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Sample records for replica package model

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  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. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Modelling of a DNA packaging motor

    Institute of Scientific and Technical Information of China (English)

    Qian Jun; Xie Ping; Xue Xiao-Guang; Wang Peng-Ye

    2009-01-01

    During the assembly of many viruses, a powerful molecular motor packages the genome into a preassembled capsid. The Bacillus subtilis phage φ29 is an excellent model system to investigate the DNA packaging mechanism because of its highly efficient in vitro DNA packaging activity and the development of a single-molecule packaging assay. Here we make use of structural and biochemical experimental data to build a physical model of DNA packaging by the φ29 DNA packaging motor. Based on the model, various dynamic behaviours such as the packaging rate, pause frequency and slip frequency under different ATP concentrations, ADP concentrations, external loads as well as capsid fillings are studied by using Monte Carlo simulation. Good agreement is obtained between the simulated and available experimental results. Moreover, we make testable predictions that should guide future experiments related to motor function.

  1. The Model 9977 Radioactive Material Packaging Primer

    Energy Technology Data Exchange (ETDEWEB)

    Abramczyk, G. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-10-09

    The Model 9977 Packaging is a single containment drum style radioactive material (RAM) shipping container designed, tested and analyzed to meet the performance requirements of Title 10 the Code of Federal Regulations Part 71. A radioactive material shipping package, in combination with its contents, must perform three functions (please note that the performance criteria specified in the Code of Federal Regulations have alternate limits for normal operations and after accident conditions): Containment, the package must “contain” the radioactive material within it; Shielding, the packaging must limit its users and the public to radiation doses within specified limits; and Subcriticality, the package must maintain its radioactive material as subcritical

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Dynamic modelling of packaging material flow systems.

    Science.gov (United States)

    Tsiliyannis, Christos A

    2005-04-01

    A dynamic model has been developed for reused and recycled packaging material flows. It allows a rigorous description of the flows and stocks during the transition to new targets imposed by legislation, product demand variations or even by variations in consumer discard behaviour. Given the annual reuse and recycle frequency and packaging lifetime, the model determines all packaging flows (e.g., consumption and reuse) and variables through which environmental policy is formulated, such as recycling, waste and reuse rates and it identifies the minimum number of variables to be surveyed for complete packaging flow monitoring. Simulation of the transition to the new flow conditions is given for flows of packaging materials in Greece, based on 1995--1998 field inventory and statistical data.

  7. 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.

  8. Economic tour package model using heuristic

    Science.gov (United States)

    Rahman, Syariza Abdul; Benjamin, Aida Mauziah; Bakar, Engku Muhammad Nazri Engku Abu

    2014-07-01

    A tour-package is a prearranged tour that includes products and services such as food, activities, accommodation, and transportation, which are sold at a single price. Since the competitiveness within tourism industry is very high, many of the tour agents try to provide attractive tour-packages in order to meet tourist satisfaction as much as possible. Some of the criteria that are considered by the tourist are the number of places to be visited and the cost of the tour-packages. Previous studies indicate that tourists tend to choose economical tour-packages and aiming to visit as many places as they can cover. Thus, this study proposed tour-package model using heuristic approach. The aim is to find economical tour-packages and at the same time to propose as many places as possible to be visited by tourist in a given geographical area particularly in Langkawi Island. The proposed model considers only one starting point where the tour starts and ends at an identified hotel. This study covers 31 most attractive places in Langkawi Island from various categories of tourist attractions. Besides, the allocation of period for lunch and dinner are included in the proposed itineraries where it covers 11 popular restaurants around Langkawi Island. In developing the itinerary, the proposed heuristic approach considers time window for each site (hotel/restaurant/place) so that it represents real world implementation. We present three itineraries with different time constraints (1-day, 2-day and 3-day tour-package). The aim of economic model is to minimize the tour-package cost as much as possible by considering entrance fee of each visited place. We compare the proposed model with our uneconomic model from our previous study. The uneconomic model has no limitation to the cost with the aim to maximize the number of places to be visited. Comparison between the uneconomic and economic itinerary has shown that the proposed model have successfully achieved the objective that

  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. Accuracy and reproducibility of dental replica models reconstructed by different rapid prototyping techniques

    NARCIS (Netherlands)

    Hazeveld, Aletta; Huddleston Slater, James J. R.; Ren, Yijin

    INTRODUCTION: Rapid prototyping is a fast-developing technique that might play a significant role in the eventual replacement of plaster dental models. The aim of this study was to investigate the accuracy and reproducibility of physical dental models reconstructed from digital data by several rapid

  11. Flexible Rasch Mixture Models with Package psychomix

    Directory of Open Access Journals (Sweden)

    Hannah Frick

    2012-05-01

    Full Text Available Measurement invariance is an important assumption in the Rasch model and mixture models constitute a flexible way of checking for a violation of this assumption by detecting unobserved heterogeneity in item response data. Here, a general class of Rasch mixture models is established and implemented in R, using conditional maximum likelihood estimation of the item parameters (given the raw scores along with flexible specification of two model building blocks: (1 Mixture weights for the unobserved classes can be treated as model parameters or based on covariates in a concomitant variable model. (2 The distribution of raw score probabilities can be parametrized in two possible ways, either using a saturated model or a specification through mean and variance. The function raschmix( in the R package psychomix provides these models, leveraging the general infrastructure for fitting mixture models in the flexmix package. Usage of the function and its associated methods is illustrated on artificial data as well as empirical data from a study of verbally aggressive behavior.

  12. 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.

  13. Volvo Logistics Corporation Returnable Packaging System : a model for analysing cost savings when switching packaging system

    OpenAIRE

    2008-01-01

    This thesis is a study for analysing costs affected by packaging in a producing industry. The purpose is to develop a model that will calculate and present possible cost savings for the customer by using Volvo Logistics Corporations, VLC’s, returnable packaging instead of other packaging solutions. The thesis is based on qualitative data gained from both theoretical and empirical studies. The methodology for gaining information has been to study theoretical sources such as course literature a...

  14. 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.

  15. Neural Network Program Package for Prosody Modeling

    Directory of Open Access Journals (Sweden)

    J. Santarius

    2004-04-01

    Full Text Available This contribution describes the programme for one part of theautomatic Text-to-Speech (TTS synthesis. Some experiments (for example[14] documented the considerable improvement of the naturalness ofsynthetic speech, but this approach requires completing the inputfeature values by hand. This completing takes a lot of time for bigfiles. We need to improve the prosody by other approaches which useonly automatically classified features (input parameters. Theartificial neural network (ANN approach is used for the modeling ofprosody parameters. The program package contains all modules necessaryfor the text and speech signal pre-processing, neural network training,sensitivity analysis, result processing and a module for the creationof the input data protocol for Czech speech synthesizer ARTIC [1].

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. topicmodels: An R Package for Fitting Topic Models

    Directory of Open Access Journals (Sweden)

    Bettina Grun

    2011-05-01

    Full Text Available Topic models allow the probabilistic modeling of term frequency occurrences in documents. The fitted model can be used to estimate the similarity between documents as well as between a set of specified keywords using an additional layer of latent variables which are referred to as topics. The R package topicmodels provides basic infrastructure for fitting topic models based on data structures from the text mining package tm. The package includes interfaces to two algorithms for fitting topic models: the variational expectation-maximization algorithm provided by David M. Blei and co-authors and an algorithm using Gibbs sampling by Xuan-Hieu Phan and co-authors.

  3. Power Electronic Packaging Design, Assembly Process, Reliability and Modeling

    CERN Document Server

    Liu, Yong

    2012-01-01

    Power Electronic Packaging presents an in-depth overview of power electronic packaging design, assembly,reliability and modeling. Since there is a drastic difference between IC fabrication and power electronic packaging, the book systematically introduces typical power electronic packaging design, assembly, reliability and failure analysis and material selection so readers can clearly understand each task's unique characteristics. Power electronic packaging is one of the fastest growing segments in the power electronic industry, due to the rapid growth of power integrated circuit (IC) fabrication, especially for applications like portable, consumer, home, computing and automotive electronics. This book also covers how advances in both semiconductor content and power advanced package design have helped cause advances in power device capability in recent years. The author extrapolates the most recent trends in the book's areas of focus to highlight where further improvement in materials and techniques can d...

  4. 教育资源网格模型及副本创建策略%Education Resource Grid Model and Replica Creation Strategies

    Institute of Scientific and Technical Information of China (English)

    邢长明; 刘方爱; 杨林; 厉文

    2009-01-01

    教育资源网格是解决目前分布式教育资源共享问题的有效手段.针对中小学教育资源共享问题,提出了层次式的教育资源网格模型,定义了各层节点的功能.通过与欧洲数据网格对比,分析了教育资源网格的特点.基于层次式的教育资源网格,对影响副本创建策略性能的因素进行了分析,然后引入网络带宽和文件大小两个参数,提出了一种动态副本创建策略(dynamic replica creation strategy,简称EDRS).利用数据网格模拟工具OptorSim构建了教育资源网格虚拟环境,分析比较了EDRS策略与Caching-LRU策略、Caching-LFU策略和基于经济模型的副本创建策略的性能.最后,综合各项指标分析了不同策略对教育资源网格系统性能的影响.结果表明,EDRS策略在教育资源网格应用中有着更好的系统性能.%The education resource grid is an effective measure to solve the problem of sharing distributed education resources at present. First, with regard to the education resource sharing in secondary and elementary schools, a hierarchy model of education resource grid is proposed and the functions of nodes in each layer are defined in this paper. By comparing with the European Data Grid, the education resource grid is analyzed with its characteristics. Then based on the hierarchy grid model, some factors, which influence the performance of replica creation strategy, are analyzed and a dynamic replica creation strategy (EDRS) is proposed by introducing two parameters, i.e., the network bandwidth and file size. With the data grid simulation tool OptorSim, the performances of EDRS with Caching-LRU, Caching-LFU and the economic model strategy are compared respectively. At last, the influence of different strategies on the performance of the education resource grid system is analyzed by synthesizing each parameter. The result indicates that the EDRS has a better system performance in applications of the education resource

  5. 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.

  6. ZONE package of the Central Valley Hydrologic Model

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital dataset defines the model grid, active cells in model layers 2 and 3, and geologic province arrays of the ZONE package used in the transient hydrologic...

  7. Asynchronous replica exchange software for grid and heterogeneous computing

    Science.gov (United States)

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

    2015-11-01

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

  8. Asynchronous Replica Exchange Software for Grid and Heterogeneous Computing

    Science.gov (United States)

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

    2015-01-01

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

  9. 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...

  10. 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.

  11. The gRbase package for graphical modelling in R

    DEFF Research Database (Denmark)

    Højsgaard, Søren; Dethlefsen, Claus

    We have developed a package, called , consisting of a number of classes and associated methods to support the analysis of data using graphical models. It is developed for the open source language, R, and is available for several platforms. The package is intended to be widely extendible and flexi...... these building blocks can be combined and integrated with inference engines in the special cases of hierarchical log-linear models (undirected models). gRbase gRbase dynamicGraph...... and flexible so that package developers may implement further types of graphical models using the available methods. contains methods for representing data, specification of models using a formal language, and is linked to , an interactive graphical user interface for manipulating graphs. We show how...

  12. An Overview on R Packages for Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Haibin Qiu

    2014-05-01

    Full Text Available The aim of this study is to present overview on R packages for structural equation modeling. Structural equation modeling, a statistical technique for testing and estimating causal relations using an amalgamation of statistical data and qualitative causal hypotheses, allow both confirmatory and exploratory modeling, meaning they are matched to both hypothesis testing and theory development. R project or R language, a free and popular programming language and computer software surroundings for statistical computing and graphics, is popularly used among statisticians for developing statistical computer software and data analysis. The major finding is that it is necessary to build excellent and enough structural equation modeling packages for R users to do research. Numerous packages for structural equation modeling of R project are introduced in this study and most of them are enclosed in the Comprehensive R Archive Network task view Psychometrics.

  13. Structural Equation Modeling Diagnostics Using R Package Semdiag and EQS

    Science.gov (United States)

    Yuan, Ke-Hai; Zhang, Zhiyong

    2012-01-01

    Yuan and Hayashi (2010) introduced 2 scatter plots for model and data diagnostics in structural equation modeling (SEM). However, the generation of the plots requires in-depth understanding of their underlying technical details. This article develops and introduces an R package semdiag for easily drawing the 2 plots. With a model specified in EQS…

  14. Mass Transfer Model for a Breached Waste Package

    Energy Technology Data Exchange (ETDEWEB)

    C. Hsu; J. McClure

    2004-07-26

    The degradation of waste packages, which are used for the disposal of spent nuclear fuel in the repository, can result in configurations that may increase the probability of criticality. A mass transfer model is developed for a breached waste package to account for the entrainment of insoluble particles. In combination with radionuclide decay, soluble advection, and colloidal transport, a complete mass balance of nuclides in the waste package becomes available. The entrainment equations are derived from dimensionless parameters such as drag coefficient and Reynolds number and based on the assumption that insoluble particles are subjected to buoyant force, gravitational force, and drag force only. Particle size distributions are utilized to calculate entrainment concentration along with geochemistry model abstraction to calculate soluble concentration, and colloid model abstraction to calculate colloid concentration and radionuclide sorption. Results are compared with base case geochemistry model, which only considers soluble advection loss.

  15. Mathematical Model and Programming in VBA Excel for Package Calculation

    Directory of Open Access Journals (Sweden)

    João Daniel Reis Lessa

    2016-05-01

    Full Text Available The industrial logistics is a fundamental pillar for the survival of companies in the actual increasingly competitive market. It is not exclusively about controlling the flow of external material between suppliers and the company, but for developing a detailed study of how to plan, control, handle and package those materials as well. Logistics activities must ensure the maximum efficiency in using corporate resources once they do not add value to the final product. The creation of a logistic plan, for each piece of the company’s production, has to adapt the demand parameters, seasonal or not, in the timeline. Thus, the definition of packaging (transportation and consumption must adjust in accordance with the demand, in order to allow the logistic planning to work, constantly, with order of economy batches. The packaging calculation for each part in every demand can become well complicated due to the large amount of parts in the production process. Automating the calculation process for choosing the right package for each piece is an effective method in logistics planning. This article will expose a simple and practical mathematical model for automating the packaging calculation and a logic program, created in Visual Basic language in the Excel software, used for creating graphic designs that show how the packages are being filled.

  16. Linear latent variable models: the lava-package

    DEFF Research Database (Denmark)

    Holst, Klaus Kähler; Budtz-Jørgensen, Esben

    2013-01-01

    An R package for specifying and estimating linear latent variable models is presented. The philosophy of the implementation is to separate the model specification from the actual data, which leads to a dynamic and easy way of modeling complex hierarchical structures. Several advanced features are...... interface covering a broad range of non-linear generalized structural equation models is described. The model and software are demonstrated in data of measurements of the serotonin transporter in the human brain....

  17. 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.

  18. dMODELS: A software package for modeling volcanic deformation

    Science.gov (United States)

    Battaglia, Maurizio

    2017-04-01

    dMODELS is a software package that includes the most common source models used to interpret deformation measurements near active volcanic centers. The emphasis is on estimating the parameters of analytical models of deformation by inverting data from the Global Positioning System (GPS), Interferometric Synthetic Aperture Radar (InSAR), tiltmeters and strainmeters. Source models include: (a) pressurized spherical, ellipsoidal and sill-like magma chambers in an elastic, homogeneous, flat half-space; (b) pressurized spherical magma chambers with topography corrections; and (c) the solutions for a dislocation (fracture) in an elastic, homogeneous, flat half-space. All of the equations have been extended to include deformation and strain within the Earth's crust (as opposed to only at the Earth's surface) and verified against finite element models. Although actual volcanic sources are not embedded cavities of simple shape, we assume that these models may reproduce the stress field created by the actual magma intrusion or hydrothermal fluid injection. The dMODELS software employs a nonlinear inversion algorithm to determine the best-fit parameters for the deformation source by searching for the minimum of the cost function χv2 (chi square per degrees of freedom). The non-linear inversion algorithm is a combination of local optimization (interior-point method) and random search. This approach is more efficient for hyper-parameter optimization than trials on a grid. The software has been developed using MATLAB, but compiled versions that can be run using the free MATLAB Compiler Runtime (MCR) module are available for Windows 64-bit operating systems. The MATLAB scripts and compiled files are open source and intended for teaching and research. The software package includes both functions for forward modeling and scripts for data inversion. A software demonstration will be available during the meeting. You are welcome to contact the author at mbattaglia@usgs.gov for

  19. A Kinetic Model for Predicting the Relative Humidity in Modified Atmosphere Packaging and Its Application in Lentinula edodes Packages

    Directory of Open Access Journals (Sweden)

    Li-xin Lu

    2013-01-01

    Full Text Available Adjusting and controlling the relative humidity (RH inside package is crucial for ensuring the quality of modified atmosphere packaging (MAP of fresh produce. In this paper, an improved kinetic model for predicting the RH in MAP was developed. The model was based on heat exchange and gases mass transport phenomena across the package, gases heat convection inside the package, and mass and heat balances accounting for the respiration and transpiration behavior of fresh produce. Then the model was applied to predict the RH in MAP of fresh Lentinula edodes (one kind of Chinese mushroom. The model equations were solved numerically using Adams-Moulton method to predict the RH in model packages. In general, the model predictions agreed well with the experimental data, except that the model predictions were slightly high in the initial period. The effect of the initial gas composition on the RH in packages was notable. In MAP of lower oxygen and higher carbon dioxide concentrations, the ascending rate of the RH was reduced, and the RH inside packages was saturated slowly during storage. The influence of the initial gas composition on the temperature inside package was not much notable.

  20. MODEL 9975 SHIPPING PACKAGE FABRICATION PROBLEMS AND SOLUTIONS

    Energy Technology Data Exchange (ETDEWEB)

    May, C; Allen Smith, A

    2008-05-07

    The Model 9975 Shipping Package is the latest in a series (9965, 9968, etc.) of radioactive material shipping packages that have been the mainstay for shipping radioactive materials for several years. The double containment vessels are relatively simple designs using pipe and pipe cap in conjunction with the Chalfont closure to provide a leak-tight vessel. The fabrication appears simple in nature, but the history of fabrication tells us there are pitfalls in the different fabrication methods and sequences. This paper will review the problems that have arisen during fabrication and precautions that should be taken to meet specifications and tolerances. The problems and precautions can also be applied to the Models 9977 and 9978 Shipping Packages.

  1. Expanded Content Envelope For The Model 9977 Packaging

    Energy Technology Data Exchange (ETDEWEB)

    Abramczyk, G. A.; Loftin, B. M.; Nathan, S. J.; Bellamy, J. S.

    2013-07-30

    An Addendum was written to the Model 9977 Safety Analysis Report for Packaging adding a new content consisting of DOE-STD-3013 stabilized plutonium dioxide materials to the authorized Model 9977 contents. The new Plutonium Oxide Content (PuO{sub 2}) Envelope will support the Department of Energy shipment of materials between Los Alamos National Laboratory and Savannah River Site facilities. The new content extended the current content envelope boundaries for radioactive material mass and for decay heat load and required a revision to the 9977 Certificate of Compliance prior to shipment. The Addendum documented how the new contents/configurations do not compromise the safety basis presented in the 9977 SARP Revision 2. The changes from the certified package baseline and the changes to the package required to safely transport this material is discussed.

  2. VR Lab ISS Graphics Models Data Package

    Science.gov (United States)

    Paddock, Eddie; Homan, Dave; Bell, Brad; Miralles, Evely; Hoblit, Jeff

    2016-01-01

    All the ISS models are saved in AC3D model format which is a text based format that can be loaded into blender and exported to other formats from there including FBX. The models are saved in two different levels of detail, one being labeled "LOWRES" and the other labeled "HIRES". There are two ".str" files (HIRES _ scene _ load.str and LOWRES _ scene _ load.str) that give the hierarchical relationship of the different nodes and the models associated with each node for both the "HIRES" and "LOWRES" model sets. All the images used for texturing are stored in Windows ".bmp" format for easy importing.

  3. High power electronics package: from modeling to implementation

    NARCIS (Netherlands)

    Yuan, C.A.; Kregting, R.; Ye, H.; Driel, W. van; Gielen, A.W.J.; Zhang, G.Q.

    2011-01-01

    Power electronics, such as high power RF components and high power LEDs, requires the combination of robust and reliable package structures, materials, and processes to guarantee their functional performance and lifetime. We started with the thermal and thermal-mechanical modeling of such component

  4. Linear latent variable models: the lava-package

    DEFF Research Database (Denmark)

    Holst, Klaus Kähler; Budtz-Jørgensen, Esben

    2013-01-01

    An R package for specifying and estimating linear latent variable models is presented. The philosophy of the implementation is to separate the model specification from the actual data, which leads to a dynamic and easy way of modeling complex hierarchical structures. Several advanced features...... are implemented including robust standard errors for clustered correlated data, multigroup analyses, non-linear parameter constraints, inference with incomplete data, maximum likelihood estimation with censored and binary observations, and instrumental variable estimators. In addition an extensive simulation...

  5. 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.

  6. The R Package bgmm : Mixture Modeling with Uncertain Knowledge

    Directory of Open Access Journals (Sweden)

    Przemys law Biecek

    2012-04-01

    Full Text Available Classical supervised learning enjoys the luxury of accessing the true known labels for the observations in a modeled dataset. Real life, however, poses an abundance of problems, where the labels are only partially defined, i.e., are uncertain and given only for a subsetof observations. Such partial labels can occur regardless of the knowledge source. For example, an experimental assessment of labels may have limited capacity and is prone to measurement errors. Also expert knowledge is often restricted to a specialized area and is thus unlikely to provide trustworthy labels for all observations in the dataset. Partially supervised mixture modeling is able to process such sparse and imprecise input. Here, we present an R package calledbgmm, which implements two partially supervised mixture modeling methods: soft-label and belief-based modeling. For completeness, we equipped the package also with the functionality of unsupervised, semi- and fully supervised mixture modeling. On real data we present the usage of bgmm for basic model-fitting in all modeling variants. The package can be applied also to selection of the best-fitting from a set of models with different component numbers or constraints on their structures. This functionality is presented on an artificial dataset, which can be simulated in bgmm from a distribution defined by a given model.

  7. 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.

  8. A Common Platform for Graphical Models in R: The gRbase Package

    Directory of Open Access Journals (Sweden)

    Claus Dethlefsen

    2005-12-01

    Full Text Available The gRbase package is intended to set the framework for computer packages for data analysis using graphical models. The gRbase package is developed for the open source language, R, and is available for several platforms. The package is intended to be widely extendible and flexible so that package developers may implement further types of graphical models using the available methods. The gRbase package consists of a set of S version 3 classes and associated methods for representing data and models. The package is linked to the dynamicGraph package (Badsberg 2005, an interactive graphical user interface for manipulating graphs.In this paper, we show how these building blocks can be combined and integrated with inference engines in the special cases of hierarchical loglinear models. We also illustrate how to extend the package to deal with other types of graphical models, in this case the graphical Gaussian models.

  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. 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.

  11. Mixed Frequency Data Sampling Regression Models: The R Package midasr

    Directory of Open Access Journals (Sweden)

    Eric Ghysels

    2016-08-01

    Full Text Available When modeling economic relationships it is increasingly common to encounter data sampled at different frequencies. We introduce the R package midasr which enables estimating regression models with variables sampled at different frequencies within a MIDAS regression framework put forward in work by Ghysels, Santa-Clara, and Valkanov (2002. In this article we define a general autoregressive MIDAS regression model with multiple variables of different frequencies and show how it can be specified using the familiar R formula interface and estimated using various optimization methods chosen by the researcher. We discuss how to check the validity of the estimated model both in terms of numerical convergence and statistical adequacy of a chosen regression specification, how to perform model selection based on a information criterion, how to assess forecasting accuracy of the MIDAS regression model and how to obtain a forecast aggregation of different MIDAS regression models. We illustrate the capabilities of the package with a simulated MIDAS regression model and give two empirical examples of application of MIDAS regression.

  12. PKgraph: an R package for graphically diagnosing population pharmacokinetic models.

    Science.gov (United States)

    Sun, Xiaoyong; Wu, Kai; Cook, Dianne

    2011-12-01

    Population pharmacokinetic (PopPK) modeling has become increasing important in drug development because it handles unbalanced design, sparse data and the study of individual variation. However, the increased complexity of the model makes it more of a challenge to diagnose the fit. Graphics can play an important and unique role in PopPK model diagnostics. The software described in this paper, PKgraph, provides a graphical user interface for PopPK model diagnosis. It also provides an integrated and comprehensive platform for the analysis of pharmacokinetic data including exploratory data analysis, goodness of model fit, model validation and model comparison. Results from a variety of modeling fitting software, including NONMEM, Monolix, SAS and R, can be used. PKgraph is programmed in R, and uses the R packages lattice, ggplot2 for static graphics, and rggobi for interactive graphics.

  13. Package models and the information crisis of prebiotic evolution.

    Science.gov (United States)

    Silvestre, Daniel A M M; Fontanari, José F

    2008-05-21

    The coexistence between different types of templates has been the choice solution to the information crisis of prebiotic evolution, triggered by the finding that a single RNA-like template cannot carry enough information to code for any useful replicase. In principle, confining d distinct templates of length L in a package or protocell, whose survival depends on the coexistence of the templates it holds in, could resolve this crisis provided that d is made sufficiently large. Here we review the prototypical package model of Niesert et al. [1981. Origin of life between Scylla and Charybdis. J. Mol. Evol. 17, 348-353] which guarantees the greatest possible region of viability of the protocell population, and show that this model, and hence the entire package approach, does not resolve the information crisis. In particular, we show that the total information stored in a viable protocell (Ld) tends to a constant value that depends only on the spontaneous error rate per nucleotide of the template replication mechanism. As a result, an increase of d must be followed by a decrease of L, so that the net information gain is null.

  14. Deconvolution Estimation in Measurement Error Models: The R Package decon

    Directory of Open Access Journals (Sweden)

    Xiao-Feng Wang

    2011-03-01

    Full Text Available Data from many scientific areas often come with measurement error. Density or distribution function estimation from contaminated data and nonparametric regression with errors in variables are two important topics in measurement error models. In this paper, we present a new software package decon for R, which contains a collection of functions that use the deconvolution kernel methods to deal with the measurement error problems. The functions allow the errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the fast Fourier transform algorithm for density estimation with error-free data to the deconvolution kernel estimation. We discuss the practical selection of the smoothing parameter in deconvolution methods and illustrate the use of the package through both simulated and real examples.

  15. COMPUTATIONAL MODELLING OF BUFFETING EFFECTS USING OPENFOAM SOFTWARE PACKAGE

    Directory of Open Access Journals (Sweden)

    V. T. Kalugin

    2015-01-01

    Full Text Available In this paper, the preliminary results of computational modeling of an aircraft with the airbrake deployed are presented. The calculations were performed with OpenFOAM software package. The results outlined are a part of a research project to optimise aircraft performance using a perforated airbrake. Within this stage of the project OpenFOAM software package with hybrid RANS-LES approach was tested in respect to a given configuration of the aircraft, airbrake and then has been compared with the test data. For the worst case the amplitude of the peak force acting on the tail fin can be up to 6 times higher than the average value without airbrake deployed. To reduce unsteady loads acting on the tailfin, perforation of the airbrake was proposed.

  16. RECERTIFICATION OF THE MODEL 9977 RADIOACTIVE MATERIAL PACKAGING

    Energy Technology Data Exchange (ETDEWEB)

    Abramczyk, G.; Bellamy, S.; Loftin, B.; Nathan, S.

