, Jing-Hua; Dong, Xiaoling; Chen, Hao; Lessl, Jason T; Ma, Lena Q

    2015-11-01

    A selective separation method based on anion exchange cartridge was developed to determine antimony (Sb) speciation in biological matrices by graphite furnace atomic absorption spectrophotometry (GFAAS). The selectivity of the cartridge towards antimonite [Sb(III)] and antimonate [Sb(V)] reversed in the presence of deionized (DI) water and 2mM citric acid. While Sb(V) was retained by the cartridge in DI water, Sb(III) was retained in citric acid media. At pH 6, Sb(III) and Sb(V) formed Sb(III)- and Sb(V)-citrate complexes, but the cartridge had higher affinity towards the Sb(III)-citrate complex. Separation of Sb(III) was tested at various concentrations in fresh and spent growth media and plant tissues. Our results showed that cartridge-based Sb speciation was successful in plant tissues, which was confirmed by HPLC-ICP-MS. The cartridge retained Sb(III) and showed 92-104% Sb(V) recovery from arsenic hyperaccumulator Pteris vittata roots treated with Sb(III) and Sb(V). The cartridge procedure is an effective alternative for Sb speciation, offering low cost, reproducible results, and simple Sb analysis using GFAAS.

  11. A New Comparison Of Vertical Ground Heat Exchanger Design Methods For Residential Applications

    Energy Technology Data Exchange (ETDEWEB)

    Shonder, John A [ORNL; Baxter, David V [ORNL; Thornton, Jeff W. [Thermal Energy Systems Specialists, Inc.; Hughes, Patrick [ORNL

    1999-06-01

    A previous comparison of vertical ground heat exchanger design methods for geothermal heat pumps in residential applications found large disagreements in the sizes recommended by five commercially-available computer programs, even when consistent information was input to all five. The objective of this work is to repeat the comparison using updated versions of the five programs originally tested, and one new program which was not included in the previous comparison. Simulation models of two sites - one in a cooling dominated climate, and the other in a heating dominated climate - were calibrated to site-collected data and then driven with typical meteorological year data to produce consistent inputs for the six design programs. The results indicate that the programs are now much more consistent with one another. For the cooling dominated site, design lengths vary by about {+-}8%, and for the heating dominated site the design lengths vary by {+-}16%. Compared to the tests performed in 1996, there is now much more consistency among the various design algorithms.

  12. 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

  13. 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

  14. 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.

  15. An isotopic exchange method applied to the study of surface mobility in catalysis; Methode d`echange isotopique appliquee a l`etude de la mobilite de surface en catalyse

    Energy Technology Data Exchange (ETDEWEB)

    Martin, D.; Duprez, D. [LACCO, 86 - Poitiers (France)

    1994-12-31

    A method for isotopic exchange of oxygen and hydrogen on the surface of supported metal catalysts (Rh, Pt), is presented. This method allows to determine various properties of oxides used as supports (rate of exchange, quantity of exchanges species, surface and bulk diffusion coefficients) which can be correlated to some specific properties of the oxides (dehydroxylation, acidity and basicity). 5 figs., 9 refs.

  16. 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.

  17. Two-pion exchange electromagnetic current in chiral effective field theory using the method of unitary transformation

    CERN Document Server

    Koelling, S; Krebs, H; Meißner, U -G

    2009-01-01

    We derive the leading two-pion exchange contributions to the two-nucleon electromagnetic current operator in the framework of chiral effective field theory using the method of unitary transformation. Explicit results for the current and charge densities are given in momentum and coordinate space.

  18. A method for the simultaneous measurement of gas exchange and diffusion resistance of fruits and vegetables under various gas conditions

    NARCIS (Netherlands)

    Peppelenbos, H.W.; Jeksrud, W.K.

    1998-01-01

    To measure the relationship between gas exchange rates and diffusion resistance, and their changes in time, both should be measured on the same fruit or vegetable, because diffusion resistance shows large variations between individuals of the same species and cultivar. The method described enables

  19. An Assessment of Transport Property Estimation Methods for Ammonia–Water Mixtures and Their Influence on Heat Exchanger Size

    DEFF Research Database (Denmark)

    Kærn, Martin Ryhl; Modi, Anish; Jensen, Jonas Kjær

    2015-01-01

    are considered: a flue-gas-based heat recovery boiler for a combined cycle power plant and a hot-oil-based boiler for a solar thermal power plant. The different transport property methods resulted in larger differences at high pressures and temperatures, and a possible discontinuous first derivative, when using...... the interpolative methods in contrast to the corresponding state methods. Nevertheless, all possible mixture transport property combinations used herein resulted in a heat exchanger size within 4.3 % difference for the flue-gas heat recovery boiler, and within 12.3 % difference for the oil-based boiler.......Transport properties of fluids are indispensable for heat exchanger design. The methods for estimating the transport properties of ammonia–water mixtures are not well established in the literature. The few existent methods are developed from none or limited, sometimes inconsistent experimental...

  20. 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)

  1. Preparation of Nafion 117™-SnO2 Composite Membranes using an Ion-Exchange Method

    DEFF Research Database (Denmark)

    Nørgaard, Casper Frydendal; Nielsen, Ulla Gro; Skou, Eivind Morten

    Nafion 117™-SnO2 composite membranes were successfully prepared using an ion-exchange method. SnO2 was incorporated into Nafion 117™ membranes by ion-exchange in solutions of SnCl2 · 2 H2O in methanol, followed by oxidation to SnO2 in air. The content of SnO2 proved controllable by adjusting...... the concentration of the ion-exchange solution. The prepared nanocomposite membranes were characterized by XRD and 119Sn MAS NMR while the in-plane proton conductivity was found to decrease with SnO2 content when evaluated with EIS. However, the conductivity was comparable to Nafion™ at SnO2 contents below 8 wt%....

  2. Theoretical study of annealed proton-exchanged Nd $LiNbO_{3}$ channel waveguide lasers with variational method

    CERN Document Server

    De Long Zhang; Yuan Guo Xie; Guilan, Ding; Yuming, Cui; Cai He Chen

    2001-01-01

    The controllable fabrication parameters, including anneal time, initial exchange time, channel width, dependences of TM/sub 00/ mode size, corresponding effective refractive index, effective pump area, and coupling efficiency between pump and laser modes in z-cut annealed proton-exchanged (APE) Nd:LiNbO/sub 3/ channel waveguide lasers were studied by using variational method. The effect of channel width on the surface index increment and the waveguide depth was taken into account. The features of mode size and effective refractive index were summarized, discussed, and compared with previously published experimental results. The effective pump area, which is directly proportional to threshold pump power, increases strongly, slightly, and very slightly with the increase of anneal time, channel width, and initial exchange time, respectively. However, the coupling efficiency, which is directly proportional to slope efficiency, remains constant (around 0.82) no matter what changes made to these parameters. The var...

  3. 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.

  4. 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

  5. Study and verification of the superposition method used for determining the pressure losses of the heat exchangers

    Directory of Open Access Journals (Sweden)

    Petru Michal

    2015-01-01

    Full Text Available This paper deals with study of the pressure losses of the new heat convectors product line. For all devices connected to the heating circuit of the building, it‘s required to declare a tabulated values of pressure drops. The heat exchangers are manufactured in a lot of different dimensions and atypical shapes. An individual assessment of the pressure losses for each type is very time consuming. Therefore based on the resulting data of the experiments and numerical models, an electronic database was created that can be used for calculating the total values of the pressure losses in the optionally assembled exchanger. The measurements are standardly performed by the manufacturer Licon heat hydrodynamic laboratory and the numerical models are carried out in COMSOL Multiphysics. Different variations of the convectors geometry cause non-linear process of energy losses, which is proportionately about 30% larger for the smaller exchanger than for the larger types. The results of the experiments and the numerical simulations were in a very good conjuncture. Considerable influence of the water temperature onto the total size of incurred energy losses has been proven. This is mainly caused by the different ranges of the Reynolds number depending on the viscosity of the used liquid. Concerning to the tested method of superposition, it is not possible to easily find the characteristic values appropriate for the each individual components of the heat exchanger. Every of the components behaves differently, depend on the complexity of the exchanger. However, the correction coefficient, depended on the matrix of the exchanger, that is suitable for the entire range of the developed product line has been found.

  6. Suitability of the methylene blue test for determination of cation exchange capacity of clay minerals related to ammonium acetate method

    Science.gov (United States)

    Milošević, Maja; Logar, Mihovil; Dojčinović, Biljana; Erić, Suzana

    2015-04-01

    Cation exchange capacity (CEC) represents one of the most important parameters of clay minerals which reflects their ability to exchange cations with liquid phases in near contact. Measurement of CEC is used for characterizing sample plasticity, adsorbing and swelling properties which later define their usage in industrial purposes. Several methods have been developed over the years for determination of layer charge, charge density, charge distribution, etc. and have been published in numerous papers (Czimerova et al., 2006; Yukselen and Kaya, 2008). The main goal of present study is comparison of suitability of more recent method - methylene blue test in regard to older method - ammonium acetate for determination of CEC. For this study, we selected one montmorillonite clay (Bogovina, Serbia) and two mainly kaolinite clays (Miličinica, Serbia). Chemicals used for CEC determinations were solution of methylene blue (MB)(14*10-6M/ml) and ammonium acetate (AA) solution (1M). The obtained results are showing generally lower values in case of MB method. The main difference is due to molecular aggregation of MB on the clay surface. AA method is highly sensitive to the presence of CaO. Release of Ca ion from the sample into the solution can limit the saturation of exchange sites by the ammonium ion. This is clearly visible in case of montmorillonite clay. Fe2+ and Mg ions are difficult to move by the ammonium ion because of their ion radius, but in case of MB molecule there is no such restriction in removing them from the exchange sites. MB solution, even in a low concentration (2*10-6M/ml), is showing preferable results in moving the ions from their positions which is already visible after adding a small quantity of solution (25cm3). Both MB-titration and MB-spot test yield similar results and are much simpler methods than AA and they also give other information such as specific surface area (external and internal) whereas AA method only provides information about

  7. 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.

  8. 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.

  9. Method of estimation of sea-shelf water exchange using information on differential coastal cooling above underwater slopes

    Science.gov (United States)

    Chubarenko, Irina

    2013-04-01

    -November 2002-2009, the South-Eastern Baltic Sea, were analyzed (see poster EGU2013-7446) demonstrating typical features of the coast-sea SST-profiles above different slopes of the given region. Overall, the method of estimation of shelf-sea water exchange on the base of information on differential coastal cooling above underwater slopes works well in laboratory and numerical experiments, and its applicability at the sea scale seems to be reasonable, however it still needs verification by real measurements of water-exchange in field, which are difficult and very expensive and thus - very rare. Investigations are supported by RFBR, grants number 10-05-00540a and 13-05-01041a.

  10. Methods of Thermal Calculations for a Condensing Waste-Heat Exchanger

    Directory of Open Access Journals (Sweden)

    Rączka Paweł

    2014-12-01

    Full Text Available The paper presents the algorithms for a flue gas/water waste-heat exchanger with and without condensation of water vapour contained in flue gas with experimental validation of theoretical results. The algorithms were used for calculations of the area of a heat exchanger using waste heat from a pulverised brown coal fired steam boiler operating in a power unit with a capacity of 900 MWe. In calculation of the condensing part, the calculation results obtained with two algorithms were compared (Colburn-Hobler and VDI algorithms. The VDI algorithm allowed to take into account the condensation of water vapour for flue gas temperatures above the temperature of the water dew point. Thanks to this, it was possible to calculate more accurately the required heat transfer area, which resulted in its reduction by 19 %. In addition, the influence of the mass transfer on the heat transfer area was taken into account, which contributed to a further reduction in the calculated size of the heat exchanger - in total by 28% as compared with the Colburn-Hobler algorithm. The presented VDI algorithm was used to design a 312 kW pilot-scale condensing heat exchanger installed in PGE Belchatow power plant. Obtained experimental results are in a good agreement with calculated values.

  11. 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.

  12. Better methods will be needed to project incomes to estimate eligibility for subsidies in health insurance exchanges.

    Science.gov (United States)

    Graves, John A

    2012-07-01

    Under the Affordable Care Act, people who meet certain income eligibility criteria will be eligible for subsidies to offset costs of premiums and cost sharing for health insurance plans purchased through new health insurance exchanges. But determining the correct level of these subsidies will not be easy, because of several factors. These include the way in which eligibility will be calculated for participation in Medicaid or for subsidies through the exchanges; possibly inaccurate income projections; the use of different income time periods to determine eligibility; and fluctuations in income. I performed a simulation that shows that under the most likely methods to be used to determine eligibility for Medicaid or for receiving subsidies through exchanges, one-third of people with incomes initially judged to be below the Medicaid threshold would actually "churn" into an exchange at the end of the year. Other people would be wrongly deemed ineligible for advance subsidy payments because their projected income was too high, while still others judged eligible for subsidies would receive advance payments on those subsidies that were too high by $208 per year, on average. To reduce these errors, I recommend the adoption of a single eligibility standard based on income data derived from prior tax returns, along with generous accommodations during a given enrollment year for people who claim a change in circumstances, such as a change in income.

  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. Increasing the pump-up rate to polarize 3He gas using spin-exchange optical pumping method

    Science.gov (United States)

    Lee, Wai Tung; Tong, Xin; Rich, Dennis; Liu, Yun; Fleenor, Michael; Ismaili, Akbar; Pierce, Joshua; Hagen, Mark; Dadras, Jonny; Robertson, J. Lee

    2009-09-01

    In recent years, polarized 3He gas has increasingly been used as neutron polarizers and polarization analyzers. Two of the leading methods to polarize the 3He gas are the spin-exchange optical pumping (SEOP) method and the meta-stable exchange optical pumping (MEOP) method. At present, the SEOP setup is comparatively compact due to the fact that it does not require the sophisticated compressor system used in the MEOP method. The temperature and the laser power available determine the speed, at which the SEOP method polarizes the 3He gas. For the quantity of gas typically used in neutron scattering work, this speed is independent of the quantity of the gas required, whereas the polarizing time using the MEOP method is proportional to the quantity of gas required. Currently, using the SEOP method to polarize several bar-liters of 3He to 70% polarization would require 20-40 h. This is an order of magnitude longer than the MEOP method for the same quantity of gas and polarization. It would therefore be advantageous to speed up the SEOP process. In this article, we analyze the requirements for temperature, laser power, and the type of alkali used in order to shorten the time required to polarize 3He gas using the SEOP method.

  15. The Brazilian dilution method for ballast water exchange; O metodo de diluicao brasileiro para troca de agua de lastro

    Energy Technology Data Exchange (ETDEWEB)

    Mauro, Celso Alleluia [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas. Avaliacao e Monitoramento Ambiental]. E-mail: celso@cenpes.petrobras.com.br; Land, Claudio Goncalves [PETROBRAS, Rio de Janeiro, RJ (Brazil). Abastecimento, Logistica e Planejamento]. E-mail: cgland@petrobras.com.br; Pimenta, Jose Maria Hollanda Alvares; Barreto, Francisco Carlos Peixoto [PETROBRAS, Rio de Janeiro, RJ (Brazil). Engenharia; Brandao, Marcus Vinicius Lisboa; Marroig, Nilton Lemos [Transpetro, Rio de Janeiro, RJ (Brazil). Frota Nacional de Petroleiros. Inspetoria Geral; Tristao, Maria Luiza Braganca [PETROBRAS, Rio de Janeiro, RJ (Brazil). Centro de Pesquisas. Quimica; Fadel, Andre Luiz da Fonseca [PETROBRAS, Rio de Janeiro, RJ (Brazil). Financas Corporativa e Tesouraria; Villac, Maria Celia; Fernandes, Lohengrin; Paranhos, Rodolfo; Dias, Cristina; Bonecker, Sergio; Denise Tenenbaum [Universidade Federal, Rio de Janeiro, RJ (Brazil). Inst. de Biologia; Persich, Graziela; Garcia, Virginia; Odebrecht, Clarisse [Fundacao Universidade do Rio Grande, RS (Brazil). Dept. de Oceanografia

    2002-12-01

    In a precautionary approach and dealing with the coming International Maritime Organization (IMO) regulations on ballast water, PETROBRAS developed a new method for ballast water exchange in tankers. Differently from ordinary methods PETROBRAS method which have been called Brazilian Dilution Method (BDM) or Dilution Method involves ballast loading through the top with simultaneous unloading from the bottom of the tanks. The method proposal was firstly presented to IMO, which encouraged PETROBRAS to carry out a field trial. PETROBRAS in June 1998 carried out a trial in the product carrier M/V Lavras. A simulation study was useful to plan the trial assessing the theoretical efficiency of the method, establishing the best sampling points and comparing the BDM with the Tank Overfilling Method (TOM). Simulation showed that for the same tank shape, the water renewal in BDM is more effective than in TOM and that 90 % of water renewal could be obtained by BDM. A dye concentration variation monitoring and a biological assessment were performed and the results confirmed that over than 90 % of the ballast water was renewed after three exchanges. The method was proved safe, practical, economical and suitable to minimize the risk of exotic species transport between ports. (author)

  16. 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...

  17. An isocratic ion exchange HPLC method for the simultaneous determination of flucloxacillin and amoxicillin in a pharmaceutical formulation for injection.

    Science.gov (United States)

    Liu, Hao; Wang, Hongwu; Sunderland, V Bruce

    2005-02-23

    An isocratic ion exchange high performance liquid chromatography method was developed for the simultaneous determination of flucloxacillin and amoxicillin in pharmaceutical formulations for injections. The separation was made by a ZORBAX 300-SCX column using 0.025 M ammonium dihydrogen phosphate (adjusted to pH 2.6 with phosphoric acid)-acetonitrile (95:5) as mobile phase. The validation of the method was performed, and specificity, reproducibility, precision and accuracy were confirmed. The limits of quantification were approximately 0.2 microg/ml for each drug. Due to its simplicity and accuracy the method is particularly suitable for routine pharmaceutical quality control.

  18. UV-visible spectroscopy method for screening the chemical stability of potential antioxidants for proton exchange membrane fuel cells

    Science.gov (United States)

    Banham, Dustin; Ye, Siyu; Knights, Shanna; Stewart, S. Michael; Wilson, Mahlon; Garzon, Fernando

    2015-05-01

    A novel method based on UV-visible spectroscopy is reported for screening the chemical stability of potential antioxidant additives for proton exchange membrane fuel cells, and the chemical stabilities of three CeOx samples of varying crystallite sizes (6, 13, or 25 nm) are examined. The chemical stabilities predicted by this new screening method are compared to in-situ membrane electrode assembly (MEA) accelerated stress testing, with the results confirming that this rapid and inexpensive method can be used to accurately predict performance impacts of antioxidants.

  19. 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.

  20. A simple method for estimating cation exchange capacity from water vapor sorption

    DEFF Research Database (Denmark)

    Arthur, Emmanuel; Tuller, Markus

    2016-01-01

    (PTFs) for estimating CEC from soil water content considering hysteresis have been developed based on 203 differently-textured soils. Furthermore, we compared the performance of the new PTFs with existing PTFs that predict CEC from clay content, organic carbon, soil pH and specific surface area. The new...... of the new PTFs, thus a simple measure of soil water content at an arbitrary relative humidity can provide reasonably accurate CEC estimates for large scale studies.......Knowledge of soil cation exchange capacity (CEC) is crucial for soil fertility considerations, sorption and release of polar and non-polar compounds, engineering applications, and other biogeochemical processes. Standard procedures such as the ammonium acetate or the BaCl2 compulsive exchange...

  1. 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.

  2. COMPUTATIONAL METHODS AND CHALLENGES IN HYDROGEN/DEUTERIUM EXCHANGE MASS SPECTROMETRY

    OpenAIRE

    2016-01-01

    Hydrogen/Deuterium exchange (HDX) has been applied, since the 1930s, as an analytical tool to study the structure and dynamics of (small) biomolecules. The popularity of using HDX to study proteins increased drastically in the last two decades due to the successful combination with mass spectrometry (MS). Together with this growth in popularity, several technological advances have been made, such as improved quenching and fragmentation. As a consequence of these experimental improvemen...