    2013-06-05

    The Model 9977 Packaging was initially issued a Certificate of Compliance (CoC) by the Department of Energy’s Office of Environmental Management (DOE-EM) for the transportation of radioactive material (RAM) in the Fall of 2007. This first CoC was for a single radioactive material and two packing configurations. In the five years since that time, seven Addendums have been written to the Safety Analysis Report for Packaging (SARP) and five Letter Amendments have been written that have authorized either new RAM contents or packing configurations, or both. This paper will discuss the process of updating the 9977 SARP to include all the contents and configurations, including the addition of a new content, and its submittal for recertification.

  17. dglars: An R Package to Estimate Sparse Generalized Linear Models

    Directory of Open Access Journals (Sweden)

    Luigi Augugliaro

    2014-09-01

    Full Text Available dglars is a publicly available R package that implements the method proposed in Augugliaro, Mineo, and Wit (2013, developed to study the sparse structure of a generalized linear model. This method, called dgLARS, is based on a differential geometrical extension of the least angle regression method proposed in Efron, Hastie, Johnstone, and Tibshirani (2004. The core of the dglars package consists of two algorithms implemented in Fortran 90 to efficiently compute the solution curve: a predictor-corrector algorithm, proposed in Augugliaro et al. (2013, and a cyclic coordinate descent algorithm, proposed in Augugliaro, Mineo, and Wit (2012. The latter algorithm, as shown here, is significantly faster than the predictor-corrector algorithm. For comparison purposes, we have implemented both algorithms.

  18. Universality class of replica symmetry breaking, scaling behavior, and the low-temperature fixed-point order function of the Sherrington-Kirkpatrick model.

    Science.gov (United States)

    Oppermann, R; Schmidt, M J

    2008-12-01

    A scaling theory of replica symmetry breaking (RSB) in the Sherrington-Kirkpatrick (SK) model is presented in the framework of critical phenomena for the scaling regime of large RSB orders kappa , small temperatures T , and small (homogeneous) magnetic fields H . We employ the pseudodynamical picture [R. Oppermann, M. J. Schmidt, and D. Sherrington, Phys. Rev. Lett. 98, 127201 (2007)], where two critical points CP1 and CP2 are associated with the order function's pseudodynamical limits lim_{a-->infinity}q(a)=1 and lim_{a-->0}q(a)=0 at (T=0 , H=0 , 1kappa=0) . CP1 - and CP2 -dominated contributions to the free energy functional F[q(a)] require an unconventional scaling hypothesis. We determine the scaling contributions in accordance with detailed numerical self-consistent solutions for up to 200 orders of RSB. Power laws, scaling functions, and crossover lines are obtained. CP1 -dominated behavior is found for the nonequilibrium susceptibility, which decays like chi_{1}=kappa;{-53}f_{1}(Tkappa;{-53}) , for the entropy, which obeys S(T=0) approximately chi_{1};{2} , and for the subclass of diverging parameters a_{i}=kappa;{53}f_{a_{i}}(Tkappa;{-53}) [describing Parisi box sizes m_{i}(T) identical witha_{i}(T)T ], with f_{1}(zeta) approximately zeta and f_{a_{i}}(zeta) approximately 1zeta for zeta-->infinity , while f(0) is finite. CP2 -dominated behavior, controlled by the magnetic field H while temperature is irrelevant, is retrieved in the plateau height (or width) of the order function q(a) according to q_{pl}(H)=kappa;{-1}f_{pl}(H;{23}kappa;{-1}) with f_{pl}mid R:(zeta)mid R:_{zeta-->infinity} approximately zeta and f_{pl}(0) finite. Divergent characteristic RSB orders kappa_{CP1}(T) approximately T;{-35} and kappa_{CP2}(H) approximately H;{-23} , respectively, describe the crossover from mean field SK- to RSB-critical behavior with rational-valued exponents extracted with high precision from our RSB data. The order function q(a) is obtained as a fixed

  19. Fitting Additive Binomial Regression Models with the R Package blm

    Directory of Open Access Journals (Sweden)

    Stephanie Kovalchik

    2013-09-01

    Full Text Available The R package blm provides functions for fitting a family of additive regression models to binary data. The included models are the binomial linear model, in which all covariates have additive effects, and the linear-expit (lexpit model, which allows some covariates to have additive effects and other covariates to have logisitc effects. Additive binomial regression is a model of event probability, and the coefficients of linear terms estimate covariate-adjusted risk differences. Thus, in contrast to logistic regression, additive binomial regression puts focus on absolute risk and risk differences. In this paper, we give an overview of the methodology we have developed to fit the binomial linear and lexpit models to binary outcomes from cohort and population-based case-control studies. We illustrate the blm packages methods for additive model estimation, diagnostics, and inference with risk association analyses of a bladder cancer nested case-control study in the NIH-AARP Diet and Health Study.

  20. scoringRules - A software package for probabilistic model evaluation

    Science.gov (United States)

    Lerch, Sebastian; Jordan, Alexander; Krüger, Fabian

    2016-04-01

    Models in the geosciences are generally surrounded by uncertainty, and being able to quantify this uncertainty is key to good decision making. Accordingly, probabilistic forecasts in the form of predictive distributions have become popular over the last decades. With the proliferation of probabilistic models arises the need for decision theoretically principled tools to evaluate the appropriateness of models and forecasts in a generalized way. Various scoring rules have been developed over the past decades to address this demand. Proper scoring rules are functions S(F,y) which evaluate the accuracy of a forecast distribution F , given that an outcome y was observed. As such, they allow to compare alternative models, a crucial ability given the variety of theories, data sources and statistical specifications that is available in many situations. This poster presents the software package scoringRules for the statistical programming language R, which contains functions to compute popular scoring rules such as the continuous ranked probability score for a variety of distributions F that come up in applied work. Two main classes are parametric distributions like normal, t, or gamma distributions, and distributions that are not known analytically, but are indirectly described through a sample of simulation draws. For example, Bayesian forecasts produced via Markov Chain Monte Carlo take this form. Thereby, the scoringRules package provides a framework for generalized model evaluation that both includes Bayesian as well as classical parametric models. The scoringRules package aims to be a convenient dictionary-like reference for computing scoring rules. We offer state of the art implementations of several known (but not routinely applied) formulas, and implement closed-form expressions that were previously unavailable. Whenever more than one implementation variant exists, we offer statistically principled default choices.

  1. 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.

  2. gems: An R Package for Simulating from Disease Progression Models

    Directory of Open Access Journals (Sweden)

    Nello Blaser

    2015-03-01

    Full Text Available Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death, displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

  3. A Thermodynamic Model for Genome Packaging in Hepatitis B Virus.

    Science.gov (United States)

    Kim, Jehoon; Wu, Jianzhong

    2015-10-20

    Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electron microscopy and x-ray diffraction, much less is known about the molecular driving forces underlying genome assembly in an intracellular environment and its in vivo interactions with the capsid proteins. Here we study the thermodynamic basis of the pregenomic RNA encapsidation in human Hepatitis B virus in vivo using a coarse-grained molecular model that captures the essential components of nonspecific intermolecular interactions. The thermodynamic model is used to examine how the electrostatic interaction between the packaged RNA and the highly charged C-terminal domains (CTD) of capsid proteins regulate the nucleocapsid formation. The theoretical model predicts optimal RNA content in Hepatitis B virus nucleocapsids with different CTD lengths in good agreement with mutagenesis measurements, confirming the predominant role of electrostatic interactions and molecular excluded-volume effects in genome packaging. We find that the amount of encapsidated RNA is not linearly correlated with the net charge of CTD tails as suggested by earlier theoretical studies. Our thermodynamic analysis of the nucleocapsid structure and stability indicates that ∼10% of the CTD residues are free from complexation with RNA, resulting in partially exposed CTD tails. The thermodynamic model also predicts the free energy of complex formation between macromolecules, which corroborates experimental results for the impact of CTD truncation on the nucleocapsid stability.

  4. DYNSTALL: Subroutine package with a dynamic stall model

    Energy Technology Data Exchange (ETDEWEB)

    Bjoerck, Anders [Aeronautical Research Inst. of Sweden, Bromma (Sweden)

    2001-03-01

    A subroutine package, called DYNSTALL, for the calculation of 2D unsteady airfoil aerodynamics is described. The subroutines are written in FORTRAN. DYNSTALL is basically an implementation of the Beddoes-Leishman dynamic stall model. This model is a semi-empirical model for dynamic stall. It includes, however, also models for attached flow unsteady aerodynamics. It is complete in the sense that it treats attached flow as well as separated flow. Semi-empirical means that the model relies on empirically determined constants. Semi because the constants are constants in equations with some physical interpretation. It requires the input of 2D airfoil aerodynamic data via tables as function of angle of attack. The method is intended for use in an aeroelastic code with the aerodynamics solved by blade/element method. DYNSTALL was written to work for any 2D angles of attack relative to the airfoil, e.g. flow from the rear of an airfoil.

  5. SPOTting Model Parameters Using a Ready-Made Python Package.

    Science.gov (United States)

    Houska, Tobias; Kraft, Philipp; Chamorro-Chavez, Alejandro; Breuer, Lutz

    2015-01-01

    The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.

  6. SPOTting Model Parameters Using a Ready-Made Python Package.

    Directory of Open Access Journals (Sweden)

    Tobias Houska

    Full Text Available The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool, an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI. We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.

  7. Technical Review Report for the Model 9975-96 Package Safety Analysis Report for Packaging (S-SARP-G-00003, Revision 0, January 2008)

    Energy Technology Data Exchange (ETDEWEB)

    West, M

    2009-05-22

    This Technical Review Report (TRR) documents the review, performed by the Lawrence Livermore National Laboratory (LLNL) Staff, at the request of the U.S. Department of Energy (DOE), on the Safety Analysis Report for Packaging, Model 9975, Revision 0, dated January 2008 (S-SARP-G-00003, the SARP). The review includes an evaluation of the SARP, with respect to the requirements specified in 10 CFR 71, and in International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1. The Model 9975-96 Package is a 35-gallon drum package design that has evolved from a family of packages designed by DOE contractors at the Savannah River Site. Earlier package designs, i.e., the Model 9965, the Model 9966, the Model 9967, and the Model 9968 Packagings, were originally designed and certified in the early 1980s. In the 1990s, updated package designs that incorporated design features consistent with the then newer safety requirements were proposed. The updated package designs at the time were the Model 9972, the Model 9973, the Model 9974, and the Model 9975 Packagings, respectively. The Model 9975 Package was certified by the Packaging Certification Program, under the Office of Safety Management and Operations. The safety analysis of the Model 9975-85 Packaging is documented in the Safety Analysis Report for Packaging, Model 9975, B(M)F-85, Revision 0, dated December 2003. The Model 9975-85 Package is certified by DOE Certificate of Compliance (CoC) package identification number, USA/9975/B(M)F-85, for the transportation of Type B quantities of uranium metal/oxide, {sup 238}Pu heat sources, plutonium/uranium metals, plutonium/uranium oxides, plutonium composites, plutonium/tantalum composites, {sup 238}Pu oxide/beryllium metal.

  8. VAR, SVAR and SVEC Models: Implementation Within R Package vars

    Directory of Open Access Journals (Sweden)

    Bernhard Pfaff

    2008-02-01

    Full Text Available The structure of the package vars and its implementation of vector autoregressive, structural vector autoregressive and structural vector error correction models are explained in this paper. In addition to the three cornerstone functions VAR(, SVAR( and SVEC( for estimating such models, functions for diagnostic testing, estimation of a restricted models, prediction, causality analysis, impulse response analysis and forecast error variance decomposition are provided too. It is further possible to convert vector error correction models into their level VAR representation. The different methods and functions are elucidated by employing a macroeconomic data set for Canada. However, the focus in this writing is on the implementation part rather than the usage of the tools at hand.

  9. MNP: R Package for Fitting the Multinomial Probit Model

    Directory of Open Access Journals (Sweden)

    Kosuke Imai

    2005-05-01

    Full Text Available MNP is a publicly available R package that fits the Bayesian multinomial probit model via Markov chain Monte Carlo. The multinomial probit model is often used to analyze the discrete choices made by individuals recorded in survey data. Examples where the multinomial probit model may be useful include the analysis of product choice by consumers in market research and the analysis of candidate or party choice by voters in electoral studies. The MNP software can also fit the model with different choice sets for each individual, and complete or partial individual choice orderings of the available alternatives from the choice set. The estimation is based on the efficient marginal data augmentation algorithm that is developed by Imai and van Dyk (2005.

  10. Continuous Time Structural Equation Modeling with R Package ctsem

    Directory of Open Access Journals (Sweden)

    Charles C. Driver

    2017-04-01

    Full Text Available We introduce ctsem, an R package for continuous time structural equation modeling of panel (N > 1 and time series (N = 1 data, using full information maximum likelihood. Most dynamic models (e.g., cross-lagged panel models in the social and behavioural sciences are discrete time models. An assumption of discrete time models is that time intervals between measurements are equal, and that all subjects were assessed at the same intervals. Violations of this assumption are often ignored due to the difficulty of accounting for varying time intervals, therefore parameter estimates can be biased and the time course of effects becomes ambiguous. By using stochastic differential equations to estimate an underlying continuous process, continuous time models allow for any pattern of measurement occasions. By interfacing to OpenMx, ctsem combines the flexible specification of structural equation models with the enhanced data gathering opportunities and improved estimation of continuous time models. ctsem can estimate relationships over time for multiple latent processes, measured by multiple noisy indicators with varying time intervals between observations. Within and between effects are estimated simultaneously by modeling both observed covariates and unobserved heterogeneity. Exogenous shocks with different shapes, group differences, higher order diffusion effects and oscillating processes can all be simply modeled. We first introduce and define continuous time models, then show how to specify and estimate a range of continuous time models using ctsem.

  11. Alloy Design Workbench-Surface Modeling Package Developed

    Science.gov (United States)

    Abel, Phillip B.; Noebe, Ronald D.; Bozzolo, Guillermo H.; Good, Brian S.; Daugherty, Elaine S.

    2003-01-01

    NASA Glenn Research Center's Computational Materials Group has integrated a graphical user interface with in-house-developed surface modeling capabilities, with the goal of using computationally efficient atomistic simulations to aid the development of advanced aerospace materials, through the modeling of alloy surfaces, surface alloys, and segregation. The software is also ideal for modeling nanomaterials, since surface and interfacial effects can dominate material behavior and properties at this level. Through the combination of an accurate atomistic surface modeling methodology and an efficient computational engine, it is now possible to directly model these types of surface phenomenon and metallic nanostructures without a supercomputer. Fulfilling a High Operating Temperature Propulsion Components (HOTPC) project level-I milestone, a graphical user interface was created for a suite of quantum approximate atomistic materials modeling Fortran programs developed at Glenn. The resulting "Alloy Design Workbench-Surface Modeling Package" (ADW-SMP) is the combination of proven quantum approximate Bozzolo-Ferrante-Smith (BFS) algorithms (refs. 1 and 2) with a productivity-enhancing graphical front end. Written in the portable, platform independent Java programming language, the graphical user interface calls on extensively tested Fortran programs running in the background for the detailed computational tasks. Designed to run on desktop computers, the package has been deployed on PC, Mac, and SGI computer systems. The graphical user interface integrates two modes of computational materials exploration. One mode uses Monte Carlo simulations to determine lowest energy equilibrium configurations. The second approach is an interactive "what if" comparison of atomic configuration energies, designed to provide real-time insight into the underlying drivers of alloying processes.

  12. SPOTting model parameters using a ready-made Python package

    Science.gov (United States)

    Houska, Tobias; Kraft, Philipp; Breuer, Lutz

    2015-04-01

    The selection and parameterization of reliable process descriptions in ecological modelling is driven by several uncertainties. The procedure is highly dependent on various criteria, like the used algorithm, the likelihood function selected and the definition of the prior parameter distributions. A wide variety of tools have been developed in the past decades to optimize parameters. Some of the tools are closed source. Due to this, the choice for a specific parameter estimation method is sometimes more dependent on its availability than the performance. A toolbox with a large set of methods can support users in deciding about the most suitable method. Further, it enables to test and compare different methods. We developed the SPOT (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of modules, to analyze and optimize parameters of (environmental) models. SPOT comes along with a selected set of algorithms for parameter optimization and uncertainty analyses (Monte Carlo, MC; Latin Hypercube Sampling, LHS; Maximum Likelihood, MLE; Markov Chain Monte Carlo, MCMC; Scuffled Complex Evolution, SCE-UA; Differential Evolution Markov Chain, DE-MCZ), together with several likelihood functions (Bias, (log-) Nash-Sutcliff model efficiency, Correlation Coefficient, Coefficient of Determination, Covariance, (Decomposed-, Relative-, Root-) Mean Squared Error, Mean Absolute Error, Agreement Index) and prior distributions (Binomial, Chi-Square, Dirichlet, Exponential, Laplace, (log-, multivariate-) Normal, Pareto, Poisson, Cauchy, Uniform, Weibull) to sample from. The model-independent structure makes it suitable to analyze a wide range of applications. We apply all algorithms of the SPOT package in three different case studies. Firstly, we investigate the response of the Rosenbrock function, where the MLE algorithm shows its strengths. Secondly, we study the Griewank function, which has a challenging response surface for

  13. 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.

  14. Technical Review Report for the Model 9978-96 Package Safety Analysis Report for Packaging (S-SARP-G-00002, Revision 1, March 2009)

    Energy Technology Data Exchange (ETDEWEB)

    West, M

    2009-03-06

    This Technical Review Report (TRR) documents the review, performed by Lawrence Livermore National Laboratory (LLNL) Staff, at the request of the Department of Energy (DOE), on the 'Safety Analysis Report for Packaging (SARP), Model 9978 B(M)F-96', Revision 1, March 2009 (S-SARP-G-00002). The Model 9978 Package complies with 10 CFR 71, and with 'Regulations for the Safe Transport of Radioactive Material-1996 Edition (As Amended, 2000)-Safety Requirements', International Atomic Energy Agency (IAEA) Safety Standards Series No. TS-R-1. The Model 9978 Packaging is designed, analyzed, fabricated, and tested in accordance with Section III of the American Society of Mechanical Engineers Boiler and Pressure Vessel Code (ASME B&PVC). The review presented in this TRR was performed using the methods outlined in Revision 3 of the DOE's 'Packaging Review Guide (PRG) for Reviewing Safety Analysis Reports for Packages'. The format of the SARP follows that specified in Revision 2 of the Nuclear Regulatory Commission's Regulatory Guide 7.9, i.e., 'Standard Format and Content of Part 71 Applications for Approval of Packages for Radioactive Material'. Although the two documents are similar in their content, they are not identical. Formatting differences have been noted in this TRR, where appropriate. The Model 9978 Packaging is a single containment package, using a 5-inch containment vessel (5CV). It uses a nominal 35-gallon drum package design. In comparison, the Model 9977 Packaging uses a 6-inch containment vessel (6CV). The Model 9977 and Model 9978 Packagings were developed concurrently, and they were referred to as the General Purpose Fissile Material Package, Version 1 (GPFP). Both packagings use General Plastics FR-3716 polyurethane foam as insulation and as impact limiters. The 5CV is used as the Primary Containment Vessel (PCV) in the Model 9975-96 Packaging. The Model 9975-96 Packaging also has the 6CV as its Secondary

  15. Use of advanced modeling techniques to optimize thermal packaging designs.

    Science.gov (United States)

    Formato, Richard M; Potami, Raffaele; Ahmed, Iftekhar

    2010-01-01

    Through a detailed case study the authors demonstrate, for the first time, the capability of using advanced modeling techniques to correctly simulate the transient temperature response of a convective flow-based thermal shipper design. The objective of this case study was to demonstrate that simulation could be utilized to design a 2-inch-wall polyurethane (PUR) shipper to hold its product box temperature between 2 and 8 °C over the prescribed 96-h summer profile (product box is the portion of the shipper that is occupied by the payload). Results obtained from numerical simulation are in excellent agreement with empirical chamber data (within ±1 °C at all times), and geometrical locations of simulation maximum and minimum temperature match well with the corresponding chamber temperature measurements. Furthermore, a control simulation test case was run (results taken from identical product box locations) to compare the coupled conduction-convection model with a conduction-only model, which to date has been the state-of-the-art method. For the conduction-only simulation, all fluid elements were replaced with "solid" elements of identical size and assigned thermal properties of air. While results from the coupled thermal/fluid model closely correlated with the empirical data (±1 °C), the conduction-only model was unable to correctly capture the payload temperature trends, showing a sizeable error compared to empirical values (ΔT > 6 °C). A modeling technique capable of correctly capturing the thermal behavior of passively refrigerated shippers can be used to quickly evaluate and optimize new packaging designs. Such a capability provides a means to reduce the cost and required design time of shippers while simultaneously improving their performance. Another advantage comes from using thermal modeling (assuming a validated model is available) to predict the temperature distribution in a shipper that is exposed to ambient temperatures which were not bracketed

  16. glmulti: An R Package for Easy Automated Model Selection with (Generalized Linear Models

    Directory of Open Access Journals (Sweden)

    Vincent Calcagno

    2010-10-01

    Full Text Available We introduce glmulti, an R package for automated model selection and multi-model inference with glm and related functions. From a list of explanatory variables, the provided function glmulti builds all possible unique models involving these variables and, optionally, their pairwise interactions. Restrictions can be specified for candidate models, by excluding specific terms, enforcing marginality, or controlling model complexity. Models are fitted with standard R functions like glm. The n best models and their support (e.g., (QAIC, (QAICc, or BIC are returned, allowing model selection and multi-model inference through standard R functions. The package is optimized for large candidate sets by avoiding memory limitation, facilitating parallelization and providing, in addition to exhaustive screening, a compiled genetic algorithm method. This article briefly presents the statistical framework and introduces the package, with applications to simulated and real data.

  17. File-based replica management

    CERN Document Server

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

    2005-01-01

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

  18. PtProcess: An R Package for Modelling Marked Point Processes Indexed by Time

    Directory of Open Access Journals (Sweden)

    David Harte

    2010-10-01

    Full Text Available This paper describes the package PtProcess which uses the R statistical language. The package provides a unified approach to fitting and simulating a wide variety of temporal point process or temporal marked point process models. The models are specified by an intensity function which is conditional on the history of the process. The user needs to provide routines for calculating the conditional intensity function. Then the package enables one to carry out maximum likelihood fitting, goodness of fit testing, simulation and comparison of models. The package includes the routines for the conditional intensity functions for a variety of standard point process models. The package is intended to simplify the fitting of point process models indexed by time in much the same way as generalized linear model programs have simplified the fitting of various linear models. The primary examples used in this paper are earthquake sequences but the package is intended to have a much wider applicability.

  19. The Computer-Aided Analytic Process Model. Operations Handbook for the Analytic Process Model Demonstration Package

    Science.gov (United States)

    1986-01-01

    Research Note 86-06 THE COMPUTER-AIDED ANALYTIC PROCESS MODEL : OPERATIONS HANDBOOK FOR THE ANALYTIC PROCESS MODEL DE ONSTRATION PACKAGE Ronald G...ic Process Model ; Operations Handbook; Tutorial; Apple; Systems Taxonomy Mod--l; Training System; Bradl1ey infantry Fighting * Vehicle; BIFV...8217. . . . . . . .. . . . . . . . . . . . . . . . * - ~ . - - * m- .. . . . . . . item 20. Abstract -continued companion volume-- "The Analytic Process Model for

  20. AGING PERFORMANCE OF MODEL 9975 PACKAGE FLUOROELASTOMER O-RINGS

    Energy Technology Data Exchange (ETDEWEB)

    Hoffman, E.; Daugherty, W.; Skidmore, E.; Dunn, K.; Fisher, D.

    2011-05-31

    The influence of temperature and radiation on Viton{reg_sign} GLT and GLT-S fluoroelastomer O-rings is an ongoing research focus at the Savannah River National Laboratory. The O-rings are credited for leaktight containment in the Model 9975 shipping package used for transportation of plutonium-bearing materials. At the Savannah River Site, the Model 9975 packages are being used for interim storage. Primary research efforts have focused on surveillance of O-rings from actual packages, leak testing of seals at bounding aging conditions and the effect of aging temperature on compression stress relaxation behavior, with the goal of service life prediction for long-term storage conditions. Recently, an additional effort to evaluate the effect of aging temperature on the oxidation of the materials has begun. Degradation in the mechanical properties of elastomers is directly related to the oxidation of the polymer. Sensitive measurements of the oxidation rate can be performed in a more timely manner than waiting for a measurable change in mechanical properties, especially at service temperatures. Measuring the oxidation rate therefore provides a means to validate the assumption that the degradation mechanisms(s) do not change from the elevated temperatures used for accelerated aging and the lower service temperatures. Monitoring the amount of oxygen uptake by the material over time at various temperatures can provide increased confidence in lifetime predictions. Preliminary oxygen consumption analysis of a Viton GLT-based fluoroelastomer compound (Parker V0835-75) using an Oxzilla II differential oxygen analyzer in the temperature range of 40-120 C was performed. Early data suggests oxygen consumption rates may level off within the first 100,000 hours (10-12 years) at 40 C and that sharp changes in the degradation mechanism (stress-relaxation) are not expected over the temperature range examined. This is consistent with the known long-term heat aging resistance of

  1. The R Package threg to Implement Threshold Regression Models

    Directory of Open Access Journals (Sweden)

    Tao Xiao

    2015-08-01

    This new package includes four functions: threg, and the methods hr, predict and plot for threg objects returned by threg. The threg function is the model-fitting function which is used to calculate regression coefficient estimates, asymptotic standard errors and p values. The hr method for threg objects is the hazard-ratio calculation function which provides the estimates of hazard ratios at selected time points for specified scenarios (based on given categories or value settings of covariates. The predict method for threg objects is used for prediction. And the plot method for threg objects provides plots for curves of estimated hazard functions, survival functions and probability density functions of the first-hitting-time; function curves corresponding to different scenarios can be overlaid in the same plot for comparison to give additional research insights.

  2. 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.

  3. Thermo-mechanical model optimization of HB-LED packaging

    NARCIS (Netherlands)

    Yuan, C.A.; Erinc, M.; Gielen, A.W.J.; Waal, A. van der; Driel, W. van; Zhang, K.

    2011-01-01

    Lighting is an advancing phenomenon both on the technology and on the market level due to the rapid development of the solid state lighting technology. The efforts in improving the efficacy of high brightness LED's (HB-LED) have concentrated on the packaging architecture. Packaging plays a significa

  4. Aluminum Laminates in Beverage Packaging: Models and Experiences

    Directory of Open Access Journals (Sweden)

    Gabriella Bolzon

    2015-08-01

    Full Text Available Aluminum laminates are among the main components of beverage packaging. These layered material systems are coupled to paperboard plies except in the cap opening area, where the human force limit sets a requirement on the material properties to allow open-ability and the mechanical characteristics are of particular interest. Experimental investigations have been carried out on this composite and on its components by either traditional or full-field measurement techniques. The interpretation of the collected data has been supported by the simulation of the performed tests considering either a homogenized material model or the individual laminate layers. However, different results may be recovered from similar samples due to physical factors like the material processing route and the embedded defectiveness. In turn, the conclusions may vary depending on the model assumptions. This contribution focuses on the physical effects and on the modeling of the large localized deformation induced by material singularities. This topic is discussed at the light of some experimental results.

  5. A Replica Placement Game Model for P2P Storage%一种 P2P 存储下的副本放置博弈模型*

    Institute of Scientific and Technical Information of China (English)

    宋玮; 朱兵章

    2013-01-01

      Replica balance in P2P storage system will affect usability greatly. Considering selfishness of peers, designs game model of P2P storage system. By using simple equilibrium achieving algo-rithm and effective P2P overlay network routing structure, designs game initiating and mainte-nance mechanism, which makes sure of balance in replica distribution. This model can bring great advantages of scalability, decentralized control and reliability and provide new solution for increasing demands on data storage.%  对等网络存储系统中副本的均衡性将影响的系统的可用性。考虑对等节点在放置数据副本时的自私性,建立 P2P 存储下的博弈模型,采用简单的博弈获取均衡算法,并借助 P2P 覆盖网络有效的路由结构与更新算法,设计博弈的发起及维护机制。模型保证数据副本在对等节点间的均衡分布,使 P2P 存储系统具有由良好的扩展性,分散控制和可靠性,为日益增长的数据存储需求提供新的解决方案。

  6. 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.

  7. AN ADA LINEAR ALGEBRA PACKAGE MODELED AFTER HAL/S

    Science.gov (United States)

    Klumpp, A. R.

    1994-01-01

    This package extends the Ada programming language to include linear algebra capabilities similar to those of the HAL/S programming language. The package is designed for avionics applications such as Space Station flight software. In addition to the HAL/S built-in functions, the package incorporates the quaternion functions used in the Shuttle and Galileo projects, and routines from LINPAK that solve systems of equations involving general square matrices. Language conventions in this package follow those of HAL/S to the maximum extent practical and minimize the effort required for writing new avionics software and translating existent software into Ada. Valid numeric types in this package include scalar, vector, matrix, and quaternion declarations. (Quaternions are fourcomponent vectors used in representing motion between two coordinate frames). Single precision and double precision floating point arithmetic is available in addition to the standard double precision integer manipulation. Infix operators are used instead of function calls to define dot products, cross products, quaternion products, and mixed scalar-vector, scalar-matrix, and vector-matrix products. The package contains two generic programs: one for floating point, and one for integer. The actual component type is passed as a formal parameter to the generic linear algebra package. The procedures for solving systems of linear equations defined by general matrices include GEFA, GECO, GESL, and GIDI. The HAL/S functions include ABVAL, UNIT, TRACE, DET, INVERSE, TRANSPOSE, GET, PUT, FETCH, PLACE, and IDENTITY. This package is written in Ada (Version 1.2) for batch execution and is machine independent. The linear algebra software depends on nothing outside the Ada language except for a call to a square root function for floating point scalars (such as SQRT in the DEC VAX MATHLIB library). This program was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

  8. AN ADA LINEAR ALGEBRA PACKAGE MODELED AFTER HAL/S

    Science.gov (United States)

    Klumpp, A. R.

    1994-01-01

    This package extends the Ada programming language to include linear algebra capabilities similar to those of the HAL/S programming language. The package is designed for avionics applications such as Space Station flight software. In addition to the HAL/S built-in functions, the package incorporates the quaternion functions used in the Shuttle and Galileo projects, and routines from LINPAK that solve systems of equations involving general square matrices. Language conventions in this package follow those of HAL/S to the maximum extent practical and minimize the effort required for writing new avionics software and translating existent software into Ada. Valid numeric types in this package include scalar, vector, matrix, and quaternion declarations. (Quaternions are fourcomponent vectors used in representing motion between two coordinate frames). Single precision and double precision floating point arithmetic is available in addition to the standard double precision integer manipulation. Infix operators are used instead of function calls to define dot products, cross products, quaternion products, and mixed scalar-vector, scalar-matrix, and vector-matrix products. The package contains two generic programs: one for floating point, and one for integer. The actual component type is passed as a formal parameter to the generic linear algebra package. The procedures for solving systems of linear equations defined by general matrices include GEFA, GECO, GESL, and GIDI. The HAL/S functions include ABVAL, UNIT, TRACE, DET, INVERSE, TRANSPOSE, GET, PUT, FETCH, PLACE, and IDENTITY. This package is written in Ada (Version 1.2) for batch execution and is machine independent. The linear algebra software depends on nothing outside the Ada language except for a call to a square root function for floating point scalars (such as SQRT in the DEC VAX MATHLIB library). This program was developed in 1989, and is a copyrighted work with all copyright vested in NASA.

  9. Analysis of Ecodesign Implementation and Solutions for Packaging Waste System by Using System Dynamics Modeling

    Science.gov (United States)

    Berzina, Alise; Dace, Elina; Bazbauers, Gatis

    2010-01-01

    This paper discusses the findings of a research project which explored the packaging waste management system in Latvia. The paper focuses on identifying how the policy mechanisms can promote ecodesign implementation and material efficiency improvement and therefore reduce the rate of packaging waste accumulation in landfill. The method used for analyzing the packaging waste management policies is system dynamics modeling. The main conclusion is that the existing legislative instruments can be used to create an effective policy for ecodesign implementation but substantially higher tax rates on packaging materials and waste disposal than the existing have to be applied.

  10. ShapeSelectForest: a new r package for modeling landsat time series

    Science.gov (United States)

    Mary Meyer; Xiyue Liao; Gretchen Moisen; Elizabeth. Freeman

    2015-01-01

    We present a new R package called ShapeSelectForest recently posted to the Comprehensive R Archival Network. The package was developed to fit nonparametric shape-restricted regression splines to time series of Landsat imagery for the purpose of modeling, mapping, and monitoring annual forest disturbance dynamics over nearly three decades. For each pixel and spectral...

  11. DMU - A Package for Analyzing Multivariate Mixed Models in quantitative Genetics and Genomics

    DEFF Research Database (Denmark)

    Madsen, Per; Jensen, Just; Labouriau, Rodrigo;

    The DMU-package for Analyzing Multivariate Mixed Models has been developed over a period of more than 25 years. This paper gives an overview of new features and the recent developments around the DMU-package, including: Genomic prediction (SNP-BLUP, G-BLUP and “One-Step”), Genome-wide association...

  12. 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.

  13. 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.

  14. 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.

  15. Advanced parametrical modelling of 24 GHz radar sensor IC packaging components

    Science.gov (United States)

    Kazemzadeh, R.; John, W.; Wellmann, J.; Bala, U. B.; Thiede, A.

    2011-08-01

    This paper deals with the development of an advanced parametrical modelling concept for packaging components of a 24 GHz radar sensor IC used in automotive driver assistance systems. For fast and efficient design of packages for system-in-package modules (SiP), a simplified model for the description of parasitic electromagnetic effects within the package is desirable, as 3-D field computation becomes inefficient due to the high density of conductive elements of the various signal paths in the package. By using lumped element models for the characterization of the conductive components, a fast indication of the design's signal-quality can be gained, but so far does not offer enough flexibility to cover the whole range of geometric arrangements of signal paths in a contemporary package. This work pursues to meet the challenge of developing a flexible and fast package modelling concept by defining parametric lumped-element models for all basic signal path components, e.g. bond wires, vias, strip lines, bumps and balls.

  16. visCOS: An R-package to evaluate model performance of hydrological models

    Science.gov (United States)

    Klotz, Daniel; Herrnegger, Mathew; Wesemann, Johannes; Schulz, Karsten

    2016-04-01

    The evaluation of model performance is a central part of (hydrological) modelling. Much attention has been given to the development of evaluation criteria and diagnostic frameworks. (Klemeš, 1986; Gupta et al., 2008; among many others). Nevertheless, many applications exist for which objective functions do not yet provide satisfying summaries. Thus, the necessity to visualize results arises in order to explore a wider range of model capacities, be it strengths or deficiencies. Visualizations are usually devised for specific projects and these efforts are often not distributed to a broader community (e.g. via open source software packages). Hence, the opportunity to explicitly discuss a state-of-the-art presentation technique is often missed. We therefore present a comprehensive R-package for evaluating model performance by visualizing and exploring different aspects of hydrological time-series. The presented package comprises a set of useful plots and visualization methods, which complement existing packages, such as hydroGOF (Zambrano-Bigiarini et al., 2012). It is derived from practical applications of the hydrological models COSERO and COSEROreg (Kling et al., 2014). visCOS, providing an interface in R, represents an easy-to-use software package for visualizing and assessing model performance and can be implemented in the process of model calibration or model development. The package provides functions to load hydrological data into R, clean the data, process, visualize, explore and finally save the results in a consistent way. Together with an interactive zoom function of the time series, an online calculation of the objective functions for variable time-windows is included. Common hydrological objective functions, such as the Nash-Sutcliffe Efficiency and the Kling-Gupta Efficiency, can also be evaluated and visualized in different ways for defined sub-periods like hydrological years or seasonal sections. Many hydrologists use long-term water-balances as a

  17. Extended Rasch Modeling: The eRm Package for the Application of IRT Models in R

    Directory of Open Access Journals (Sweden)

    Patrick Mair

    2007-02-01

    Full Text Available Item response theory models (IRT are increasingly becoming established in social science research, particularly in the analysis of performance or attitudinal data in psychology, education, medicine, marketing and other fields where testing is relevant. We propose the R package eRm (extended Rasch modeling for computing Rasch models and several extensions. A main characteristic of some IRT models, the Rasch model being the most prominent, concerns the separation of two kinds of parameters, one that describes qualities of the subject under investigation, and the other relates to qualities of the situation under which the response of a subject is observed. Using conditional maximum likelihood (CML estimation both types of parameters may be estimated independently from each other. IRT models are well suited to cope with dichotomous and polytomous responses, where the response categories may be unordered as well as ordered. The incorporation of linear structures allows for modeling the effects of covariates and enables the analysis of repeated categorical measurements. The eRm package fits the following models: the Rasch model, the rating scale model (RSM, and the partial credit model (PCM as well as linear reparameterizations through covariate structures like the linear logistic test model (LLTM, the linear rating scale model (LRSM, and the linear partial credit model (LPCM. We use an unitary, efficient CML approach to estimate the item parameters and their standard errors. Graphical and numeric tools for assessing goodness-of-fit are provided.

  18. Dynamic modelling and PID loop control of an oil-injected screw compressor package

    Science.gov (United States)

    Poli, G. W.; Milligan, W. J.; McKenna, P.

    2017-08-01

    A significant amount of time is spent tuning the PID (Proportional, Integral and Derivative) control loops of a screw compressor package due to the unique characteristics of the system. Common mistakes incurred during the tuning of a PID control loop include improper PID algorithm selection and unsuitable tuning parameters of the system resulting in erratic and inefficient operation. This paper details the design and development of software that aims to dynamically model the operation of a single stage oil injected screw compressor package deployed in upstream oil and gas applications. The developed software will be used to assess and accurately tune PID control loops present on the screw compressor package employed in controlling the oil pressures, temperatures and gas pressures, in a bid to improve control of the operation of the screw compressor package. Other applications of the modelling software will include its use as an evaluation tool that can estimate compressor package performance during start up, shutdown and emergency shutdown processes. The paper first details the study into the fundamental operational characteristics of each of the components present on the API 619 screw compressor package and then discusses the creation of a dynamic screw compressor model within the MATLAB/Simulink software suite. The paper concludes by verifying and assessing the accuracy of the created compressor model using data collected from physical screw compressor packages.

  19. truncSP: An R Package for Estimation of Semi-Parametric Truncated Linear Regression Models

    Directory of Open Access Journals (Sweden)

    Maria Karlsson

    2014-05-01

    Full Text Available Problems with truncated data occur in many areas, complicating estimation and inference. Regarding linear regression models, the ordinary least squares estimator is inconsistent and biased for these types of data and is therefore unsuitable for use. Alternative estimators, designed for the estimation of truncated regression models, have been developed. This paper presents the R package truncSP. The package contains functions for the estimation of semi-parametric truncated linear regression models using three different estimators: the symmetrically trimmed least squares, quadratic mode, and left truncated estimators, all of which have been shown to have good asymptotic and ?nite sample properties. The package also provides functions for the analysis of the estimated models. Data from the environmental sciences are used to illustrate the functions in the package.

  20. A critical review of constitutive models for solders in electronic packaging

    National Research Council Canada - National Science Library

    Chen, Gang; Zhao, Xiaochen; Wu, Hao

    2017-01-01

    .... Because the failure of the whole electronic packaging is often induced by the failure of solders, modeling and simulation of solder joint performance are quite important in ensuring the quality...

  1. Use of GEANT4 programme package for radiation technological modeling problems

    CERN Document Server

    Bratchenko, M I

    2001-01-01

    The results of pilot computer experiments directed toward the application of Geant4 package for modeling of gamma radiation dose distributions in homogeneous phantoms are presented. we demonstrate the potential of the package it self and of the developed add-on software modules for the calculations of three-dimensional absorbed dose distributions taking into account the design and geometry of model irradiators and phantoms.

  2. 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

  3. 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.

  4. Effects of deceptive packaging and product involvement on purchase intention: an elaboration likelihood model perspective.

    Science.gov (United States)

    Lammers, H B

    2000-04-01

    From an Elaboration Likelihood Model perspective, it was hypothesized that postexposure awareness of deceptive packaging claims would have a greater negative effect on scores for purchase intention by consumers lowly involved rather than highly involved with a product (n = 40). Undergraduates who were classified as either highly or lowly (ns = 20 and 20) involved with M&Ms examined either a deceptive or non-deceptive package design for M&Ms candy and were subsequently informed of the deception employed in the packaging before finally rating their intention to purchase. As anticipated, highly deceived subjects who were low in involvement rated intention to purchase lower than their highly involved peers. Overall, the results attest to the robustness of the model and suggest that the model has implications beyond advertising effects and into packaging effects.

  5. Packaging tomorrow : modelling the material input for European packaging in the 21st century

    NARCIS (Netherlands)

    Hekkert, M.P.; Joosten, L.A.J.; Worrell, E.

    2006-01-01

    This report is a result of the MATTER project (MATerials Technology for CO2 Emission Reduction). The project focuses on CO2 emission reductions that are related to the Western European materials system. The total impact of the reduction options for different scenario's will be modeled in MARKAL (MAR

  6. CML based estimation of extended Rasch models with the eRm package in R

    Directory of Open Access Journals (Sweden)

    PATRICK MAIR

    2007-03-01

    Full Text Available This paper presents an open source tool for computing extended Rasch models. It is realized in R (R Development Core Team, 2006 and available as package eRm. In addition to ordinary Rasch models extended models such as linear logistic test models, (linear rating scale models and (linear partial credit models can be estimated. A striking feature of this package is the implementation of conditional maximum likelihood estimation techniques which relate directly to Rasch's original concept of specific objectivity. The mathematical and epistemological benefits of this estimation method are discussed. Moreover, the capabilities of the eRm routine with respect to structural item response designs are demonstrated.

  7. Model-grid and hydraulic-property data arrays of the MULT package of the Central Valley Hydrologic Model

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital dataset defines the model-grid and hydraulic-property data arrays of the Multiplier (MULT) Package used in the transient hydrologic model of the Central...

  8. PyXel: A Python Package for Astronomical X-ray Data Modeling

    Science.gov (United States)

    Ogrean, Georgiana

    2016-06-01

    PyXel is an new Python package for modeling astronomical X-ray imaging data. It is built on NumPy, SciPy, matplotlib, and Astropy, and distributed under an open-source license. The package aims to provide a common set of image analysis tools for astronomers working with extended X-ray sources. I will present an overview of its existing and planned features, and analysis examples based on public Chandra data.

  9. Technical Review Report for the Safety Analysis Report for Packaging Model 9977 S-SARP-G-00001 Revision 2

    Energy Technology Data Exchange (ETDEWEB)

    DiSabatino, A; Hafner, R; West, M

    2007-10-04

    This Technical Review Report (TRR) summarizes the review findings for the Safety Analysis Report for Packaging (SARP) for the Model 9977 B(M)F-96 shipping container. The content analyzed for this submittal is Content Envelope C.1, Heat Sources, in assemblies of Radioisotope Thermoelectric Generators or food-pack cans. The SARP under review, i.e., S-SARP-G-00001, Revision 2 (August 2007), was originally referred to as the General Purpose Fissile Material Package. The review presented in this TRR was performed using the methods outlined in Revision 3 of the Department of Energy's (DOE's) Packaging Review Guide (PRG) for Reviewing Safety Analysis Reports for Packages. The format of the SARP follows that specified in Revision 2 of the Nuclear Regulatory Commission's, Regulatory Guide 7.9, i.e., Standard Format and Content of Part 71 Applications for Approval of Packages for Radioactive Material. Although the two documents are similar in their content, they are not identical. Formatting differences have been noted in this TRR, where appropriate. The Model 9977 Package is a 35-gallon drum package design that has evolved from a family of packages designed by DOE contractors at the Savannah River Site. The Model 9977 Package design includes a single, 6-inch diameter, stainless steel pressure vessel containment system (i.e., the 6CV) that was designed and fabricated in accordance with Section III, Subsection NB, of the American Society of Mechanical Engineers Boiler & Pressure Vessel Code. The earlier package designs, i.e., the Model 9965, 9966, 9967 and 9968 Packages, were originally designed and certified in the 1980s. In the 1990s, updated package designs that incorporated design features consistent with new safety requirements, based on International Atomic Energy Agency guidelines, were proposed. The updated package designs were the Model 9972, 9973, 9974 and 9975 Packages, respectively. The Model 9975 Package was certified by the Packaging Certification

  10. Modular modeling system for building distributed hydrologic models with a user-friendly software package

    Science.gov (United States)

    Wi, S.; Ray, P. A.; Brown, C.

    2015-12-01

    A software package developed to facilitate building distributed hydrologic models in a modular modeling system is presented. The software package provides a user-friendly graphical user interface that eases its practical use in water resources-related research and practice. The modular modeling system organizes the options available to users when assembling models according to the stages of hydrological cycle, such as potential evapotranspiration, soil moisture accounting, and snow/glacier melting processes. The software is intended to be a comprehensive tool that simplifies the task of developing, calibrating, validating, and using hydrologic models through the inclusion of intelligent automation to minimize user effort, and reduce opportunities for error. Processes so far automated include the definition of system boundaries (i.e., watershed delineation), climate and geographical input generation, and parameter calibration. Built-in post-processing toolkits greatly improve the functionality of the software as a decision support tool for water resources system management and planning. Example post-processing toolkits enable streamflow simulation at ungauged sites with predefined model parameters, and perform climate change risk assessment by means of the decision scaling approach. The software is validated through application to watersheds representing a variety of hydrologic regimes.

  11. The Langevin Approach: An R Package for Modeling Markov Processes

    Directory of Open Access Journals (Sweden)

    Philip Rinn

    2016-08-01

    Full Text Available We describe an 'R' package developed by the research group 'Turbulence, Wind energy' 'and Stochastics' (TWiSt at the Carl von Ossietzky University of Oldenburg, which extracts the (stochastic evolution equation underlying a set of data or measurements. The method can be directly applied to data sets with one or two stochastic variables. Examples for the one-dimensional and two-dimensional cases are provided. This framework is valid under a small set of conditions which are explicitly presented and which imply simple preliminary test procedures to the data. For Markovian processes involving Gaussian white noise, a stochastic differential equation is derived straightforwardly from the time series and captures the full dynamical properties of the underlying process. Still, even in the case such conditions are not fulfilled, there are alternative versions of this method which we discuss briefly and provide the user with the necessary bibliography.

  12. Modeling sustainable groundwater management: packaging and sequencing of policy interventions.

    Science.gov (United States)

    Esteban, Encarna; Dinar, Ariel

    2013-04-15

    Of the many studies estimating effectiveness of policy reforms most have been considering various types of policy reforms in isolation from each other. Such pattern has also been the case in water resource regulations. In the case of groundwater almost all policy interventions considered in the literature have been implemented individually, without taking into account the possible interactions and impacts among them. In this paper, we focus on two policy instruments: water quota and uniform water tax. The paper demonstrates how packaging and sequencing sets of policy interventions, with possible triggers to initiate their time of implementation, may be more effective in achieving a sustainable groundwater management than single policies when environmental externalities exist. The policy instruments are applied to the Western la Mancha aquifer in Southeast Spain, a major aquifer that is managed by a command and control approach. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. The Langevin Approach: An R Package for Modeling Markov Processes

    CERN Document Server

    Rinn, Philip; Wächter, Matthias; Peinke, Joachim

    2016-01-01

    We describe an R package developed by the research group Turbulence, Wind energy and Stochastics (TWiSt) at the Carl von Ossietzky University of Oldenburg, which extracts the (stochastic) evolution equation underlying a set of data or measurements. The method can be directly applied to data sets with one or two stochastic variables. Examples for the one-dimensional and two-dimensional cases are provided. This framework is valid under a small set of conditions which are explicitly presented and which imply simple preliminary test procedures to the data. For Markovian processes involving Gaussian white noise, a stochastic differential equation is derived straightforwardly from the time series and captures the full dynamical properties of the underlying process. Still, even in the case such conditions are not fulfilled, there are alternative versions of this method which we discuss briefly and provide the user with the necessary bibliography.

  14. Safety analysis report for packaging, Oak Ridge Y-12 Plant, model DC-1 package with HEU oxide contents. Change pages for Rev.1

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-01-18

    This Safety Analysis Report for Packaging for the Oak Ridge Y-12 Plant for the Model DC-1 package with highly enriched uranium (HEU) oxide contents has been prepared in accordance with governing regulations form the Nuclear Regulatory Commission and the Department of Transportation and orders from the Department of energy. The fundamental safety requirements addressed by these regulations and orders pertain to the containment of radioactive material, radiation shielding, and nuclear subcriticality. This report demonstrates how these requirements are met.

  15. 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.

  16. 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...

  17. A MATLAB Package for Markov Chain Monte Carlo with a Multi-Unidimensional IRT Model

    Directory of Open Access Journals (Sweden)

    Yanyan Sheng

    2008-11-01

    Full Text Available Unidimensional item response theory (IRT models are useful when each item is designed to measure some facet of a unified latent trait. In practical applications, items are not necessarily measuring the same underlying trait, and hence the more general multi-unidimensional model should be considered. This paper provides the requisite information and description of software that implements the Gibbs sampler for such models with two item parameters and a normal ogive form. The software developed is written in the MATLAB package IRTmu2no. The package is flexible enough to allow a user the choice to simulate binary response data with multiple dimensions, set the number of total or burn-in iterations, specify starting values or prior distributions for model parameters, check convergence of the Markov chain, as well as obtain Bayesian fit statistics. Illustrative examples are provided to demonstrate and validate the use of the software package.

  18. Random forest methodology for model-based recursive partitioning: the mobForest package for R

    OpenAIRE

    Garge, Nikhil R; Bobashev, Georgiy; Eggleston, Barry

    2013-01-01

    Background Recursive partitioning is a non-parametric modeling technique, widely used in regression and classification problems. Model-based recursive partitioning is used to identify groups of observations with similar values of parameters of the model of interest. The mob() function in the party package in R implements model-based recursive partitioning method. This method produces predictions based on single tree models. Predictions obtained through single tree models are very sensitive to...

  19. Development and application of compact models of packages based on DELPHI methodology

    CERN Document Server

    Parry, J; Shidore, S

    1997-01-01

    The accurate prediction of the temperatures of critical electronic parts at the package- board- and system-level is seriously hampered by the lack of reliable, standardised input data for the characterisation of the thermal $9 behaviour of these parts. The recently completed collaborative European project, DELPHI has been concerned with the creation and experimental validation of thermal models (both detailed and compact) of a range of electronic parts, $9 including mono-chip packages. This paper demonstrates the reliable performance of thermal compact models in a range of applications, by comparison with the detailed models from which they were derived. (31 refs).

  20. Modeling and simulation for microelectronic packaging assembly manufacturing, reliability and testing

    CERN Document Server

    Liu, Sheng

    2011-01-01

    Although there is increasing need for modeling and simulation in the IC package design phase, most assembly processes and various reliability tests are still based on the time consuming ""test and try out"" method to obtain the best solution. Modeling and simulation can easily ensure virtual Design of Experiments (DoE) to achieve the optimal solution. This has greatly reduced the cost and production time, especially for new product development. Using modeling and simulation will become increasingly necessary for future advances in 3D package development.  In this book, Liu and Liu allow people

  1. ltm: An R Package for Latent Variable Modeling and Item Response Analysis

    Directory of Open Access Journals (Sweden)

    Dimitris Rizopoulos

    2006-11-01

    Full Text Available The R package ltm has been developed for the analysis of multivariate dichotomous and polytomous data using latent variable models, under the Item Response Theory approach. For dichotomous data the Rasch, the Two-Parameter Logistic, and Birnbaum's Three-Parameter models have been implemented, whereas for polytomous data Semejima's Graded Response model is available. Parameter estimates are obtained under marginal maximum likelihood using the Gauss-Hermite quadrature rule. The capabilities and features of the package are illustrated using two real data examples.

  2. [download] (969dlmap: An R Package for Mixed Model QTL and Association Analysis

    Directory of Open Access Journals (Sweden)

    B. Emma Huang

    2012-08-01

    Full Text Available dlmap is a software package capable of mapping quantitative trait loci (QTL in a variety of genetic studies. Unlike most other QTL mapping packages, dlmap is built on a linear mixed model platform, and thus can simultaneously handle multiple sources of genetic and environmental variation. Furthermore, it can accommodate both experimental crosses and association mapping populations within a versatile modeling framework. The software implements a mapping algorithm with separate detection and localization stages in a user-friendly manner. It accepts data in various common formats, has a flexible modeling environment, and summarizes results both graphically and numerically.

  3. The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

    Science.gov (United States)

    Chaouiya, Claudine; Keating, Sarah M; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P; Le Novère, Nicolas; Helikar, Tomáš

    2015-09-04

    Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

  4. 'spup' - an R package for uncertainty propagation analysis in spatial environmental modelling

    Science.gov (United States)

    Sawicka, Kasia; Heuvelink, Gerard

    2017-04-01

    Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability and being able to deal with case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected visualization methods that are understandable by non-experts with limited background in

  5. 'spup' - an R package for uncertainty propagation in spatial environmental modelling

    Science.gov (United States)

    Sawicka, Kasia; Heuvelink, Gerard

    2016-04-01

    Computer models have become a crucial tool in engineering and environmental sciences for simulating the behaviour of complex static and dynamic systems. However, while many models are deterministic, the uncertainty in their predictions needs to be estimated before they are used for decision support. Currently, advances in uncertainty propagation and assessment have been paralleled by a growing number of software tools for uncertainty analysis, but none has gained recognition for a universal applicability, including case studies with spatial models and spatial model inputs. Due to the growing popularity and applicability of the open source R programming language we undertook a project to develop an R package that facilitates uncertainty propagation analysis in spatial environmental modelling. In particular, the 'spup' package provides functions for examining the uncertainty propagation starting from input data and model parameters, via the environmental model onto model predictions. The functions include uncertainty model specification, stochastic simulation and propagation of uncertainty using Monte Carlo (MC) techniques, as well as several uncertainty visualization functions. Uncertain environmental variables are represented in the package as objects whose attribute values may be uncertain and described by probability distributions. Both numerical and categorical data types are handled. Spatial auto-correlation within an attribute and cross-correlation between attributes is also accommodated for. For uncertainty propagation the package has implemented the MC approach with efficient sampling algorithms, i.e. stratified random sampling and Latin hypercube sampling. The design includes facilitation of parallel computing to speed up MC computation. The MC realizations may be used as an input to the environmental models called from R, or externally. Selected static and interactive visualization methods that are understandable by non-experts with limited background in

  6. 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

  7. 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.

  8. Independencies Induced from a Graphical Markov Model After Marginalization and Conditioning: The R Package ggm

    Directory of Open Access Journals (Sweden)

    Giovanni M. Marchetti

    2006-02-01

    Full Text Available We describe some functions in the R package ggm to derive from a given Markov model, represented by a directed acyclic graph, different types of graphs induced after marginalizing over and conditioning on some of the variables. The package has a few basic functions that find the essential graph, the induced concentration and covariance graphs, and several types of chain graphs implied by the directed acyclic graph (DAG after grouping and reordering the variables. These functions can be useful to explore the impact of latent variables or of selection effects on a chosen data generating model.