  3. Monte Carlo Planning Method Estimates Planning Horizons during Interactive Social Exchange.

    Directory of Open Access Journals (Sweden)

    Andreas Hula

    2015-06-01

    Full Text Available Reciprocating interactions represent a central feature of all human exchanges. They have been the target of various recent experiments, with healthy participants and psychiatric populations engaging as dyads in multi-round exchanges such as a repeated trust task. Behaviour in such exchanges involves complexities related to each agent's preference for equity with their partner, beliefs about the partner's appetite for equity, beliefs about the partner's model of their partner, and so on. Agents may also plan different numbers of steps into the future. Providing a computationally precise account of the behaviour is an essential step towards understanding what underlies choices. A natural framework for this is that of an interactive partially observable Markov decision process (IPOMDP. However, the various complexities make IPOMDPs inordinately computationally challenging. Here, we show how to approximate the solution for the multi-round trust task using a variant of the Monte-Carlo tree search algorithm. We demonstrate that the algorithm is efficient and effective, and therefore can be used to invert observations of behavioural choices. We use generated behaviour to elucidate the richness and sophistication of interactive inference.

  4. Stratosphere-troposphere exchange in an extratropical cyclone, calculated with a Lagrangian method

    Directory of Open Access Journals (Sweden)

    M. Sigmond

    Full Text Available A Lagrangian technique is developed and applied to calculate stratosphere-troposphere exchange in an extratropical cyclone. This exchange is computed from the potential vorticity or PV along trajectories, calculated from ECMWF circulation data. Special emphasis is put on the statistical significance of the results. The computed field of the cross-tropopause flux is dominated by elongated patterns of statistically significant large downward and small upward fluxes. The downward fluxes mainly occur in the lower part of the considered tropopause folds. The upward fluxes are found near the entrance of the folds, in the tropopause ridges. The ratio between the area averaged downward and upward cross-tropopause fluxes increases with increasing strength of the cyclone. Since the largest fluxes are shown to occur in the regions with the largest wind shear, where PV-mixing is thought to cause large cross-tropopause fluxes, the results are expected to be reliable, at least in a qualitative sense. The position of a tropopause fold along the northwest coast of Africa is confirmed by total ozone observations. The results indicate that the applied Lagrangian technique is an appropriate tool for diagnosing stratosphere-troposphere exchange.

    Key words: Meteorology and atmospheric dynamics (general circulation; mesoscale meteorology; middle atmosphere dynamics

  5. A simple method for differentiation of monoisotopic drug metabolites with hydrogen-deuterium exchange liquid chromatography/electrospray mass spectrometry.

    Science.gov (United States)

    Tolonen, Ari; Turpeinen, Miia; Uusitalo, Jouko; Pelkonen, Olavi

    2005-05-01

    A simple but efficient method for determination of labile protons in drug metabolites using post-column infusion of deuterium oxide (D2O) in liquid chromatography/mass spectrometry (LC/MS) experiments with electrospray ionization and time-of-flight mass spectrometry is described. The number of exchangeable protons in analytes, i.e. hydroxyl, amine, thiol and carboxylic acid protons, can easily be determined by comparing the increase in m/z values after H/D-exchange occurring online between a HPLC column and electrospray ion source. Especially, the hydroxyl metabolites and S/N-oxides with the same accurate mass can be distinguished. A good degree of exchange was obtained in repeatable experiments. Only a low consumption of D2O is needed in a very easy and rapidly set-up procedure. The method is applied in the study of metabolites of omeprazole and imipramine in human and mouse in vitro samples, respectively, together with exact mass data obtained from time-of-flight mass spectrometric experiments.

  6. 外汇储备的组合预报法%Foreign exchange reserve combined forecasting method

    Institute of Scientific and Technical Information of China (English)

    毛志杰; 曹杰; 朱奇; 吴武清; 陈敏

    2012-01-01

    Firstly, it makes an in-depth study on the econometric relationship between the quarter increment of the foreign exchange reserve in China and the main macro-economic variables. It finds that the macro-economic situation have great effect on the increase of foreign exchange reserves. Secondly, for the first time, it puts forward the combined forecasting method of R2 weight, which uses R2 statistics as the combined forecasting weight to combine the different models' results. With this method, we got the stable and accurate result that the foreign exchange reserves will increase continuously. Finally, it gives some suggestions.%通过深入研究我国外汇储备季度增量与主要宏观经济变量的计量关系,发现宏观经济形势对外汇储备增长有重要影响.提出R2权重组合预报法,该方法将R2统计量作为模型预测结果组合的权重,对不同模型的预测结果进行组合加权,得到了较为稳定而且准确的预报结果:外汇储备规模将会持续增长.对此结果提出了相应的政策建议.

  7. 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....

  8. 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.

  9. 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.

  10. Forecasting abrupt changes in foreign exchange markets: method using dynamical network marker

    Science.gov (United States)

    Oya, Shunsuke; Aihara, Kazuyuki; Hirata, Yoshito

    2014-11-01

    We apply the idea of dynamical network markers (Chen et al 2012 Sci. Rep. 2 342) to foreign exchange markets so that early warning signals can be provided for any abrupt changes. The dynamical network marker constructed achieves a high odds ratio for forecasting these sudden changes. In addition, we also extend the notion of the dynamical network marker by using recurrence plots so that the notion can be applied to delay coordinates and point processes. Thus, the dynamical network marker is useful in a variety of contexts in science, technology, and society.

  11. EXTRACTION OF CITRIC ACID FROM FERMENTATION BROTH USING ION—EXCHANGE METHOD

    Institute of Scientific and Technical Information of China (English)

    LiuZuozhen; WangXiangyang; 等

    1998-01-01

    A number of ion-exchange resins were tested on their capacity to adsorb citric acid,among them resin 335,d315, Amberlite IRA-35 and IRA-68 exhibited higher adsorption capacity.We chose resin 335 and D315 to be used for extraction of citric acid from fermentation broth,followed by elution with 10% ammonia liquor,decoloration with K-15 carbon and removal of ammonia with resin 732,converting citrate of free citric acid with a concentration of 10% and an amount of readily carbonizable substance meeting the GB 8269-87 standard.

  12. 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...

  13. A CORBA-based object framework with patient identification translation and dynamic linking. Methods for exchanging patient data.

    Science.gov (United States)

    Wang, C; Ohe, K

    1999-03-01

    Exchanging and integration of patient data across heterogeneous databases and institutional boundaries offers many problems. We focused on two issues: (1) how to identify identical patients between different systems and institutions while lacking universal patient identifiers; and (2) how to link patient data across heterogeneous databases and institutional boundaries. To solve these problems, we created a patient identification (ID) translation model and a dynamic linking method in the Common Object Request Broker Architecture (CORBA) environment. The algorithm for the patient ID translation is based on patient attribute matching plus computer-based human checking; the method for dynamic linking is temporal mapping. By implementing these methods into computer systems with help of the distributed object computing technology, we built a prototype of a CORBA-based object framework in which the patient ID translation and dynamic linking methods were embedded. Our experiments with a Web-based user interface using the object framework and dynamic linking-through the object framework were successful. These methods are important for exchanging and integrating patient data across heterogeneous databases and institutional boundaries.

  14. ExchanGE processes in mountainous Regions (EGER – overview of design, methods, and first results

    Directory of Open Access Journals (Sweden)

    T. Foken

    2011-09-01

    Full Text Available To investigate the energy, matter and reactive and non-reactive trace gas exchange between the atmosphere and a spruce forest in the German mountain region, two intensive measuring periods were conducted at the FLUXNET site Waldstein-Weidenbrunnen in September/October 2007 and June/July 2008. They were part of the project "ExchanGE processes in mountainous Regions" (EGER. Beyond a brief description of the experiment and links to the already published results of both experiments, the main focus of the paper is the problem of the coupling of the trunk space, the canopy and the atmosphere. Therefore, the relevant coherent structures were analyzed in different canopy levels and an already published coupling classification was applied to gradients and fluxes. It could be shown that fluxes above the canopy are only related to the gradient between the canopy and the atmosphere in the case of a fully coupled system. Changes in the concentration of especially reactive trace gases (NO-NO2-O3 and HONO could only be interpreted together with the coupling stage. Finally it was pointed out that the combination of air chemical measurements with micrometeorological turbulence measurements is urgently needed to understand the biosphere-atmosphere interaction.

  15. Modified Perfluorocarbon Tracer Method for Measuring Effective Multizone Air Exchange Rates

    Directory of Open Access Journals (Sweden)

    Masashi Gamo

    2010-08-01

    Full Text Available A modified procedure was developed for the measurement of the effective air exchange rate, which represents the relationship between the pollutants emitted from indoor sources and the residents’ level of exposure, by placing the dosers of tracer gas at locations that resemble indoor emission sources. To measure the 24-h-average effective air exchange rates in future surveys based on this procedure, a low-cost, easy-to-use perfluorocarbon tracer (PFT doser with a stable dosing rate was developed by using double glass vials, a needle, a polyethylene-sintered filter, and a diffusion tube. Carbon molecular sieve cartridges and carbon disulfide (CS2 were used for passive sampling and extraction of the tracer gas, respectively. Recovery efficiencies, sampling rates, and lower detection limits for 24-h sampling of hexafluorobenzene, octafluorotoluene, and perfluoroallylbenzene were 40% ± 3%, 72% ± 5%, and 84% ± 6%; 10.5 ± 1.1, 14.4 ± 1.4, and 12.2 ± 0.49 mL min−1; and 0.20, 0.17, and 0.26 μg m–3, respectively.

  16. Preparation and characterization of 5-sulphosalicylic acid doped tetraethoxysilane composite ion-exchange material by sol–gel method

    Energy Technology Data Exchange (ETDEWEB)

    Rehman, Suhail-ul; Islam, Nasarul; Ahad, Sozia; Fatima, Syed Zeeshan; Pandith, Altaf Hussain, E-mail: altafpandit23@gmail.com

    2013-09-15

    Highlights: • Sulphosalicylic acid doped tetraethoxysilane composite is prepared by sol–gel method. •Its X-ray diffraction studies suggest that it is crystalline in nature. • This material shows selectivity for Mg(II) and Ni(II) ions in aqueous solutions. • Separation of Ni(II) from binary mixtures was successfully achieved on this material. -- Abstract: In this manuscript, we report the preparation and characterization of sulphosalicylic doped tetraethoxysilane (SATEOS), composite material by sol–gel method as a new ion exchanger for the removal of Ni(II) from aqueous solution. The fine granular material was prepared by acid catalyzed condensation polymerization through sol–gel mechanism in the presence of cationic surfactant. The material has an ion exchange capacity of 0.64 mequiv./g(dry) for sodium ions, 0.60 mequiv./g(dry) for potassium ions, 1.84 mequiv./g(dry) for magnesium ions, 1.08 mequiv./g(dry) for calcium ions and 1.36 mequiv./g(dry) for strontium ions. Its X-ray diffraction studies suggest that it is crystalline in nature. The material has been characterized by SEM, IR, TGA and DTG so as to identify the various functional groups and ion exchange sites present in this material. Quantum chemical computations at DFT/B3LYP/6-311G (d,p) level on model systems were performed to substantiate the structural conclusions based ion instrumental techniques. Investigations into the elution behaviour, ion exchange reversibility and distribution capacities of this material towards certain environmentally hazardous metal ions are also performed. The material shows good chemical stability towards acidic conditions and exhibits fast elution of exchangeable H{sup +} ions under neutral conditions. This material shows remarkable selectivity for Ni(II) and on the basis of its K{sub d} value (4 × 10{sup 2} in 0.01 M HClO{sub 4}) some binary separations of Ni(II) from other metal ions are performed.

  17. [Evaluation of remote sensing extraction methods for vegetation phenology based on flux tower net ecosystem carbon exchange data].

    Science.gov (United States)

    Mou, Min-Jie; Zhu, Wen-Quan; Wang, Ling-Li; Xu, Ying-Jun; Liu, Jian-Hong

    2012-02-01

    Taking the vegetation phenological metrics derived from the net ecosystem carbon exchange (NEE) data of 72 flux towers in North America as the references, a comprehensive evaluation was conducted on the three typical classes of remote sensing extraction methods (threshold method, moving average method, and function fitting method) for vegetation phenology from the aspects of feasibility and accuracy. The results showed that the local midpoint threshold method had the highest feasibility and accuracy for extracting vegetation phenology, followed by the first derivative method based on fitted Logistic function. The feasibility and accuracy of moving average method were determined by the moving window size. As for the MODJS 16 d composited time-series normalized difference vegetation index (NDVI), the moving average method had preferable performance when the window size was set as 15. The global threshold method performed quite poor in the feasibility and accuracy. Though the values of the phenological metrics extracted by the curvature change rate method based on fitted Logistic function and the corresponding ones derived from NEE data had greater differences, there existed a strong correlation between them, indicating that the vegetation phenological metrics extracted by the curvature change rate method could reflect the real temporal and spatial variations of vegetation phenology.

  18. 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....

  19. 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.

  20. 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.

  1. Fast synthesis of dopamine-coated Fe3O4 nanoparticles through ligand-exchange method

    Institute of Scientific and Technical Information of China (English)

    Peng An; Fang Zuo; Yuan Peng Wu; Jun Hua Zhang; Zhao Hui Zheng; Xiao Bin Ding; Yu Xing Peng

    2012-01-01

    A fast approach was described for the synthesis of water-dispersible monodisperse dopamine-coated Fe3O4 nanoparticles (DA-Fe3O4) with uniform size and shape via ligand-exchange of oleic acid on Fe3O4 using only 2 min.The prepared DA-Fe3O4 nanoparticles were characterized by transmission electron microscopy,Fourier transform infrared spectrometry,and vibrating sample magnetometer.The results indicated that the resulting DA-Fe3O4 nanoparticles had an average diameter of about 19.2 nm.The magnetic saturation value of the prepared DA-Fe3O4 nanoparticles was determined to be 72.87 emu/g,which indicating a wellestablished superparamagnetic property.

  2. Controllable Synthesis of Mn6+ Doped Nanoparticles by a Facile Anion Exchange Method

    Science.gov (United States)

    Zhang, Xiaowen; Li, Yang; Liao, Chenxing; Chen, Zhi; Qiu, Jianrong

    2017-01-01

    Fluorescence imaging in the second near-infrared window (NIR-II, 1000-1400 nm) is attracting extensive attention. Mn6+ doped BaSO4 with broadband emission from 900 nm to 1400 nm is emerging as a new class of NIR phosphor for fluorescence imaging. Manganese has diverse valence states, thus it is difficult to prevent valence change of Mn6+ during traditional synthesis process. In this work, BaSO4:Mn6+ nanoparticles with uniform size and morphology were first successfully prepared through a fast liquid-solid solution route at room temperature. The nanoparticles exhibit broadband NIR emission from Mn6+ when excited by 808 nm lasers. This convenient strategy, based on an efficient anion exchange reaction, is proved effective for synthesizing nano-sized materials. The results reveal that our strategy has great potential in fabricating special valence state ion doped nanomaterials.

  3. A comparison of positron emission particle tracking (PEPT) methods for analysis of a tube-in-shell heat exchanger

    Science.gov (United States)

    Wiggins, Cody; Patel, Nitant; Ruggles, Arthur

    2016-03-01

    A positron emission particle tracking (PEPT) study of a stainless steel tube-in-shell heat exchanger is performed. Studies are performed using two different energy window settings. A new multiple particle tracking technique is introduced and used in this analysis. Results are compared to those obtained with previously established multiple particle tracking technique. Both techniques are found to be capable of flow imaging through opaque surfaces. No significant difference is observed between energy window settings using either method. Results from both methods are found to be qualitatively similar; however, it is observed that the new method exhibits consistently lower measurement uncertainty across the field of view of the scanner and is robust against the adverse effects of stationary particles in the flow field.

  4. Simple and low cost method for metal-based micro-capillary channels for heat exchanger use

    Science.gov (United States)

    Ogbonnaya, E.; Champagne, C.; Weiss, L.

    2013-11-01

    In this work, we present an alternative, low cost method for the fabrication of a heat exchanger utilizing metal-based microchannels using the UV-LiGA technique. Lithography is used to pattern dry film negative photoresist (Ordyl P-50100) on the substrate. The resist is laminated over the substrate and exposed with a UV source. The use of dry film resist allows for simple and inexpensive microchannel patterns without requiring advanced cleanroom equipment. Following the lithography process, electrodeposition of metals is used to fill the recesses patterned in the resist. In this work, nickel has been electroplated into the bounding resist structure. After electroplating, the remaining resist is dissolved leaving free standing metal structures. The fabricated exchanger is then evaluated based on thermal absorption of simulated waste heat sources and capillary action of the metal channels themselves. Channels are fabricated to heights of 60, 70 and 90 μm respectively on copper substrate using these methods. Working fluid mass transfer rate from the heated microchannel heat exchanger (MHE) is utilized as a basic metric of operation. The mass transfer rate recorded from the nickel-based MHE is 2.19, 2.81 and 3.20 mg s-1 respectively for the different channel heights. This implies an effective thermal power consumption rate of 1.66, 2.13 and 2.42 kW m-2 respectively. By contrast, an MHE fabricated with 115 and 142 μm tall channels on silicon substrate is shown to evaporate up to 2.84 and 3.04 mg s-1 respectively, giving an effective thermal power consumption of 2.15 and 2.31 kW m-2 respectively. An investigation of working fluid contact angle with the electroplated nickel surface is also presented. The surface is found to be a porous structure stemming from the electroplating process.

  5. A rapid method for direct detection of metabolic conversion and magnetization exchange with application to hyperpolarized substrates

    Science.gov (United States)

    Larson, Peder E. Z.; Kerr, Adam B.; Leon Swisher, Christine; Pauly, John M.; Vigneron, Daniel B.

    2012-12-01

    In this work, we present a new MR spectroscopy approach for directly observing nuclear spins that undergo exchange, metabolic conversion, or, generally, any frequency shift during a mixing time. Unlike conventional approaches to observe these processes, such as exchange spectroscopy (EXSY), this rapid approach requires only a single encoding step and thus is readily applicable to hyperpolarized MR in which the magnetization is not replenished after T1 decay and RF excitations. This method is based on stimulated-echoes and uses phase-sensitive detection in conjunction with precisely chosen echo times in order to separate spins generated during the mixing time from those present prior to mixing. We are calling the method Metabolic Activity Decomposition Stimulated-echo Acquisition Mode or MAD-STEAM. We have validated this approach as well as applied it in vivo to normal mice and a transgenic prostate cancer mouse model for observing pyruvate-lactate conversion, which has been shown to be elevated in numerous tumor types. In this application, it provides an improved measure of cellular metabolism by separating [1-13C]-lactate produced in tissue by metabolic conversion from [1-13C]-lactate that has flowed into the tissue or is in the blood. Generally, MAD-STEAM can be applied to any system in which spins undergo a frequency shift.

  6. Synthesis of calcium silicates by Pechini method and exchanging ions of sodium alginate-calcium chloride

    Energy Technology Data Exchange (ETDEWEB)

    Flores-Garay, K.A.; Martinez-Luevanos, A.; Cruz-Ortiz, B.R.; Garcia-Cerda, L.A.; Lopez-Badillo, C.M.