  9. LanHEP - a package for automatic generation of Feynman rules in gauge models

    CERN Document Server

    Semenov, A Yu

    1996-01-01

    We consider the general problem of derivation of the Feynman rules for the matrix elements in momentum representation from the given Lagrangian in coordinate space invariant under the transformation of some gauge group. LanHEP package presented in this paper allows to define in a convenient way the gauge model Lagrangian in canonical form and then to generate automatically the Feynman rules that can be used in the following calculation of the physical processes by means of CompHEP package. The detailed description of LanHEP commands is given and several examples of LanHEP applications (QED, QCD, Standard Model in the t'Hooft-Feynman gauge) are presented.

  10. 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.

  11. Finite element modelling for the investigation of edge effect in acoustic micro imaging of microelectronic packages

    Science.gov (United States)

    Shen Lee, Chean; Zhang, Guang-Ming; Harvey, David M.; Ma, Hong-Wei; Braden, Derek R.

    2016-02-01

    In acoustic micro imaging of microelectronic packages, edge effect is often presented as artifacts of C-scan images, which may potentially obscure the detection of defects such as cracks and voids in the solder joints. The cause of edge effect is debatable. In this paper, a 2D finite element model is developed on the basis of acoustic micro imaging of a flip-chip package using a 230 MHz focused transducer to investigate acoustic propagation inside the package in attempt to elucidate the fundamental mechanism that causes the edge effect. A virtual transducer is designed in the finite element model to reduce the coupling fluid domain, and its performance is characterised against the physical transducer specification. The numerical results showed that the under bump metallization (UBM) structure inside the package has a significant impact on the edge effect. Simulated wavefields also showed that the edge effect is mainly attributed to the horizontal scatter, which is observed in the interface of silicon die-to-the outer radius of solder bump. The horizontal scatter occurs even for a flip-chip package without the UBM structure.

  12. Release Mathematical Model of Active Agent from Packaging Material into Food

    Directory of Open Access Journals (Sweden)

    Xiuling Huang

    2013-01-01

    Full Text Available Active packaging is an innovative packaging technology by which active compounds are released from the package to enhance the quality and microbial safety for a wide range of foods. The problem of active ingredient release through the bilayer packaging food system is studied from a theoretical viewpoint. A release model is built to provide predictions of concentration and amount of active ingredient. The equations are built based on Fickian diffusion, and numerical solutions are obtained through finite difference. Different diffusion coefficients DP and DC of active ingredient in different packaging layers, partition coefficient kCP at the interface of outer layer and inner layer, partition coefficient kFC at the interface of inner layer and food, and mass transfer coefficient hm at the interface of inner layer and food are considered in the model. The effects of kCP, thicknesses of outer layer and inner layer, CP0, DP, DC, kFC, and hm on the release are discussed. Corresponding conclusions and analysis are given.

  13. 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 ...

  14. MODEL 9975 LIFE EXTENSION TEST PACKAGE 3 - INTERIM REPORT - JANUARY 2017

    Energy Technology Data Exchange (ETDEWEB)

    Daugherty, W. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2017-01-31

    Life extension package LE3 (9975-03203) has been instrumented and subjected to an elevated temperature environment for approximately 8 years. During this time, the cane fiberboard has been maintained at a maximum temperature of ~160 - 165 °F, which was established by a combination of internal (19 watts) and external heat sources. Several tests and parameters were used to characterize the package components. Results from these tests generally indicate agreement between this full-scale shipping package and small-scale laboratory tests on fiberboard samples, including the degradation models based on the laboratory tests. These areas of agreement include the rate of change of fiberboard weight, dimensions and density, and change in fiberboard thermal conductivity. Corrosion of the lead shield occurred at a high rate during the first several weeks of aging, but dropped significantly after most of the moisture in the fiberboard migrated away from the lead shield. Dimensional measurements of the lead shield indicate that no significant creep deformation has occurred. This is consistent with literature data that predict a very small creep deformation for the time at temperature experienced by this package. The SCV O-rings were verified to remain leak-tight after ~5 years aging at an average temperature of ~170 °F. This package provides an example of the extent to which moisture within a typical fiberboard assembly can redistribute in the presence of a temperature gradient such as might be created by a 19 watt internal heat load. The majority of water within the fiberboard migrated to the bottom layers of fiberboard, with approximately 2 kg of water (2 liters) eventually escaping from the package. Two conditions have developed that are not consistent with package certification requirements. The axial gap at the top of the package increased to a maximum value of 1.549 inches, exceeding the 1 inch criterion. In addition, staining and/or corrosion have formed in a few spots

  15. 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.

  16. Performance of Nonmigratory Iron Chelating Active Packaging Materials in Viscous Model Food Systems.

    Science.gov (United States)

    Roman, Maxine J; Decker, Eric A; Goddard, Julie M

    2015-09-01

    Many packaged food products undergo quality deterioration due to iron promoted oxidative reactions. Recently, we have developed a nonmigratory iron chelating active packaging material that represents a novel approach to inhibit oxidation of foods while addressing consumer demands for "cleanˮ labels. A challenge to the field of nonmigratory active packaging is ensuring that surface-immobilized active agents retain activity in a true food system despite diffusional limitations. Yet, the relationship between food viscosity and nonmigratory active packaging activity retention has never been characterized. The objective of this study was to investigate the influence of food viscosity on iron chelation by a nonmigratory iron chelating active packaging material. Methyl cellulose was added to aqueous buffered iron solutions to yield model systems with viscosities ranging from ∼1 to ∼10(5)  mPa·s, representing viscosities ranging from beverage to mayonnaise. Iron chelation was quantified by material-bound iron content using colorimetry and inductively coupled plasma-optical emission spectrometry (ICP-OES).  Maximum iron chelation was reached in solutions up to viscosity ∼10(2)  mPa·s. In more viscous solutions (up to ∼10(4)  mPa·s), there was a significant decrease in iron chelating capacity (P influence of different food hydrocolloids on the performance of nonmigratory iron chelating active packaging was characterized. Methyl cellulose and carrageenan did not compete with the material for specific iron chelation (P > 0.05). Materials retained 32% to 45% chelating capacity when in contact with competitively chelating hydrocolloids guar gum, locust bean gum, and xanthan gum. This work demonstrates the potential application of nonmigratory iron chelating active packaging in liquid and semi-liquid foods to allow for the removal of synthetic chelators, while maintaining food quality.

  17. An R package for fitting age, period and cohort models

    Directory of Open Access Journals (Sweden)

    Adriano Decarli

    2014-11-01

    Full Text Available In this paper we present the R implementation of a GLIM macro which fits age-period-cohort model following Osmond and Gardner. In addition to the estimates of the corresponding model, owing to the programming capability of R as an object oriented language, methods for printing, plotting and summarizing the results are provided. Furthermore, the researcher has fully access to the output of the main function (apc which returns all the models fitted within the function. It is so possible to critically evaluate the goodness of fit of the resulting model.

  18. Multilevel IRT Modeling in Practice with the Package mlirt

    NARCIS (Netherlands)

    Fox, Jean-Paul

    2007-01-01

    Variance component models are generally accepted for the analysis of hierarchical structured data. A shortcoming is that outcome variables are still treated as measured without an error. Unreliable variables produce biases in the estimates of the other model parameters. The variability of the relati

  19. ergm: A Package to Fit, Simulate and Diagnose Exponential-Family Models for Networks

    Directory of Open Access Journals (Sweden)

    David R. Hunter

    2008-12-01

    Full Text Available We describe some of the capabilities of the ergm package and the statistical theory underlying it. This package contains tools for accomplishing three important, and inter-related, tasks involving exponential-family random graph models (ERGMs: estimation, simulation, and goodness of fit. More precisely, ergm has the capability of approximating a maximum likelihood estimator for an ERGM given a network data set; simulating new network data sets from a fitted ERGM using Markov chain Monte Carlo; and assessing how well a fitted ERGM does at capturing characteristics of a particular network data set.

  20. PyXel: A Python Package for Astronomical X-ray Data Modeling

    Science.gov (United States)

    Ogrean, Georgiana

    2017-01-01

    PyXel is a open-source Python package for modeling astronomical X-ray imaging data. It is primarily built on NumPy, SciPy, Astropy, and emcee. The package aims to provide a common set of image analysis tools for astronomers working with extended X-ray sources. I will present an overview of its features, and analysis examples based on public Chandra data.The code is available for download on GitHub (https://github.com/gogrean/PyXel), and contributions to it are welcome.

  1. airGRteaching: an R-package designed for teaching hydrology with lumped hydrological models

    Science.gov (United States)

    Thirel, Guillaume; Delaigue, Olivier; Coron, Laurent; Andréassian, Vazken; Brigode, Pierre

    2017-04-01

    Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2016), called airGR (Coron et al., 2016, 2017), to make these models widely available. Although its initial target public was hydrological modellers, the package is already used for educational purposes. Indeed, simple models allow for rapidly visualising the effects of parameterizations and model components on flows hydrographs. In order to avoid the difficulties that students may have when manipulating R and datasets, we developed (Delaigue and Coron, 2016): - Three simplified functions to prepare data, calibrate a model and run a simulation - Simplified and dynamic plot functions - A shiny (Chang et al., 2016) interface that connects this R-package to a browser-based visualisation tool. On this interface, the students can use different hydrological models (including the possibility to use a snow-accounting model), manually modify their parameters and automatically calibrate their parameters with diverse objective functions. One of the visualisation tabs of the interface includes observed precipitation and temperature, simulated snowpack (if any), observed and simulated

  2. Certified reference materials for food packaging specific migration tests: development, validation and modelling

    NARCIS (Netherlands)

    Stoffers, N.H.

    2005-01-01

    Keywords:certified reference materials; diffusion; food contact materials; food packaging; laurolactam; migration modelling; nylon; specific migration This thesis compiles several research topics

  3. Predictive modeling of migration from packaging materials into food products for regulatory purposes

    NARCIS (Netherlands)

    Helmroth, I.E.; Rijk, R.; Dekker, M.; Jongen, W.M.F.

    2002-01-01

    Migration of low-molecular weight compounds is one of the most important problems of packaging plastics and other plastics intended to come into contact with food products. Since migration experiments are time consuming and expensive, predictive modelling has been introduced as a promising alternati

  4. robustlmm: An R Package for Robust Estimation of Linear Mixed-Effects Models

    Directory of Open Access Journals (Sweden)

    Manuel Koller

    2016-12-01

    Full Text Available As any real-life data, data modeled by linear mixed-effects models often contain outliers or other contamination. Even little contamination can drive the classic estimates far away from what they would be without the contamination. At the same time, datasets that require mixed-effects modeling are often complex and large. This makes it difficult to spot contamination. Robust estimation methods aim to solve both problems: to provide estimates where contamination has only little influence and to detect and flag contamination. We introduce an R package, robustlmm, to robustly fit linear mixed-effects models. The package's functions and methods are designed to closely equal those offered by lme4, the R package that implements classic linear mixed-effects model estimation in R. The robust estimation method in robustlmm is based on the random effects contamination model and the central contamination model. Contamination can be detected at all levels of the data. The estimation method does not make any assumption on the data's grouping structure except that the model parameters are estimable. robustlmm supports hierarchical and non-hierarchical (e.g., crossed grouping structures. The robustness of the estimates and their asymptotic efficiency is fully controlled through the function interface. Individual parts (e.g., fixed effects and variance components can be tuned independently. In this tutorial, we show how to fit robust linear mixed-effects models using robustlmm, how to assess the model fit, how to detect outliers, and how to compare different fits.

  5. 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.

  6. pyBSM: A Python package for modeling imaging systems

    Science.gov (United States)

    LeMaster, Daniel A.; Eismann, Michael T.

    2017-05-01

    There are components that are common to all electro-optical and infrared imaging system performance models. The purpose of the Python Based Sensor Model (pyBSM) is to provide open source access to these functions for other researchers to build upon. Specifically, pyBSM implements much of the capability found in the ERIM Image Based Sensor Model (IBSM) V2.0 along with some improvements. The paper also includes two use-case examples. First, performance of an airborne imaging system is modeled using the General Image Quality Equation (GIQE). The results are then decomposed into factors affecting noise and resolution. Second, pyBSM is paired with openCV to evaluate performance of an algorithm used to detect objects in an image.

  7. VHDL Models with Usage of the LFSR_PCKG Package

    Directory of Open Access Journals (Sweden)

    J. Mitrych

    2002-04-01

    Full Text Available LFSRs (Linear Feedback Shift Registers are very often used in theBIST (Built-In Self-Test methodology. Implementation of the LFSRs tothe design or application of digital system, which supports BISTtechniques or which only uses these LFSRs, can be done by VHDLlanguage. This paper presents VHDL models of the devices andsubroutines (e.g. test pattern generators, signature analysers. Modelsare based on LFSR structures with usage of the LFSR_PCKG packagedescribed in the (Kovalsky and Vlcek, 2001, which can be usedin the applications supporting BIST techniques. Devices are describedas behavioural and structural models. These models and descriptions canbe used e.g. in the (Kovalsky, 2001. The LFSR_PCKG was modifiedand new approach is presented. Naturally, there are presented somesynthesis conclusions of the VHDL models and applications in thispaper.

  8. Predictive modelling for packaging design: equilibrium modified atmosphere packages of fresh-cut vegetables subjected to a simulated distribution chain.

    Science.gov (United States)

    Jacxsens, L; Devlieghere, F; Debevere, J

    2002-03-01

    The impact of temperature fluctuations in a simulated cold distribution chain, typical of commercial practice, was investigated on both the microbial and sensorial quality of equilibrium modified atmosphere (EMA) packaged minimally processed vegetables. The internal O2 concentration of the designed packages could be predicted for the different steps of the simulated distribution chain by applying an integrated mathematical system. The internal atmosphere in the packages remained in its aerobic range during storage in the chain due to the application of high permeable packaging films for O2 and CO2. Spoilage microorganisms were proliferating fast on minimally processed bell peppers and lettuce. Yeasts showed to be the shelf-life limiting group. Visual properties limited the sensorial shelf-life. Listeria monocytogenes was able to multiply on cucumber slices, survived on minimally processed lettuce and decreased in number on bell peppers due to the combination of low pH and refrigeration. Aeromonas caviae was multiplying on both cucumber slices and mixed lettuce, but was as well inhibited by the low pH of bell peppers. Storage temperature control was found to be of paramount importance for the microbial (spoilage and safety) and sensorial quality evaluation of EMA-packaged minimally processed vegetables.

  9. Program package for constructing analytical models of industrial robots

    Energy Technology Data Exchange (ETDEWEB)

    Vukobratovich, M.; Kirchanskiy, N.

    Complex multidimensional nonlinear dynamic systems are controlled with the use of control computers differing in their complexity, from large ones at the level of the modeling of the dynamics of the system and synthesis of the control algorithm to microcomputers directly controlling the system. One of the main decisive problems in controlling an industrial robot is the generation of a dynamic on-line model. For this purpose, a separate microcomputer or several computers operating in the multiprocessor mode are used. The existing methods of robot dynamics simulation which are based on the equations of Newton-Euler, Lagrange and others require a large number of numerical operations and they cannot be realized in real time: the time spent on the construction of a model is several times greater than that acceptable for the computer. This is explained by the following factors: complexity of the mathematical model, the use of a high-level language for programming, the desire to construct an algorithm of a general kind, which leads to high redundancy of numerical operations; the use of recursion relations, which excludes the possibility of performing parallel operations during the realization in a computer. Special characteristics of the construction of a program system which is to a considerable degree free of the above drawbacks is considered below. Instead of directly constructing a model in the numerical form on the basis of one of the approaches of classical mechanics, the concept of constructing a model in symbols is proposed here. It is possible to show that in this way it is possible to obtain a compact mathematical model which requires fewer numerical operations (multiplication, addition) for its realization by two orders in comparison with the methods used earlier. 9 references, 2 tables.

  10. Inferring 3D Articulated Models for Box Packaging Robot

    CERN Document Server

    Yang, Heran; Cong, Matthew; Saxena, Ashutosh

    2011-01-01

    Given a point cloud, we consider inferring kinematic models of 3D articulated objects such as boxes for the purpose of manipulating them. While previous work has shown how to extract a planar kinematic model (often represented as a linear chain), such planar models do not apply to 3D objects that are composed of segments often linked to the other segments in cyclic configurations. We present an approach for building a model that captures the relation between the input point cloud features and the object segment as well as the relation between the neighboring object segments. We use a conditional random field that allows us to model the dependencies between different segments of the object. We test our approach on inferring the kinematic structure from partial and noisy point cloud data for a wide variety of boxes including cake boxes, pizza boxes, and cardboard cartons of several sizes. The inferred structure enables our robot to successfully close these boxes by manipulating the flaps.

  11. bspmma: An R Package for Bayesian Semiparametric Models for Meta-Analysis

    Directory of Open Access Journals (Sweden)

    Deborah Burr

    2012-07-01

    Full Text Available We introduce an R package, bspmma, which implements a Dirichlet-based random effects model specific to meta-analysis. In meta-analysis, when combining effect estimates from several heterogeneous studies, it is common to use a random-effects model. The usual frequentist or Bayesian models specify a normal distribution for the true effects. However, in many situations, the effect distribution is not normal, e.g., it can have thick tails, be skewed, or be multi-modal. A Bayesian nonparametric model based on mixtures of Dirichlet process priors has been proposed in the literature, for the purpose of accommodating the non-normality. We review this model and then describe a competitor, a semiparametric version which has the feature that it allows for a well-defined centrality parameter convenient for determining whether the overall effect is significant. This second Bayesian model is based on a different version of the Dirichlet process prior, and we call it the "conditional Dirichlet model". The package contains functions to carry out analyses based on either the ordinary or the conditional Dirichlet model, functions for calculating certain Bayes factors that provide a check on the appropriateness of the conditional Dirichlet model, and functions that enable an empirical Bayes selection of the precision parameter of the Dirichlet process. We illustrate the use of the package on two examples, and give an interpretation of the results in these two different scenarios.

  12. A modular approach for item response theory modeling with the R package flirt.

    Science.gov (United States)

    Jeon, Minjeong; Rijmen, Frank

    2016-06-01

    The new R package flirt is introduced for flexible item response theory (IRT) modeling of psychological, educational, and behavior assessment data. flirt integrates a generalized linear and nonlinear mixed modeling framework with graphical model theory. The graphical model framework allows for efficient maximum likelihood estimation. The key feature of flirt is its modular approach to facilitate convenient and flexible model specifications. Researchers can construct customized IRT models by simply selecting various modeling modules, such as parametric forms, number of dimensions, item and person covariates, person groups, link functions, etc. In this paper, we describe major features of flirt and provide examples to illustrate how flirt works in practice.

  13. Unified Geostatistical Modeling for Data Fusion and Spatial Heteroskedasticity with R Package ramps

    Directory of Open Access Journals (Sweden)

    Brian J. Smith

    2008-03-01

    Full Text Available This article illustrates usage of the ramps R package, which implements the reparameterized and marginalized posterior sampling (RAMPS algorithm for complex Bayesian geostatistical models. The RAMPS methodology allows joint modeling of areal and point-source data arising from the same underlying spatial process. A reparametrization of variance parameters facilitates slice sampling based on simplexes, which can be useful in general when multiple variances are present. Prediction at arbitrary points can be made, which is critical in applications where maps are needed. Our implementation takes advantage of sparse matrix operations in the Matrix package and can provide substantial savings in computing time for large datasets. A user-friendly interface, similar to the nlme mixed effects models package, enables users to analyze datasets with little programming effort. Support is provided for numerous spatial and spatiotemporal correlation structures, user-defined correlation structures, and non-spatial random effects. The package features are illustrated via a synthetic dataset of spatially correlated observation distributed across the state of Iowa, USA.

  14. Documentation pckage for the RFID temperature monitoring system (Of Model 9977 packages at NTS).

    Energy Technology Data Exchange (ETDEWEB)

    Chen, K.; Tsai, H.; Decision and Information Sciences

    2009-02-20

    The technical basis for extending the Model 9977 shipping package periodic maintenance beyond the one-year interval to a maximum of five years is based on the performance of the O-ring seals and the environmental conditions. The DOE Packaging Certification Program (PCP) has tasked Argonne National Laboratory to develop a Radio-Frequency Identification (RFID) temperature monitoring system for use by the facility personnel at DAF/NTS. The RFID temperature monitoring system, depicted in the figure below, consists of the Mk-1 RFId tags, a reader, and a control computer mounted on a mobile platform that can operate as a stand-alone system, or it can be connected to the local IT network. As part of the Conditions of Approval of the CoC, the user must complete the prescribed training to become qualified and be certified for operation of the RFID temperature monitoring system. The training course will be administered by Argonne National Laboratory on behalf of the Headquarters Certifying Official. This is a complete documentation package for the RFID temperature monitoring system of the Model 9977 packagings at NTS. The documentation package will be used for training and certification. The table of contents are: Acceptance Testing Procedure of MK-1 RFID Tags for DOE/EM Nuclear Materials Management Applications; Acceptance Testing Result of MK-1 RFID Tags for DOE/EM Nuclear Materials Management Applications; Performance Test of the Single Bolt Seal Sensor for the Model 9977 Packaging; Calibration of Built-in Thermistors in RFID Tags for Nevada Test Site; Results of Calibration of Built-in Thermistors in RFID Tags; Results of Thermal Calibration of Second Batch of MK-I RFID Tags; Procedure for Installing and Removing MK-1 RFID Tag on Model 9977 Drum; User Guide for RFID Reader and Software for Temperature Monitoring of Model 9977 Drums at NTS; Software Quality Assurance Plan (SQAP) for the ARG-US System; Quality Category for the RFID Temperature Monitoring System; The

  15. Estimating the Multilevel Rasch Model: With the lme4 Package

    Directory of Open Access Journals (Sweden)

    Harold Doran

    2007-02-01

    Full Text Available Traditional Rasch estimation of the item and student parameters via marginal maximum likelihood, joint maximum likelihood or conditional maximum likelihood, assume individuals in clustered settings are uncorrelated and items within a test that share a grouping structure are also uncorrelated. These assumptions are often violated, particularly in educational testing situations, in which students are grouped into classrooms and many test items share a common grouping structure, such as a content strand or a reading passage. Consequently, one possible approach is to explicitly recognize the clustered nature of the data and directly incorporate random effects to account for the various dependencies. This article demonstrates how the multilevel Rasch model can be estimated using the functions in R for mixed-effects models with crossed or partially crossed random effects. We demonstrate how to model the following hierarchical data structures: a individuals clustered in similar settings (e.g., classrooms, schools, b items nested within a particular group (such as a content strand or a reading passage, and c how to estimate a teacher × content strand interaction.

  16. 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.

  17. DEMONSTRATION OF EQUIVALENCY OF CANE AND SOFTWOOD BASED CELOTEX FOR MODEL 9975 SHIPPING PACKAGES

    Energy Technology Data Exchange (ETDEWEB)

    Watkins, R; Jason Varble, J

    2008-05-27

    Cane-based Celotex{trademark} has been used extensively in various Department of Energy (DOE) packages as a thermal insulator and impact absorber. Cane-based Celotex{trademark} fiberboard was only manufactured by Knight-Celotex Fiberboard at their Marrero Plant in Louisiana. However, Knight-Celotex Fiberboard shut down their Marrero Plant in early 2007 due to impacts from hurricane Katrina and other economic factors. Therefore, cane-based Celotex{trademark} fiberboard is no longer available for use in the manufacture of new shipping packages requiring the material as a component. Current consolidation plans for the DOE Complex require the procurement of several thousand new Model 9975 shipping packages requiring cane-based Celotex{trademark} fiberboard. Therefore, an alternative to cane-based Celotex{trademark} fiberboard is needed. Knight-Celotex currently manufactures Celotex{trademark} fiberboard from other cellulosic materials, such as hardwood and softwood. A review of the relevant literature has shown that softwood-based Celotex{trademark} meets all parameters important to the Model 9975 shipping package.

  18. 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.

  19. The Computer-Aided Analytic Process Model. Operations Handbook for the APM (Analytic Process Model) Demonstration Package. Appendix

    Science.gov (United States)

    1986-01-01

    The Analytic Process Model for System Design and Measurement: A Computer-Aided Tool for Analyzing Training Systems and Other Human-Machine Systems. A...separate companion volume--The Computer-Aided Analytic Process Model : Operations Handbook for the APM Demonstration Package is also available under

  20. Estimating Population Abundance Using Sightability Models: R SightabilityModel Package

    Directory of Open Access Journals (Sweden)

    John R. Fieberg

    2012-11-01

    Full Text Available Sightability models are binary logistic-regression models used to estimate and adjust for visibility bias in wildlife-population surveys (Steinhorst and Samuel 1989. Estimation proceeds in 2 stages: (1 Sightability trials are conducted with marked individuals, and logistic regression is used to estimate the probability of detection as a function of available covariates (e.g., visual obstruction, group size. (2 The fitted model is used to adjust counts (from future surveys for animals that were not observed. A modified Horvitz-Thompson estimator is used to estimate abundance: counts of observed animal groups are divided by their inclusion probabilites (determined by plot-level sampling probabilities and the detection probabilities estimated from stage 1. We provide a brief historical account of the approach, clarifying and documenting suggested modifications to the variance estimators originally proposed by Steinhorst and Samuel (1989. We then introduce a new R package, SightabilityModel, for estimating abundance using this technique. Lastly, we illustrate the software with a series of examples using data collected from moose (Alces alces in northeastern Minnesota and mountain goats (Oreamnos americanus in Washington State.

  1. A two-dimensional simulation model for the molded underfill process in flip chip packaging

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Xue Ru; Young, Wen Bin [National Cheng Kung University, Tainan (China)

    2015-07-15

    The flip chip process involves the deposition of solder bumps on the chip surface and their subsequent direct attachment and connection to a substrate. Underfilling traditional flip chip packaging is typically performed following a two-step approach. The first step uses capillary force to fill the gap between the chip and the substrate, and the second step uses epoxy molding compound (EMC) to overmold the package. Unlike traditional flip chip packaging, the molded underfill (MUF) concept uses a single-step approach to simultaneously achieve both underfill and overmold. MUF is a simpler and faster process. In this study, a 2D numerical model is developed to simulate the front movement of EMC flow and the void formation for different geometric parameters. The 2D model simplifies the procedures of geometric modeling and reduces the modeling time for the MUF simulation. Experiments are conducted to verify the prediction results of the model. The effect on void formation for different geometric parameters is investigated using a 2D model.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. Distributed Lag Linear and Non-Linear Models in R: The Package dlnm

    Directory of Open Access Journals (Sweden)

    Antonio Gasparrini

    2011-08-01

    Full Text Available Distributed lag non-linear models (DLNMs represent a modeling framework to flexibly describe associations showing potentially non-linear and delayed effects in time series data. This methodology rests on the definition of a crossbasis, a bi-dimensional functional space expressed by the combination of two sets of basis functions, which specify the relationships in the dimensions of predictor and lags, respectively. This framework is implemented in the R package dlnm, which provides functions to perform the broad range of models within the DLNM family and then to help interpret the results, with an emphasis on graphical representation. This paper offers an overview of the capabilities of the package, describing the conceptual and practical steps to specify and interpret DLNMs with an example of application to real data.

  7. 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

  8. Introducing COZIGAM: An R Package for Unconstrained and Constrained Zero-Inflated Generalized Additive Model Analysis

    Directory of Open Access Journals (Sweden)

    Hai Liu

    2010-10-01

    Full Text Available Zero-inflation problem is very common in ecological studies as well as other areas. Nonparametric regression with zero-inflated data may be studied via the zero-inflated generalized additive model (ZIGAM, which assumes that the zero-inflated responses come from a probabilistic mixture of zero and a regular component whose distribution belongs to the 1-parameter exponential family. With the further assumption that the probability of non-zero-inflation is some monotonic function of the mean of the regular component, we propose the constrained zero-inflated generalized additive model (COZIGAM for analyzingzero-inflated data. When the hypothesized constraint obtains, the new approach provides a unified framework for modeling zero-inflated data, which is more parsimonious and efficient than the unconstrained ZIGAM. We have developed an R package COZIGAM which contains functions that implement an iterative algorithm for fitting ZIGAMs and COZIGAMs to zero-inflated data basedon the penalized likelihood approach. Other functions included in the package are useful for model prediction and model selection. We demonstrate the use of the COZIGAM package via some simulation studies and a real application.