    2016-07-01

    Calcium silicates samples were synthesized using tetraethyl orthosilicate (TEOS) and by Pechini methodology assisted with ion-exchange of sodium alginate, followed by a heat treatment of 800°C by two hours. A, B and C samples were obtained using 1.7×10−3M, 3.4×10−3M and 5.1×10−3M of TEOS, respectively, and without heat treatment; these samples were characterized by thermogravimetric analysis (TGA) and infrared spectroscopy with attenuated total reflectance (FTIR-ATR). Furthermore, samples A800, B800 and C800 obtained using a heat treatment of 800° by two hours were characterized by FTIR-ATR, absorption technique (BET), X-ray diffraction (XRD) and by scanning electron microscopy. The XRD patterns indicate that sample A800 contains olivine (Ca2SiO4) in orthorhombic phase and wollastonite-2M (CaSiO3); sample B800 showed the earlier phases and quartz (SiO2), whereas sample C800 contains wollastonite phases and larnite-2M (Ca2SiO4). (Author)

  7. Detecting proton exchange membrane fuel cell hydrogen leak using electrochemical impedance spectroscopy method

    Science.gov (United States)

    Mousa, Ghassan; Golnaraghi, Farid; DeVaal, Jake; Young, Alan

    2014-01-01

    When a proton exchange membrane (PEM) fuel cell runs short of hydrogen, it suffers from a reverse potential fault that, when driven by neighboring cells, can lead to anode catalyst degradation and holes in the membrane due to local heat generation. As a result, hydrogen leaks through the electrically-shorted membrane-electrode assembly (MEA) without being reacted, and a reduction in fuel cell voltage is noticed. Such voltage reduction can be detected by using electrochemical impedance spectroscopy (EIS). To fully understand the reverse potential fault, the effect of hydrogen crossover leakage in a commercial MEA is measured by EIS at different differential pressures between the anode and cathode. Then the signatures of these leaky cells were compared with the signatures of a no-leaky cells at different oxygen concentrations with the same current densities. The eventual intent of this early stage work is to develop an on-board diagnostics system that can be used to detect and possibly prevent cell reversal failures, and to permit understanding the status of crossover or transfer leaks versus time in operation.

  8. Probable causes of damage of heat-exchange tubes of low-pressure-exchanges of PND-3 type and repair methods

    Science.gov (United States)

    Trifonov, N. N.; Esin, S. B.; Nikolaenkova, E. K.; Sukhorukov, Yu. G.; Svyatkin, F. A.; Sintsova, T. G.; Modestov, V. S.

    2017-08-01

    The structures of low-pressure heaters (LPH), which are installed at nuclear power plants with the K-1000-60/1500 type turbine plants are considered. It was revealed that only the PND-3 type low-pressure heaters have the damages of the heat exchange tubes. For a short operation life, the number of the damaged heat-exchange tubes of PND-3 is approximately 50 pcs for Kalinin NPP and 100-150 pcs for Balakovo NPP. The low-pressure heaters were manufactured at AO Ural Plant of Chemical Machine-Building "Uralkhimmash," OAO Taganrog Boiler-Making Works "Krasny Kotelshchik," and Vitkovice Machinery Group, but the damage nature of the heat-exchange tubes is identical for all PND-3. The damages occur in the place of passage of the heat exchange tubes through the first, the second, and the third partitions over the lower tube plate (the first path of the turbine condensate). Hydraulic shocks can be one of the possible causes of the damage of the heat-exchange tubes of PND-3. The analysis of the average thermal and dynamic loads of the tube systems of PND-1-PND-4 revealed that PND-3 by the thermal power are loaded 1.4-1.6 times and by the dynamic effects are loaded 1.8-2.0 times more than the remaining LPHs. Another possible cause of damage can be the cascaded drain of the separate into PND-4 and then through the drainage heat exchange into PND-3. An additional factor can be the structure of the condensate drainage unit. The advanced system of the heating steam flow and pumping scheme of the separate drain using the existing drainage pumps of PND-3 for K-1000-60/1500 turbine plants for Balakovo and Kalinin NPPs were proposed. The considered decisions make it possible to reduce the flow rate of the heating steam condensate from PND-3 into PND-4 and the speed of the heating steam in the tube space of PND-3 and eliminate the occurrence of hydraulic shocks and damages of the heat exchanger tubes.

  9. Orbital-dependent exchange-correlation functionals in density-functional theory realized by the FLAPW method

    Energy Technology Data Exchange (ETDEWEB)

    Betzinger, Markus

    2011-12-14

    In this thesis, we extended the applicability of the full-potential linearized augmented-plane-wave (FLAPW) method, one of the most precise, versatile and generally applicable electronic structure methods for solids working within the framework of density-functional theory (DFT), to orbital-dependent functionals for the exchange-correlation (xc) energy. Two different schemes that deal with orbital-dependent functionals, the Kohn-Sham (KS) and the generalized Kohn-Sham (gKS) formalism, have been realized. Hybrid functionals, combining some amount of the orbital-dependent exact exchange energy with local or semi-local functionals of the density, are implemented within the gKS scheme. We work in particular with the PBE0 hybrid of Perdew, Burke, and Ernzerhof. Our implementation relies on a representation of the non-local exact exchange potential - its calculation constitutes the most time consuming step in a practical calculation - by an auxiliary mixed product basis (MPB). In this way, the matrix elements of the Hamiltonian corresponding to the non-local potential become a Brillouin-zone (BZ) sum over vector-matrix-vector products. Several techniques are developed and explored to further accelerate our numerical scheme. We show PBE0 results for a variety of semiconductors and insulators. In comparison with experiment, the PBE0 functional leads to improved band gaps and an improved description of localized states. Even for the ferromagnetic semiconductor EuO with localized 4f electrons, the electronic and magnetic properties are correctly described by the PBE0 functional. Subsequently, we discuss the construction of the local, multiplicative exact exchange (EXX) potential from the non-local, orbital-dependent exact exchange energy. For this purpose we employ the optimized effective potential (OEP) method. Central ingredients of the OEP equation are the KS wave-function response and the single-particle density response function. We show that a balance between the LAPW

  10. A Case for Rhetorical Method: Criticism, Theory, and the Exchange of Jean Baudrillard

    OpenAIRE

    Gogan, Brian James

    2011-01-01

    This dissertation uses the case of Jean Baudrillard to argue that successful critics must consider rhetorical method as it relates to theory. Throughout this dissertation, I follow Edwin Black in using the term rhetorical method to describe the procedures a rhetor uses to guide composition. The project's two main goals are, first, to demonstrate how rhetorical method can serve as a foundation for worthwhile criticism, and, second, to outline a Baudrillardian rhetoric. In order to meet these g...

  11. Public outcry: madness masks method on Manhattan's energy exchange

    Energy Technology Data Exchange (ETDEWEB)

    Faulkner, P.

    2000-01-01

    Operation of the NYMEX, a division of the New York Mercantile Exchange that deals almost exclusively in crude oil, heating oil, natural gas, electricity, propane, platinum and palladium trading, is described. The NYMEX where the big forces affecting the market such as OPEC, rising demands, limited oil production and tanker capacity, lagging natural gas supplies, pipeline bottlenecks, and cold snaps are translated into economic values, is considered by insiders as the best guarantee against under- or over-pricing, despite the appearance of bedlam and complete chaos. They consider commodity trading a service rather than an added risk in the energy industry. i. e. the NYMEX is seen as a model of order for transactions on a huge scale, aimed at establishing the value, at any given time under any given circumstances, of standardized energy commodities and sales-volume contracts at agreed points. NYMEX's chief strength is that it provides a completely visible and continuous measurement of value. It is also a factory, generating multiple financial instruments for hedging against risks of unfavorable price movements in the future. The anonymity of the buyers and sellers directing the traders is considered a crucial element of the system, ensuring that the market is about the commodity, not about who is producing or using it. Hedging is a key service wherein sellers (mostly oil companies) sell futures contracts to lock in prices to protect their sources of revenue, should market values fall. Buyers make the deals because they believe that prices will go the other way. Industry insiders maintain that hedgers do not try to make a killing on the market. That is the realm of speculators who are most often high income amateurs. By taking the opposite sides of bids or offers, they provide the market with liquidity.

  12. 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。

  13. Charge-constrained auxiliary-density-matrix methods for the Hartree–Fock exchange contribution

    DEFF Research Database (Denmark)

    Merlot, Patrick; Izsak, Robert; Borgoo, Alex;

    2014-01-01

    Three new variants of the auxiliary-density-matrix method (ADMM) of Guidon, Hutter, and VandeVondele [J. Chem. Theory Comput. 6, 2348 (2010)] are presented with the common feature thatthey have a simplified constraint compared with the full orthonormality requirement of the earlier ADMM1 method...

  14. Estimation of Instantaneous Gas Exchange in Flow-Through Respirometry Systems: A Modern Revision of Bartholomew's Z-Transform Method.

    Directory of Open Access Journals (Sweden)

    Hodjat Pendar

    Full Text Available Flow-through respirometry systems provide accurate measurement of gas exchange over long periods of time. However, these systems have limitations in tracking rapid changes. When an animal infuses a metabolic gas into the respirometry chamber in a short burst, diffusion and airflow in the chamber gradually alter the original signal before it arrives at the gas analyzer. For single or multiple bursts, the recorded signal is smeared or mixed, which may result in dramatically altered recordings compared to the emitted signal. Recovering the original metabolic signal is a difficult task because of the inherent ill conditioning problem. Here, we present two new methods to recover the fast dynamics of metabolic patterns from recorded data. We first re-derive the equations of the well-known Z-transform method (ZT method to show the source of imprecision in this method. Then, we develop a new model of analysis for respirometry systems based on the experimentally determined impulse response, which is the response of the system to a very short unit input. As a result, we present a major modification of the ZT method (dubbed the 'EZT method' by using a new model for the impulse response, enhancing its precision to recover the true metabolic signals. The second method, the generalized Z-transform (GZT method, was then developed by generalizing the EZT method; it can be applied to any flow-through respirometry system with any arbitrary impulse response. Experiments verified that the accuracy of recovering the true metabolic signals is significantly improved by the new methods. These new methods can be used more broadly for input estimation in variety of physiological systems.

  15. Comparison between methods using copper, lanthanum, and colorimetry for the determination of the cation exchange capacity of plant cell walls.

    Science.gov (United States)

    Wehr, J Bernhard; Blamey, F Pax C; Menzies, Neal W

    2010-04-28

    The determination of the cation exchange capacity (CEC) of plant cell walls is important for many physiological studies. We describe the determination of cell wall CEC by cation binding, using either copper (Cu) or lanthanum (La) ions, and by colorimetry. Both cations are strongly bound by cell walls, permitting fast and reproducible determinations of the CEC of small samples. However, the dye binding methods using two cationic dyes, Methylene Blue and Toluidine Blue, overestimated the CEC several-fold. Column and centrifugation methods are proposed for CEC determination by Cu or La binding; both provide similar results. The column method involves packing plant material (2-10 mg dry mass) in a chromatography column (10 mL) and percolating with 20 bed volumes of 1 mM La or Cu solution, followed by washing with deionized water. The centrifugation method uses a suspension of plant material (1-2 mL) that is centrifuged, and the pellet is mixed three times with 10 pellet volumes of 1 mM La or Cu solution followed by centrifugation and final washing with deionized water. In both methods the amount of La or Cu bound to the material was determined by spectroscopic methods.

  16. Near-infrared spectroscopic observation of the ageing process in archaeological wood using a deuterium exchange method.

    Science.gov (United States)

    Tsuchikawa, Satoru; Yonenobu, Hitoshi; Siesler, H W

    2005-03-01

    The ageing degradation of the fine wood structure of dry-exposed archaeological wood was investigated by Fourier transform near-infrared spectroscopy with the aid of a deuterium exchange method. The archaeological wood sample was taken from an old wooden temple in Japan (late 7th century), which has been designated as a UNESCO world heritage site. Comparing the analytical results with those of a modern wood sample of the same species, the ageing process of archaeological wood was clarified as a change in the state of order on a macromolecular structural level. It can be concluded from NIR spectra that the amorphous region, and partially semi-crystalline region, in cellulose, hemicellulose, and lignin decreased by the ageing degradation, whereas the crystalline region in cellulose was not affected by the ageing. The accessibility of the diffusant to effect H/D-exchange was monitored by an OH-related absorption band obtained from FT-NIR transmission spectroscopy and characteristically varied with the ageing process of the wood samples, the absorption bands characteristic of a specific state of order and the diffusion agent. Finally, we proposed a morphological model to describe the variation of the fine structure of the microfibrils in the cell wall with ageing degradation. The state of microfibrils changed loosely by ageing, so that elementary fibrils were arranged loosely under 5 A, whereas several elementary fibrils in the modern wood were arranged in very close proximity under 3 A to each other.

  17. [Exchange of medical imaging and data information in radiotherapy: needs, methods and current limits].

    Science.gov (United States)

    Manens, J P

    1997-01-01

    Extension of the image network within radiotherapy departments provides the technical infrastructure which is made necessary by the rapid evolution of techniques in the field of diagnosis and treatment in radiotherapy. The system is aimed at managing the whole set of data (textual data and images) that are needed for planning and control of treatments. The radiotherapy network addresses two objectives: managing both the information necessary for treatment planning (target volumes definition, planning dosimetry) and the control of all parameters involved during the patient's treatment under the treatment unit. The major challenge is to improve the quality of treatment. Multimodal imaging is a major advance as it allows the use of new dosimetry and simulation techniques. The need for standards to exchange medical imaging information is now recognized by all the institutions and a majority of users and manufacturers. It is widely accepted that the lack of standard has been one of the fundamental obstacles in the deployment of operational "Picture Archiving Communication Systems". The International Standard Organisation Open System Interconnection model is the standard reference mode used to describe network protocols. The network is based on the Ethernet and TCP/IP protocol that provides the means to interconnect imaging devices and workstations dedicated to specific image processing or machines used in radiotherapy. The network uses Ethernet cabled on twisted-pair (10 BaseT) or optical fibres in a star-shaped physical layout. Dicom V3.0 supports fundamental network interactions: transfer of images (computerized tomography magnetic resonance imaging query and retrieve of images), printing on network attached cameras, support of HIS/RIS related interfacing and image management. The supplement to the Dicom standard, Dicom RT, specifies five data objects known in Dicom as Information Object Definition for relevant radiotherapy. Dicom RT objects can provide a mean for

  18. 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.

  19. Selective catalytic reduction of NOx with NH3 over a Cu-SSZ-13 catalyst prepared by a solid state ion exchange method

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Di; Gao, Feng; Peden, Charles HF; Li, Junhui; Kamasamudram, Krishna; Epling, William S.

    2014-06-01

    A novel solid state method was developed to synthesize Cu-SSZ-13 catalysts with excellent NH3-SCR performance and durable hydrothermal stability. After the solid state ion exchange (SSIE) process, the SSZ framework structure and surface area was maintained. In-situ DRIFTS and NH3-TPD experiments provide evidence that isolated Cu ions were successfully exchanged into the pores, which are the active centers for the NH3-SCR reaction.

  20. Parametric analysis of proton exchange membrane fuel cell performance by using the Taguchi method and a neural network

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Sheng-Ju; Shiah, Sheau-Wen [Department of Power Vehicle and Systems Engineering, Chung Cheng Institute of Technology, National Defense University, No. 190, Sanyuan 1st Street, Ta-Hsi, Taoyuan, Taiwan 335 (China); Yu, Wei-Lung [Graduate School of Defense Science, Chung Cheng Institute of Technology, National Defense University, No. 190, Sanyuan 1st Street, Ta-Hsi, Taoyuan, Taiwan 335 (China)

    2009-01-15

    This study proposes a novel parameter optimization method, capable of integrating the neural network and the Taguchi method for parametric analysis of proton exchange membrane fuel cell (PEMFC) performance. Numerous parameters affecting the PEMFC performance are analyzed, such as fuel cell operating temperatures, cathode and anode humidification temperatures, operating pressures, and reactant flow rate. In the traditional design of experiments, the Taguchi method has been popularly utilized in engineering. However, the parameter levels selected to form the orthogonal array in the Taguchi method are discrete, preventing the estimation of the real optimum. This study used the Taguchi method to acquire the primary optimums of the operating parameters in the PEMFC. Each row in the orthogonal array together with its relative responses was used to establish a set of training patterns (input/target pair) to the neural network. The neural network can then construct relationships between the control factors and responses in the PEMFC. The actual optimums of the operating parameters in the PEMFC were obtained by the trained neural network. Experimental results are presented for identifying the proposed approach, which is useful in improving performance for PEMFC and developing electrical system on advanced vehicles and ships. (author)

  1. Die casting process assessment using single minute exchange of dies (SMED method

    Directory of Open Access Journals (Sweden)

    M. Perinić

    2009-07-01

    Full Text Available Die casting process uses high productive level machines. Machine capacity utilization is a key goal in achieving minimum time consumption. Changeover procedure during die casting process is recognized as possible area for reducing time consumption. The SMED method has been improved by additional procedures simultaneously applying the 5S method. Their contribution is evident in recognition of internal and external activities, particularly while transferring internal activities into external ones in as many numbers as possible, by minimizing at the same moment the internal ones. The validity of the method and procedures are verified by an example application of die casting foundry for casting automobile parts. Significant time savings have been achieved with minimum investment.

  2. A Novel Mobile Personalized Recommended Method Based on Money Flow Model for Stock Exchange

    Directory of Open Access Journals (Sweden)

    Qingzhen Xu

    2014-01-01

    Full Text Available Personalized recommended method is widely used to recommend commodities for target customers in e-commerce sector. The core idea of merchandise personalized recommendation can be applied to financial field, which can also achieve stock personalized recommendation. This paper proposes a new recommended method using collaborative filtering based on user fuzzy clustering and predicts the trend of those stocks based on money flow. We use M/G/1 queue system with multiple vacations and server close-down time to measure practical money flow. Based on the indicated results of money flow, we can select the more valued stock to recommend to investors. The experimental results show that the proposed method provides investors with reliable practical investment guidance and receiving more returns.

  3. 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.

  4. 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...

  5. Selected Ratio and Bankruptcy Early-Warning Method Analysis of Competitiveness of Wood Sector Companies Listed on Warsaw Stock Exchange

    Directory of Open Access Journals (Sweden)

    Justyna Biernacka

    2012-09-01

    Full Text Available This paper presents the analysis of economic conditions of wood sector companies listed on the Warsaw Stock Exchange. Among many measures of ratio analysis, the three most frequently used groups of indicators - profitability, debt and liquidity were selected. For a comprehensive presentation of the situation of each company, the Mączyńska & Zawadzki’s model was used as the bankruptcy early warning method. Two furniture industry companies, two wood-based panel industry companies, two pulp and paper industry entities, a representative of sawmilling industry and a company of wood-based panels and furniture industry were analyzed. The analysis showed that companies with stabile position in the market have the best economic conditions, and these were namely the pulp and paper industry and furniture industry.

  6. Selection of Numerical Methods and Their Application to the Thermo-Ecological Life Cycle Cost of Heat Exchanger Components

    Directory of Open Access Journals (Sweden)

    Lucyna Czarnowska

    2015-06-01

    Full Text Available Thermo-ecological cost with the inclusion of life cycle (TEC-LC is defined as the cumulative exergy consumption of non-renewable natural resources associated with any product and its life cycle, taking into account the necessity to prevent and compensate losses caused by depletion of natural resources and the release of harmful substances into the environment. The problem of collecting data for solving TEC-LC equations is not the only one which can be faced in determining this indicator. The selection of the calculation method could also affect obtained results due to the accuracy of the selected algorithm. Numerical stability is particularly important in the case of large sets of data and in this case operations on large matrixes. The issue with a set of TEC-LC balanced equations is examined and compared on the basis of heat exchanger components.

  7. Application of Multivariate Statistical Methods to Urban and Regional Planning. Exchange Bibliography No. 136.

    Science.gov (United States)

    Cherukupalle, Nirmala devi

    This bibliography contains works that illustrate and apply multivariate statistical methods in the analysis of empirical data in the field of urban and regional planning. The bibliography has been designed for use by planning students and the professional planner. The first section of the bibliography lists some elementary and intermediate level…

  8. 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...

  9. Proteomics-based, multivariate random forest method for prediction of protein separation behavior during cation-exchange chromatography.

    Science.gov (United States)

    Swanson, Ryan K; Xu, Ruo; Nettleton, Dan; Glatz, Charles E

    2012-08-01

    The most significant cost of recombinant protein production lies in the optimization of the downstream purification methods, mainly due to a lack of knowledge of the separation behavior of the host cell proteins (HCP). To reduce the effort required for purification process development, this work was aimed at modeling the separation behavior of a complex mixture of proteins in cation-exchange chromatography (CEX). With the emergence of molecular pharming as a viable option for the production of recombinant pharmaceutical proteins, the HCP mixture chosen was an extract of corn germ. Aqueous two phase system (ATPS) partitioning followed by two-dimensional electrophoresis (2DE) provided data on isoelectric point, molecular weight and surface hydrophobicity of the extract and step-elution fractions. A multivariate random forest (MVRF) method was then developed using the three characterization variables to predict the elution pattern of individual corn HCP. The MVRF method achieved an average root mean squared error (RMSE) value of 0.0406 (fraction of protein eluted in each CEX elution step) for all the proteins that were characterized, providing evidence for the effectiveness of both the characterization method and the analysis approach for protein purification applications.

  10. Stochastic reconstruction and a scaling method to determine effective transport coefficients of a proton exchange membrane fuel cell catalyst layer

    Energy Technology Data Exchange (ETDEWEB)

    Barbosa, R. [Centro de Investigacion en Energia, UNAM, Privada Xochicalco S/N, 62580 Temixco (Mexico); Andaverde, J. [Centro de Investigacion en Ingenieria y Ciencias Aplicadas, UAEM, Av. Universidad 1001, Col. Chamilpa, 62210 Cuernavaca (Mexico); Escobar, B. [Instituto Tecnologico de Cancun, Av. Kabah 3, 77515 Cancun (Mexico); Cano, U. [Instituto de Investigaciones Electricas, Av. Reforma 113, col. Palmira, 62490 Cuernavaca (Mexico)

    2011-02-01

    This work uses a method for the stochastic reconstruction of catalyst layers (CLs) proposing a scaling method to determine effective transport properties in proton exchange membrane fuel cell (PEMFC). The algorithm that generates the numerical grid makes use of available information before and after manufacturing the CL. The structures so generated are characterized statistically by two-point correlation functions and by the resultant pore size distribution. As an example of this method, the continuity equation for charge transport is solved directly on the three-dimensional grid of finite control volumes (FCVs), to determine effective electrical and proton conductivities of different structures. The stochastic reconstruction and the electrical and proton conductivity of a 45 {mu}m side size cubic sample of a CL, represented by more than 3.3 x 10{sup 12} FVCs were realized in a much shorter time compared with non-scaling methods. Variables studied in an example of CL structure were: (i) volume fraction of dispersed electrolyte, (ii) total CL porosity and (iii) pore size distribution. Results for the conduction efficiency for this example are also presented. (author)

  11. Advanced analytical method of nereistoxin using mixed-mode cationic exchange solid-phase extraction and GC/MS.

    Science.gov (United States)

    Park, Yujin; Choe, Sanggil; Lee, Heesang; Jo, Jiyeong; Park, Yonghoon; Kim, Eunmi; Pyo, Jaesung; Jung, Jee H

    2015-07-01

    Nereistoxin(NTX) was originated from a marine annelid worm Lumbriconereis heteropoda and its analogue pesticides including cartap, bensultap, thiocyclam and thiobensultap have been commonly used in agriculture, because of their low toxicity and high insecticidal activity. However, NTX has been reported about its inhibitory neuro toxicity in human and animal body, by blocking nicotinic acetylcholine receptor and it cause significant neuromuscular toxicity, resulting in respiratory failure. We developed a new method to determine NTX in biological fluid. The method involves mixed-mode cationic exchange based solid phase extraction and gas chromatography/mass spectrometry for final identification and quantitative analysis. The limit of detection and recovery were substantially better than those of other methods using liquid-liquid extraction or headspace solid phase microextraction. The good recoveries (97±14%) in blood samples were obtained and calibration curves over the range 0.05-20 mg/L have R2 values greater than 0.99. The developed method was applied to a fatal case of cartap intoxication of 74 years old woman who ingested cartap hydrochloride for suicide. Cartap and NTX were detected from postmortem specimens and the cause of the death was ruled to be nereistoxin intoxication. The concentrations of NTX were 2.58 mg/L, 3.36 mg/L and 1479.7 mg/L in heart, femoral blood and stomach liquid content, respectively. The heart blood/femoral blood ratio of NTX was 0.76.

  12. An alternative preparation method for ion exchanged catalysts: Solid state redox reaction

    DEFF Research Database (Denmark)

    Schneider, E.; Hagen, A.; Grunwaldt, J.-D.

    2004-01-01

    A new method for modifying zeolites with zinc is proposed. The solid state redox reaction between metallic zinc and ZSM-5 zeolites with different Si/Al ratios was investigated by temperature programmed hydrogen evolution (TPHE), X-ray absorption near edge structure (XANES) and diffuse reflectance...... infrared Fourier transform spectroscopy (DRIFTS). The evolution of hydrogen was detected at temperatures above 620 K. The source of hydrogen was the solid state redox reaction of the metal with protons of the support. The samples exhibit catalytic activity in ethane aromatization indicating that zinc...... should be located at the same sites as in catalysts prepared by conventional methods. Combination of XANES and catalytic activity point to zinc being mainly present in tetrahedral geometry under reaction conditions....

  13. 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).

  14. 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.

  15. Validation of a pH gradient-based ion-exchange chromatography method for high-resolution monoclonal antibody charge variant separations.

    Science.gov (United States)

    Rea, Jennifer C; Moreno, G Tony; Lou, Yun; Farnan, Dell

    2011-01-25

    Ion-exchange chromatography is widely used for profiling the charge heterogeneity of proteins, including monoclonal antibodies. Despite good resolving power and robustness, ionic strength-based ion-exchange separations are product-specific and time-consuming to develop. We have previously reported a novel pH-based separation of proteins by cation exchange chromatography that was multi-product, high-resolution, and robust against variations in sample matrix salt concentration and pH. In this study, a pH gradient-based separation method using cation exchange chromatography was evaluated in a mock validation. This method was shown to be robust for monoclonal antibodies and suitable for its intended purpose of charge heterogeneity analysis. Simple mixtures of defined buffer components were used to generate the pH gradients that separated closely related antibody species. Validation characteristics, such as precision and linearity, were evaluated. Robustness to changes in protein load, buffer pH and column oven temperature was demonstrated. The stability-indicating capability of this method was determined using thermally stressed antibody samples. In addition, intermediate precision was demonstrated using multiple instruments, multiple analysts, multiple column lots, and different column manufacturers. Finally, the precision for this method was compared to conventional ion-exchange chromatography and imaged capillary isoelectric focusing. These results demonstrate the superior precision and robustness of this multi-product method, which can be used for the high-throughput evaluation of in-process and final product samples.

  16. 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.

  17. Research Objects for Sharing and Exchanging Research Data and Methods in Earth Science

    Science.gov (United States)

    Gómez Pérez, José Manuel; Palma, Raul

    2016-04-01

    Scientists in data-intensive disciplines increasingly call for models that go beyond the publication of datasets, allowing systematic capture of the lifecycle of scientific investigations and providing a single entry point for accessing information about (to name a few) the hypotheses investigated, the datasets used, the computations, observations and experiments carried out, their outcomes and provenance, the conclusions and findings that were derived, and even the scientists involved in a particular investigation. In this scenario, Research Objects provide a structured means to encapsulate such information and the associated methods involved, along with essential metadata and annotations aimed at both humans and computers. Research objects are therefore portable units of scientific knowledge that enable the sharing, preservation, scholarly communication, validation, and re-use of scientific outcomes. In this presentation we will focus on the application of the Research Object concept in observational disciplines and particularly Earth Science. We will present the main concepts behind research objects and discuss the challenges involved in the extension and adaptation of existing practices, modelling vocabularies, middleware and tools for these disciplines. By deploying research object technologies in Earth Science, we aim to enhance the portability of scientific materials and methods, the collaboration capabilities within and between teams of earth scientists, the quality and long-term preservation capabilities of the methods, and the means to communicate, validate and measure the impact of scientific outcomes. This work is being conducted in the context of the Horizon2020 EVER-EST project, the main objective of which is the development of a research object-centric virtual research environment for Earth Science communities.

  18. An alternative preparation method for ion exchanged catalysts: Solid state redox reaction

    DEFF Research Database (Denmark)

    Schneider, E.; Hagen, A.; Grunwaldt, J.-D.

    2004-01-01

    A new method for modifying zeolites with zinc is proposed. The solid state redox reaction between metallic zinc and ZSM-5 zeolites with different Si/Al ratios was investigated by temperature programmed hydrogen evolution (TPHE), X-ray absorption near edge structure (XANES) and diffuse reflectance...... infrared Fourier transform spectroscopy (DRIFTS). The evolution of hydrogen was detected at temperatures above 620 K. The source of hydrogen was the solid state redox reaction of the metal with protons of the support. The samples exhibit catalytic activity in ethane aromatization indicating that zinc...

  19. Replica casting technique for micro Fresnel lenses characterization

    DEFF Research Database (Denmark)

    Gasparin, Stefania; Tosello, Guido; Hansen, Hans Nørgaard

    2012-01-01

    The available measuring techniques are not always suitable for the characterization of optical surfaces such as Fresnel lenses or polished specimens. A way to overcome these challenges is to reproduce the optical components surface using a polymer casting method and to measure the replicated surf...

  20. Investigation on the micromilled surface characterization through replica technology

    DEFF Research Database (Denmark)

    Baruffi, Federico; Parenti, P.; Cacciatore, F.

    2016-01-01

    . This represents an open issue that, in some cases, can be tackled by adopting the replication technology. The method consists in obtaining the replicated surface and performing its measurement using suitable measuring systems. This paper evaluates the actual performance of a commercial replication product...

  1. Assessment of Cation Exchange Membrane Method and Estimation of Potassium Critical Values

    Institute of Scientific and Technical Information of China (English)

    SHENJIANBO; J.J.SCHOENAU; 等

    1996-01-01

    Soil and tissue analyses are usually used in identifying potassium(K) deficiencies and predicting K fertilizer requirements of crops.The critical levels of both soil and fresh leaf tissue at seventh leaf stage were developed and assessed for canola,chickpea and sunflower grown on two saskatchewan,soils,with six rates of K fertilizer supply.in a growth chamber experiment.The available potassium in soils was detemined by two methods:1)resin strip extraction,and 2)NH4OAC extraction.The potassium in fresh leaves was determined at seventh leaf stage by a simple procedure using a common garlic press and injector to extract the plant sap and testing the sap with a handheld ion selection electrode meter,The results showed significant relationships between the resin strip extractable K and NH4OAC extractable K,and between the plant uptake of total K and the supple of available K in the soils determined by the two methods.Good relationships were also found between the potassium in fresh leaves and the plant uptake of totak K for canola,chickpea and sunflower.The resin strip extraction for K was calibrated using common NH4OAC extraction,and recommended for routine analyses because of its simplicity and sensitivity.

  2. Influence of Thermal Conductivity on Interface Shape during Growth of Sapphire Crystal Using a Heat-Exchanger-Method

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    The internal radiative contributed on heat transfer will enhance the heat transport inside the crystalline phase during growth the transparent sapphire crystal using a heat-exchanger-method (HEM). The artificially enhanced thermal conductivity of the solid to include the internal radiation effect was used in the present study. Numerical simulations using FIDAP were performed to investigate the effects of the thermal conductivity on the shape of the melt-crystal interface, the temperature distribution, and the velocity distribution. Heat transfer (including radiation) from the furnace to the crucible and heat extraction from the heat exchanger can be modeled by the convection boundary conditions. In the present study, we focus on the influence of the conductivity on the shape of the melt-crystal interface. Therefore, the effect of the others growth parameters during the HEM crystal growth was neglected. For the homogenous conductivity (km=kS=k), the maximum convexity decreases as k increases and the rate of maximum convexity increases for a higher conductivity is less abrupt than for a lower conductivity. For the no homogenous conductivity (km≠kS), the higher solid's kS generates lower maximum convexity and the variation in maximum convexity was less abrupt for the different melt's km. The maximum convexity decreases slightly as the enhance conductivity of the sapphire crystal increases. The effects of the anisotropic conductivity of the sapphire crystal were also addressed. The maximum convexity of the melt-crystal interface decreases when the radial conductivity (ksr) of the crystal increases. The maximum convexity increases as the axial conductivity (ksz) of the crucible increases.

  3. Progress in remote sensing of global land surface heat fluxes and evaporations with a turbulent heat exchange parameterization method

    Science.gov (United States)

    Chen, Xuelong; Su, Bob

    2017-04-01

    Remote sensing has provided us an opportunity to observe Earth land surface with a much higher resolution than any of GCM simulation. Due to scarcity of information for land surface physical parameters, up-to-date GCMs still have large uncertainties in the coupled land surface process modeling. One critical issue is a large amount of parameters used in their land surface models. Thus remote sensing of land surface spectral information can be used to provide information on these parameters or assimilated to decrease the model uncertainties. Satellite imager could observe the Earth land surface with optical, thermal and microwave bands. Some basic Earth land surface status (land surface temperature, canopy height, canopy leaf area index, soil moisture etc.) has been produced with remote sensing technique, which already help scientists understanding Earth land and atmosphere interaction more precisely. However, there are some challenges when applying remote sensing variables to calculate global land-air heat and water exchange fluxes. Firstly, a global turbulent exchange parameterization scheme needs to be developed and verified, especially for global momentum and heat roughness length calculation with remote sensing information. Secondly, a compromise needs to be innovated to overcome the spatial-temporal gaps in remote sensing variables to make the remote sensing based land surface fluxes applicable for GCM model verification or comparison. A flux network data library (more 200 flux towers) was collected to verify the designed method. Important progress in remote sensing of global land flux and evaporation will be presented and its benefits for GCM models will also be discussed. Some in-situ studies on the Tibetan Plateau and problems of land surface process simulation will also be discussed.

  4. Alternative purification method for recombinant measles viral nucleoprotein expressed in insect cells by ion-exchange chromatography.

    Science.gov (United States)

    Lee, Han Saem; Kim, You-Jin; Yang, Jeongsun; Yoon, Hee Sook; Kim, Seung Tae; Kim, Kisoon

    2014-03-01

    Recombinant measles virus nucleoproteins (rMeV N) and fusion (F) proteins were characterized as major antigenic proteins expressed in insect cells mediated by recombinant baculoviruses (rBVs). Band intensities were analyzed by Western blotting to recognize IgG and IgM antibodies against the rMeV N and F proteins in human sera and cerebrospinal fluids (CSFs) from patients with measles infections. Positive results from the blots using the rMeV N were consistent with the results of enzyme-linked immunosorbent assays (ELISAs) in which whole viral proteins were used as antigens. Human sera and CSFs reacted more strongly with the rMeV N than with the rMeV F proteins prepared in an identical expression system. For efficient and reliable purification, ion-exchange chromatography using Source Q anion resin was applied, and high-purity rMeV N protein was harvested. To characterize the similarity with the native viral protein to purified N protein, structural mimicry of purified recombinant proteins with intact rMeV N was shown through transmission electron microscopy, and the truncation and the phosphorylation status of the expressed protein were analyzed. These results suggest that the rMeV N purified by ion-exchange chromatography has features similar to those of naïve N including a self-assembled structure, phosphorylation and antigenic function. Thus, these expression and purification methods can be applied to the large-scale production of the rMeV N, which is essential for the development of new diagnostic tools and vaccines for acute and chronic MeV infections.

  5. An Active-Distributed Temperature Sensing method to quantify groundwater - surface water exchanges

    Science.gov (United States)

    Simon, Nataline; Bour, Olivier; Lavenant, Nicolas; Faucheux, Mickaël; Fovet, Ophélie; Longuevergne, Laurent

    2017-04-01

    Understanding and quantifying groundwater and surface water interactions are key elements for the management of water quality and quantity, but also for the preservation of groundwater dependent ecosystems and riparian habitat. We developed a methodology to quantify groundwater and surface water interactions, by setting up an active heat tracer experiment using fiber-optic distributed temperature sensing (FO-DTS). The experimental setup consists in heating an armoured fiber-optic cable that has been previously deployed along the streambed within the sediments. Then, the increase in temperature along the heated cable is a function of the thermal properties of the sediments and of the fluid flow velocity within the sediments. The cable is heated electrically through the steel armouring of the cable while the elevations in temperature are continuously monitored. We tested this methodology on the Kerbernez catchment, located in south-western Brittany (France) and which is part of the AgrHys hydrological observatory. We deploy the cable in a first-order stream within this small agricultural catchment (0.12 km2). Temperature was monitored along 60 meters of stream with a spatial and temporal resolution respectively equal to 29 cm and 30 s. To interpret the data, we used an analytical solution developed for geothermal energy that considers advection and conduction of temperature in porous media. To validate the use of the analytical solution and to define the limits of the method, a 2D numerical model has been developed. This model simulates heat transport and conduction with steady state fluid flow using the Conjugate Heat Transfer module of COMSOL Multiphysics ®. During heating and cooling, the measured temperature was particularly variable along the section with temperature increases that range between 16 to 36°C. This variability can directly be associated with local variations of water fluxes by applying the appropriate analytical solution. Henceforth, it is

  6. 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.

  7. Methods for promoting knowledge exchange and networking among young professionals in the aerospace sector-IAF's IPMC workshop 2013 insights

    Science.gov (United States)

    Monzon, Amalio; Chow, Tiffany; Guthrie, Paul; Lu, Zhuoyan; Chuma, Constant; He, Huang; Kuzkov, Sergii

    2016-01-01

    During the next decades, the aerospace community will pursue goals such as human exploration beyond the Moon, commercialization and cost reduction of space activities or sustainability of air transport and space operations, bringing relevant economic, environmental and social benefits to the society. Young professionals development is a critical success factor to enable these goals and in consequence is an area of significant interest. This paper focuses on the methods for promoting knowledge exchange and networking among Young Professionals. On the one hand, it analyzes the different activities currently used for that purpose by the organizations of the sector as well as explores the opportunities to reinforce these methods. On the other hand, it presents the results of a survey addressed to Young Professionals and aimed at identifying their needs, expectations and benefits perceived in relation with these activities. This study was conducted as part of the IAF's (International Astronautical Federation) IPMC (International Programme/Project Management Committee) Workshop held during the International Astronautical Congress (IAC) 2013 in Beijing, whose objective was to provide Young Professionals a forum to share experiences and to discuss ideas and needs, and which counted with more than fifty delegates representing IAF member organizations from all around the world.

  8. Development of a method to estimate the lifespan of proton exchange membrane fuel cell using electrochemical impedance spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Ju-hyung; Lee, Jong-Hak; Choi, Woojin [Department of Electrical Engineering, Soongsil University, 1-1 Sangdo-dong, Dongjak-gu, Seoul 156-743 (Korea); Park, Kyung-Won [Department of Chemical/Environmental Engineering, Soongsil University, 1-1 Sangdo-dong, Dongjak-gu, Seoul 156-743 (Korea); Sun, Hee-Young [Samsung Advanced Institute of Technology, Mt. 14-1, Nongseo-dong, Giheung-gu, Yongin-si, Gyeonggi-do 446-712 (Korea); Oh, Jae-Hyuk [Samsung Electronics, 416 Maetan-dong, Youngtong-gu, Suwon-si, Gyeonggi-do 443-370 (Korea)

    2010-09-15

    This paper proposes a new method for estimating the state and lifespan of fuel cells in operation by fuel cell equivalent impedance modeling by electrochemical impedance spectroscopy (EIS) and observing degradation. The performance change of fuel cells takes place in the form of changes in each parameter value comprising an equivalent AC impedance circuit; monitoring such changes allows for the prediction of the state and lifespan of a fuel cell. In the experiments, the AC impedance of high-temperature proton exchange membrane (PEM) fuel cells was measured at constant time intervals during their continuous operation for over 2200 h. The expression for the lifespan of a fuel cell was deduced by curve fitting the changes in each parameter to a polynomial. Electric double layer capacitance and charge transfer resistance, which show the reduction reaction of the cathode, were used as major parameters for judging the degradation; a method of using time constants is proposed to more accurately estimate the degree of degradation. In addition, an algorithm that can evaluate the soundness and lifespan of a fuel cell is proposed; it compares the measured time constant of the fuel cell being tested with that of average lifespan fuel cell. (author)

  9. Generalized ensemble method applied to study systems with strong first order transitions

    Science.gov (United States)

    Małolepsza, E.; Kim, J.; Keyes, T.