  9. XCAT/DRASIM: a realistic CT/human-model simulation package

    Science.gov (United States)

    Fung, George S. K.; Stierstorfer, Karl; Segars, W. Paul; Taguchi, Katsuyuki; Flohr, Thomas G.; Tsui, Benjamin M. W.

    2011-03-01

    The aim of this research is to develop a complete CT/human-model simulation package by integrating the 4D eXtended CArdiac-Torso (XCAT) phantom, a computer generated NURBS surface based phantom that provides a realistic model of human anatomy and respiratory and cardiac motions, and the DRASIM (Siemens Healthcare) CT-data simulation program. Unlike other CT simulation tools which are based on simple mathematical primitives or voxelized phantoms, this new simulation package has the advantages of utilizing a realistic model of human anatomy and physiological motions without voxelization and with accurate modeling of the characteristics of clinical Siemens CT systems. First, we incorporated the 4D XCAT anatomy and motion models into DRASIM by implementing a new library which consists of functions to read-in the NURBS surfaces of anatomical objects and their overlapping order and material properties in the XCAT phantom. Second, we incorporated an efficient ray-tracing algorithm for line integral calculation in DRASIM by computing the intersection points of the rays cast from the x-ray source to the detector elements through the NURBS surfaces of the multiple XCAT anatomical objects along the ray paths. Third, we evaluated the integrated simulation package by performing a number of sample simulations of multiple x-ray projections from different views followed by image reconstruction. The initial simulation results were found to be promising by qualitative evaluation. In conclusion, we have developed a unique CT/human-model simulation package which has great potential as a tool in the design and optimization of CT scanners, and the development of scanning protocols and image reconstruction methods for improving CT image quality and reducing radiation dose.

  10. 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.

  11. 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.

  12. 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.

  13. 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,...

  14. Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R

    DEFF Research Database (Denmark)

    O'Connell, Jarad Michael; Højsgaard, Søren

    2011-01-01

    This paper describes the R package mhsmm which implements estimation and prediction methods for hidden Markov and semi-Markov models for multiple observation sequences. Such techniques are of interest when observed data is thought to be dependent on some unobserved (or hidden) state. Hidden Markov...... models only allow a geometrically distributed sojourn time in a given state, while hidden semi-Markov models extend this by allowing an arbitrary sojourn distribution. We demonstrate the software with simulation examples and an application involving the modelling of the ovarian cycle of dairy cows...

  15. metaSEM: an R package for meta-analysis using structural equation modeling.

    Science.gov (United States)

    Cheung, Mike W-L

    2014-01-01

    The metaSEM package provides functions to conduct univariate, multivariate, and three-level meta-analyses using a structural equation modeling (SEM) approach via the OpenMx package in the R statistical platform. It also implements the two-stage SEM approach to conducting fixed- and random-effects meta-analytic SEM on correlation or covariance matrices. This paper briefly outlines the theories and their implementations. It provides a summary on how meta-analyses can be formulated as structural equation models. The paper closes with a conclusion on several relevant topics to this SEM-based meta-analysis. Several examples are used to illustrate the procedures in the supplementary material.

  16. Implementing a Simulation Study Using Multiple Software Packages for Structural Equation Modeling

    Directory of Open Access Journals (Sweden)

    Sunbok Lee

    2015-07-01

    Full Text Available A Monte Carlo simulation study is an essential tool for evaluating the behavior of various quantitative methods including structural equation modeling (SEM under various conditions. Typically, a large number of replications are recommended for a Monte Carlo simulation study, and therefore automating a Monte Carlo simulation study is important to get the desired number of replications for a simulation study. This article is intended to provide concrete examples for automating a Monte Carlo simulation study using some standard software packages for SEM: Mplus, LISREL, SAS PROC CALIS, and R package lavaan. Also, the equivalence between the multilevel SEM and hierarchical linear modeling (HLM is discussed, and relevant examples are provided. It is hoped that the codes in this article can provide some building blocks for researchers to write their own code to automate simulation procedures.

  17. 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.

  18. An Elastic Plastic Contact Model with Strain Hardening for the LAMMPS Granular Package

    Energy Technology Data Exchange (ETDEWEB)

    Kuhr, Bryan [Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States); Brake, Matthew Robert [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Component Science and Mechanics; Lechman, Jeremy B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Nanoscale and Reactive Processes

    2015-03-01

    The following details the implementation of an analytical elastic plastic contact model with strain hardening for normal im pacts into the LAMMPS granular package. The model assumes that, upon impact, the co llision has a period of elastic loading followed by a period of mixed elastic plas tic loading, with contributions to each mechanism estimated by a hyperbolic seca nt weight function. This function is implemented in the LAMMPS source code as the pair style gran/ep/history. Preliminary tests, simulating the pouring of pure nickel spheres, showed the elastic/plastic model took 1.66x as long as similar runs using gran/hertz/history.

  19. CASE ANALYSIS OF INNOVATION IN THE PACKAGING INDUSTRY USING THE CYCLIC INNOVATION MODEL

    OpenAIRE

    Ford, Nicholas; Trott, Paul; Simms, Chris; Hartmann, Dap

    2014-01-01

    This paper builds upon Berkhout et al.’s (2010) cyclic innovation model (CIM). This model was shown to provide an effective framework for understanding and managing the innovation process and to address many of the shortcomings of previous models. Building on that article we have applied CIM to an in-depth case study featuring a formable paperboard technology within the packaging industry. Using data gathered from 28 interviews conducted over a three year period, CIM, for the first time, is a...

  20. Numerical modeling and validation of squeezed-film damping in vacuum-packaged industrial MEMS

    Science.gov (United States)

    Syed, Wajih U.; Brimmo, Ayoola; Waheed, Owais; Bojesomo, Alabi; Hassan Ali, Mohamed; Ocak, Ilker; Chengliang, Sun; Chatterjee, Aveek; Elfadel, Ibrahim (Abe M.

    2017-07-01

    Several high-performance, industrial micro-electromechanical (MEM) devices, such as gyroscopes, magnetometers, high-Q resonators and piezoelectric energy harvesters, require wafer bonding and packaging under near-vacuum conditions. One very challenging aspect of the design, verification and characterisation of these devices is to predict their performance characteristics in the presence of any residual gases post-packaging. Such gases contribute to the energy losses resulting from device surfaces squeezing or sliding against the gas films within the device cavities. In this paper, we fully expose the modelling assumptions used in commercial FEM tools to estimate the squeezed-film damping (SFD) experienced by MEM devices that are packaged under near-vacuum conditions. We also explain the various meshing options to enable the extraction of the most accurate Q factors under existing SFD assumptions. In addition, we compare the computational results across a variety of commercial FEM codes against measurements obtained under realistic vacuum conditions for an industrial high-Q magnetometer. These measurements suggest that existing computational models may deviate by as much as 25% on Q factor values for gas flow regimes under operating cavity pressures of less than 1 Torr.

  1. Radiative transfer modeling through terrestrial atmosphere and ocean accounting for inelastic processes: Software package SCIATRAN

    Science.gov (United States)

    Rozanov, V. V.; Dinter, T.; Rozanov, A. V.; Wolanin, A.; Bracher, A.; Burrows, J. P.

    2017-06-01

    SCIATRAN is a comprehensive software package which is designed to model radiative transfer processes in the terrestrial atmosphere and ocean in the spectral range from the ultraviolet to the thermal infrared (0.18-40 μm). It accounts for multiple scattering processes, polarization, thermal emission and ocean-atmosphere coupling. The main goal of this paper is to present a recently developed version of SCIATRAN which takes into account accurately inelastic radiative processes in both the atmosphere and the ocean. In the scalar version of the coupled ocean-atmosphere radiative transfer solver presented by Rozanov et al. [61] we have implemented the simulation of the rotational Raman scattering, vibrational Raman scattering, chlorophyll and colored dissolved organic matter fluorescence. In this paper we discuss and explain the numerical methods used in SCIATRAN to solve the scalar radiative transfer equation including trans-spectral processes, and demonstrate how some selected radiative transfer problems are solved using the SCIATRAN package. In addition we present selected comparisons of SCIATRAN simulations with those published benchmark results, independent radiative transfer models, and various measurements from satellite, ground-based, and ship-borne instruments. The extended SCIATRAN software package along with a detailed User's Guide is made available for scientists and students, who are undertaking their own research typically at universities, via the web page of the Institute of Environmental Physics (IUP), University of Bremen: http://www.iup.physik.uni-bremen.de.

  2. strucchange: An R Package for Testing for Structural Change in Linear Regression Models

    Directory of Open Access Journals (Sweden)

    Achim Zeileis

    2002-01-01

    Full Text Available This paper reviews tests for structural change in linear regression models from the generalized fluctuation test framework as well as from the F test (Chow test framework. It introduces a unified approach for implementing these tests and presents how these ideas have been realized in an R package called strucchange. Enhancing the standard significance test approach the package contains methods to fit, plot and test empirical fluctuation processes (like CUSUM, MOSUM and estimates-based processes and to compute, plot and test sequences of F statistics with the supF , aveF and expF test. Thus, it makes powerful tools available to display information about structural changes in regression relationships and to assess their significance. Furthermore, it is described how incoming data can be monitored.

  3. Application of Tube-Packaged FBG Strain Sensor in Vibration Experiment of Submarine Pipeline Model

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Optical fiber sensors have received increasing attention in the fields of aeronautic and civil engineering for their superior ability to stand explosion, immunity to electromagnetic interference and high accuracy, especially fit for measurement applications in harsh environment. In this study, a novel FBG (fiber Bragg grating) strain sensor, which is packaged in a 1.2 mm stainless steel tube with epoxy resin, is developed. Experiments are conducted on the universal material testing machine to calibrate its strain transferring characteristics. The sensor has the advantages of small size, high precision and flexible use, and exhibits promising potentials. Five tube-packaged strain FBG sensors have been applied to the vibration experiment of a submarine pipeline model. The strain measured with the FBG sensor agrees well with that measured with the electric resistance strain sensor.

  4. Groundwater flow and solute transport modelling from within R: Development of the RMODFLOW and RMT3DMS packages.

    Science.gov (United States)

    Rogiers, Bart

    2015-04-01

    Since a few years, an increasing number of contributed R packages is becoming available, in the field of hydrology. Hydrological time series analysis packages, lumped conceptual rainfall-runoff models, distributed hydrological models, weather generators, and different calibration and uncertainty estimation methods are all available. Also a few packages are available for solving partial differential equations. Subsurface hydrological modelling is however still seldomly performed in R, or with codes interfaced with R, despite the fact that excellent geostatistical packages, model calibration/inversion options and state-of-the-art visualization libraries are available. Moreover, other popular scientific programming languages like matlab and python have packages for pre- and post-processing files of MODFLOW (Harbaugh 2005) and MT3DMS (Zheng 2010) models. To fill this gap, we present here the development versions of the RMODFLOW and RMT3DMS packages, which allow pre- and post-processing MODFLOW and MT3DMS input and output files from within R. File reading and writing functions are currently available for different packages, and plotting functions are foreseen making use of the ggplot2 package (plotting system based on the grammar of graphics; Wickham 2009). The S3 generic-function object oriented programming style is used for this. An example is provided, making modifications to an existing model, and visualization of the model output. References Harbaugh, A. (2005). MODFLOW-2005: The US Geological Survey Modular Ground-water Model--the Ground-water Flow Process, U.S. Geological Survey Techniques and Methods 6-A16 (p. 253). Wickham, H. (2009). ggplot2: elegant graphics for data analysis. Springer New York, 2009. Zheng, C. (2010). MT3DMS v5.3, a modular three-dimensional multispecies transport model for simulation of advection, dispersion and chemical reactions of contaminants in groundwater systems. Supplemental User's Guide. (p. 56).

  5. 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.

  6. msSurv: An R Package for Nonparametric Estimation of Multistate Models

    Directory of Open Access Journals (Sweden)

    Nicole Ferguson

    2012-09-01

    Full Text Available We present an R package, msSurv, to calculate the marginal (that is, not conditional on any covariates state occupation probabilities, the state entry and exit time distributions, and the marginal integrated transition hazard for a general, possibly non-Markov, multistate system under left-truncation and right censoring. For a Markov model, msSurv also calculates and returns the transition probability matrix between any two states. Dependent censoring is handled via modeling the censoring hazard through observable covariates. Pointwise confidence intervals for the above mentioned quantities are obtained and returned for independent censoring from closed-form variance estimators and for dependent censoring using the bootstrap.

  7. Linear Quantile Mixed Models: The lqmm Package for Laplace Quantile Regression

    Directory of Open Access Journals (Sweden)

    Marco Geraci

    2014-05-01

    Full Text Available Inference in quantile analysis has received considerable attention in the recent years. Linear quantile mixed models (Geraci and Bottai 2014 represent a ?exible statistical tool to analyze data from sampling designs such as multilevel, spatial, panel or longitudinal, which induce some form of clustering. In this paper, I will show how to estimate conditional quantile functions with random e?ects using the R package lqmm. Modeling, estimation and inference are discussed in detail using a real data example. A thorough description of the optimization algorithms is also provided.

  8. Modeling of Stress Corrosion Cracking for High Level Radioactive-Waste Packages

    Energy Technology Data Exchange (ETDEWEB)

    Lu, S C; Gordon, G M; Andresen, P L; Herrera, M L

    2003-06-20

    A stress corrosion cracking (SCC) model has been adapted for performance prediction of high level radioactive-waste packages to be emplaced in the proposed Yucca Mountain radioactive-waste repository. SCC is one form of environmentally assisted cracking due to three factors, which must be present simultaneously: metallurgical susceptibility, critical environment, and static (or sustained) tensile stresses. For waste packages of the proposed Yucca Mountain repository, the outer barrier material is Alloy 22, a highly corrosion resistant alloy, the environment is represented by the water film present on the surface of the waste package from dripping or deliquescence of soluble salts present in any surface deposits, and the stress is principally the weld induced residual stress. SCC has historically been separated into ''initiation'' and ''propagation'' phases. Initiation of SCC will not occur on a smooth surface if the surface stress is below a threshold value defined as the threshold stress. Cracks can also initiate at and propagate from flaws (or defects) resulting from manufacturing processes (such as welding). To account for crack propagation, the slip dissolution/film rupture (SDFR) model is adopted to provide mathematical formulas for prediction of the crack growth rate. Once the crack growth rate at an initiated SCC is determined, the time to through-wall penetration for the waste package can be calculated. The SDFR model relates the advance (or propagation) of cracks, subsequent to the crack initiation from bare metal surface, to the metal oxidation transients that occur when the protective film at the crack tip is continually ruptured and repassivated. A crack, however, may reach the ''arrest'' state before it enters the ''propagation'' phase. There exists a threshold stress intensity factor, which provides a criterion for determining if an initiated crack or pre

  9. 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 ...

  10. Performance Evaluation of O-Ring Seals in Model 9975 Packaging Assemblies (U)

    Energy Technology Data Exchange (ETDEWEB)

    Skidmore, Eric

    1998-12-28

    The Materials Consultation Group of SRTC has completed a review of existing literature and data regarding the useable service life of Viton{reg_sign} GLT fluoroelastomer O-rings currently used in the Model 9975 packaging assemblies. Although the shipping and transportation period is normally limited to 2 years, it is anticipated that these packages will be used for longer-term storage of Pu-bearing materials in KAMS (K-Area Materials Storage) prior to processing or disposition in the APSF (Actinide Packaging and Storage Facility). Based on the service conditions and review of available literature, Materials Consultation concludes that there is sufficient existing data to establish the technical basis for storage of Pu-bearing materials using Parker Seals O-ring compound V835-75 (or equivalent) for up to 10 years following the 2-year shipping period. Although significant physical deterioration of the O-rings and release of product is not expected, definite changes in physical properties will occur. However, due to the complex relationship between elastomer formulation, seal properties, and competing degradation mechanisms, the actual degree of property variation and impact upon seal performance is difficult to predict. Therefore, accelerated aging and/or surveillance programs are recommended to validate the assumptions outlined in this report and to assess the long-term performance of O-ring seals under actual service conditions. Such programs could provide a unique opportunity to develop nonexistent long-term performance data, as well as address storage extension issues if necessary.

  11. 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.

  12. Bayesian ensemble refinement by replica simulations and reweighting.

    Science.gov (United States)

    Hummer, Gerhard; Köfinger, Jürgen

    2015-12-28

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

  13. 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.

  14. DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results

    Directory of Open Access Journals (Sweden)

    Gizzatkulov Nail M

    2010-08-01

    Full Text Available Abstract Background Systems biology research and applications require creation, validation, extensive usage of mathematical models and visualization of simulation results by end-users. Our goal is to develop novel method for visualization of simulation results and implement it in simulation software package equipped with the sophisticated mathematical and computational techniques for model development, verification and parameter fitting. Results We present mathematical simulation workbench DBSolve Optimum which is significantly improved and extended successor of well known simulation software DBSolve5. Concept of "dynamic visualization" of simulation results has been developed and implemented in DBSolve Optimum. In framework of the concept graphical objects representing metabolite concentrations and reactions change their volume and shape in accordance to simulation results. This technique is applied to visualize both kinetic response of the model and dependence of its steady state on parameter. The use of the dynamic visualization is illustrated with kinetic model of the Krebs cycle. Conclusion DBSolve Optimum is a user friendly simulation software package that enables to simplify the construction, verification, analysis and visualization of kinetic models. Dynamic visualization tool implemented in the software allows user to animate simulation results and, thereby, present them in more comprehensible mode. DBSolve Optimum and built-in dynamic visualization module is free for both academic and commercial use. It can be downloaded directly from http://www.insysbio.ru.

  15. A new vector radiative transfer model as a part of SCIATRAN 3.0 software package.

    Science.gov (United States)

    Rozanov, Alexei; Rozanov, Vladimir; Burrows, John P.

    The SCIATRAN 3.0 package is a result of further development of the SCIATRAN 2.x software family which, similar to previous versions, comprises a radiative transfer model and a retrieval block. A major improvement was achieved in comparison to previous software versions by adding the vector mode to the radiative transfer model. Thus, the well-established Discrete Ordinate solver can now be run in the vector mode to calculate the scattered solar radiation including polarization, i.e., to simulate all four components of the Stockes vector. Similar to the scalar version, the simulations can be performed for any viewing geometry typical for atmospheric observations in the UV-Vis-NIR spectral range (nadir, limb, off-axis, etc.) as well as for any observer position within or outside the Earth's atmosphere. Similar to the precursor version, the new model is freely available for non-commercial use via the web page of the University of Bremen. In this presentation a short description of the software package, especially of the new vector radiative transfer model will be given, including remarks on the availability for the scientific community. Furthermore, comparisons to other vector models will be shown and some example problems will be considered where the polarization of the observed radiation must be accounted for to obtain high quality results.

  16. Simulation-based Bayesian inference for latent traits of item response models: Introduction to the ltbayes package for R.

    Science.gov (United States)

    Johnson, Timothy R; Kuhn, Kristine M

    2015-12-01

    This paper introduces the ltbayes package for R. This package includes a suite of functions for investigating the posterior distribution of latent traits of item response models. These include functions for simulating realizations from the posterior distribution, profiling the posterior density or likelihood function, calculation of posterior modes or means, Fisher information functions and observed information, and profile likelihood confidence intervals. Inferences can be based on individual response patterns or sets of response patterns such as sum scores. Functions are included for several common binary and polytomous item response models, but the package can also be used with user-specified models. This paper introduces some background and motivation for the package, and includes several detailed examples of its use.

  17. 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.

  18. 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...

  19. Environmental and economic benefit of recycling model of packaging waste:a case study on aluminum

    Institute of Scientific and Technical Information of China (English)

    Huang Pingsha

    2004-01-01

    In order to achieve sustainable utilization of natural resources, save energy and protect environment and ecosystem, it is important for a region or a nation to develop and implement a viable waste recycling model from both theoretical and practical point of view. Some packaging recycling models operated in developed countries are introduced in this article. Aluminium can recovery and recycling is emphasized. Cost effective, economic and environmental benefit of different models are compared and analyzed. The result shows that all recycling models have their characteristics due to the initial purpose of recovery and the situation of the implementing country. However, all the models contribute to the reduction of municipal solid waste disposal and resources conservation.

  20. 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.

  1. Highly-optimized TWSM software package for seismic diffraction modeling adapted for GPU-cluster

    Science.gov (United States)

    Zyatkov, Nikolay; Ayzenberg, Alena; Aizenberg, Arkady

    2015-04-01

    Oil producing companies concern to increase resolution capability of seismic data for complex oil-and-gas bearing deposits connected with salt domes, basalt traps, reefs, lenses, etc. Known methods of seismic wave theory define shape of hydrocarbon accumulation with nonsufficient resolution, since they do not account for multiple diffractions explicitly. We elaborate alternative seismic wave theory in terms of operators of propagation in layers and reflection-transmission at curved interfaces. Approximation of this theory is realized in the seismic frequency range as the Tip-Wave Superposition Method (TWSM). TWSM based on the operator theory allows to evaluate of wavefield in bounded domains/layers with geometrical shadow zones (in nature it can be: salt domes, basalt traps, reefs, lenses, etc.) accounting for so-called cascade diffraction. Cascade diffraction includes edge waves from sharp edges, creeping waves near concave parts of interfaces, waves of the whispering galleries near convex parts of interfaces, etc. The basic algorithm of TWSM package is based on multiplication of large-size matrices (make hundreds of terabytes in size). We use advanced information technologies for effective realization of numerical procedures of the TWSM. In particular, we actively use NVIDIA CUDA technology and GPU accelerators allowing to significantly improve the performance of the TWSM software package, that is important in using it for direct and inverse problems. The accuracy, stability and efficiency of the algorithm are justified by numerical examples with curved interfaces. TWSM package and its separate components can be used in different modeling tasks such as planning of acquisition systems, physical interpretation of laboratory modeling, modeling of individual waves of different types and in some inverse tasks such as imaging in case of laterally inhomogeneous overburden, AVO inversion.

  2. Utilizing an Adaptive Grey Model for Short-Term Time Series Forecasting: A Case Study of Wafer-Level Packaging

    Directory of Open Access Journals (Sweden)

    Che-Jung Chang

    2013-01-01

    Full Text Available The wafer-level packaging process is an important technology used in semiconductor manufacturing, and how to effectively control this manufacturing system is thus an important issue for packaging firms. One way to aid in this process is to use a forecasting tool. However, the number of observations collected in the early stages of this process is usually too few to use with traditional forecasting techniques, and thus inaccurate results are obtained. One potential solution to this problem is the use of grey system theory, with its feature of small dataset modeling. This study thus uses the AGM(1,1 grey model to solve the problem of forecasting in the pilot run stage of the packaging process. The experimental results show that the grey approach is an appropriate and effective forecasting tool for use with small datasets and that it can be applied to improve the wafer-level packaging process.

  3. 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

  4. PyMT: A Python package for model-coupling in the Earth sciences

    Science.gov (United States)

    Hutton, E.

    2016-12-01

    The current landscape of Earth-system models is not only broad in scientific scope, but also broad in type. On the one hand, the large variety of models is exciting, as it provides fertile ground for extending or linking models together in novel ways to answer new scientific questions. However, the heterogeneity in model type acts to inhibit model coupling, model development, or even model use. Existing models are written in a variety of programming languages, operate on different grids, use their own file formats (both for input and output), have different user interfaces, have their own time steps, etc. Each of these factors become obstructions to scientists wanting to couple, extend - or simply run - existing models. For scientists whose main focus may not be computer science these barriers become even larger and become significant logistical hurdles. And this is all before the scientific difficulties of coupling or running models are addressed. The CSDMS Python Modeling Toolkit (PyMT) was developed to help non-computer scientists deal with these sorts of modeling logistics. PyMT is the fundamental package the Community Surface Dynamics Modeling System uses for the coupling of models that expose the Basic Modeling Interface (BMI). It contains: Tools necessary for coupling models of disparate time and space scales (including grid mappers) Time-steppers that coordinate the sequencing of coupled models Exchange of data between BMI-enabled models Wrappers that automatically load BMI-enabled models into the PyMT framework Utilities that support open-source interfaces (UGRID, SGRID,CSDMS Standard Names, etc.) A collection of community-submitted models, written in a variety of programminglanguages, from a variety of process domains - but all usable from within the Python programming language A plug-in framework for adding additional BMI-enabled models to the framework In this presentation we intoduce the basics of the PyMT as well as provide an example of coupling

  5. SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

    Science.gov (United States)

    Noel, Jeffrey K; Levi, Mariana; Raghunathan, Mohit; Lammert, Heiko; Hayes, Ryan L; Onuchic, José N; Whitford, Paul C

    2016-03-01

    Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

  6. SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

    Directory of Open Access Journals (Sweden)

    Jeffrey K Noel

    2016-03-01

    Full Text Available Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.

  7. Modeling viscoelastic deformation of the earth due to surface loading by commercial finite element package - ABAQUS

    Science.gov (United States)

    Kit Wong, Ching; Wu, Patrick

    2017-04-01

    Wu (2004) developed a transformation scheme to model viscoelatic deformation due to glacial loading by commercial finite element package - ABAQUS. Benchmark tests confirmed that this method works extremely well on incompressible earth model. Bangtsson & Lund (2008),however, showed that the transformation scheme would lead to incorrect results if compressible material parameters are used. Their study implies that Wu's method of stress transformation is inadequate to model the load induced deformation of a compressible earth under the framework of ABAQUS. In light of this, numerical experiments are carried out to find if there exist other methods that serve this purpose. All the tested methods are not satisfying as the results failed to converge through iterations, except at the elastic limit. Those tested methods will be outlined and the results will be presented. Possible reasons of failure will also be discussed. Bängtsson, E., & Lund, B. (2008). A comparison between two solution techniques to solve the equations of glacially induced deformation of an elastic Earth. International journal for numerical methods in engineering, 75(4), 479-502. Wu, P. (2004). Using commercial finite element packages for the study of earth deformations, sea levels and the state of stress. Geophysical Journal International, 158(2), 401-408.

  8. Implementation of the GFS physical package in the GRAPES regional model: single column experiment

    Science.gov (United States)

    Chen, Baode; Huang, Wei; Bao, Jian-wen

    2015-04-01

    There is a growing concern about coupling among physical components in NWP models. The Physics package of the NCEP Global Forecast System (GFS) has been considerably turned and connection among various components is well considered. Thus, the full GFS physical package was implemented into the GRAPES-MESO and its single column version as well. Using the data collected at ARM Southern Great Plain site during the summer 1997 Intensive Observing Period, several experiments of single-column model (SCM) were conducted to test performance of a set of original physical processes of GRAPES(CTL experiment) and the GFS physics package implemented(GFS experiment). Temperature, moisture, radiation, surface heat flux, surface air temperature and precipitation are evaluated. It is found that potential temperature and vapor mixing ratio simulated by GFS experiment is more accurate than that of CTL experiment. Errors of surface downward solar and long-wave radiation simulated by GFS experiment are less than that of CTL experiment and upward latent and sensible heat flux are also better agreeing with observation. The maximum and minimum 2-m air temperatures of the GFS experiment are close to observation compared with that of CTL experiment. Analysis of precipitation simulated shows that both sets of physical processes well reproduce heavy rainfall events. Failure and delay of moderate rainfall events and over predictions of drizzle events are commonly found for two sets of experiments. For the case of three rainfall events, the errors of potential temperature and vapor mixing ratio simulated by GFS experiment were smaller than that of CTL experiment. It is shown that the late occurrences of rainfall are resulted from a more stable temperature profile and lower moisture simulated in boundary layer than those from the observation prior to rainfall. When the simulated rainfall occurs, the simulated temperature and moisture become more favorable to the precipitation than observation.