    2015-09-01

    At strong first-order phase transitions, the entropy versus energy or, at constant pressure, enthalpy, exhibits convex behavior, and the statistical temperature curve correspondingly exhibits an S-loop or back-bending. In the canonical and isothermal-isobaric ensembles, with temperature as the control variable, the probability density functions become bimodal with peaks localized outside of the S-loop region. Inside, states are unstable, and as a result simulation of equilibrium phase coexistence becomes impossible. To overcome this problem, a method was proposed by Kim, Keyes and Straub [1], where optimally designed generalized ensemble sampling was combined with replica exchange, and denoted generalized replica exchange method (gREM). This new technique uses parametrized effective sampling weights that lead to a unimodal energy distribution, transforming unstable states into stable ones. In the present study, the gREM, originally developed as a Monte Carlo algorithm, was implemented to work with molecular dynamics in an isobaric ensemble and coded into LAMMPS, a highly optimized open source molecular simulation package. The method is illustrated in a study of the very strong solid/liquid transition in water.

  10. Development and validation of an ion-exchange chromatography method for heparin and its impurities in heparin products.

    Science.gov (United States)

    Thiangthum, Sumate; Vander Heyden, Yvan; Buchberger, Wolfgang; Viaene, Johan; Prutthiwanasan, Brompoj; Suntornsuk, Leena

    2014-11-01

    An anion-exchange liquid chromatography method for the determination of heparin and its impurities (dermatan sulfate and oversulfated chondroitin sulfate) was developed using chemometric-assisted optimization, including multivariate experimental design and response surface methodology. The separation of heparin, dermatan sulfate, and oversulfated chondroitin sulfate (Rs above 2.0) was achieved on a Dionex RF IC IonPac AS22 column with a gradient elution of 10-70% of 2.5 M sodium chloride and 20 mM Tris phosphate buffer (pH 2.1) at a flow rate of 0.6 mL/min and UV detection at 215 nm. Method validation shows good linearity (r > 0.99), acceptable precision (%relative standard deviations <11.4%) and trueness (%recovery of 92.3-103.9%) for all analytes. The limits of detection for dermatan sulfate and oversulfated chondroitin sulfate are equivalent to 0.11% w/w (10.5 μg/mL) and 0.07% w/w (7.2 μg/mL), while the limits of quantification are 0.32% w/w (31.5 μg/mL) and 0.22% w/w (22.0 μg/mL) relative to heparin, respectively. The method is specific for heparin, dermatan sulfate, and oversulfated chondroitin sulfate without interference from mobile phase and sample matrices and could be used for accurate quantitation the drug and its impurities in a single run. Applications of the method reveal contents of heparin between 90.3 and 97.8%. Dermatan sulfate and oversulfated chondroitin sulfate were not detected in any of the real-life samples.

  11. Did you have an impact? A theory-based method for planning and evaluating knowledge-transfer and exchange activities in occupational health and safety.

    Science.gov (United States)

    Kramer, Desré M; Wells, Richard P; Carlan, Nicolette; Aversa, Theresa; Bigelow, Philip P; Dixon, Shane M; McMillan, Keith

    2013-01-01

    Few evaluation tools are available to assess knowledge-transfer and exchange interventions. The objective of this paper is to develop and demonstrate a theory-based knowledge-transfer and exchange method of evaluation (KEME) that synthesizes 3 theoretical frameworks: the promoting action on research implementation of health services (PARiHS) model, the transtheoretical model of change, and a model of knowledge use. It proposes a new term, keme, to mean a unit of evidence-based transferable knowledge. The usefulness of the evaluation method is demonstrated with 4 occupational health and safety knowledge transfer and exchange (KTE) implementation case studies that are based upon the analysis of over 50 pre-existing interviews. The usefulness of the evaluation model has enabled us to better understand stakeholder feedback, frame our interpretation, and perform a more comprehensive evaluation of the knowledge use outcomes of our KTE efforts.

  12. Optimization of the polypyrrole-coating parameters for proton exchange membrane fuel cell bipolar plates using the Taguchi method

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yan; Northwood, Derek O. [Department of Mechanical, Automotive, and Materials Engineering, University of Windsor, 401 Sunset Avenue, Windsor, Ontario (Canada)

    2008-10-15

    In order to overcome the high price, weight and volume of non-porous graphite bipolar plates, metallic bipolar plates are being investigated as a substitute material. However, metallic materials can corrode under proton exchange membrane fuel cell (PEMFC) working conditions, leading to a degradation in the performance of the membrane. Previous work had shown that a polypyrrole coating on SS316L can significantly increase the corrosion resistance of the base material. In this study, a Taguchi design of experiment method was used to optimize the process parameters for the polypyrrole coating so as to produce the maximum corrosion resistance. Potentiodynamic and potentiostatic tests were used to determine the corrosion resistance of the polypyrrole-coated SS316L. Scanning electron microscopy (SEM) with energy dispersive X-ray (EDX) was used to characterize the coating thickness and coating appearance. Inductively coupled plasma optical emission spectroscopy (ICP-OES) was used to determine the metal ion concentration in the solution after corrosion. The interfacial contact resistance of SS316L with carbon paper was measured both before and after coating with polypyrrole. (author)

  13. Similarity measure and topology evolution of foreign exchange markets using dynamic time warping method: Evidence from minimal spanning tree

    Science.gov (United States)

    Wang, Gang-Jin; Xie, Chi; Han, Feng; Sun, Bo

    2012-08-01

    In this study, we employ a dynamic time warping method to study the topology of similarity networks among 35 major currencies in international foreign exchange (FX) markets, measured by the minimal spanning tree (MST) approach, which is expected to overcome the synchronous restriction of the Pearson correlation coefficient. In the empirical process, firstly, we subdivide the analysis period from June 2005 to May 2011 into three sub-periods: before, during, and after the US sub-prime crisis. Secondly, we choose NZD (New Zealand dollar) as the numeraire and then, analyze the topology evolution of FX markets in terms of the structure changes of MSTs during the above periods. We also present the hierarchical tree associated with the MST to study the currency clusters in each sub-period. Our results confirm that USD and EUR are the predominant world currencies. But USD gradually loses the most central position while EUR acts as a stable center in the MST passing through the crisis. Furthermore, an interesting finding is that, after the crisis, SGD (Singapore dollar) becomes a new center currency for the network.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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...

  19. The Comparison of Methods Artificial Neural Network with Linear Regression Using Specific Variables for Prediction Stock Price in Tehran Stock Exchange

    CERN Document Server

    Ahangar, Reza Gharoie; Pournaghshband, Hassan

    2010-01-01

    In this paper, researchers estimated the stock price of activated companies in Tehran (Iran) stock exchange. It is used Linear Regression and Artificial Neural Network methods and compared these two methods. In Artificial Neural Network, of General Regression Neural Network method (GRNN) for architecture is used. In this paper, first, researchers considered 10 macro economic variables and 30 financial variables and then they obtained seven final variables including 3 macro economic variables and 4 financial variables to estimate the stock price using Independent components Analysis (ICA). So, we presented an equation for two methods and compared their results which shown that artificial neural network method is more efficient than linear regression method.

  20. Enhanced salt-removal percentage in capacitive deionization with addition of ion-exchange membrane using carbon electrode synthesized with freezing thawing method

    Science.gov (United States)

    Sari, Intan Permata; Endarko

    2016-04-01

    Ion-exchange membrane technology has shown a great potential to enhance the desalting efficiency. Ion-exchange membranes are placed in front of the electrodes so that the charged ions can be selectively passed through the membrane layer and captured by the oppositely charged electrode more quickly, so as to increase the efficiency of desalination. In this research, carbon electrodes have been synthesized from an activated carbon (700 - 1400 m2/g) and polyvinyl alcohol (PVA) as a binder using freezing thawing method. A solution with 180 µS/cm NaCl was pumped to the capacitive deionization (CDI) cell using a Boyu Submersible pump (model SP-601) at a flow rate of 25 mL/min and the voltage was set at 2 V. The result showed that the CDI cell with ion-exchange membrane (MCDI) has the salt removal efficiency greater than the CDI cell without ion-exchange membrane. The salt-removal percentage of MCDI was achieved at 66.36%, meanwhile the CDI cell without ion-exchange membrane resulted in 54.4%.

  1. 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

  2. Simple (17) O NMR method for studying electron self-exchange reaction between UO2 (2+) and U(4+) aqua ions in acidic solution.

    Science.gov (United States)

    Bányai, István; Farkas, Ildikó; Tóth, Imre

    2016-06-01

    (17) O NMR spectroscopy is proven to be suitable and convenient method for studying the electron exchange by following the decrease of (17) O-enrichment in U(17) OO(2+) ion in the presence of U(4+) ion in aqueous solution. The reactions have been performed at room temperature using I = 5 M ClO4 (-) ionic medium in acidic solutions in order to determine the kinetics of electron exchange between the U(4+) and UO2 (2+) aqua ions. The rate equation is given as R = a[H(+) ](-2)  + R', where R' is an acid independent parallel path. R' depends on the concentration of the uranium species according to the following empirical rate equation: R' = k1 [UO(2 +) ](1/2) [U(4 +) ](1/2)  + k2 [UO(2 +) ](3/2) [U(4 +) ](1/2) . The mechanism of the inverse H(+) concentration-dependent path is interpreted as equilibrium formation of reactive UO2 (+) species from UO2 (2+) and U(4+) aqua ions and its electron exchange with UO2 (2+) . The determined rate constant of this reaction path is in agreement with the rate constant of UO2 (2+) -UO2 (+) , one electron exchange step calculated by Marcus theory, match the range given experimentally of it in an early study. Our value lies in the same order of magnitude as the recently calculated ones by quantum chemical methods. The acid independent part is attributed to the formation of less hydrolyzed U(V) species, i.e. UO(3+) , which loses enrichment mainly by electron exchange with UO2 (2+) ions. One can also conclude that (17) O NMR spectroscopy, or in general NMR spectroscopy with careful kinetic analysis, is a powerful tool for studying isotope exchange reactions without the use of sophisticated separation processes. Copyright © 2015 John Wiley & Sons, Ltd.

  3. Overcoming strong metastabilities with the LLR method

    CERN Document Server

    Lucini, Biagio; Langfeld, Kurt

    2016-01-01

    In previous work, it has been shown that the recently proposed LLR method is very efficient at overcoming strong metastabilities that arise near first-order phase transition points. Here we present a systematic study of the performance of the algorithm near (pseudo-)critical points for $q$-state Potts models with $q$ as large as 20, in two and three dimensions. In particular, we shall focus our study on the ergodicity of the replica exchange step and the underlying physical mechanism. When compared with both analytical and numerical results present in the literature, our determinations of thermodynamic observables (including the order-disorder interface tension at criticality) show an impressive degree of relative accuracy (up to $2.5 \\times 10^{-6}$), which confirms the reliability and the efficiency of the proposed approach.

  4. 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

  5. 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...

  6. 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.

  7. Optimization of ion exchange sigmoidal gradients using hybrid models: Implementation of quality by design in analytical method development.

    Science.gov (United States)

    Joshi, Varsha S; Kumar, Vijesh; Rathore, Anurag S

    2017-03-31

    Thorough product understanding is one of the basic tenets for successful implementation of Quality by Design (QbD). Complexity encountered in analytical characterization of biotech therapeutics such as monoclonal antibodies (mAbs) requires novel, simpler, and generic approaches towards product characterization. This paper presents a methodology for implementation of QbD for analytical method development. Optimization of an analytical cation exchange high performance liquid chromatography (CEX-HPLC) method utilizing a sigmoidal gradient has been performed using a hybrid mechanistic model that is based on Design of experiment (DOE) based studies. Since sigmodal gradients are much more complex than the traditional linear gradients and have a large number of input parameters (five) for optimization, the number of DOE experiments required for a full factorial design to estimate all the main effects as well as the interactions would be too large (243). To address this problem, a mechanistic model was used to simulate the analytical separation for the DOE and then the results were used to build an empirical model. The mechanistic model used in this work is a more versatile general rate model in combination of modified Langmuir binding kinetics. The modified Langmuir model is capable of modelling the impact of nonlinear changes in the concentration of the salt modifier. Further, to get the input and output profiles of mAb and salts/buffers, the HPLC system, consisting of the mixer, detectors, and tubing was modelled as a sequence of dispersed plug flow reactors and continuous stirred tank reactors (CSTR). The experimental work was limited to calibration of the HPLC system and finding the model parameters through three linear gradients. To simplify the optimization process, only three peaks in the centre of the profile (main product and the adjacent acidic and basic variants) were chosen to determine the final operating condition. The regression model made from the DoE data

  8. 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.

  9. The Sherrington-Kirkpatrick spin glass model in the presence of a random field with a joint Gaussian probability density function for the exchange interactions and random fields

    Science.gov (United States)

    Hadjiagapiou, Ioannis A.

    2014-03-01

    The magnetic systems with disorder form an important class of systems, which are under intensive studies, since they reflect real systems. Such a class of systems is the spin glass one, which combines randomness and frustration. The Sherrington-Kirkpatrick Ising spin glass with random couplings in the presence of a random magnetic field is investigated in detail within the framework of the replica method. The two random variables (exchange integral interaction and random magnetic field) are drawn from a joint Gaussian probability density function characterized by a correlation coefficient ρ. The thermodynamic properties and phase diagrams are studied with respect to the natural parameters of both random components of the system contained in the probability density. The de Almeida-Thouless line is explored as a function of temperature, ρ and other system parameters. The entropy for zero temperature as well as for non zero temperatures is partly negative or positive, acquiring positive branches as h0 increases.

  10. An easy method for the preparation of anion exchange membranes: Graft-polymerization of ionic liquids in porous supports

    NARCIS (Netherlands)

    Merle, Geraldine; Chairuna, Annisa; Ven, van de Erik; Nijmeijer, Kitty

    2013-01-01

    A novel way for anion exchange membrane (AEM) preparation has been investigated, avoiding the use of expensive and toxic chemicals. This new synthetic approach to prepare AEMs was based on the use of a porous polybenzylimidazole membrane as support in which functionalized ILs were introduced and sub

  11. An ion-exchange method for selective separation of palladium, platinum and rhodium from solutions obtained by leaching automotive catalytic converters.

    Science.gov (United States)

    Gaita, R; Al-Bazi, S J

    1995-02-01

    An ion-exchange method has been developed for the separation of palladium, platinum and rhodium from a solution that is highly acidic and contains a considerable amount of lead, aluminum, iron and cerium, obtained by leaching a used honeycomb type automotive catalytic converter. A column of Amberlite IRA-93 anion-exchange resin was found appropriate to recover platinum metals from the pregnant solution. Selective stripping of these metals from the resin was achieved by eluting rhodium first with 6.0M hydrochloric acid, then palladium with a 1% ammonia solution at ambient temperature, and platinum with 5% of the reagent at elevated temperatures. Optimum conditions for leaching these metals from the catalyst were 5.0M hydrochloric acid and 0.4M sodium chlorate at 70 degrees C. This method can be applied to both analytical as well as large scale operations. It is simple, economical, and relatively safe for human exposure and the environment.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. Calculation Method of Finned Tube Condensing Heat Exchanger for Natural Gas Water Heater%天然气热水器翅片式冷凝换热器的计算方法

    Institute of Scientific and Technical Information of China (English)

    崔永章; 钱申贤

    2000-01-01

    分析了冷凝翅片换热器传热过程和主要参量,提出了天然气热水器冷凝翅片换热器的设计方法。%On the basis of theory analysis of heat transfer process and major parameters in finned tube condensing heat exchanger, a method is derived for calculating heat exchange of condensing finned tube heat exchanger.

  4. Method to obtain absolute impurity density profiles combining charge exchange and beam emission spectroscopy without absolute intensity calibrationa)

    Science.gov (United States)

    Kappatou, A.; Jaspers, R. J. E.; Delabie, E.; Marchuk, O.; Biel, W.; Jakobs, M. A.

    2012-10-01

    Investigation of impurity transport properties in tokamak plasmas is essential and a diagnostic that can provide information on the impurity content is required. Combining charge exchange recombination spectroscopy (CXRS) and beam emission spectroscopy (BES), absolute radial profiles of impurity densities can be obtained from the CXRS and BES intensities, electron density and CXRS and BES emission rates, without requiring any absolute calibration of the spectra. The technique is demonstrated here with absolute impurity density radial profiles obtained in TEXTOR plasmas, using a high efficiency charge exchange spectrometer with high etendue, that measures the CXRS and BES spectra along the same lines-of-sight, offering an additional advantage for the determination of absolute impurity densities.

  5. Method to obtain absolute impurity density profiles combining charge exchange and beam emission spectroscopy without absolute intensity calibration

    Energy Technology Data Exchange (ETDEWEB)

    Kappatou, A.; Delabie, E. [FOM Institute DIFFER - Dutch Institute for Fundamental Energy Research, Association EURATOM-FOM, 3430 BE Nieuwegein (Netherlands); Jaspers, R. J. E.; Jakobs, M. A. [Science and Technology of Nuclear Fusion, Eindhoven University of Technology, 5600 MB Eindhoven (Netherlands); Marchuk, O.; Biel, W. [Institute for Energy and Climate Research, Forschungszentrum Julich GmbH, Trilateral Euregio Cluster, 52425 Julich (Germany)

    2012-10-15

    Investigation of impurity transport properties in tokamak plasmas is essential and a diagnostic that can provide information on the impurity content is required. Combining charge exchange recombination spectroscopy (CXRS) and beam emission spectroscopy (BES), absolute radial profiles of impurity densities can be obtained from the CXRS and BES intensities, electron density and CXRS and BES emission rates, without requiring any absolute calibration of the spectra. The technique is demonstrated here with absolute impurity density radial profiles obtained in TEXTOR plasmas, using a high efficiency charge exchange spectrometer with high etendue, that measures the CXRS and BES spectra along the same lines-of-sight, offering an additional advantage for the determination of absolute impurity densities.

  6. Preparation of Nafion 117™-SnO2 Composite Membranes using an Ion-Exchange Method

    DEFF Research Database (Denmark)

    Nørgaard, Casper Frydendal; Nielsen, Ulla Gro; Skou, Eivind Morten

    2012-01-01

    ∙ 2 H2O used in the ion-exchange step, compositions ranging from 2 to 8 wt% SnO2 with SnO2 homogeneously distributed as nanoparticles were obtained. The prepared nanocomposite membranes were characterized by powder XRD, 119Sn MAS NMR spectroscopy, electrochemical impedance spectroscopy, water uptake......, tensile stress-strain measurements and thermogravimetric analysis. A SnO2 content around 4 wt% gave a significant increase in membrane stiffness without losses in conductivity....

  7. Solution strategies for finite elements and finite volumes methods applied to flow and heat transfer problem in U-shaped geothermal exchangers

    Science.gov (United States)

    Egidi, Nadaniela; Giacomini, Josephin; Maponi, Pierluigi

    2016-06-01

    Matter of this paper is the study of the flow and the corresponding heat transfer in a U-shaped heat exchanger. We propose a mathematical model that is formulated as a forced convection problem for incompressible and Newtonian fluids and results in the unsteady Navier-Stokes problem. In order to get a solution, we discretise the equations with both the Finite Elements Method and the Finite Volumes Method. These procedures give rise to a non-symmetric indefinite quadratic system of equations. Thus, three regularisation techniques are proposed to make approximations effective and ideas to compare their results are provided.

  8. Design method for heat exchanger of stirling cycle machines; Sutaringu saikuru kikan ni okeru netsu kokanki no sekkei shuho

    Energy Technology Data Exchange (ETDEWEB)

    Sekiya, H. [Sanyo Electric Co., Ltd., Tokyo (Japan)

    1999-11-10

    Recently, the Stirling cycle organization attracts the attention as 1 of the countermeasure to the global environmental problem, and the tendency of various application equipment developments heightens. The main factor is in constructing CFC elimination refrigeration air conditioner, and the development example as an engine for power source of refrigerating machine used in the ultra-low-temperature region and equipment variously is reported. In this paper, practical design tool and design examination case are introduced, while design technique of heat exchanger, which is the most important in design development of these, ST refrigerating machine and ST engines is described. (NEDO)

  9. Impact of river stage prediction methods on stream-aquifer exchanges in a hydro(geo)logical model at the regional scale

    Science.gov (United States)

    Saleh, F.; Flipo, N.; de Fouquet, C.

    2012-04-01

    The main objective of this study is to provide a realistic simulation of river stage in regional river networks in order to improve the quantification of stream-aquifer exchanges and better assess the associated aquifer responses that are often impacted by the magnitude and the frequency of the river stage fluctuations. The study focuses on the Oise basin (17 000 km2, part of the 65 000 km2 Seine basin in Northern France) where stream-aquifer exchanges cannot be assessed directly by experimental methods. Nowadays numerical methods are the most appropriate approaches for assessing stream-aquifer exchanges at this scale. A regional distributed process-based hydro(geo)logical model, Eau-Dyssée, is used, which aims at the integrated modeling of the hydrosystem to manage the various elements involved in the quantitative and qualitative aspects of water resources. Eau-Dyssée simulates pseudo 3D flow in aquifer systems solving the diffusivity equation with a finite difference numerical scheme. River flow is simulated with a Muskingum model. In addition to the in-stream discharge, a river stage estimate is needed to calculate the water exchange at the stream-aquifer interface using the Darcy law. Three methods for assessing in-stream river stages are explored to determine the most appropriate representation at regional scale over 25 years (1980-2005). The first method consists in defining rating curves for each cell of a 1D Saint-Venant hydraulic model. The second method consists in interpolating observed rating curves (at gauging stations) onto the river cells of the hydro(geo)logical model. The interpolation technique is based on geostatistics. The last method assesses river stage using Manning equation with a simplified rectangular cross-section (water depth equals the hydraulic radius). Compared to observations, the geostatistical and the Manning methodologies lead to slightly less accurate (but still acceptable) results offering a low computational cost opportunity

  10. Thermal Response Testing Results of Different Types of Borehole Heat Exchangers: An Analysis and Comparison of Interpretation Methods

    Directory of Open Access Journals (Sweden)

    Angelo Zarrella

    2017-06-01

    Full Text Available The design phase of ground source heat pump systems is an extremely important one as many of the decisions made at that time can affect the system’s energy performance as well as installation and operating costs. The current study examined the interpretation of thermal response testing measurements used to evaluate the equivalent ground thermal conductivity and thus to design the system. All the measurements were taken at the same geological site located in Molinella, Bologna (Italy where a variety of borehole heat exchangers (BHEs had been installed and investigated within the project Cheap-GSHPs (Cheap and efficient application of reliable Ground Source Heat exchangers and Pumps of the European Union’s Horizon 2020 research and innovation program. The measurements were initially analyzed in accordance with the common interpretation based on the first-order approximation of the solution for the infinite line source model and then by utilizing the complete solutions of both the infinite line and cylinder source models. An inverse numerical approach based on a detailed model that considers the current geometry of the BHE and the axial heat transfer as well as the effect of weather on the ground surface was also used. Study findings revealed that the best result was generally obtained using the inverse numerical interpretation.

  11. Capture and isotopic exchange method for water and hydrogen isotopes on zeolite catalysts up to technical scale for pre-study of processing highly tritiated water

    Energy Technology Data Exchange (ETDEWEB)

    Michling, R.; Braun, A.; Cristescu, I.; Dittrich, H.; Gramlich, N.; Lohr, N. [Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Glugla, M.; Shu, W.; Willms, S. [ITER Organization, Saint-Paul-lez-Durance (France)

    2015-03-15

    Highly tritiated water (HTW) may be generated at ITER by various processes and, due to the excessive radio toxicity, the self-radiolysis and the exceedingly corrosive property of HTW, a potential hazard is associated with its storage and process. Therefore, the capture and exchange method for HTW utilizing Molecular Sieve Beds (MSB) was investigated in view of adsorption capacity, isotopic exchange performance and process parameters. For the MSB, different types of zeolite were selected. All zeolite materials were additionally coated with platinum. The following work comprised the selection of the most efficient zeolite candidate based on detailed parametric studies during the H{sub 2}/D{sub 2}O laboratory scale exchange experiments (about 25 g zeolite per bed) at the Tritium Laboratory Karlsruhe (TLK). For the zeolite, characterization analytical techniques such as Infrared Spectroscopy, Thermogravimetry and online mass spectrometry were implemented. Followed by further investigation of the selected zeolite catalyst under full technical operation, a MSB (about 22 kg zeolite) was processed with hydrogen flow rates up to 60 mol*h{sup -1} and deuterated water loads up to 1.6 kg in view of later ITER processing of arising HTW. (authors)

  12. CAPITAL ASSET PRICING MODEL METHOD USED IN MEASURING AND ANALYZING COMPANIES LISTED IN PEFINDO25 AT INDONESIA STOCK EXCHANGE PERIOD 2015

    Directory of Open Access Journals (Sweden)

    Francis M HUTABARAT

    2016-08-01

    Full Text Available The industry in Indonesia is an interesting business to capitalize. In Indonesia many companies were established since it is profitable. The capital market serves as an economic pillar in most countries. Indonesia is a rich country, rich in many ways especially in natural resources. However, the industry has its ups and downs in the stock market. It is interesting to see the performance of the companies listed in the Indonesia Stock Exchange.  This study aimed to measure and analyze companies listed in Pefindo25 at Indonesian Stock Exchange using Capital Asset Pricing Model. The sample used is 25 companies listed at Pefindo25 index. Based on the results of the study, it can conclude that after analyzing the companies listed in the Indonesian Stock Exchange using Capital Asset Pricing Model that based on Beta analysis, the companies have the type of stocks that are aggressive and defensive. With positive and negative return. The company with aggressive beta shows that the company tend to face higher risk, as JPFA find itself with positif return 15.47% expected return. And companies with defensive type of stocks tend to have positive return such as: FISH, STTP, AISA, APLN, and others since they are not sensitive to market changes. It is recommended for further research to look on this CAPM method in analyzing the stock investment.

  13. Development of a new analysis method evaluating adsorption energies for the respective ion-exchanged sites on alkali-metal ion-exchanged ZSM-5 utilizing CO as a probe molecule: IR-spectroscopic and calorimetric studies combined with a DFT method.

    Science.gov (United States)

    Kumashiro, Ryotaro; Fujie, Kazuhiko; Kondo, Aki; Mori, Toshinori; Nagao, Mahiko; Kobayashi, Hisayoshi; Kuroda, Yasushige

    2009-07-07

    For alkali-metal ion-exchanged ZSM-5 zeolites (MZSM-5; M: Li, Na, K, Rb, Cs) the analysis of ion-exchangeable sites was performed by means of a combined method based on IR spectroscopic and calorimetric measurements using CO as the probe molecule. The heat of adsorption of CO was found to be correlated with an IR frequency of stretching vibration of C-O in the adsorbed species. It was revealed that there exists at least two types of sites capable of ion-exchanging; for the lithium ion-exchanged ZSM-5 (LiZSM-5) CO adsorption on each type of site is evaluated to give a set of IR bands and heats of adsorption, 2195 cm(-1) and 49 kJ mol(-1), 2185 cm(-1) and 39 kJ mol(-1) with the aid of the newly developed method utilizing the data obtained from a combined microcalorimetric and IR-spectroscopic study. Such types of data were also obtained for Na- and K-ion-exchanged ZSM-5 samples. Furthermore, a linear relationship between the differential heat of adsorption (q(diff)) evaluated and the shift of wavenumber of the C-O stretching vibration from that of a gaseous CO molecule (Deltanu) was established for the systems of MZSM-5-CO, and the bonding nature of the CO molecule with each site can be explained in terms of the electrostatic force. The model of each adsorption site was also examined by the quantum calculation method (density functional theory: DFT). The trends obtained from the experimental data may be substantially supported by the calculation method even adopting a model as simple as the ZSM-5-type zeolite: the composition of MAlSi(4)O(4)H(12).

  14. 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.

  15. Non-noble metal based electro-catalyst compositions for proton exchange membrane based water electrolysis and methods of making

    Energy Technology Data Exchange (ETDEWEB)

    Kumta, Prashant N.; Kadakia, Karan Sandeep; Datta, Moni Kanchan; Velikokhatnyi, Oleg

    2017-02-07

    The invention provides electro-catalyst compositions for an anode electrode of a proton exchange membrane-based water electrolysis system. The compositions include a noble metal component selected from the group consisting of iridium oxide, ruthenium oxide, rhenium oxide and mixtures thereof, and a non-noble metal component selected from the group consisting of tantalum oxide, tin oxide, niobium oxide, titanium oxide, tungsten oxide, molybdenum oxide, yttrium oxide, scandium oxide, cooper oxide, zirconium oxide, nickel oxide and mixtures thereof. Further, the non-noble metal component can include a dopant. The dopant can be at least one element selected from Groups III, V, VI and VII of the Periodic Table. The compositions can be prepared using a surfactant approach or a sol gel approach. Further, the compositions are prepared using noble metal and non-noble metal precursors. Furthermore, a thin film containing the compositions can be deposited onto a substrate to form the anode electrode.

  16. Cliché fabrication method using precise roll printing process with 5 um pattern width

    Science.gov (United States)

    Shin, Yejin; Kim, Inyoung; Oh, Dong-Ho; Lee, Taik-Min

    2016-09-01

    Among the printing processes for printed electronic devices, gravure offset and reverse offset method have drawn attention for its fine pattern printing possibility. These printing methods use cliché, which has critical effect on the final product precision and quality. In this research, a novel precise cliché replica method is proposed. It consists of copper sputtering, precise mask pattern printing with 5 um width using reverse offset printing, Ni electroplating, lift-off, etching, and DLC coating. We finally compare the fabricated replica cliché with the original one and print out precise patterns using the replica cliché.

  17. 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.

  18. 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.

  19. An enzymatic method for the determination of fructans in foods and food products - Comparison of the results by high performance anion exchange chromatography with pulsed amperemetric detection

    DEFF Research Database (Denmark)

    Andersen, Rikke; Sørensen, A.

    1999-01-01

    effects than the fructanase reported as normally used. The method is tested on ten standard substances and five fructan products, and nine foods and food products are also analysed. The enzymatic measurement of the released sugars is confirmed by measurements done by high performance anion exchange......We report a new and non-equipment demanding method of measuring the content of fructans as well as the contents of free glucose, free fructose and sucrose in foods and food products enzymatically. This method comprises hydrolysis of fructans into D-glucose and D-fructose enzymatically...... and measurement of the released sugars enzymatically. Sucrose is hydrolysed by alpha-glucosidase instead of beta-fructosidase, which is normally used. In addition, sucrose is measured in the form of D-fructose instead of the typical D-glucose form, and the fructanase used to hydrolyse the fructans has fewer side...

  20. Nanoscale study of reactive transport in catalyst layer of proton exchange membrane fuel cells with precious and non-precious catalysts using lattice Boltzmann method

    CERN Document Server

    Chen, Li; Kang, Qinjun; Holby, Edward F; Tao, Wen-Quan

    2014-01-01

    High-resolution porous structures of catalyst layer (CL) with multicomponent in proton exchange membrane fuel cells are reconstructed using a reconstruction method called quartet structure generation set. Characterization analyses of nanoscale structures are implemented including pore size distribution, specific area and phase connectivity. Pore-scale simulation methods based on the lattice Boltzmann method are developed and used to predict the macroscopic transport properties including effective diffusivity and proton conductivity. Nonuniform distributions of ionomer in CL generates more tortuous pathway for reactant transport and greatly reduces the effective diffusivity. Tortuosity of CL is much higher than conventional Bruggeman equation adopted. Knudsen diffusion plays a significant role in oxygen diffusion and significantly reduces the effective diffusivity. Reactive transport inside the CL is also investigated. Although the reactive surface area of non-precious metal catalyst (NPMC) CL is much higher t...

  1. 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 ...

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Application of a GC-ECD for measurements of biosphere–atmosphere exchange fluxes of peroxyacetyl nitrate using the relaxed eddy accumulation and gradient method

    Directory of Open Access Journals (Sweden)

    A. Moravek

    2014-02-01

    Full Text Available Peroxyacetyl nitrate (PAN may constitute a significant fraction of reactive nitrogen in the atmosphere. Current knowledge about the biosphere–atmosphere exchange of PAN is limited and only few studies have investigated the deposition of PAN to terrestrial ecosystems. We developed a flux measurement system for the determination of biosphere–atmosphere exchange fluxes of PAN using both the hyperbolic relaxed eddy accumulation (HREA method and the modified Bowen ratio (MBR method. The system consists of a modified, commercially available gas chromatograph with electron capture detection (GC-ECD, Meteorologie Consult GmbH, Germany. Sampling was performed by trapping PAN onto two pre-concentration columns; during HREA operation one was used for updraft and one for downdraft events and during MBR operation the two columns allowed simultaneous sampling at two measurement heights. The performance of the PAN flux measurement system was tested at a natural grassland site, using fast response ozone (O3 measurements as a proxy for both methods. The measured PAN fluxes were comparatively small (daytime PAN deposition was on average −0.07 nmol m−2 s−1 and, thus, prone to significant uncertainties. A major challenge in the design of the system was the resolution of the small PAN mixing ratio differences. Consequently, the study focuses on the performance of the analytical unit and a detailed analysis of errors contributing to the overall uncertainty. The error of the PAN mixing ratio differences ranged from 4 to 15 ppt during the MBR and between 18 and 26 ppt during the HREA operation, while during daytime measured PAN mixing ratios were of similar magnitude. Choosing optimal settings for both the MBR and HREA method, the study shows that the HREA method did not have a significant advantage towards the MBR method under well mixed conditions as it was expected.

  10. 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.

  11. 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.

  12. 人民币均衡汇率估计:粘性价格目标区模型方法%Estimating Equilibrium Exchange Rate of Renminbi-A Method of Target Scope of Sticky Price Model

    Institute of Scientific and Technical Information of China (English)

    窦祥胜; 杨炘

    2004-01-01

    The managedfloating exchange rate system is one of special manifestations of target zone system,and actually it is a quasi-target zone system. Hence RMB equilibrium exchange rate may be estimated by use of the method of exchange rate target zone model. At present, the sticky-price model is one of best models, and it is a extension of flex-price model. The model is based on assumptions of price inertia and output decided by demand. Under those assumptions and the condition of the commodity and the currency market equilibrium, a stochastic differential equation may be established, and in the light of theequation,we may get a exchange rate function. Our research indicates a good outcome may be made,applying the sticky-price model to estimate RMB equilibrium exchange rate.

  13. Improving a free air breathing proton exchange membrane fuel cell through the Maximum Efficiency Point Tracking method

    Science.gov (United States)

    Higuita Cano, Mauricio; Mousli, Mohamed Islam Aniss; Kelouwani, Sousso; Agbossou, Kodjo; Hammoudi, Mhamed; Dubé, Yves

    2017-03-01

    This work investigates the design and validation of a fuel cell management system (FCMS) which can perform when the fuel cell is at water freezing temperature. This FCMS is based on a new tracking technique with intelligent prediction, which combined the Maximum Efficiency Point Tracking with variable perturbation-current step and the fuzzy logic technique (MEPT-FL). Unlike conventional fuel cell control systems, our proposed FCMS considers the cold-weather conditions, the reduction of fuel cell set-point oscillations. In addition, the FCMS is built to respond quickly and effectively to the variations of electric load. A temperature controller stage is designed in conjunction with the MEPT-FL in order to operate the FC at low-temperature values whilst tracking at the same time the maximum efficiency point. The simulation results have as well experimental validation suggest that propose approach is effective and can achieve an average efficiency improvement up to 8%. The MEPT-FL is validated using a Proton Exchange Membrane Fuel Cell (PEMFC) of 500 W.

  14. Role of Corporate Governance Application in Practice of Creative Accounting Methods-Applied Study on Listed Companies in Khartoum Exchange

    Directory of Open Access Journals (Sweden)

    Sayed A. Bala

    2013-12-01

    Full Text Available The purpose of the research is the definition of Corporate Governance and its principles, importance, objectives, and knowledge of its role in reducing the practice of Creative Accounting, as well as its role in raising the efficiency of companies’ performance and Quality of Accounting Information. In this regard, the researcher used a descriptive analytical approach and looked into the theoretical and field relevant studies of Arabs and foreigners with the induction and presentation of the most important results, and the development of what supports the development of Corporate Governance and it is use in raising the efficiency of companies’ performance, and reducing the practice of Creative Accounting, with a field Study on Listed Companies in Khartoum Stock Exchange. The research came up with several conclusions, such as the influential role of Corporate Governance in raising the efficiency of its financial and administrative performance. Besides, Corporate Governance has an effective role in determining the Quality of Accounting Information and reducing the practice of Creative Accounting.

  15. Analytical Method for Sugar Profile in Pet Food and Animal Feeds by High-Performance Anion-Exchange Chromatography with Pulsed Amperometric Detection.

    Science.gov (United States)

    Ellingson, David J; Anderson, Phillip; Berg, Daniel P

    2016-01-01

    There is a need for a standardized, accurate, rugged, and consistent method to measure for sugars in pet foods and animal feeds. Many traditional standard sugar methods exist for other matrixes, but when applied in collaborative studies there was poor agreement and sources of error identified with those standard methods. The advancement in technology over the years has given us the ability to improve on these standard methods of analysis. A method is described here that addresses these common issues and was subjected to a single-laboratory validation to assess performance on a wide variety of pet foods and animal feeds. Of key importance to the method performance is the sample preparation before extraction, type of extraction solvent, postextraction cleanup, and, finally, optimized chromatography using high-performance anion exchange chromatography with pulsed amperometric detection. The results obtained from the validation demonstrate how typical issues seen with these matrixes can influence performance of sugar analysis. The results also demonstrate that this method is fit-for-purpose and can meet the challenges of sugar analysis in pet food and animal feeds to lay the foundation for a standardized method of analysis.