  9. 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)

  10. 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.

  11. Packaging fluency

    DEFF Research Database (Denmark)

    Mocanu, Ana; Chrysochou, Polymeros; Bogomolova, Svetlana

    2011-01-01

    Research on packaging stresses the need for packaging design to read easily, presuming fast and accurate processing of product-related information. In this paper we define this property of packaging as “packaging fluency”. Based on the existing marketing and cognitive psychology literature...... on packaging design and processing fluency, our aim is to define and conceptualise packaging fluency. We stress the important role of packaging fluency since it is anticipated that a fluent package would influence the evaluative judgments for a product. We conclude this paper by setting the research agenda...

  12. The production-distribution problem with order acceptance and package delivery: models and algorithm

    Directory of Open Access Journals (Sweden)

    Khalili Majid

    2016-01-01

    Full Text Available The production planning and distribution are among the most important decisions in the supply chain. Classically, in this problem, it is assumed that all orders have to produced and separately delivered; while, in practice, an order may be rejected if the cost that it brings to the supply chain exceeds its revenue. Moreover, orders can be delivered in a batch to reduce the related costs. This paper considers the production planning and distribution problem with order acceptance and package delivery to maximize the profit. At first, a new mathematical model based on mixed integer linear programming is developed. Using commercial optimization software, the model can optimally solve small or even medium sized instances. For large instances, a solution method, based on imperialist competitive algorithms, is also proposed. Using numerical experiments, the proposed model and algorithm are evaluated.

  13. Application of Thermal Network Model to Transient Thermal Analysis of Power Electronic Package Substrate

    Directory of Open Access Journals (Sweden)

    Masaru Ishizuka

    2011-01-01

    Full Text Available In recent years, there is a growing demand to have smaller and lighter electronic circuits which have greater complexity, multifunctionality, and reliability. High-density multichip packaging technology has been used in order to meet these requirements. The higher the density scale is, the larger the power dissipation per unit area becomes. Therefore, in the designing process, it has become very important to carry out the thermal analysis. However, the heat transport model in multichip modules is very complex, and its treatment is tedious and time consuming. This paper describes an application of the thermal network method to the transient thermal analysis of multichip modules and proposes a simple model for the thermal analysis of multichip modules as a preliminary thermal design tool. On the basis of the result of transient thermal analysis, the validity of the thermal network method and the simple thermal analysis model is confirmed.

  14. CFD modeling to improve safe and efficient distribution of chlorine dioxide gas for packaging fresh produce

    Science.gov (United States)

    The efficiency of the packaging system in inactivating food borne pathogens and prolonging the shelf life of fresh-cut produce is influenced by the design of the package apart from material and atmospheric conditions. Three different designs were considered to determine a specific package design ens...

  15. 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)].

  16. Implementation of New Process Models for Tailored Polymer Composite Structures into Processing Software Packages

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Ba Nghiep; Jin, Xiaoshi; Wang, Jin; Phelps, Jay; Tucker III, Charles L.; Kunc, Vlastimil; Bapanapalli, Satish K.; Smith, Mark T.

    2010-02-23

    This report describes the work conducted under the Cooperative Research and Development Agreement (CRADA) (Nr. 260) between the Pacific Northwest National Laboratory (PNNL) and Autodesk, Inc. to develop and implement process models for injection-molded long-fiber thermoplastics (LFTs) in processing software packages. The structure of this report is organized as follows. After the Introduction Section (Section 1), Section 2 summarizes the current fiber orientation models developed for injection-molded short-fiber thermoplastics (SFTs). Section 3 provides an assessment of these models to determine their capabilities and limitations, and the developments needed for injection-molded LFTs. Section 4 then focuses on the development of a new fiber orientation model for LFTs. This model is termed the anisotropic rotary diffusion - reduced strain closure (ARD-RSC) model as it explores the concept of anisotropic rotary diffusion to capture the fiber-fiber interaction in long-fiber suspensions and uses the reduced strain closure method of Wang et al. to slow down the orientation kinetics in concentrated suspensions. In contrast to fiber orientation modeling, before this project, no standard model was developed to predict the fiber length distribution in molded fiber composites. Section 5 is therefore devoted to the development of a fiber length attrition model in the mold. Sections 6 and 7 address the implementations of the models in AMI, and the conclusions drawn from this work is presented in Section 8.

  17. Inference in Graphical Gaussian Models with Edge and Vertex Symmetries with the gRc Package for R

    DEFF Research Database (Denmark)

    Højsgaard, Søren; Lauritzen, Steffen L

    2007-01-01

    In this paper we present the R package gRc for statistical inference in graphical Gaussian models in which symmetry restrictions have been imposed on the concentration or partial correlation matrix. The models are represented by coloured graphs where parameters associated with edges or vertices o...... of same colour are restricted to being identical. We describe algorithms for maximum likelihood estimation and discuss model selection issues. The paper illustrates the practical use of the gRc package......In this paper we present the R package gRc for statistical inference in graphical Gaussian models in which symmetry restrictions have been imposed on the concentration or partial correlation matrix. The models are represented by coloured graphs where parameters associated with edges or vertices...

  18. Nonlinearities and transit times in soil organic matter models: new developments in the SoilR package

    Science.gov (United States)

    Sierra, Carlos; Müller, Markus

    2016-04-01

    SoilR is an R package for implementing diverse models representing soil organic matter dynamics. In previous releases of this package, we presented the implementation of linear first-order models with any number of pools as well as radiocarbon dynamics. We present here new improvements of the package regarding the possibility to implement models with nonlinear interactions among state variables and the possibility to calculate ages and transit times for nonlinear models with time dependencies. We show here examples on how to implement model structures with Michaelis-Menten terms for explicit microbial growth and resource use efficiency, and Langmuir isotherms for representing adsorption of organic matter to mineral surfaces. These nonlinear terms can be implemented for any number of organic matter pools, microbial functional groups, or mineralogy, depending on user's requirements. Through a simple example, we also show how transit times of organic matter in soils are controlled by the time-dependencies of the input terms.

  19. A suite of R packages for web-enabled modeling and analysis of surface waters

    Science.gov (United States)

    Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

    2014-12-01

    Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

  20. CSR behavior and aging model for the Viton© Fluorelastomer O-rings in the 9975 shipping package

    Energy Technology Data Exchange (ETDEWEB)

    Mcwilliams, A. J. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Daugherty, W. L. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Skidmore, T. E. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-12-01

    The 9975 Type B shipping package is used within the DOE complex for shipping special nuclear materials. This package is re-certified annually in accordance with Safety Analysis Report for Packaging (SARP) requirements. The package is also used at the Savannah River Site as part of the long-term storage configuration of special nuclear materials. As such, the packages do not undergo annual recertification during storage, with uncertainty as to how long some of the package components will meet their functional requirements in the storage environment. The packages are currently approved for up to 15 years storage, and work continues to provide a technical basis to extend that period. This report describes efforts by the Savannah River National Laboratory (SRNL) to extend the service life estimate of Viton® GLT and GLT-S fluoroelastomer O-rings used in the 9975 shipping package. O-rings of both GLT and GLT-S compositions are undergoing accelerated aging at elevated temperature, and are periodically tested for compression stress relaxation (CSR) behavior. The CSR behavior of O-rings was evaluated at temperatures from 175 to 400 °F. These collective data were used to develop predictive models for extrapolation of CSR behavior to relevant service temperatures (< 156 °F). The predictive model developed from the CSR data conservatively indicates a service life of approximately 37 years for Viton GLT O-rings at the maximum effective service temperature of 156 °F. The estimated service life for Viton GLT-S O-rings is significantly longer.

  1. 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.

  2. demogR: A Package for the Construction and Analysis of Age-structured Demographic Models in R

    Directory of Open Access Journals (Sweden)

    James Holland Jones

    2007-08-01

    Full Text Available The analysis of matrix population models has become a fundamental tool in ecology, conservation biology, and life history theory. In this paper, I present demogR, a package for analyzing age-structured population models in R. The package includes tools for the construction and analysis of matrix population models. In addition to the standard analyses commonly used in evolutionary demography and conservation biology, demogR contains a variety of tools from classical demography. This includes the construction of period life tables, and the generation of model mortality and fertility schedules for human populations. The tools in demogR are generally applicable to age-structured populations but are particularly useful for analyzing problems in human ecology. I illustrate some of the capabilities of the package by doing an evolutionary demographic analysis of several human populations.

  3. 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.

  4. Packaging fluency

    DEFF Research Database (Denmark)

    Mocanu, Ana; Chrysochou, Polymeros; Bogomolova, Svetlana

    2011-01-01

    Research on packaging stresses the need for packaging design to read easily, presuming fast and accurate processing of product-related information. In this paper we define this property of packaging as “packaging fluency”. Based on the existing marketing and cognitive psychology literature on pac...

  5. The last developments of the airGR R-package, an open source software for rainfall-runoff modelling

    Science.gov (United States)

    Thirel, Guillaume; Delaigue, Olivier; Coron, Laurent; Perrin, Charles; Andréassian, Vazken

    2017-04-01

    Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years with the main objectives of designing models as efficient as possible in terms of streamflow simulation, applicable to a wide range of catchments and having low data requirements. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2016), called airGR (Coron et al., 2016, 2017), to make these models widely available. It includes: - the water balance annual GR1A model, - the monthly GR2M model, - three versions of the daily model, namely GR4J, GR5J and GR6J, - the hourly GR4H model, - a degree-day snow model CemaNeige. The airGR package has been designed to facilitate the use by non-expert users and allow the addition of evaluation criteria, models or calibration algorithm selected by the end-user. Each model core is coded in FORTRAN to ensure low computational time. The other package functions (i.e. mainly the calibration algorithm and the efficiency criteria) are coded in R. The package is also used for educational purposes. It allows for convenient implementation of model inter-comparisons and large sample hydrology experiments. The airGR package undergoes continuous developments for improving the efficiency, computational time

  6. 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

  7. Application of the Finite Elemental Analysis to Modeling Temperature Change of the Vaccine in an Insulated Packaging Container during Transport.

    Science.gov (United States)

    Ge, Changfeng; Cheng, Yujie; Shen, Yan

    2013-01-01

    This study demonstrated an attempt to predict temperatures of a perishable product such as vaccine inside an insulated packaging container during transport through finite element analysis (FEA) modeling. In order to use the standard FEA software for simulation, an equivalent heat conduction coefficient is proposed and calculated to describe the heat transfer of the air trapped inside the insulated packaging container. The three-dimensional, insulated packaging container is regarded as a combination of six panels, and the heat flow at each side panel is a one-dimension diffusion process. The transit-thermal analysis was applied to simulate the heat transition process from ambient environment to inside the container. Field measurements were carried out to collect the temperature during transport, and the collected data were compared to the FEA simulation results. Insulated packaging containers are used to transport temperature-sensitive products such as vaccine and other pharmaceutical products. The container is usually made of an extruded polystyrene foam filled with gel packs. World Health Organization guidelines recommend that all vaccines except oral polio vaccine be distributed in an environment where the temperature ranges between +2 to +8 °C. The primary areas of concern in designing the packaging for vaccine are how much of the foam thickness and gel packs should be used in order to keep the temperature in a desired range, and how to prevent the vaccine from exposure to freezing temperatures. This study uses numerical simulation to predict temperature change within an insulated packaging container in vaccine cold chain. It is our hope that this simulation will provide the vaccine industries with an alternative engineering tool to validate vaccine packaging and project thermal equilibrium within the insulated packaging container.

  8. Microelectronic packaging

    CERN Document Server

    Datta, M; Schultze, J Walter

    2004-01-01

    Microelectronic Packaging analyzes the massive impact of electrochemical technologies on various levels of microelectronic packaging. Traditionally, interconnections within a chip were considered outside the realm of packaging technologies, but this book emphasizes the importance of chip wiring as a key aspect of microelectronic packaging, and focuses on electrochemical processing as an enabler of advanced chip metallization.Divided into five parts, the book begins by outlining the basics of electrochemical processing, defining the microelectronic packaging hierarchy, and emphasizing the impac

  9. MuLV packaging systems as models for estimating/measuring retrovirus recombination frequency.

    Science.gov (United States)

    Patience, C; Takeuch, Y; Cosset, F L; Weiss, R A

    2001-01-01

    Interaction of retrovirus vectors and endogenous retroviruses present in packaging cell lines and target cells may result in the formation of recombinant viruses. Using sensitive RT-PCR assays, we have investigated human and murine gene therapy packaging cell lines for the incorporation of endogenous retrovirus transcripts into murine leukaemia virus (MLV) vector particles and whether vector genomes are incorporated into human endogenous retrovirus (HERV) particles. VL30 endogenous retrovirus sequences were packaged in particles produced by the murine AM12 packaging system. For every seven MLV-derived -galactosidase beta-Gal vector genomes present in the particles, one copy of VL30 was also packaged. Although human FLY packaging cells expressed HERV transcripts (HERV-K, HuRT, type C, and RTVL-H), none was detectable in the MLV vector particles released from the cells. Non-specific packaging of the MLV gag-pol expression vector transcripts was detected in the FLY virions at a low level (one in 17,000 sequences). In other experiments, gag proteins produced by HERV-K particles present in human teratocarcinoma cells did not appear to package MLV-based vectors that expressed Gal transcripts. These findings indicate that retrovirus vectors interact with human packaging cells to produce retrovirus particles that are far less contaminated by endogenous viral sequences or other types of extraneous particles than murine packaging cells.

  10. ARM Cloud Radar Simulator Package for Global Climate Models Value-Added Product

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yuying [North Carolina State Univ., Raleigh, NC (United States); Xie, Shaocheng [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-05-01

    It has been challenging to directly compare U.S. Department of Energy (DOE) Atmospheric Radiation Measurement (ARM) Climate Research Facility ground-based cloud radar measurements with climate model output because of limitations or features of the observing processes and the spatial gap between model and the single-point measurements. To facilitate the use of ARM radar data in numerical models, an ARM cloud radar simulator was developed to converts model data into pseudo-ARM cloud radar observations that mimic the instrument view of a narrow atmospheric column (as compared to a large global climate model [GCM] grid-cell), thus allowing meaningful comparison between model output and ARM cloud observations. The ARM cloud radar simulator value-added product (VAP) was developed based on the CloudSat simulator contained in the community satellite simulator package, the Cloud Feedback Model Intercomparison Project (CFMIP) Observation Simulator Package (COSP) (Bodas-Salcedo et al., 2011), which has been widely used in climate model evaluation with satellite data (Klein et al., 2013, Zhang et al., 2010). The essential part of the CloudSat simulator is the QuickBeam radar simulator that is used to produce CloudSat-like radar reflectivity, but is capable of simulating reflectivity for other radars (Marchand et al., 2009; Haynes et al., 2007). Adapting QuickBeam to the ARM cloud radar simulator within COSP required two primary changes: one was to set the frequency to 35 GHz for the ARM Ka-band cloud radar, as opposed to 94 GHz used for the CloudSat W-band radar, and the second was to invert the view from the ground to space so as to attenuate the beam correctly. In addition, the ARM cloud radar simulator uses a finer vertical resolution (100 m compared to 500 m for CloudSat) to resolve the more detailed structure of clouds captured by the ARM radars. The ARM simulator has been developed following the COSP workflow (Figure 1) and using the capabilities available in COSP

  11. McCoy cell line as a possible model containing CD4+ receptors for the study of HIV-1 replication Células de linhagem McCoy como um possível modelo contendo receptores CD4+ para estudos da replicação do HIV

    Directory of Open Access Journals (Sweden)

    Yeda L. Nogueira

    2003-08-01

    Full Text Available Several studies have recently shown the use of recombinant rabies virus as potential vector-viral vaccine for HIV-1. The sequence homology between gp 120 and rabies virus glycoprotein has been reported. The McCoy cell line has therefore been used to show CD4+ or CD4+ like receptors. Samples of HIV-1 were isolated, when plasma of HIV-1 positive patients was inoculated in the McCoy cell line. The virus infection was then studied during successive virus passages. The proteins released in the extra cellular medium were checked for protein activity, by exposure to SDS Electrophoresis and blotting to nitro-cellulose filter, then reacting with sera of HIV positive and negative patients. Successive passages were performed, and showed viral replication, membrane permeabilization, the syncytium formation, and the cellular lysis (cytopathic effect. Flow cytometry analysis shows clear evidence that CD4+ receptors are present in this cell line, which enhances the likelihood of easy isolation and replication of HIV. The results observed allow the use of this cell line as a possible model for isolating HIV, as well as for carrying out studies of the dynamics of viral infection in several situations, including exposure to drugs in pharmacological studies, and possibly studies and analyses of the immune response in vaccine therapies.Recentes estudos demonstraram o uso do vírus raiva como modelo vetor para produzir vacinas expressando as glicoproteínas do vírus HIV-1. A homologia na seqüência entre gp120 do vírus HIV-1 e a glicoproteína G do vírus rábico já foi previamente relatada. Devido a estes fatos a linhagem de célula McCoy utilizada com sucesso para a replicação do vírus rábico foi utilizada para demonstrar a replicação do HIV-1. Amostra de HIV-1 foi isolada de plasma de um paciente soro positivo e inoculada em células de linhagem McCoy e então a infecção viral foi estudada em passagens sucessivas do vírus nesta célula. As prote

  12. A flexible open-source toolbox for robust end-member modelling analysis - The R-package EMMAgeo

    Science.gov (United States)

    Dietze, Michael; Dietze, Elisabeth

    2013-04-01

    Interpreting geomorphological and sedimentological processes from grain-size data in environmental archives typically runs into problems when source- and process-related grain-size distributions become mixed during deposition. A powerful approach to overcome this ambiguity is to statistically "unmix" the samples. Typical algorithms use eigenspace decomposition and techniques of dimension reduction. This contribution presents a package for the free statistical software R. Some of the great advantages of R and R-packages are the open code structure, flexibility and low programming effort. The package contains a series of flexible, ready-to-use functions to perform different tasks of data tests, preparation, modelling and visualisation. The package originated from a recently presented Matlab-based end-member modelling algorithm (Dietze et al., 2012, SedGeol). It supports simple modelling of grain-size end-member loadings and scores (eigenspace extraction, factor rotation, data scaling, non-negative least squares solving) along with several measures of model quality. The package further provides preprocessing tools (e.g. grain-size scale conversions, tests of data structure, weight factor limit inference, determination of minimum, optimum and maximum number of meaningful end-members) and allows to model data sets with artificial or user-defined end-member loadings. EMMAgeo also supports inferring uncertainty estimation from a series of plausible model runs and the determination of robust end-members. The contribution presents important package functions, thereby illustrating how large data sets of artificial and natural grain-size samples from different depositional environments can be analysed to infer quantified process-related proxies.

  13. airGR: a suite of lumped hydrological models in an R-package

    Science.gov (United States)

    Coron, Laurent; Perrin, Charles; Delaigue, Olivier; Andréassian, Vazken; Thirel, Guillaume

    2016-04-01

    Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years with the main objectives of designing models as efficient as possible in terms of streamflow simulation, applicable to a wide range of catchments and having low data requirements. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2015), called airGR, to make these models widely available. It includes: - the water balance annual GR1A (Mouehli et al., 2006), - the monthly GR2M (Mouehli, 2003) models, - three versions of the daily model, namely GR4J (Perrin et al., 2003), GR5J (Le Moine, 2008) and GR6J (Pushpalatha et al., 2011), - the hourly GR4H model (Mathevet, 2005), - a degree-day snow module CemaNeige (Valéry et al., 2014). The airGR package has been designed to facilitate the use by non-expert users and allow the addition of evaluation criteria, models or calibration algorithms selected by the end-user. Each model core is coded in FORTRAN to ensure low computational time. The other package functions (i.e. mainly the calibration algorithm and the efficiency criteria) are coded in R. The package is already used for educational purposes. The presentation will detail the main functionalities of the package and present a case

  14. Geochemistry Model Abstraction and Sensitivity Studies for the 21 PWR CSNF Waste Package

    Energy Technology Data Exchange (ETDEWEB)

    P. Bernot; S. LeStrange; E. Thomas; K. Zarrabi; S. Arthur

    2002-10-29

    The CSNF geochemistry model abstraction, as directed by the TWP (BSC 2002b), was developed to provide regression analysis of EQ6 cases to obtain abstracted values of pH (and in some cases HCO{sub 3}{sup -} concentration) for use in the Configuration Generator Model. The pH of the system is the controlling factor over U mineralization, CSNF degradation rate, and HCO{sub 3}{sup -} concentration in solution. The abstraction encompasses a large variety of combinations for the degradation rates of materials. The ''base case'' used EQ6 simulations looking at differing steel/alloy corrosion rates, drip rates, and percent fuel exposure. Other values such as the pH/HCO{sub 3}{sup -} dependent fuel corrosion rate and the corrosion rate of A516 were kept constant. Relationships were developed for pH as a function of these differing rates to be used in the calculation of total C and subsequently, the fuel rate. An additional refinement to the abstraction was the addition of abstracted pH values for cases where there was limited O{sub 2} for waste package corrosion and a flushing fluid other than J-13, which has been used in all EQ6 calculation up to this point. These abstractions also used EQ6 simulations with varying combinations of corrosion rates of materials to abstract the pH (and HCO{sub 3}{sup -} in the case of the limiting O{sub 2} cases) as a function of WP materials corrosion rates. The goodness of fit for most of the abstracted values was above an R{sup 2} of 0.9. Those below this value occurred during the time at the very beginning of WP corrosion when large variations in the system pH are observed. However, the significance of F-statistic for all the abstractions showed that the variable relationships are significant. For the abstraction, an analysis of the minerals that may form the ''sludge'' in the waste package was also presented. This analysis indicates that a number a different iron and aluminum minerals may form in

  15. A bunswik lens model of consumer health judgments of packaged foods

    DEFF Research Database (Denmark)

    Orquin, Jacob Lund

    2014-01-01

    representativeness. The study revealed that the objective healthfulness criterion is highly predictable on the basis of cues such as the food category, brand, carbohydrate content, and whether the food is a typical “light” product. However, consumer judgments of food healthfulness are based almost entirely...... criterion was calculated for each product according to its specific nutrition values using a validated nutrition profile. The lens model included explicit cues such as nutrition values, nutrition and health claims, food category, and brand and implicit cues such a packaging design and category...... on the food category and to a lesser extent on the brand and consumer familiarity with the product. The results are in conflict with consumers’ self-reported use of nutrition information but are in accordance with findings from studies using implicit methods....

  16. Optimal Non-Invasive Fault Classification Model for Packaged Ceramic Tile Quality Monitoring Using MMW Imaging

    Science.gov (United States)

    Agarwal, Smriti; Singh, Dharmendra

    2016-04-01

    Millimeter wave (MMW) frequency has emerged as an efficient tool for different stand-off imaging applications. In this paper, we have dealt with a novel MMW imaging application, i.e., non-invasive packaged goods quality estimation for industrial quality monitoring applications. An active MMW imaging radar operating at 60 GHz has been ingeniously designed for concealed fault estimation. Ceramic tiles covered with commonly used packaging cardboard were used as concealed targets for undercover fault classification. A comparison of computer vision-based state-of-the-art feature extraction techniques, viz, discrete Fourier transform (DFT), wavelet transform (WT), principal component analysis (PCA), gray level co-occurrence texture (GLCM), and histogram of oriented gradient (HOG) has been done with respect to their efficient and differentiable feature vector generation capability for undercover target fault classification. An extensive number of experiments were performed with different ceramic tile fault configurations, viz., vertical crack, horizontal crack, random crack, diagonal crack along with the non-faulty tiles. Further, an independent algorithm validation was done demonstrating classification accuracy: 80, 86.67, 73.33, and 93.33 % for DFT, WT, PCA, GLCM, and HOG feature-based artificial neural network (ANN) classifier models, respectively. Classification results show good capability for HOG feature extraction technique towards non-destructive quality inspection with appreciably low false alarm as compared to other techniques. Thereby, a robust and optimal image feature-based neural network classification model has been proposed for non-invasive, automatic fault monitoring for a financially and commercially competent industrial growth.

  17. CARBayes: An R Package for Bayesian Spatial Modeling with Conditional Autoregressive Priors

    Directory of Open Access Journals (Sweden)

    Duncan Lee

    2013-11-01

    Full Text Available Conditional autoregressive models are commonly used to represent spatial autocorrelation in data relating to a set of non-overlapping areal units, which arise in a wide variety of applications including agriculture, education, epidemiology and image analysis. Such models are typically specified in a hierarchical Bayesian framework, with inference based on Markov chain Monte Carlo (MCMC simulation. The most widely used software to fit such models is WinBUGS or OpenBUGS, but in this paper we introduce the R package CARBayes. The main advantage of CARBayes compared with the BUGS software is its ease of use, because: (1 the spatial adjacency information is easy to specify as a binary neighbourhood matrix; and (2 given the neighbourhood matrix the models can be implemented by a single function call in R. This paper outlines the general class of Bayesian hierarchical models that can be implemented in the CARBayes software, describes their implementation via MCMC simulation techniques, and illustrates their use with two worked examples in the fields of house price analysis and disease mapping.

  18. 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...

  19. A Mathematical Model of the Modified Atmosphere Packaging (MAP System for the Gas Transmission Rate of Fruit Produce

    Directory of Open Access Journals (Sweden)

    Li Li

    2010-01-01

    Full Text Available A mathematical model to predict oxygen, carbon dioxide, and water vapour exchanges in non-perforated and micro-perforated modified atmosphere packaging films has successfully been proposed. The transmission rate of gases was measured for films with thickness of 0.03 and 0.05 mm, perforation diameters of 0.5 and 2.0 mm, and temperatures of 0, 10 and 20 °C. Under most conditions, the increase in temperature and perforation diameter increased the transmission rate of oxygen, carbon dioxide, and water vapour, whereas the increase in film thickness decreased the transmission rate of the various gases. Validation of the proposed modified atmosphere packaging model was found to yield good prediction for gas concentrations and percentage losses in the mass of the produce after comparison with the experimental results of modified atmosphere packaging for tomato (Lycopersicon esculentum.

  20. Logistic random effects regression models: a comparison of statistical packages for binary and ordinal outcomes

    Directory of Open Access Journals (Sweden)

    Steyerberg Ewout W

    2011-05-01

    Full Text Available Abstract Background Logistic random effects models are a popular tool to analyze multilevel also called hierarchical data with a binary or ordinal outcome. Here, we aim to compare different statistical software implementations of these models. Methods We used individual patient data from 8509 patients in 231 centers with moderate and severe Traumatic Brain Injury (TBI enrolled in eight Randomized Controlled Trials (RCTs and three observational studies. We fitted logistic random effects regression models with the 5-point Glasgow Outcome Scale (GOS as outcome, both dichotomized as well as ordinal, with center and/or trial as random effects, and as covariates age, motor score, pupil reactivity or trial. We then compared the implementations of frequentist and Bayesian methods to estimate the fixed and random effects. Frequentist approaches included R (lme4, Stata (GLLAMM, SAS (GLIMMIX and NLMIXED, MLwiN ([R]IGLS and MIXOR, Bayesian approaches included WinBUGS, MLwiN (MCMC, R package MCMCglmm and SAS experimental procedure MCMC. Three data sets (the full data set and two sub-datasets were analysed using basically two logistic random effects models with either one random effect for the center or two random effects for center and trial. For the ordinal outcome in the full data set also a proportional odds model with a random center effect was fitted. Results The packages gave similar parameter estimates for both the fixed and random effects and for the binary (and ordinal models for the main study and when based on a relatively large number of level-1 (patient level data compared to the number of level-2 (hospital level data. However, when based on relatively sparse data set, i.e. when the numbers of level-1 and level-2 data units were about the same, the frequentist and Bayesian approaches showed somewhat different results. The software implementations differ considerably in flexibility, computation time, and usability. There are also differences in

  1. BPACK -- A computer model package for boiler reburning/co-firing performance evaluations. User`s manual, Volume 1

    Energy Technology Data Exchange (ETDEWEB)

    Wu, K.T.; Li, B.; Payne, R.