  16. Drug delivery system for an anticancer agent, chlorogenate-Zn/Al-layered double hydroxide nanohybrid synthesised using direct co-precipitation and ion exchange methods

    Energy Technology Data Exchange (ETDEWEB)

    Barahuie, Farahnaz [Materials Synthesis and Characterization Laboratory, Institute of Advanced Technology (ITMA), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Hussein, Mohd Zobir, E-mail: mzobir@putra.upm.edu.my [Materials Synthesis and Characterization Laboratory, Institute of Advanced Technology (ITMA), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Arulselvan, Palanisamy [Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Fakurazi, Sharida [Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Zainal, Zulkarnain [Materials Synthesis and Characterization Laboratory, Institute of Advanced Technology (ITMA), Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia)

    2014-09-15

    A nano-structured drug-inorganic clay hybrid involving an active anticancer compound, which is chlorogenic acid (CA) intercalated into Zn/Al-layered double hydroxide, has been assembled via ion-exchange and co-precipitation methods to form a nanohybrid CZAE (a chlorogenic acid-Zn/Al nanohybrid synthesised using an ion-exchange method) and CZAC (a chlorogenic acid-Zn/Al nanohybrid synthesised using a direct method), respectively. The X-ray diffraction (XRD) results confirmed that the CA-LDH had a hybrid structure in which the anionic chlorogenate is arranged between the interlayers as a horizontal monolayer at 90 and 20° angles from the x axis for CZAE and CZAC, respectively. Both nanohybrids have the properties of mesoporous materials. The high loading percentage of chlorogenic acid (approximately 43.2% for CZAE and 45.3% for CZAC) with basal spacings of 11.7 and 12.6 Å for CZAE and CZAC, respectively, corroborates the successful intercalation of chlorogenic acid into the interlayer gallery of layered double hydroxides. Free chlorogenic acid and the synthesised nanocomposites (CZAE, CZAC) were assessed for their cytotoxicity against various cancer cells. The Fourier transform infrared data supported the formation of both nanohybrids, and a thermal analysis showed that the nanohybrids are more thermally stable than their counterparts. The chlorogenate shows a sustained release, and the release rate of chlorogenate from CZAE and CZAC nanohybrids at pH 7.4 is remarkably lower than that at pH 4.8 due to their different release mechanisms. The release rate of chlorogenate from both nanohybrids can be described as pseudo-second order. The present investigation revealed the potential of the nanohybrids to enhance the in vitro anti-tumour effect of chlorogenic acid in liver and lung cancer cells in vitro. - Highlights: • We intercalated chlorogenic into Zn/Al-layered double hydroxide by ion-exchange and coprecipitation methods. • The two methods gave nanocomposites

  17. An experimental study on the thermal and fouling characteristics in a washable shell and helically coiled heat exchanger by the Wilson plot method

    Energy Technology Data Exchange (ETDEWEB)

    Koo, Kyoung Min; Ahn, Young Chull [Pusan National University, Busan (Korea, Republic of); Hwang, Jun Hyeon; Hur, Hyun; Na, Byung Chul; Hwang, Yoon Jae; Kim, Byung Soon [LG Electronics, Changwon (Korea, Republic of); Lee, Jae Keun [EcoEnergy Research Institute, Busan (Korea, Republic of)

    2016-06-15

    Brazed plate heat exchangers (BPHEX) are broadly used in water source heat pump systems for their large heat transfer capacity. Despite their high heat transfer rate, their high-performance rate tends to decrease sharply, due to fouling and they cannot be cleaned. So the thermal and fouling resistances of washable Shell and helically coiled tube heat exchangers (SCHEX) are designed and experimentally investigated in this study. Heat exchangers with two different tube types are studied and compared with a brazed plate heat exchanger. The overall thermal resistance coefficient of the heat exchangers as determined by using Wilson plots is 38% lower than that of the brazed plate heat exchanger at a Reynolds number of 2460. Fouling test results revealed that regular maintenance and physical cleaning can be used to maintain the thermal resistance of fouling of the washable heat exchanger at a level equal to or less than that of the brazed plate heat exchanger.

  18. 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

  19. 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

  20. Comparative study of selected parallel tempering methods

    Science.gov (United States)

    Malakis, A.; Papakonstantinou, T.

    2013-07-01

    We review several parallel tempering schemes and examine their main ingredients for accuracy and efficiency. The present study covers two selection methods of temperatures and several choices for the exchange of replicas, including a recent novel all-pair exchange method. We compare the resulting schemes and measure specific heat errors and efficiency using the two-dimensional (2D) Ising model. Our tests suggest that an earlier proposal for using numbers of local moves related to the canonical correlation times is one of the key ingredients for increasing efficiency, and protocols using cluster algorithms are found to be very effective. Some of the protocols are also tested for efficiency and ground state production in 3D spin-glass models where we find that a simple nearest-neighbor approach using a local n-fold-way algorithm is the most effective. Finally, we present evidence that the asymptotic limits of the ground state energy for the isotropic case and for an anisotropic case of the 3D spin-glass model are very close and may even coincide.

  1. Application of the Vertex Exchange Method to estimate a semi-parametric mixture model for the MIC density of Escherichia coli isolates tested for susceptibility against ampicillin.

    Science.gov (United States)

    Jaspers, Stijn; Verbeke, Geert; Böhning, Dankmar; Aerts, Marc

    2016-01-01

    In the last decades, considerable attention has been paid to the collection of antimicrobial resistance data, with the aim of monitoring non-wild-type isolates. This monitoring is performed based on minimum inhibition concentration (MIC) values, which are collected through dilution experiments. We present a semi-parametric mixture model to estimate the entire MIC density on the continuous scale. The parametric first component is extended with a non-parametric second component and a new back-fitting algorithm, based on the Vertex Exchange Method, is proposed. Our data example shows how to estimate the MIC density for Escherichia coli tested for ampicillin and how to use this estimate for model-based classification. A simulation study was performed, showing the promising behavior of the new method, both in terms of density estimation as well as classification.

  2. 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

    BACKGROUND: Previous studies have demonstrated that the combination of olfactory ensheathing cells (OECs) and neurotrophic factor-3 (NT-3) in the rat lateral ventricle can promote nerve axonal regeneration and myelin sheath repair. However, this effect remains very short-lived.OBJECTIVE: To transfect NT-3 into OECs and to observe the biological activity of OEC-expressing NT-3.DESIGN, TIME AND SETI'ING: This genetic engineering, in vitro experiment was performed in the Provincial Hospital Affiliated to Shandong University between January 2007 and October 2008.MATERIALS: Trizol Reagent kit was purchased from Gibco, USA; reverse transcription kit, NT-3Emax lmmunoAssay System reagent was purchased from Promega, USA.METHODS: Neonatal Wistar rat OECs were established as primary cultures and were transfected with pN2A-NT-3 viral vector. The OECs with the highest virus titer and stable cellular growth served as the transfection group; OECs transfected with NT-3-free retrovirus carrier pN2A served as theempty vector group; un-transfected OECs served as the control group. After adherence, the logarithmically cultured PC12-TrkC cells were plated in OECs supernatant from the transfectJon and empty vector groups, as well as 20 μL PBS, and cultured for 4 days.MAIN OUTCOME MEASURES: NT-3 mRNA expression in OECs, fluorescence of NT-3-positivecells in the transfection group and control group; influence of OECs secreting NT-3 on the differentiation ratio of PC12-TrkC cells.RESULTS: NT-3 mRNA expression was observed 24 hours after transfeotion and lasted for 28 days,which was greater than the control and empty vector groups (P<0.01). A large number ofNT-3-positive cells were observed in the transfection group, and immunofluorescence was greaterthan the control and empty vector groups. PC12-TrkC cells co-cultured with OECs from thetransfection group exhibited a thick and long cell process, increased cell density, and thedifferentiation ratio was increased (P < 0.01).CONCLUSION

  3. 'Living' controlled in situ gelling systems: thiol-disulfide exchange method toward tailor-made biodegradable hydrogels.

    Science.gov (United States)

    Wu, De-Cheng; Loh, Xian Jun; Wu, Yun-Long; Lay, Chee Leng; Liu, Ye

    2010-11-03

    A 'living' controlled hydrogel formation method was first reported to create loose and compact in situ biodegradable hydrogels. The method executed under mild reaction conditions can conveniently tailor the hydrogel properties, and it has the potential to develop into a powerful tool for the design, synthesis, and self-assembly of novel tailor-made biomaterials and drug delivery systems.

  4. 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

  5. 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.

  6. 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

  7. Influence of the crucible geometry on the shape of the melt crystal interface during growth of sapphire crystal using a heat exchanger method

    Science.gov (United States)

    Chen, Jyh-Chen; Lu, Chung-Wei

    2004-05-01

    Computer simulations using the commercial code FIDAP, which is based on finite element techniques, were performed to investigate the effect of the shape of the crucible on the temperature distribution, velocity distribution and shape of the melt-crystal interface, during the application of the heat exchanger method (HEM) of growing sapphire crystals. Heat transfer from the furnace to the crucible and heat extraction from the heat exchanger can be modeled by the convection boundary conditions. Cylindrical crucibles with differently curved corners at their base are considered. The curved base of the crucible decreases the convexity of the melt-crystal interface and suppresses the appearance of "hot spots". A hemispherically shaped crucible base yields the lowest maximum convexity. The variation in convexity of the melt-crystal interface is less abrupt for a cylindrical crucible with curved corners at the base than one without curved corners. The effects of the thickness and the conductivity of the crucible are also addressed. The convexity of the melt-crystal interface decreases as the thickness of the crucible wall increases. The convexity also declines as the conductivity of the crucible increases.

  8. 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.

  9. 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.

  10. The hybrid experimental simplex algorithm--an alternative method for 'sweet spot' identification in early bioprocess development: case studies in ion exchange chromatography.

    Science.gov (United States)

    Konstantinidis, Spyridon; Chhatre, Sunil; Velayudhan, Ajoy; Heldin, Eva; Titchener-Hooker, Nigel

    2012-09-19

    The capacity to locate efficiently a subset of experimental conditions necessary for the identification of an operating envelope is a key objective in many studies. We have shown previously how this can be performed by using the simplex algorithm and this paper now extends the approach by augmenting the established simplex method to form a novel hybrid experimental simplex algorithm (HESA) for identifying 'sweet spots' during scouting development studies. The paper describes the new algorithm and illustrates its use in two bioprocessing case studies conducted in a 96-well filter plate format. The first investigates the effect of pH and salt concentration on the binding of green fluorescent protein, isolated from Escherichia coli homogenate, to a weak anion exchange resin and the second examines the impact of salt concentration, pH and initial feed concentration upon the binding capacities of a FAb', isolated from E. coli lysate, to a strong cation exchange resin. Compared with the established algorithm, HESA was better at delivering valuable information regarding the size, shape and location of operating 'sweet spots' that could then be further investigated and optimized with follow up studies. To test how favorably these features of HESA compared with conventional DoE (design of experiments) methods, HESA results were also compared with approaches including response surface modeling experimental designs. The results show that HESA can return 'sweet spots' that are equivalently or better defined than those obtained from DoE approaches. At the same time the deployment of HESA to identify bioprocess-relevant operating boundaries was accompanied by comparable experimental costs to those of DoE methods. HESA is therefore a viable and valuable alternative route for identifying 'sweet spots' during scouting studies in bioprocess development.

  11. Drug delivery system for an anticancer agent, chlorogenate-Zn/Al-layered double hydroxide nanohybrid synthesised using direct co-precipitation and ion exchange methods

    Science.gov (United States)

    Barahuie, Farahnaz; Hussein, Mohd Zobir; Arulselvan, Palanisamy; Fakurazi, Sharida; Zainal, Zulkarnain

    2014-09-01

    A nano-structured drug-inorganic clay hybrid involving an active anticancer compound, which is chlorogenic acid (CA) intercalated into Zn/Al-layered double hydroxide, has been assembled via ion-exchange and co-precipitation methods to form a nanohybrid CZAE (a chlorogenic acid-Zn/Al nanohybrid synthesised using an ion-exchange method) and CZAC (a chlorogenic acid-Zn/Al nanohybrid synthesised using a direct method), respectively. The X-ray diffraction (XRD) results confirmed that the CA-LDH had a hybrid structure in which the anionic chlorogenate is arranged between the interlayers as a horizontal monolayer at 90 and 20° angles from the x axis for CZAE and CZAC, respectively. Both nanohybrids have the properties of mesoporous materials. The high loading percentage of chlorogenic acid (approximately 43.2% for CZAE and 45.3% for CZAC) with basal spacings of 11.7 and 12.6 Å for CZAE and CZAC, respectively, corroborates the successful intercalation of chlorogenic acid into the interlayer gallery of layered double hydroxides. Free chlorogenic acid and the synthesised nanocomposites (CZAE, CZAC) were assessed for their cytotoxicity against various cancer cells. The Fourier transform infrared data supported the formation of both nanohybrids, and a thermal analysis showed that the nanohybrids are more thermally stable than their counterparts. The chlorogenate shows a sustained release, and the release rate of chlorogenate from CZAE and CZAC nanohybrids at pH 7.4 is remarkably lower than that at pH 4.8 due to their different release mechanisms. The release rate of chlorogenate from both nanohybrids can be described as pseudo-second order. The present investigation revealed the potential of the nanohybrids to enhance the in vitro anti-tumour effect of chlorogenic acid in liver and lung cancer cells in vitro.

  12. Developing bulk exchange spring magnets

    Energy Technology Data Exchange (ETDEWEB)

    Mccall, Scott K.; Kuntz, Joshua D.

    2017-06-27

    A method of making a bulk exchange spring magnet by providing a magnetically soft material, providing a hard magnetic material, and producing a composite of said magnetically soft material and said hard magnetic material to make the bulk exchange spring magnet. The step of producing a composite of magnetically soft material and hard magnetic material is accomplished by electrophoretic deposition of the magnetically soft material and the hard magnetic material to make the bulk exchange spring magnet.

  13. Long repetition time experiments for measurement of concentrations in systems with chemical exchange and undergoing temporal variation-comparison of methods with and without correction for saturation

    Science.gov (United States)

    Galbán, Craig J.; Spencer, Richard G. S.

    2003-02-01

    The purpose of this paper is to compare two methods for quantifying metabolite concentrations using the one-pulse experiment for a sample undergoing chemical exchange and subject to an intervention or other temporal variation. The methods, LATR-C (Long Acquisition TR (interpulse delay); Corrected for partial saturation) and LATR-NC (Long Acquisition TR; Not Corrected), are compared in terms of signal-to-noise ratio, SNR, per unit time and quantitation errors. Parameters relevant to the isolated perfused rat heart are used as a specific application, although the results are general. We assume throughout that spin-lattice relaxation times, T1, do not change. For a given flip angle, θ, TR's are calculated which result in maximal SNR per unit time under 10%, 5%, and 1% constraints on quantitation errors. Additional simulations were performed to demonstrate explicitly the dependence of the quantitation errors on TR for a fixed θ. We find (i) if the allowed error is large, and when both metabolite concentrations and rate constants vary, LATR-C permits use of shorter TR, and hence yields greater SNR per unit time, than LATR-NC; (ii) for small allowed error, the two methods give similar TR's and SNR per unit time, so that the simpler LATR-NC experiment may be preferred; (iii) large values of θ result in similar constrained TR's and hence SNR per unit time for the two methods; (iv) the ratio of concentrations of metabolites with similar T1 exhibit similar errors for the two methods.

  14. Removal of infused water predominantly during insertion (water exchange) is consistently associated with an increase in adenoma detection rate - review of data in randomized controlled trials (RCTs) of water-related methods.

    Science.gov (United States)

    Leung, Fw; Harker, Jo; Leung, Jw; Siao-Salera, Rm; Mann, Sk; Ramirez, Fc; Friedland, S; Amato, A; Radaelli, F; Paggi, S; Terruzzi, V; Hsieh, Yh

    2011-07-01

    INTRODUCTION: Variation in outcomes in RcTs comparing water-related methods and air insufflation raises challenging questions regarding the new approach. This report reviews impact of water exchange - simultaneous infusion and removal of infused water during insertion on adenoma detection rate (ADR) defined as proportion of patients with a least one adenoma of any size. METHODS: Medline (2008-2011) searches, abstract of 2011 Digestive Disease Week (DDW) meeting and personal communications were considered to identify RcTs that compared water-related methods and air insufflation to aid insertion of colonoscope. RESULTS: Since 2008, eleven reports of RcTs (6 published, 1 submitted and 4 abstracts, n=1728) described ADR in patients randomized to be examined by air and water-related methods. The water-related methods differed in timing of removal of the infused water -predominantly during insertion (water exchange) (n=825) or predominantly during withdrawal (water immersion) (n=903). Water immersion was associated with both increases and decreases in ADR compared to respective air method patients and the net overall change (-7%) was significant. On the other hand water exchange was associated with increases in ADR consistently and the net changes (overall, 8%; proximal overall, 11%; and proximal Comparative data generated the hypothesis that significantly larger increases in overall and proximal colon ADRs were associated with water exchange than water immersion or air insufflation during insertion. The hypothesis should be evaluated by RCTs to elucidate the mechanism of water exchange on adenoma detection.

  15. A Novel Ion-exchange Method for the Synthesis of Nano-SnO/micro-C Hybrid Structure as High Capacity Anode Material in Lithium Ion Batteries

    Institute of Scientific and Technical Information of China (English)

    Zhi Tan; Zhenhua Sun; Qi Guo; Haihua Wang; Dangsheng Su

    2013-01-01

    A novel and simple ion-exchange method was developed for the synthesis of nano-SnO/micro-C hybrid structure.The structure of the as prepared nano-SnO/micro-C was directly revealed by scanning electron microscopy (SEM)and transmission electron microscopy (TEM).SnO particles with the size about 25 nm were well confined in amorphous carbon microparticles.Carbon matrix in micrometer scale not only acts as a protective buffer for the SnO nanoparticles during the battery cycling processes,but also avoids the shortcomings of nanostructures,such as low tap density and potential safety threats.Electrochemical behaviors of the nano-SnO/micro-C were tested as anode material in lithium ion batteries.The initial reversible capacity is 508 mA h g-1,and the reversible capacity after 60 cycles is 511 mA h g-1,indicating good capacity retention ability.

  16. Synthesis of electrocatalysts by the Bönnemann method for the oxidation of methanol and the mixture H2/CO in a Proton Exchange Membrane Fuel Cell

    Directory of Open Access Journals (Sweden)

    Franco E. G.

    2002-01-01

    Full Text Available The synthesis of ternary electrocatalysts Pt/Ru/Mo type were performed according to the Bönnemann method and characterized by the following techniques: energy dispersive analysis (EDX, X-rays diffraction (XRD, cyclic voltammetry (CV and polarization curves (E vs. i for the oxidation of H2, H2/CO and methanol in a Proton Exchange Membrane Fuel Cell (PEMFC. Catalysts structure consists of highly dispersed nanocrystals in carbon support, with an average particle size of 2 nm. The results of cyclic voltammetry suggest an enhancement of the catalyst electroactivity with the addition of cocatalysts. Polarization curves indicate that Pt/Ru/Mo systems could be employed as electrode material for PEM fuel cell for technological application.

  17. Low-cost conversion of polycrystalline silicon into sheet by HEM and FAST. [Heat Exchanger Method and Fixed Abrasive Slicing Technique

    Science.gov (United States)

    Khattak, C. P.; Schmid, F.

    1980-01-01

    The conversion of polycrystalline silicon to sheet form (the wafers produced are 10 cm x 10 cm cross section with minimum surface damage) by the Heat Exchanger Method (HEM) and multi-wire Fixed Abrasive Slicing Technique (FAST), as a means of reducing the cost of solar arrays for adaptation of photovoltaic technology for terrestrial applications, is given. A schematic of a HEM furnace, which includes a silica crucible, and developments in the HEM process are presented. A new machine for slicing with wire was designed and fabricated. The high-speed slicer has been used to slice 19 wafers per cm from 10 cm diameter crystals. Both HEM and FAST are low-cost processes and they have the potential of giving one of the lowest add-on costs ($6.24 and $6.48 per square meter of sheet respectively, with the combination add-on cost of $14.87 per square meter) of this conversion.

  18. Low-cost conversion of polycrystalline silicon into sheet by HEM and FAST. [Heat Exchanger Method and Fixed Abrasive Slicing Technique

    Science.gov (United States)

    Khattak, C. P.; Schmid, F.

    1980-01-01

    The conversion of polycrystalline silicon to sheet form (the wafers produced are 10 cm x 10 cm cross section with minimum surface damage) by the Heat Exchanger Method (HEM) and multi-wire Fixed Abrasive Slicing Technique (FAST), as a means of reducing the cost of solar arrays for adaptation of photovoltaic technology for terrestrial applications, is given. A schematic of a HEM furnace, which includes a silica crucible, and developments in the HEM process are presented. A new machine for slicing with wire was designed and fabricated. The high-speed slicer has been used to slice 19 wafers per cm from 10 cm diameter crystals. Both HEM and FAST are low-cost processes and they have the potential of giving one of the lowest add-on costs ($6.24 and $6.48 per square meter of sheet respectively, with the combination add-on cost of $14.87 per square meter) of this conversion.

  19. Comparison of the clinical effects between catheter exchange methods in geriatric patients with tunneled cuffed hemodialysis catheters

    Institute of Scientific and Technical Information of China (English)

    周参新

    2012-01-01

    Objective To compare the infection-free and overall survival between first and subsequent tunneled cuffed hemodialysis catheters in geriatric patients. Methods The study involved 57 geriatric patients [32 male,25 female; mean age(72.4±6.7) years]undergoing maintenance hemodialysis in our blood

  20. 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

  1. Leaf Histology--Two Modern Methods.

    Science.gov (United States)

    Freeman, H. E.