    1992-06-01

    This manual presents and describes a package of computer models uniquely developed for boiler thermal performance and emissions evaluations by the Energy and Environmental Research Corporation. The model package permits boiler heat transfer, fuels combustion, and pollutant emissions predictions related to a number of practical boiler operations such as fuel-switching, fuels co-firing, and reburning NO{sub x} reductions. The models are adaptable to most boiler/combustor designs and can handle burner fuels in solid, liquid, gaseous, and slurried forms. The models are also capable of performing predictions for combustion applications involving gaseous-fuel reburning, and co-firing of solid/gas, liquid/gas, gas/gas, slurry/gas fuels. The model package is conveniently named as BPACK (Boiler Package) and consists of six computer codes, of which three of them are main computational codes and the other three are input codes. The three main codes are: (a) a two-dimensional furnace heat-transfer and combustion code: (b) a detailed chemical-kinetics code; and (c) a boiler convective passage code. This user`s manual presents the computer model package in two volumes. Volume 1 describes in detail a number of topics which are of general users` interest, including the physical and chemical basis of the models, a complete description of the model applicability, options, input/output, and the default inputs. Volume 2 contains a detailed record of the worked examples to assist users in applying the models, and to illustrate the versatility of the codes.

  2. 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.

  3. 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,...

  4. MODEL 9977 B(M)F-96 SAFETY ANALYSIS REPORT FOR PACKAGING

    Energy Technology Data Exchange (ETDEWEB)

    Abramczyk, G; Paul Blanton, P; Kurt Eberl, K

    2006-05-18

    This Safety Analysis Report for Packaging (SARP) documents the analysis and testing performed on and for the 9977 Shipping Package, referred to as the General Purpose Fissile Package (GPFP). The performance evaluation presented in this SARP documents the compliance of the 9977 package with the regulatory safety requirements for Type B packages. Per 10 CFR 71.59, for the 9977 packages evaluated in this SARP, the value of ''N'' is 50, and the Transport Index based on nuclear criticality control is 1.0. The 9977 package is designed with a high degree of single containment. The 9977 complies with 10 CFR 71 (2002), Department of Energy (DOE) Order 460.1B, DOE Order 460.2, and 10 CFR 20 (2003) for As Low As Reasonably Achievable (ALARA) principles. The 9977 also satisfies the requirements of the Regulations for the Safe Transport of Radioactive Material--1996 Edition (Revised)--Requirements. IAEA Safety Standards, Safety Series No. TS-R-1 (ST-1, Rev.), International Atomic Energy Agency, Vienna, Austria (2000). The 9977 package is designed, analyzed and fabricated in accordance with Section III of the American Society of Mechanical Engineers (ASME) Boiler and Pressure Vessel (B&PV) Code, 1992 edition.

  5. A Comparative Study of BDD Packages for Probabilistic Symbolic Model Checking

    NARCIS (Netherlands)

    van Dijk, Tom; Hahn, Ernst Moritz; Jansen, D.N.; Li, Yong; Neele, Thomas; Stoelinga, Mariëlle Ida Antoinette; Turrini, Andrea; Zhang, Lijun

    2015-01-01

    Symbolic data structures using Binary Decision Diagrams (BDDs) have been successfully used in the last decades to analyse large systems. While various BDD and MTBDD packages have been developed in the community, the CUDD package remains the default choice of most of the symbolic (probabilistic)

  6. Code package MAG c user tool for numerical modeling of 1D shock wave and dynamic processes in solids

    Science.gov (United States)

    Rudenko, Vladimir; Shaburov, Michail

    1999-06-01

    Design and theoretical and numerical preparation of shock wave experiments require, as a rule, conduction of a large amount of calculations. Usually preparation of a problem for numerical solution, calculation and processing of the results is done be programmers c mathematicians. The appearance of powerful personal computers and interface tools allows to develop such user-oriented programs that a researcher can handle them without the help of a mathematician, even if he does not have special programming background. Code package MAG for numerical solution of 1D system of equations of hydrodynamics, elastoplastics, heat conduction and magnetic hydrodynamic. A number of modern models of elastoplastics and kinetics of power materials is implemented in it. The package includes libraries of equations of state, thermal physical and electromagnetic properties of substances. The code package is an interactive visual medium providing a user with the following capabilities: ? Input and edit initial data for a problem; ? Calculate separate problems, as well as series of problems with a possibility of automatic variation of parameters; ? View the modeled phenomena dynamically using the means of visualization; ? Control the process of calculation: terminate the calculation, change parameters, make express-processing of the results, continue the calculation etc.; ? Process the numerical results producing final plots and tables; ? Record and store numerical results in databases, including the formats supported by Microsoft Word, Acces, Exel; ? Make dynamic visual comparison of the results of several simultaneous calculations; ? Carry out automatic numerical optimization of a selected experimental scheme. The package is easy in use, allows prompt input and convenient information processing. The validity of numerical results obtained with the package MAG has been proved by numerous hydrodynamic experiments and comparisons with numerical results from similar programs. The package was

  7. Software Package \\Nesvetay-3D" for modeling three-dimensional flows of monatomic rarefied gas

    Directory of Open Access Journals (Sweden)

    V. A. Titarev

    2014-01-01

    Full Text Available Analysis of three-dimensional rarefied gas flowsin microdevices (micropipes, micropumps etc and over re-entry vehicles requires development of methods of computational modelling. One of such methods is the direct numerical solution of the Boltzmann kinetic equation for the velocity distribution function with either exact or approximate (model collision integral. At present, for flows of monatomic rarefied gas the Shakhov model kinetic equation, also called S-model, has gained wide-spread use. The equation can be regarded as a model equation of the incomplete thirdorder approximation. Despite its relative simplicity, the S-model is still a complicated integrodifferential equation of high dimension. The numerical solution of such an equation requires high-accuracy parallel methods.The present work is a review of recent results concerning the development and application of three-dimensional computer package Nesvetay-3D intended for modelling of rarefied gas flows. The package solves Boltzmann kinetic equation with the BGK (Krook and Shakhov model collision integrals using the discrete velocity approach. Calculations are carried out in non-dimensional variables. A finite integration domain and a mesh are introduced in the molecular velocity space. Next, the kinetic equation is re-written as a system of kinetic equations for each of the discrete velocities. The system is solved using an implicit finite-volume method of Godunov type. The steady-state solution is computed by a time marching method. High order of spatial accuracy is achieved by using a piece-wise linear representation of the distribution function in each spatial cell. In general, the coefficients of such an approximation are found using the least-square method. Arbitrary unstructured meshes in the physical space can be used in calculations, which allow considering flows over objects of general geometrical shape. Conservative property of the method with respect to the model collision

  8. MCMC Methods for Multi-Response Generalized Linear Mixed Models: The MCMCglmm R Package

    Directory of Open Access Journals (Sweden)

    Jarrod Had

    2010-02-01

    Full Text Available Generalized linear mixed models provide a flexible framework for modeling a range of data, although with non-Gaussian response variables the likelihood cannot be obtained in closed form. Markov chain Monte Carlo methods solve this problem by sampling from a series of simpler conditional distributions that can be evaluated. The R package MCMCglmm implements such an algorithm for a range of model fitting problems. More than one response variable can be analyzed simultaneously, and these variables are allowed to follow Gaussian, Poisson, multi(binominal, exponential, zero-inflated and censored distributions. A range of variance structures are permitted for the random effects, including interactions with categorical or continuous variables (i.e., random regression, and more complicated variance structures that arise through shared ancestry, either through a pedigree or through a phylogeny. Missing values are permitted in the response variable(s and data can be known up to some level of measurement error as in meta-analysis. All simu- lation is done in C/ C++ using the CSparse library for sparse linear systems.

  9. UCVM: An Open Source Software Package for Querying and Visualizing 3D Velocity Models

    Science.gov (United States)

    Gill, D.; Small, P.; Maechling, P. J.; Jordan, T. H.; Shaw, J. H.; Plesch, A.; Chen, P.; Lee, E. J.; Taborda, R.; Olsen, K. B.; Callaghan, S.

    2015-12-01

    Three-dimensional (3D) seismic velocity models provide foundational data for ground motion simulations that calculate the propagation of earthquake waves through the Earth. The Southern California Earthquake Center (SCEC) has developed the Unified Community Velocity Model (UCVM) package for both Linux and OS X. This unique framework provides a cohesive way for querying and visualizing 3D models. UCVM v14.3.0, supports many Southern California velocity models including CVM-S4, CVM-H 11.9.1, and CVM-S4.26. The last model was derived from 26 full-3D tomographic iterations on CVM-S4. Recently, UCVM has been used to deliver a prototype of a new 3D model of central California (CCA) also based on full-3D tomographic inversions. UCVM was used to provide initial plots of this model and will be used to deliver CCA to users when the model is publicly released. Visualizing models is also possible with UCVM. Integrated within the platform are plotting utilities that can generate 2D cross-sections, horizontal slices, and basin depth maps. UCVM can also export models in NetCDF format for easy import into IDV and ParaView. UCVM has also been prototyped to export models that are compatible with IRIS' new Earth Model Collaboration (EMC) visualization utility. This capability allows for user-specified horizontal slices and cross-sections to be plotted in the same 3D Earth space. UCVM was designed to help a wide variety of researchers. It is currently being use to generate velocity meshes for many SCEC wave propagation codes, including AWP-ODC-SGT and Hercules. It is also used to provide the initial input to SCEC's CyberShake platform. For those interested in specific data points, the software framework makes it easy to extract P and S wave propagation speeds and other material properties from 3D velocity models by providing a common interface through which researchers can query earth models for a given location and depth. Also included in the last release was the ability to add small

  10. MEMS packaging

    CERN Document Server

    Hsu , Tai-Ran

    2004-01-01

    MEMS Packaging discusses the prevalent practices and enabling techniques in assembly, packaging and testing of microelectromechanical systems (MEMS). The entire spectrum of assembly, packaging and testing of MEMS and microsystems, from essential enabling technologies to applications in key industries of life sciences, telecommunications and aerospace engineering is covered. Other topics included are bonding and sealing of microcomponents, process flow of MEMS and microsystems packaging, automated microassembly, and testing and design for testing.The Institution of Engineering and Technology is

  11. Development of the CCP-200 mathematical model for Syzran CHPP using the Thermolib software package

    Science.gov (United States)

    Usov, S. V.; Kudinov, A. A.

    2016-04-01

    Simplified cycle diagram of the CCP-200 power generating unit of Syzran CHPP containing two gas turbines PG6111FA with generators, two steam recovery boilers KUP-110/15-8.0/0.7-540/200, and one steam turbine Siemens SST-600 (one-cylinder with two variable heat extraction units of 60/75 MW in heatextraction and condensing modes, accordingly) with S-GEN5-100 generators was presented. Results of experimental guarantee tests of the CCP-200 steam-gas unit are given. Brief description of the Thermolib application for the MatLab Simulink software package is given. Basic equations used in Thermolib for modeling thermo-technical processes are given. Mathematical models of gas-turbine plant, heat-recovery steam generator, steam turbine and integrated plant for power generating unit CCP-200 of Syzran CHPP were developed with the help of MatLab Simulink and Thermolib. The simulation technique at different ambient temperature values was used in order to get characteristics of the developed mathematical model. Graphic comparison of some characteristics of the CCP-200 simulation model (gas temperature behind gas turbine, gas turbine and combined cycle plant capacity, high and low pressure steam consumption and feed water consumption for high and low pressure economizers) with actual characteristics of the steam-gas unit received at experimental (field) guarantee tests at different ambient temperature are shown. It is shown that the chosen degrees of complexity, characteristics of the CCP-200 simulation model, developed by Thermolib, adequately correspond to the actual characteristics of the steam-gas unit received at experimental (field) guarantee tests; this allows considering the developed mathematical model as adequate and acceptable it for further work.

  12. 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.

  13. 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.

  14. 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.

  15. hydroPSO: A Versatile Particle Swarm Optimisation R Package for Calibration of Environmental Models

    Science.gov (United States)

    Zambrano-Bigiarini, M.; Rojas, R.

    2012-04-01

    Particle Swarm Optimisation (PSO) is a recent and powerful population-based stochastic optimisation technique inspired by social behaviour of bird flocking, which shares similarities with other evolutionary techniques such as Genetic Algorithms (GA). In PSO, however, each individual of the population, known as particle in PSO terminology, adjusts its flying trajectory on the multi-dimensional search-space according to its own experience (best-known personal position) and the one of its neighbours in the swarm (best-known local position). PSO has recently received a surge of attention given its flexibility, ease of programming, low memory and CPU requirements, and efficiency. Despite these advantages, PSO may still get trapped into sub-optimal solutions, suffer from swarm explosion or premature convergence. Thus, the development of enhancements to the "canonical" PSO is an active area of research. To date, several modifications to the canonical PSO have been proposed in the literature, resulting into a large and dispersed collection of codes and algorithms which might well be used for similar if not identical purposes. In this work we present hydroPSO, a platform-independent R package implementing several enhancements to the canonical PSO that we consider of utmost importance to bring this technique to the attention of a broader community of scientists and practitioners. hydroPSO is model-independent, allowing the user to interface any model code with the calibration engine without having to invest considerable effort in customizing PSO to a new calibration problem. Some of the controlling options to fine-tune hydroPSO are: four alternative topologies, several types of inertia weight, time-variant acceleration coefficients, time-variant maximum velocity, regrouping of particles when premature convergence is detected, different types of boundary conditions and many others. Additionally, hydroPSO implements recent PSO variants such as: Improved Particle Swarm

  16. Fullrmc, a rigid body Reverse Monte Carlo modeling package enabled with machine learning and artificial intelligence.

    Science.gov (United States)

    Aoun, Bachir

    2016-05-01

    A new Reverse Monte Carlo (RMC) package "fullrmc" for atomic or rigid body and molecular, amorphous, or crystalline materials is presented. fullrmc main purpose is to provide a fully modular, fast and flexible software, thoroughly documented, complex molecules enabled, written in a modern programming language (python, cython, C and C++ when performance is needed) and complying to modern programming practices. fullrmc approach in solving an atomic or molecular structure is different from existing RMC algorithms and software. In a nutshell, traditional RMC methods and software randomly adjust atom positions until the whole system has the greatest consistency with a set of experimental data. In contrast, fullrmc applies smart moves endorsed with reinforcement machine learning to groups of atoms. While fullrmc allows running traditional RMC modeling, the uniqueness of this approach resides in its ability to customize grouping atoms in any convenient way with no additional programming efforts and to apply smart and more physically meaningful moves to the defined groups of atoms. In addition, fullrmc provides a unique way with almost no additional computational cost to recur a group's selection, allowing the system to go out of local minimas by refining a group's position or exploring through and beyond not allowed positions and energy barriers the unrestricted three dimensional space around a group.

  17. SPICE Work Package 3: Modelling the Effects of Stratospheric Aerosol Geoengineering

    Science.gov (United States)

    Driscoll, Simon

    2015-04-01

    This talk presents the results of the SPICE Work Package 3. There is an obvious need for methods to verify the accuracy of geoengineering given no observations of a geoengineering programme. Accordingly, model ability in reproducing the observed dynamical response to volcanic eruptions is discussed using analysis of CMIP5 data and different configurations of the HadGEM2 model. With the HadGEM2-L60 model shown to be substantially better in reproducing the observed dynamical response to volcanic eruptions, simulations of GeoMIP's G4 scenario are performed. Simulated impacts of geoengineering are described, and asymmetries between the immediate onset and immediate cessation ('termination') of geoengineering are analysed. Whilst a rapid large increase in stratospheric sulphate aerosols (such as from volcanic eruptions) can cause substantial damage, most volcanic eruptions in general are not catastrophic. One may therefore suspect that an 'equal but opposite' change in radiative forcing from termination may therefore not be catastrophic, if the climatic response is simulated to be symmetric. HadGEM2 simulations reveal a substantially more rapid change in variables such as near-surface temperature and precipitation following termination than the onset, indicating that termination may be substantially more damaging and even catastrophic. Some suggestions for hemispherically asymmetric geoengineering have been proposed as a way to reduce Northern Hemisphere sea ice, for example, with lesser impacts on the rest of the climate. However, HadGEM2 simulations are performed and observations analysed following volcanic eruptions. Both indicate substantial averse consequences from hemispherically asymmetric loading of stratospheric loading on precipitation in the Sahelian region - a vulnerable region where drought has caused hundreds of thousands of deaths and created millions of refugees in the past.

  18. 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...

  19. 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...

  20. 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.

  1. 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.

  2. CYPROS - Cybernetic Program Packages

    Directory of Open Access Journals (Sweden)

    Arne Tyssø

    1980-10-01

    Full Text Available CYPROS is an interactive program system consisting of a number of special purpose packages for simulation, identification, parameter estimation and control system design. The programming language is standard FORTRAN IV and the system is implemented on a medium size computer system (Nord-10. The system is interactive and program control is obtained by the use of numeric terminals. Output is rapidly examined by extensive use of video colour graphics. The subroutines included in the packages are designed and documented according to standardization rules given by the SCL (Scandinavian Control Library organization. This simplifies the exchange of subroutines throughout the SCL system. Also, this makes the packages attractive for implementation by industrial users. In the simulation package, different integration methods are available and it can be easily used for off-line, as well as real time, simulation problems. The identification package consists of programs for single-input/single-output and multivariablc problems. Both transfer function models and state space models can be handled. Optimal test signals can be designed. The control package consists of programs based on multivariable time domain and frequency domain methods for analysis and design. In addition, there is a package for matrix and time series manipulation. CYPROS has been applied successfully to industrial problems of various kinds, and parts of the system have already been implemented on different computers in industry. This paper will, in some detail, describe the use and the contents of the packages and some examples of application will be discussed.

  3. Environmental Modeling Packages for the MSTDCL TDP: Review and Recommendations (Trousses de Modelisation Environnementale Pour le PDT DCLTCM: Revue et Recommendations)

    Science.gov (United States)

    2009-09-01

    selection of acoustic model inputs, this can be much less than that required by some of the competing packages. The NUW package was also constructed with...1314, 1980. [5] R. T. Bachman , “Parameterization of Geoacoustic Properties”, San Diego, Cal., Scripps Institution of Oceanography, 1989 [6] E. B

  4. 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.

  5. 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.

  6. 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.

  7. Three-dimensional integration and modeling a revolution in RF and wireless packaging

    CERN Document Server

    Lee, Jong-Hoon

    2007-01-01

    This book presents a step-by-step discussion of the 3D integration approach for the development of compact system-on-package (SOP) front-ends.Various examples of fully-integrated passive building blocks (cavity/microstip filters, duplexers, antennas), as well as a multilayer ceramic (LTCC) V-band transceiver front-end midule demonstrate the revolutionary effects of this approach in RF/Wireless packaging and multifunctional miniaturization.Designs covered are based on novel ideas and are presented for the first time for millimeterwave (60GHz) ultrabroadband wireless modules.Table of Contents: I

  8. An Ada Linear-Algebra Software Package Modeled After HAL/S

    Science.gov (United States)

    Klumpp, Allan R.; Lawson, Charles L.

    1990-01-01

    New avionics software written more easily. Software package extends Ada programming language to include linear-algebra capabilities similar to those of HAL/S programming language. Designed for such avionics applications as Space Station flight software. In addition to built-in functions of HAL/S, package incorporates quaternion functions used in Space Shuttle and Galileo projects and routines from LINPAK solving systems of equations involving general square matrices. Contains two generic programs: one for floating-point computations and one for integer computations. Written on IBM/AT personal computer running under PC DOS, v.3.1.

  9. An Ada Linear-Algebra Software Package Modeled After HAL/S

    Science.gov (United States)

    Klumpp, Allan R.; Lawson, Charles L.

    1990-01-01

    New avionics software written more easily. Software package extends Ada programming language to include linear-algebra capabilities similar to those of HAL/S programming language. Designed for such avionics applications as Space Station flight software. In addition to built-in functions of HAL/S, package incorporates quaternion functions used in Space Shuttle and Galileo projects and routines from LINPAK solving systems of equations involving general square matrices. Contains two generic programs: one for floating-point computations and one for integer computations. Written on IBM/AT personal computer running under PC DOS, v.3.1.

  10. Population stochastic modelling (PSM)--an R package for mixed-effects models based on stochastic differential equations.

    Science.gov (United States)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode; Overgaard, Rune Viig; Madsen, Henrik

    2009-06-01

    The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model development, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 109-141; C.W. Tornøe, R.V. Overgaard, H. Agersø, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8)) (2005) 1247-1258; R.V. Overgaard, N. Jonsson, C.W. Tornøe, H. Madsen, Non-linear mixed-effects models with stochastic differential equations: implementation of an estimation algorithm, J. Pharmacokinet. Pharmacodyn. 32 (February(1)) (2005) 85-107; U. Picchini, S. Ditlevsen, A. De Gaetano, Maximum likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODEs) with an observation link that incorporates noise. This state-space formulation only allows for observation noise and not for system noise. Extending to SDEs allows for a Wiener noise component in the system equations. This additional noise component enables handling of autocorrelated residuals originating from natural variation or systematic model error. Autocorrelated residuals are often partly ignored in PK/PD modelling although violating the hypothesis for many standard statistical tests. This article presents a package for the statistical program R that is able to handle SDEs in a mixed-effects setting. The estimation method implemented is the FOCE(1) approximation to the population likelihood which is generated from the individual likelihoods that are approximated using the Extended Kalman Filter's one-step predictions.

  11. Software Replica of Minimal Living Processes

    Science.gov (United States)

    Bersini, Hugues

    2010-04-01

    There is a long tradition of software simulations in theoretical biology to complement pure analytical mathematics which are often limited to reproduce and understand the self-organization phenomena resulting from the non-linear and spatially grounded interactions of the huge number of diverse biological objects. Since John Von Neumann and Alan Turing pioneering works on self-replication and morphogenesis, proponents of artificial life have chosen to resolutely neglecting a lot of materialistic and quantitative information deemed not indispensable and have focused on the rule-based mechanisms making life possible, supposedly neutral with respect to their underlying material embodiment. Minimal life begins at the intersection of a series of processes which need to be isolated, differentiated and duplicated as such in computers. Only software developments and running make possible to understand the way these processes are intimately interconnected in order for life to appear at the crossroad. In this paper, I will attempt to set out the history of life as the disciples of artificial life understand it, by placing these different lessons on a temporal and causal axis, showing which one is indispensable to the appearance of the next and how does it connect to the next. I will discuss the task of artificial life as setting up experimental software platforms where these different lessons, whether taken in isolation or together, are tested, simulated, and, more systematically, analyzed. I will sketch some of these existing software platforms: chemical reaction networks, Varela’s autopoietic cellular automata, Ganti’s chemoton model, whose running delivers interesting take home messages to open-minded biologists.

  12. airGR: an R-package suitable for large sample hydrology presenting a suite of lumped hydrological models

    Science.gov (United States)

    Thirel, G.; Delaigue, O.; Coron, L.; Perrin, C.; Andreassian, V.

    2016-12-01

    Lumped hydrological models are useful and convenient tools for research, engineering and educational purposes. They propose catchment-scale representations of the precipitation-discharge relationship. Thanks to their limited data requirements, they can be easily implemented and run. With such models, it is possible to simulate a number of hydrological key processes over the catchment with limited structural and parametric complexity, typically evapotranspiration, runoff, underground losses, etc. The Hydrology Group at Irstea (Antony) has been developing a suite of rainfall-runoff models over the past 30 years with the main objectives of designing models as efficient as possible in terms of streamflow simulation, applicable to a wide range of catchments and having low data requirements. This resulted in a suite of models running at different time steps (from hourly to annual) applicable for various issues including water balance estimation, forecasting, simulation of impacts and scenario testing. Recently, Irstea has developed an easy-to-use R-package (R Core Team, 2015; Coron et al., 2016), called airGR, to make these models widely available. It includes: - the water balance annual GR1A (Mouehli et al., 2006), - the monthly GR2M (Mouehli, 2003) models, - three versions of the daily model, namely GR4J (Perrin et al., 2003), GR5J (Le Moine, 2008) and GR6J (Pushpalatha et al., 2011), - the hourly GR4H model (Mathevet, 2005), - a degree-day snow module CemaNeige (Valéry et al., 2014). The airGR package has been designed to facilitate the use by non-expert users and allow the addition of evaluation criteria, models or calibration algorithm selected by the end-user. Each model core is coded in FORTRAN to ensure low computational time. The other package functions (i.e. mainly the calibration algorithm and the efficiency criteria) are coded in R. The package is already used for educational purposes. It allows for convenient implementation of model inter-comparisons and

  13. Characterization of integrated circuit packaging materials

    CERN Document Server

    Moore, Thomas

    1993-01-01

    Chapters in this volume address important characteristics of IC packages. Analytical techniques appropriate for IC package characterization are demonstrated through examples of the measurement of critical performance parameters and the analysis of key technological problems of IC packages. Issues are discussed which affect a variety of package types, including plastic surface-mount packages, hermetic packages, and advanced designs such as flip-chip, chip-on-board and multi-chip models.

  14. Drop Test Results for the Combustion Engineering Model No. ABB-2901 Fuel Pellet Package

    Energy Technology Data Exchange (ETDEWEB)

    Hafner, R S; Mok, G C; Hagler, L G

    2004-04-23

    The U.S. Nuclear Regulatory Commission (USNRC) contracted with the Packaging Review Group (PRG) at Lawrence Livermore National Laboratory (LLNL) to conduct a single, 30-ft shallow-angle drop test on the Combustion Engineering ABB-2901 drum-type shipping package. The purpose of the test was to determine if bolted-ring drum closures could fail during shallow-angle drops. The PRG at LLNL planned the test, and Defense Technologies Engineering Division (DTED) personnel from LLNL's Site-300 Test Group executed the plan. The test was conducted in November 2001 using the drop-tower facility at LLNL's Site 300. Two representatives from Westinghouse Electric Company in Columbia, South Carolina (WEC-SC); two USNRC staff members; and three PRG members from LLNL witnessed the preliminary test runs and the final test. The single test clearly demonstrated the vulnerability of the bolted-ring drum closure to shallow-angle drops-the test package's drum closure was easily and totally separated from the drum package. The results of the preliminary test runs and the 30-ft shallow-angle drop test offer valuable qualitative understandings of the shallow-angle impact.

  15. A comprehensive waste collection cost model applied to post-consumer plastic packaging waste

    NARCIS (Netherlands)

    Groot, J.J.; Bing, X.; Bos-Brouwers, H.E.J.; Bloemhof, J.M.

    2014-01-01

    Post-consumer plastic packaging waste (PPW) can be collected for recycling via source separation or post-separation. In source separation, households separate plastics from other waste before collection, whereas in post-separation waste is separated at a treatment centre after collection. There are

  16. Modelling of simultaneous two-sided migration into water and olive oil from nylon food packaging

    NARCIS (Netherlands)

    Stoffers, N.H.; Dekker, M.; Linssen, J.P.H.; Störmer, A.; Franz, R.; Boekel, van M.A.J.S.