    1984-01-01

    Two methods for examining leaf structure are presented; both methods involve use of "superglue." The first method uses the glue to form a thin, permanent, direct replica of a leaf surface on a microscope slide. The second method uses the glue to examine the three-dimensional structure of spongy mesophyll. (JN)

  2. 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.

  3. Selective and Accurate Determination Method of Propofol in Human Plasma by Mixed-Mode Cation Exchange Cartridge and GC-MS

    Directory of Open Access Journals (Sweden)

    Jae Sung Pyo

    2016-01-01

    Full Text Available A gas chromatography-mass spectrometry (GC-MS method for the determination of propofol in human plasma has been developed and validated. Propofol was extracted from human plasma by using mixed-mode cation exchange/reversed-phase (MCX cartridges. As propofol easily volatilizes during concentration, 100% methanol was injected directly into GC-MS to elute propofol. Despite avoiding concentration process of the eluted solution, lower limit of quantization (LLOQ of propofol was 25 ng/mL. The validated method exhibited good linearity (R2=0.9989 with accuracy and precision −5.8%~11.7% and 3.7%~11.6%, respectively. The other validation parameters, recovery and matrix effect, ranged from 96.6% to 99.4% and 95.3% to 101.4%, respectively. Propofol standard was quantified to evaluate possible loss due to the concentration processes, nitrogen gas and centrifugal vacuum. These two concentration processes resulted in notable decrease in the quantity of propofol, signifying avoiding any concentration processes during propofol quantification. Also, to confirm suitability of the developed method, authentic human plasma samples were analyzed. The selective assay method using MCX cartridge and GC-MS facilitated quantification of propofol in plasma sample accurately by preventing any losses due to the concentration processes.

  4. Magnetic exchange interactions and critical temperature of the nanolaminate M n2GaC from first-principles supercell methods

    Science.gov (United States)

    Thore, A.; Dahlqvist, M.; Alling, B.; Rosen, J.

    2016-02-01

    In this work, we employ and critically evaluate a first-principles approach based on supercell calculations for predicting the magnetic critical order-disorder temperature Tc. As a model material we use the recently discovered nanolaminate M n2GaC . First, we derive the exchange interaction parameters Ji j between pairs of Mn atoms on sites i and j of the bilinear Heisenberg Hamiltonian using the novel magnetic direct cluster averaging method (MDCA), and then compare the J's from the MDCA calculations to the same parameters calculated using the Connolly-Williams method. We show that the two methods yield closely matching results, but observe that the MDCA method is computationally less effective when applied to highly ordered phases such as M n2GaC . Secondly, Monte Carlo simulations are used to derive the magnetic energy, specific heat, and Tc. For M n2GaC , we find Tc=660 K . The uncertainty in the calculated Tc caused by possible uncertainties in the J's is discussed and exemplified in our case by an analysis of the impact of the statistical uncertainties of the MDCA-derived J's , resulting in a Tc distribution with a standard deviation of 133 K.

  5. Selective and Accurate Determination Method of Propofol in Human Plasma by Mixed-Mode Cation Exchange Cartridge and GC-MS.

    Science.gov (United States)

    Pyo, Jae Sung

    2016-01-01

    A gas chromatography-mass spectrometry (GC-MS) method for the determination of propofol in human plasma has been developed and validated. Propofol was extracted from human plasma by using mixed-mode cation exchange/reversed-phase (MCX) cartridges. As propofol easily volatilizes during concentration, 100% methanol was injected directly into GC-MS to elute propofol. Despite avoiding concentration process of the eluted solution, lower limit of quantization (LLOQ) of propofol was 25 ng/mL. The validated method exhibited good linearity (R (2) = 0.9989) with accuracy and precision -5.8%~11.7% and 3.7%~11.6%, respectively. The other validation parameters, recovery and matrix effect, ranged from 96.6% to 99.4% and 95.3% to 101.4%, respectively. Propofol standard was quantified to evaluate possible loss due to the concentration processes, nitrogen gas and centrifugal vacuum. These two concentration processes resulted in notable decrease in the quantity of propofol, signifying avoiding any concentration processes during propofol quantification. Also, to confirm suitability of the developed method, authentic human plasma samples were analyzed. The selective assay method using MCX cartridge and GC-MS facilitated quantification of propofol in plasma sample accurately by preventing any losses due to the concentration processes.

  6. Two solid-phase recycling method for basic ionic liquid [C4mim]Ac by macroporous resin and ion exchange resin from Schisandra chinensis fruits extract.

    Science.gov (United States)

    Ma, Chun-hui; Zu, Yuan-gang; Yang, Lei; Li, Jian

    2015-01-22

    In this study, two solid-phase recycling method for basic ionic liquid (IL) 1-butyl-3-methylimidazolium acetate ([C4mim]Ac) were studied through a digestion extraction system of extracting biphenyl cyclooctene lignans from Schisandra chinensis. The RP-HPLC detection method for [C4mim]Ac was established in order to investigate the recovery efficiency of IL. The recycling method of [C4mim]Ac is divided into two steps, the first step was the separation of lignans from the IL solution containing HPD 5000 macroporous resin, the recovery efficiency and purity of [C4mim]Ac achieved were 97.8% and 67.7%, respectively. This method cannot only separate the lignans from [C4mim]Ac solution, also improve the purity of lignans, the absorption rate of lignans in [C4mim]Ac solution was found to be higher (69.2%) than that in ethanol solution (57.7%). The second step was the purification of [C4mim]Ac by the SK1B strong acid ion exchange resin, an [C4mim]Ac recovery efficiency of 55.9% and the purity higher than 90% were achieved. Additionally, [C4mim]Ac as solvent extraction of lignans from S. chinensis was optimized, the hydrolysis temperature was 90°C and the hydrolysis time was 2h.

  7. Development of a new analytical method for the determination of sulfites in fresh meats and shrimps by ion-exchange chromatography with conductivity detection.

    Science.gov (United States)

    Iammarino, Marco; Di Taranto, Aurelia; Muscarella, Marilena; Nardiello, Donatella; Palermo, Carmen; Centonze, Diego

    2010-07-05

    An accurate and reliable analytical method, based on ion chromatography and suppressed conductivity detection, has been developed and validated for the quantitative determination of sulfites in fresh meats and shrimps. The chromatographic separation was accomplished by using an anion-exchange column eluted with sodium carbonate and sodium hydroxide. The optimized step-change elution, followed by column re-equilibration at the initial mobile phase composition, guaranteed a good resolution even toward endogenous interfering peaks, and an excellent retention time repeatability (1.1%, n=6). Good results in terms of sample extract stability, recovery efficiency were achieved with an extraction solvent mixture based on sodium hydroxide, fructose and EDTA. The method validation, performed by an in-house model according to Decision 657/2002/EC and Regulation 882/2004/EC, provided excellent results with respect to linearity (correlation coefficient up to 0.9998), limits of detection and quantification (2.7 and 8.2 mg kg(-1), respectively, expressed as SO(2)), expanded measurement uncertainty (below 10%), recovery values (ranging from 85% to 92%) and repeatability (down to 8%), demonstrating the conformity of the proposed method with the European directives. Finally, by major changes ruggedness studies, the method applicability to the quantitative analysis of cow hamburger, pork and horse sausage, and shrimps was demonstrated.

  8. Standardization of method for determining glycosylated hemoglobin (Hb A1c by cation exchange high performance liquid chromatography

    Directory of Open Access Journals (Sweden)

    Marina Venzon Antunes

    2009-12-01

    Full Text Available Hemoblobin A1c is the most important parameter for the monitoring of metabolic control of patients with diabetes mellitus. The purpose of this study was to adapt the Mono S method to a conventional HPLC system, allowing highly selective HbA1c determination without the acquisition of kits or the use of dedicated systems The results obtained were compared to the Tinaquant® immune turbidimetric method and the Bio-Rad Variant® chromatographic method. The developed method presented intra-study precision (C.V. % of 1.39-3.65 and inter-study precision (C.V. % of 2.80-3.02%. The determination coefficients among methods were: HPLC Mono S x Tinaquant®: r²: 0.9856 (n=60 and HPLC Mono S x HPLC Bio-Rad Variant®: r²: 0.9806 (n=16. A conversion equation between HPLC Mono S and Bio-Rad Variant® was calculated allowing yielding comparable and interchangeable values. The HPLC Mono-S is a precise, low-cost method which yields similar values to the Bio-Rad Variant® method on conventional HPLC equipment.A hemoglobina A1c é o parâmetro laboratorial mais importante no monitoramento do controle metabólico de pacientes portadores de diabetes melito. Dentre as metodologias existentes para a quantificação desta fração de hemoglobina, a cromatografia líquida de alta eficiência (CLAE baseada em troca catiônica apresenta a melhor precisão, sendo o método de escolha. O objetivo deste trabalho foi adaptar o método Mono S a um sistema de CLAE convencional permitindo a disponibilidade da determinação altamente seletiva de Hb A1c sem a aquisição de kits e comparar os resultados obtidos com o método imunoturbidimétrico Tinaquant® (Roche® e com o método de cromatografia líquida Bio-Rad Variant®. O método desenvolvido apresentou precisão intra-ensaio de 1,39-3,65% e inter-ensaio de 2,80-3,02%. Os coeficientes de determinação entre os métodos foram: CLAE Mono S x Tinaquant®: r² = 0,9856 (n=60 e CLAE Mono S x Bio-Rad Variant®: r² = 0,9806 (n=16

  9. Theoretical investigation of exchange bias

    Institute of Scientific and Technical Information of China (English)

    Xiong Zhi-Jie; Wang Huai-Yu; Ding Ze-Jun

    2007-01-01

    The exchange bias of bilayer magnetic films consisting of ferromagnetic (FM) and antiferromagnetic (AFM) layers in an uncompensated case is studied by use of the many-body Green's function method of quantum statistical theory.The effects of the layer thickness and temperature and the interfacial coupling strength on the exchange bias HE are investigated. The dependence of the exchange bias HE on the FM layer thickness and temperature is qualitatively in agreement with experimental results. When temperature varies, both the coercivity HC and HE decrease with the temperature increasing. For each FM thickness, there exists a least AFM thickness in which the exchange bias occurs,which is called pinning thickness.

  10. Quantifying groundwater exchange rates in a beach barrier lagoon using a radioisotopic tracer and geophysical methods: Younger Lagoon, Santa Cruz, CA

    Science.gov (United States)

    Richardson, C. M.; Swarzenski, P. W.; Johnson, C.

    2013-12-01

    Coastal lagoons are highly productive systems with a strong dependence on the physico-chemical regime of their surrounding environment. Groundwater interactions with the nearshore environment can drive ecosystem stability and productivity. Lagoons with restricted surface connectivity interact with coastal waters via subsurface flow paths that follow natural hydraulic gradients, producing a dynamic freshwater-saltwater mixing zone with submarine groundwater discharge (SGD) regions that are tidally influenced. Recent studies demonstrate the importance of SGD in maintaining nearshore ecology through a number of processes, including enhanced chemical loadings, focused biogeochemical transformations, and complex water mixing scenarios (Slomp and Van Cappellen, 2004 and Taniguchi et al., 2002). Groundwater discharge to the coastal ocean is often slow, diffuse and site-specific. Traditional methods used to evaluate SGD fluxes operate at varying scales and typically result in over or underestimates of SGD. Novel monitoring and evaluation methods are required in order to better understand how coastal aquifer systems influence multi-scalar water and nutrient budgets. Recently developed methods to determine fluid exchange rates include the use of select U- and Th-series radionuclides, multi-channel resistivity imaging, as well as the integration of temperature data and 1-D analytical modeling. Groundwater fluxes were examined in a coastal lagoon system to characterize the physics of subsurface fluid transport evidenced by visible seepage faces at low tide. Fluid exchange rates were quantified to determine the spatial and temporal variability of groundwater movement using thermal time series, water level data, and a coupled radiotracer-geophysical method. Our investigation of subsurface characteristics and groundwater fluxes using both traditional and newly-developed methods indicated that seasonal water inputs and tidal controls on water table elevation significantly

  11. Chemical exchange saturation transfer MR imaging of articular cartilage glycosaminoglycans at 3 T: Accuracy of B0 Field Inhomogeneity corrections with gradient echo method.

    Science.gov (United States)

    Wei, Wenbo; Jia, Guang; Flanigan, David; Zhou, Jinyuan; Knopp, Michael V

    2014-01-01

    Glycosaminoglycan Chemical Exchange Saturation Transfer (gagCEST) is an important molecular MRI methodology developed to assess changes in cartilage GAG concentrations. The correction for B0 field inhomogeneity is technically crucial in gagCEST imaging. This study evaluates the accuracy of the B0 estimation determined by the dual gradient echo method and the effect on gagCEST measurements. The results were compared with those from the commonly used z-spectrum method. Eleven knee patients and three healthy volunteers were scanned. Dual gradient echo B0 maps with different ∆TE values (1, 2, 4, 8, and 10 ms) were acquired. The asymmetry of the magnetization transfer ratio at 1 ppm offset referred to the bulk water frequency, MTRasym(1 ppm), was used to quantify cartilage GAG levels. The B0 shifts for all knee patients using the z-spectrum and dual gradient echo methods are strongly correlated for all ∆TE values used (r = 0.997 to 0.786, corresponding to ∆TE = 10 to 1 ms). The corrected MTRasym(1 ppm) values using the z-spectrum method (1.34% ± 0.74%) highly agree only with those using the dual gradient echo methods with ∆TE = 10 ms (1.72% ± 0.80%; r = 0.924) and 8 ms (1.50% ± 0.82%; r = 0.712). The dual gradient echo method with longer ∆TE values (more than 8 ms) has an excellent correlation with the z-spectrum method for gagCEST imaging at 3T.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Trust, confidentiality, and the acceptability of sharing HIV-related patient data: lessons learned from a mixed methods study about Health Information Exchanges

    Directory of Open Access Journals (Sweden)

    Maiorana Andre

    2012-04-01

    Full Text Available Abstract Background Concerns about the confidentiality of personal health information have been identified as a potential obstacle to implementation of Health Information Exchanges (HIEs. Considering the stigma and confidentiality issues historically associated with human immunodeficiency virus (HIV disease, we examine how trust—in technology, processes, and people—influenced the acceptability of data sharing among stakeholders prior to implementation of six HIEs intended to improve HIV care in parts of the United States. Our analyses identify the kinds of concerns expressed by stakeholders about electronic data sharing and focus on the factors that ultimately facilitated acceptability of the new exchanges. Methods We conducted 549 surveys with patients and 66 semi-structured interviews with providers and other stakeholders prior to implementation of the HIEs to assess concerns about confidentiality in the electronic sharing of patient data. The patient quantitative data were analyzed using SAS 9.2 to yield sample descriptive statistics. The analysis of the qualitative interviews with providers and other stakeholders followed an open-coding process, and convergent and divergent perspectives emerging from those data were examined within and across the HIEs. Results We found widespread acceptability for electronic sharing of HIV-related patient data through HIEs. This acceptability appeared to be driven by growing comfort with information technologies, confidence in the security protocols utilized to protect data, trust in the providers and institutions who use the technologies, belief in the benefits to the patients, and awareness that electronic exchange represents an enhancement of data sharing already taking place by other means. HIE acceptability depended both on preexisting trust among patients, providers, and institutions and on building consensus and trust in the HIEs as part of preparation for implementation. The process of HIE

  17. THE VALUATION OF INITIAL SHARE PRICE USING THE FREE CASH FLOW TO FIRM METHOD AND THE REAL OPTION METHOD IN INDONESIA STOCK EXCHANGE

    Directory of Open Access Journals (Sweden)

    Adhy Listya Paramitha

    2014-01-01

    Full Text Available The purposes of this study were to determine fair share value, to analyze the factors that influence undervalue and overvalue, and to determine the best valuation method. This study made valuation using real options method and free cash flow to firm method. The results of partial logistic regression on Free Cash Flow to Firm showed that tenor variable and equity variable had positive and significant effects, while dummy variable had a negative and significant effect. In the real option model, tenor variable and implied volatility variable had positive and significant effects, while sheets of share variable had a negative and significant effect

  18. Heterozygote Hemoglobin G-Coushatta as the Cause of a Falsely Decreased Hemoglobin A1C in an Ion-Exchange HPLC Method

    Directory of Open Access Journals (Sweden)

    Kurtoğlu Ayşegül Uğur

    2017-09-01

    Full Text Available Glycated hemoglobin (HbA1c is used for the assessment of glycemic control in patients with diabetes. The presence of genetic variants of hemoglobin can profoundly affect the accuracy of HbA1c measurement. Here, we report two cases of Hemoglobin G-Coushatta (HBB:c.68A>C variant that interferes in the measurement of HbA1c by a cation-exchange HPLC (CE-HPLC method. HbA1c was measured by a CE-HPLC method in a Tosoh HLC-723 G7 instrument. The HbA1c levels were 2.9% and 4%. These results alerted us to a possible presence of hemoglobinopathy. In the hemoglobin variant analysis, HbA2 levels were detected as 78.3% and 40.7% by HPLC using the short program for the Biorad Variant II. HbA1c levels were measured by an immunoturbidimetric assay in a Siemens Dimension instrument. HbA1c levels were reported as 5.5% and 5.3%. DNA mutation analysis was performed to detect the abnormal hemoglobin variant. Presence of Hemoglobin G-Coushatta variant was detected in the patients. The Hb G-Coushatta variants have an impact on the determination of glycated hemoglobin levels using CEHPLC resulting in a false low value. Therefore, it is necessary to use another measurement method.

  19. A pore-scale model for the cathode electrode of a proton exchange membrane fuel cell by lattice Boltzmann method

    Energy Technology Data Exchange (ETDEWEB)

    Molaeimanesh, Gholam Reza; Akbari, Mohammad Hadi [Shiraz University, Shiraz (Iran, Islamic Republic of)

    2015-03-15

    A pore-scale model based on the lattice Boltzmann method (LBM) is proposed for the cathode electrode of a PEM fuel cell with heterogeneous and anisotropic porous gas diffusion layer (GDL) and interdigitated flow field. An active approach is implemented to model multi-component transport in GDL, which leads to enhanced accuracy, especially at higher activation over-potentials. The core of the paper is the implementation of an electrochemical reaction with an active approach in a multi-component lattice Boltzmann model for the first time. After model validation, the capability of the presented model is demonstrated through a parametric study. Effects of activation over-potential, pressure differential between inlet and outlet gas channels, land width to channel width ratio, and channel width are investigated. The results show the significant influence of GDL microstructure on the oxygen distribution and current density profile.

  20. Development of a laser cleaning method for the first mirror surface of the charge exchange recombination spectroscopy diagnostics on ITER

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, A. P., E-mail: APKuznetsov@mephi.ru [National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) (Russian Federation); Buzinskij, O. I. [State Research Center Troitsk Institute for Innovation and Fusion Research (TRINITI) (Russian Federation); Gubsky, K. L.; Nikitina, E. A.; Savchenkov, A. V.; Tarasov, B. A. [National Research Nuclear University MEPhI (Moscow Engineering Physics Institute) (Russian Federation); Tugarinov, S. N. [State Research Center Troitsk Institute for Innovation and Fusion Research (TRINITI) (Russian Federation)

    2015-12-15

    A set of optical diagnostics is expected for measuring the plasma characteristics in ITER. Optical elements located inside discharge chambers are exposed to an intense radiation load, sputtering due to collisions with energetic atoms formed in the charge transfer processes, and contamination due to recondensation of materials sputtered from different parts of the construction of the chamber. Removing the films of the sputtered materials from the mirrors with the aid of pulsed laser radiation is an efficient cleaning method enabling recovery of the optical properties of the mirrors. In this work, we studied the efficiency of removal of metal oxide films by pulsed radiation of a fiber laser. Optimization of the laser cleaning conditions was carried out on samples representing metal substrates polished with optical quality with deposition of films on them imitating the chemical composition and conditions expected in ITER. It is shown that, by a proper selection of modes of radiation exposure to the surface with a deposited film, it is feasible to restore the original high reflection characteristics of optical elements.