    2005-01-01

    Nylon 6 and nylon 12 food packaging materials used as sausage casings are typically exposed to fatty food on one side and boiling water on the other during the cooking process. To simulate the migration behaviour under these conditions, a special migration cell was constructed and filled with olive

  17. Modelling of simultaneous two-sided migration into water and olive oil from nylon food packaging

    NARCIS (Netherlands)

    Stoffers, N.H.; Dekker, M.; Linssen, J.P.H.; Störmer, A.; Franz, R.; Boekel, van M.A.J.S.

    2005-01-01

    Nylon 6 and nylon 12 food packaging materials used as sausage casings are typically exposed to fatty food on one side and boiling water on the other during the cooking process. To simulate the migration behaviour under these conditions, a special migration cell was constructed and filled with olive

  18. A comprehensive waste collection cost model applied to post-consumer plastic packaging waste

    NARCIS (Netherlands)

    Groot, J.J.; Bing, X.; Bos-Brouwers, H.E.J.; Bloemhof, J.M.

    2014-01-01

    Post-consumer plastic packaging waste (PPW) can be collected for recycling via source separation or post-separation. In source separation, households separate plastics from other waste before collection, whereas in post-separation waste is separated at a treatment centre after collection. There are

  19. Analysis of mathematical models of Pseudomonas spp. growth in pallet-package pork stored at different temperatures.

    Science.gov (United States)

    Li, Miaoyun; Niu, Huimin; Zhao, Gaiming; Tian, Lu; Huang, Xianqing; Zhang, Jianwei; Tian, Wei; Zhang, Qiuhui

    2013-04-01

    Pseudomonas of pallet-packaged raw pork grown at 0, 5, 10, 15, 20 and 25°C has been studied in this paper. The modified Gompertz, Baranyi and Huang models were used for data fitting. Statistical criteria such as residual sum of squares, mean square error, Akaike's information criterion, and pseudo-R(2) were used to evaluate model performance. Results showed that there was an apparent decline in Pseudomonas growth at initial-storage phase at low temperatures. The modified Gompertz model outperformed the others at 5, 15, and 20°C, while Baranyi model was appropriate for 0 and 25°C. The Huang model was optimal at 10°C. No single model can give a consistently preferable goodness-of-fit for all growth data. The Gompertz model, with the smallest average values of RSS, AIC, MSE and the biggest pseudo-R(2) at all temperatures, is the most appropriate model to describe the growth of Pseudomonas of raw pork under pallet packaging. Copyright © 2012 Elsevier Ltd. All rights reserved.

  20. 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.

  1. 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.

  2. 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.

  3. Development of tube-packaged FBG strain sensor and application in the vibration experiment of submarine pipeline model

    Science.gov (United States)

    Ren, Liang; Li, Hong-Nan; Sun, Li; Li, Dong-Sheng

    2005-05-01

    Optical fiber sensors have received increasing attention in the fields of aeronautic and civil engineering for their superior ability of explosion proof, immunity to electromagnetic interference and high accuracy, especially fitting for measurement applications in harsh environment. In this paper, a novel FBG (fiber Bragg grating) strain sensor, which was packaged in a 1.2mm stainless steel tube by epoxy resin, was developed. Experiments were conducted on the universal material testing machine to calibrate its strain transferring characteristics. The sensor has the advantages of small size, high precision and flexible use, and demonstrates promising potentials. Ten of tube-packaged strain FBG sensors were applied in the vibration experiment of submarine pipeline model. The strain measured by FBG sensor agrees well with the electric resistance strain sensor.

  4. 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.

  5. 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.

  6. Modelled Cost-Effectiveness of a Package Size Cap and a Kilojoule Reduction Intervention to Reduce Energy Intake from Sugar-Sweetened Beverages in Australia.

    Science.gov (United States)

    Crino, Michelle; Herrera, Ana Maria Mantilla; Ananthapavan, Jaithri; Wu, Jason H Y; Neal, Bruce; Lee, Yong Yi; Zheng, Miaobing; Lal, Anita; Sacks, Gary

    2017-09-06

    Interventions targeting portion size and energy density of food and beverage products have been identified as a promising approach for obesity prevention. This study modelled the potential cost-effectiveness of: a package size cap on single-serve sugar sweetened beverages (SSBs) >375 mL ( package size cap ), and product reformulation to reduce energy content of packaged SSBs ( energy reduction ). The cost-effectiveness of each intervention was modelled for the 2010 Australia population using a multi-state life table Markov model with a lifetime time horizon. Long-term health outcomes were modelled from calculated changes in body mass index to their impact on Health-Adjusted Life Years (HALYs). Intervention costs were estimated from a limited societal perspective. Cost and health outcomes were discounted at 3%. Total intervention costs estimated in AUD 2010 were AUD 210 million. Both interventions resulted in reduced mean body weight ( package size cap : 0.12 kg; energy reduction : 0.23 kg); and HALYs gained ( package size cap : 73,883; energy reduction : 144,621). Cost offsets were estimated at AUD 750.8 million ( package size cap ) and AUD 1.4 billion ( energy reduction ). Cost-effectiveness analyses showed that both interventions were "dominant", and likely to result in long term cost savings and health benefits. A package size cap and kJ reduction of SSBs are likely to offer excellent "value for money" as obesity prevention measures in Australia.

  7. 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.

  8. Critical head, thickness of fine-grained deposit, and skeletal elastic storage arrays of the SUB package of the Central Valley Hydrologic Model

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This digital dataset defines the SUB package arrays for the model grid, critical head, thickness of fine-grained deposits, and skeletal-elastic-storage used in the...

  9. Demands placed on waste package performance testing and modeling by some general results on reliability analysis

    Energy Technology Data Exchange (ETDEWEB)

    Chesnut, D.A.

    1991-09-01

    Waste packages for a US nuclear waste repository are required to provide reasonable assurance of maintaining substantially complete containment of radionuclides for 300 to 1000 years after closure. The waiting time to failure for complex failure processes affecting engineered or manufactured systems is often found to be an exponentially-distributed random variable. Assuming that this simple distribution can be used to describe the behavior of a hypothetical single barrier waste package, calculations presented in this paper show that the mean time to failure (the only parameter needed to completely specify an exponential distribution) would have to be more than 10{sub 7} years in order to provide reasonable assurance of meeting this requirement. With two independent barriers, each would need to have a mean time to failure of only 10{sup 5} years to provide the same reliability. Other examples illustrate how multiple barriers can provide a strategy for not only achieving but demonstrating regulatory compliance.

  10. lumpR 2.0.0: an R package facilitating landscape discretisation for hillslope-based hydrological models

    Science.gov (United States)

    Pilz, Tobias; Francke, Till; Bronstert, Axel

    2017-08-01

    The characteristics of a landscape pose essential factors for hydrological processes. Therefore, an adequate representation of the landscape of a catchment in hydrological models is vital. However, many of such models exist differing, amongst others, in spatial concept and discretisation. The latter constitutes an essential pre-processing step, for which many different algorithms along with numerous software implementations exist. In that context, existing solutions are often model specific, commercial, or depend on commercial back-end software, and allow only a limited or no workflow automation at all. Consequently, a new package for the scientific software and scripting environment R, called lumpR, was developed. lumpR employs an algorithm for hillslope-based landscape discretisation directed to large-scale application via a hierarchical multi-scale approach. The package addresses existing limitations as it is free and open source, easily extendible to other hydrological models, and the workflow can be fully automated. Moreover, it is user-friendly as the direct coupling to a GIS allows for immediate visual inspection and manual adjustment. Sufficient control is furthermore retained via parameter specification and the option to include expert knowledge. Conversely, completely automatic operation also allows for extensive analysis of aspects related to landscape discretisation. In a case study, the application of the package is presented. A sensitivity analysis of the most important discretisation parameters demonstrates its efficient workflow automation. Considering multiple streamflow metrics, the employed model proved reasonably robust to the discretisation parameters. However, parameters determining the sizes of subbasins and hillslopes proved to be more important than the others, including the number of representative hillslopes, the number of attributes employed for the lumping algorithm, and the number of sub-discretisations of the representative hillslopes.

  11. IN-PACKAGE CHEMISTRY ABSTRACTION

    Energy Technology Data Exchange (ETDEWEB)

    E. Thomas

    2005-07-14

    This report was developed in accordance with the requirements in ''Technical Work Plan for Postclosure Waste Form Modeling'' (BSC 2005 [DIRS 173246]). The purpose of the in-package chemistry model is to predict the bulk chemistry inside of a breached waste package and to provide simplified expressions of that chemistry as a function of time after breach to Total Systems Performance Assessment for the License Application (TSPA-LA). The scope of this report is to describe the development and validation of the in-package chemistry model. The in-package model is a combination of two models, a batch reactor model, which uses the EQ3/6 geochemistry-modeling tool, and a surface complexation model, which is applied to the results of the batch reactor model. The batch reactor model considers chemical interactions of water with the waste package materials, and the waste form for commercial spent nuclear fuel (CSNF) waste packages and codisposed (CDSP) waste packages containing high-level waste glass (HLWG) and DOE spent fuel. The surface complexation model includes the impact of fluid-surface interactions (i.e., surface complexation) on the resulting fluid composition. The model examines two types of water influx: (1) the condensation of water vapor diffusing into the waste package, and (2) seepage water entering the waste package as a liquid from the drift. (1) Vapor-Influx Case: The condensation of vapor onto the waste package internals is simulated as pure H{sub 2}O and enters at a rate determined by the water vapor pressure for representative temperature and relative humidity conditions. (2) Liquid-Influx Case: The water entering a waste package from the drift is simulated as typical groundwater and enters at a rate determined by the amount of seepage available to flow through openings in a breached waste package.

  12. 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.

  13. Using ProModel as a simulation tools to assist plant layout design and planning: Case study plastic packaging factory

    Directory of Open Access Journals (Sweden)

    Pochamarn Tearwattanarattikal

    2008-01-01

    Full Text Available This study is about the application of a Simulation Model to assist decision making on expanding capacity and plant layout design and planning. The plant layout design concept is performed first to create the physical layouts then the simulation model used to test the capability of plant to meet various demand forecast scena. The study employed ProModel package as a tool, using the model to compare the performances in term of % utilization, characteristics of WIP and ability to meet due date. The verification and validation stages were perform before running the scenarios. The model runs daily production and then the capacity constraint resources defined by % utilization. The expanding capacity policy can be extra shift-working hours or increasing the number of machines. After expanding capacity solutions are found, the physical layout is selected based on the criterion of space available for WIP and easy flow of material.

  14. 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.

  15. [Definition of "Safety and Hygiene Packages" as a management model for the Hospital Hygiene Service (HHS)].

    Science.gov (United States)

    Raponi, Matteo; Damiani, Gianfranco; Vincenti, Sara; Wachocka, Malgorzata; Boninti, Federica; Bruno, Stefania; Quaranta, Gianluigi; Moscato, Umberto; Boccia, Stefania; Ficarra, Maria Giovanna; Specchia, Maria Lucia; Posteraro, Brunella; Berloco, Filippo; Celani, Fabrizio; Ricciardi, Walter; Laurenti, Patrizia

    2014-01-01

    The purpose of this research is to identify and formalize the Hospital Hygiene Service activities and products, evaluating them in a cost accounting management view. The ultimate aim, is to evaluate the financial adverse events prevention impact, in an Hospital Hygiene Service management. A three step methodology based on affinity grouping activities, was employed. This methodology led us to identify 4 action areas, with 23 related productive processes, and 86 available safety packages. Owing to this new methodology, we was able to implement a systematic evaluation of the furnished services.

  16. Computer aided simulation for developing a simple model to predict cooling of packaged foods

    DEFF Research Database (Denmark)

    Christensen, Martin Gram; Feyissa, Aberham Hailu; Adler-Nissen, Jens

    A new equation to predict equilibrium temperatures for cooling operations of packaged foods has been deducted from the traditional 1st order solution to Fourier’s heat transfer equations. The equation is analytical in form and only requires measurable parameters, in form of area vs. volume ratio (A...... are too laborious or impossible to conduct. The deducted equation was tested for irregular geometries, unequal heat transfer and headspace restrictions. The new equation predicted equilibrium temperature curves of the simulated cooling with a low error (1.5°C for Fourier numbers below 0.3) and good...

  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. Detection of alpha-helical coiled-coil dimer formation by spin-labeled synthetic peptides: a model parallel coiled-coil peptide and the antiparallel coiled coil formed by a replica of the ProP C-terminus.

    Science.gov (United States)

    Hillar, Alexander; Tripet, Brian; Zoetewey, David; Wood, Janet M; Hodges, Robert S; Boggs, Joan M

    2003-12-30

    Electron paramagnetic resonance spectroscopy was used to determine relative peptide orientation within homodimeric, alpha-helical coiled-coil structures. Introduction of cysteine (Cys) residues into peptides/proteins for spin labeling allows detection of their oligomerization from exchange broadening or dipolar interactions between residues within 25 A of each other. Two synthetic peptides containing Cys substitutions were used: a 35-residue model peptide and the 30-residue ProP peptide. The model peptide is known to form a stable, parallel homodimeric coiled coil, which is partially destabilized by Cys substitutions at heptad a and d positions (peptides C30a and C33d). The ProP peptide, a 30-residue synthetic peptide, corresponds to residues 468-497 of osmoregulatory transporter ProP from Escherichia coli. It forms a relatively unstable, homodimeric coiled coil that is predicted to be antiparallel in orientation. Cys was introduced in heptad g positions of the ProP peptide, near the N-terminus (K473C, creating peptide C473g) or closer to the center of the sequence (E480C, creating peptide C480g). In contrast to the destabilizing effect of Cys substitution at the core heptad a or d positions of model peptides C30a and C33d, circular dichroism spectroscopy showed that Cys substitutions at the heptad g positions of the ProP peptide had little or no effect on coiled-coil stability. Thermal denaturation analysis showed that spin labeling increased the stability of the coiled coil for all peptides. Strong exchange broadening was detected for both C30a and C33d, in agreement with a parallel structure. EPR spectra of C480g had a large hyperfine splitting of about 90 G, indicative of strong dipole-dipole interactions and a distance between spin-labeled residues of less than 9 A. Spin-spin interactions were much weaker for C473g. These results supported the hypothesis that the ProP peptide primarily formed an antiparallel coiled coil, since formation of a parallel dimer

  2. Green Packaging Development. : A way to efficient, effective and more environmental friendly packaging solutions.

    OpenAIRE

    Mian Muhammad, Masoud

    2011-01-01

    Growing pressure on the packaging design to enhance the environmental and logistics performance of a packaging system stresses the packaging designers to search new design strategies that not only fulfill logistics requirements in the supply chain, but also reduce the CO 2emissions during the packaging life cycle. This thesis focuses on the packaging design process and suggests some improvements by considering its logistics performance and CO 2emissions. A Green packaging development model wa...

  3. 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.

  4. 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.

  5. Intellectual package that uses knowledge of an object region and functional models in the planning of computations

    Energy Technology Data Exchange (ETDEWEB)

    Bukhshtab, Yu.A.; Gorlin, A.I.; Kamynin, S.S.; Koryagin, D.A.; Lyubimskiy, E.Z.

    1981-09-01

    Summary form only given, as follows. A method is proposed for constructing a system for filling a package of applied programs. The system is capable of automatic planning of computations, based on the use of knowledge of regarding the object region of the package and regarding the semantics of modules appearing in the functional filling of the package. An experimental package constructed in accordance with proposed principles is described, and an example of work with them is included.

  6. Empirical models for end-use properties prediction of LDPE: application in the flexible plastic packaging industry

    Directory of Open Access Journals (Sweden)

    Maria Carolina Burgos Costa

    2008-03-01

    Full Text Available The objective of this work is to develop empirical models to predict end use properties of low density polyethylene (LDPE resins as functions of two intrinsic properties easily measured in the polymers industry. The most important properties for application in the flexible plastic packaging industry were evaluated experimentally for seven commercial polymer grades. Statistical correlation analysis was performed for all variables and used as the basis for proper choice of inputs to each model output. Intrinsic properties selected for resin characterization are fluidity index (FI, which is essentially an indirect measurement of viscosity and weight average molecular weight (MW, and density. In general, models developed are able to reproduce and predict experimental data within experimental accuracy and show that a significant number of end use properties improve as the MW and density increase. Optical properties are mainly determined by the polymer morphology.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Drop Test Results for the Combustion Engineering Model No. ABB-2901 Fuel Pellet Shipping Package

    Energy Technology Data Exchange (ETDEWEB)

    Mok, G; Hagler, L

    2002-06-01

    Steel cylindrical drums have been used for many years to transport radioactive materials. The radioactive material inserted into the drum cavity for shipping is usually restrained within its own container or containment vessel. For additional protection, the container is surrounded or supported by components made of impact-absorbent and/or thermal-insulation materials. The components are expected to protect the container and its radioactive contents under severe transportation conditions like free drops and fires. Due to its simplicity and convenience, bolted-ring drum closures are commonly used to close many drum packages. Because the structural integrity of the drum and drum closure often play a significant role in determining the package's ability to maintain sub-criticality, shielding, and containment of the radioactive contents, regulations require that the complete drum package be tested for safety performance. The structural integrity of the drum body is relatively simple to understand and analyze, whereas analyzing the integrity of the drum closure is not so simple. In summary, the drop test accomplished its mission. Because the lid and closure device separated from the drum body in the 30-ft 17.5{sup o} shallow-angle drop, the drop test confirmed that the common drum closure with a bolted ring is vulnerable to damage by a shallow-angle drop, even though the closure has been shown to survive much steeper-angle drops. The test program also demonstrated one of the mechanisms by which the shallow-angle drop opens the common bolted-ring drum closure. The separation of the drum lid and closure device from the drum body was initiated by a large outward buckling deformation of the lid and completed with minimal assistance by the round plywood boards behind the lid. The energy spent to complete the separation appeared to be only a small fraction of the total impact energy. Limited to only one test, the present test program could not explore all possible

  12. WASTE CONTAINER AND WASTE PACKAGE PERFORMANCE MODELING TO SUPPORT SAFETY ASSESSMENT OF LOW AND INTERMEDIATE-LEVEL RADIOACTIVE WASTE DISPOSAL.

    Energy Technology Data Exchange (ETDEWEB)

    SULLIVAN, T.

    2004-06-30

    Prior to subsurface burial of low- and intermediate-level radioactive wastes, a demonstration that disposal of the wastes can be accomplished while protecting the health and safety of the general population is required. The long-time frames over which public safety must be insured necessitates that this demonstration relies, in part, on computer simulations of events and processes that will occur in the future. This demonstration, known as a Safety Assessment, requires understanding the performance of the disposal facility, waste containers, waste forms, and contaminant transport to locations accessible to humans. The objective of the coordinated research program is to examine the state-of-the-art in testing and evaluation short-lived low- and intermediate-level waste packages (container and waste form) in near surface repository conditions. The link between data collection and long-term predictions is modeling. The objective of this study is to review state-of-the-art modeling approaches for waste package performance. This is accomplished by reviewing the fundamental concepts behind safety assessment and demonstrating how waste package models can be used to support safety assessment. Safety assessment for low- and intermediate-level wastes is a complicated process involving assumptions about the appropriate conceptual model to use and the data required to support these models. Typically due to the lack of long-term data and the uncertainties from lack of understanding and natural variability, the models used in safety assessment are simplistic. However, even though the models are simplistic, waste container and waste form performance are often central to the case for making a safety assessment. An overview of waste container and waste form performance and typical models used in a safety assessment is supplied. As illustrative examples of the role of waste container and waste package performance, three sample test cases are provided. An example of the impacts of

  13. Portobello Packaging

    National Research Council Canada - National Science Library

    Thomas Grose

    2010-01-01

    ...-based foams. Bayer earned dual degrees in mechanical engineering and product design in 2007 and, with classmate Gavin Mclntyre, started the company Ecovative Design to market his creation. EcoCradle, the company's organic packaging material, was named one of the top inventions of 2009 by Popular Science. Its insulation material, Greensulate, got a ...

  14. Repository environmental parameters and models/methodologies relevant to assessing the performance of high-level waste packages in basalt, tuff, and salt

    Energy Technology Data Exchange (ETDEWEB)

    Claiborne, H.C.; Croff, A.G.; Griess, J.C.; Smith, F.J.

    1987-09-01

    This document provides specifications for models/methodologies that could be employed in determining postclosure repository environmental parameters relevant to the performance of high-level waste packages for the Basalt Waste Isolation Project (BWIP) at Richland, Washington, the tuff at Yucca Mountain by the Nevada Test Site, and the bedded salt in Deaf Smith County, Texas. Guidance is provided on the identify of the relevant repository environmental parameters; the models/methodologies employed to determine the parameters, and the input data base for the models/methodologies. Supporting studies included are an analysis of potential waste package failure modes leading to identification of the relevant repository environmental parameters, an evaluation of the credible range of the repository environmental parameters, and a summary of the review of existing models/methodologies currently employed in determining repository environmental parameters relevant to waste package performance. 327 refs., 26 figs., 19 tabs.

  15. Spallation Source Modelling for an ADS Using the MCNPX and GEANT4 Packages for Sensitivity Analysis of Reactivity

    Science.gov (United States)

    Antolin, M. Q.; Marinho, F.; Palma, D. A. P.; Martinez, A. S.

    2014-04-01

    A simulation for the time evolution of the MYRRHA conceptual reactor was developed. The SERPENT code was used to simulate the nuclear fuel depletion and the spallation source which drives the system was simulated using both MCNPX and GEANT4 packages. The obtained results for the neutron energy spectrum from the spallation are coherent with each other and were used as input for the SERPENT code which simulated a constant power operation regime. The obtained results show that the criticality of the system is not sensitive to the spallation models employed and only relative small deviations with respect to the inverse kinetic model coming from the point kinetic equations proposed by Gandini were observed.

  16. Fitting HIV Prevalence 1981 Onwards for Three Indian States Using the Goals Model and the Estimation and Projection Package

    Science.gov (United States)

    Bhatnagar, Tarun; Dutta, Tapati; Stover, John; Godbole, Sheela; Sahu, Damodar; Boopathi, Kangusamy; Bembalkar, Shilpa; Singh, Kh. Jitenkumar; Goyal, Rajat; Pandey, Arvind; Mehendale, Sanjay M.

    2016-01-01

    Models are designed to provide evidence for strategic program planning by examining the impact of different interventions on projected HIV incidence. We employed the Goals Model to fit the HIV epidemic curves in Andhra Pradesh, Maharashtra and Tamil Nadu states of India where HIV epidemic is considered to have matured and in a declining phase. Input data in the Goals Model consisted of demographic, epidemiological, transmission-related and risk group wise behavioral parameters. The HIV prevalence curves generated in the Goals Model for each risk group in the three states were compared with the epidemic curves generated by the Estimation and Projection Package (EPP) that the national program is routinely using. In all the three states, the HIV prevalence trends for high-risk populations simulated by the Goals Model matched well with those derived using state-level HIV surveillance data in the EPP. However, trends for the low- and medium-risk populations differed between the two models. This highlights the need to generate more representative and robust data in these sub-populations and consider some structural changes in the modeling equation and parameters in the Goals Model to effectively use it to assess the impact of future strategies of HIV control in various sub-populations in India at the sub-national level. PMID:27711212

  17. 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.

  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. CH Packaging Program Guidance

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2009-06-01

    The purpose of this document is to provide the technical requirements for preparation for use, operation, inspection, and maintenance of a Transuranic Package Transporter Model II (TRUPACT-II), a HalfPACT shipping package, and directly related components. This document complies with the minimum requirements as specified in the TRUPACT-II Safety Analysis Report for Packaging (SARP), HalfPACT SARP, and U.S. Nuclear Regulatory Commission (NRC) Certificates of Compliance (C of C) 9218 and 9279, respectively. In the event of a conflict between this document and the SARP or C of C, the C of C shall govern. The C of Cs state: "each package must be prepared for shipment and operated in accordance with the procedures described in Chapter 7.0, Operating Procedures, of the application." They further state: "each package must be tested and maintained in accordance with the procedures described in Chapter 8.0, Acceptance Tests and Maintenance Program of the Application." Chapter 9.0 of the SARP charges the U.S. Department of Energy (DOE) or the Waste Isolation Pilot Plant (WIPP) management and operating (M&O) contractor with assuring packaging is used in accordance with the requirements of the C of C. Because the packaging is NRC-approved, users need to be familiar with Title 10 Code of Federal Regulations (CFR) §71.8. Any time a user suspects or has indications that the conditions of approval in the C of C were not met, the Carlsbad Field Office (CBFO) shall be notified immediately. The CBFO will evaluate the issue and notify the NRC if required. In accordance with 10 CFR Part 71, certificate holders, packaging users, and contractors or subcontractors who use, design, fabricate, test, maintain, or modify the packaging shall post copies of (1) 10 CFR Part 21 regulations, (2) Section 206 of the Energy Reorganization Act of 1974, and (3) NRC Form 3, Notice to Employees. These documents must be posted in a conspicuous location where the activities subject to these regulations are

  20. CH Packaging Program Guidance

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2008-09-11

    The purpose of this document is to provide the technical requirements for preparation for use, operation, inspection, and maintenance of a Transuranic Package Transporter Model II (TRUPACT-II), a HalfPACT shipping package, and directly related components. This document complies with the minimum requirements as specified in the TRUPACT-II Safety Analysis Report for Packaging (SARP), HalfPACT SARP, and U.S. Nuclear Regulatory Commission (NRC) Certificates of Compliance (C of C) 9218 and 9279, respectively. In the event of a conflict between this document and the SARP or C of C, the C of C shall govern. The C of Cs state: "each package must be prepared for shipment and operated in accordance with the procedures described in Chapter 7.0, Operating Procedures, of the pplication." They further state: "each package must be tested and maintained in accordance with the procedures described in Chapter 8.0, Acceptance Tests and Maintenance Program of the Application." Chapter 9.0 of the SARP charges the U.S. Department of Energy (DOE) or the Waste Isolation Pilot Plant (WIPP) management and operating (M&O) contractor with assuring packaging is used in accordance with the requirements of the C of C. Because the packaging is NRC-approved, users need to be familiar with Title 10 Code of Federal Regulations (CFR) §71.8. Any time a user suspects or has indications that the conditions of approval in the C of C were not met, the Carlsbad Field Office (CBFO) shall be notified immediately. The CBFO will evaluate the issue and notify the NRC if required. In accordance with 10 CFR Part 71, certificate holders, packaging users, and contractors or subcontractors who use, design, fabricate, test, maintain, or modify the packaging shall post copies of (1) 10 CFR Part 21 regulations, (2) Section 206 of the Energy Reorganization Act of 1974, and (3) NRC Form 3, Notice to Employees. These documents must be posted in a conspicuous location where the activities subject to these regulations are

  1. Seafood Packaging

    Science.gov (United States)

    1996-01-01

    NASA's Technology Transfer Office at Stennis Space Center worked with a New Orleans seafood packaging company to develop a container to improve the shipping longevity of seafood, primarily frozen and fresh fish, while preserving the taste. A NASA engineer developed metalized heat resistant polybags with thermal foam liners using an enhanced version of the metalized mylar commonly known as 'space blanket material,' which was produced during the Apollo era.

  2. Use of food and packaging model matrices to investigate the antioxidant properties of biorefinery grass lignins.

    Science.gov (United States)

    Aguié-Béghin, Véronique; Foulon, Laurence; Soto, Paola; Crônier, David; Corti, Elena; Legée, Frédéric; Cézard, Laurent; Chabbert, Brigitte; Maillard, Marie-Noëlle; Huijgen, Wouter J J; Baumberger, Stéphanie

    2015-11-18

    The antioxidant properties of grass lignins recovered from an alkaline industrial process and from different ethanol organosolv pretreatment processes were compared using two types of tests: (i) classical radical 2,2'-diphenyl-1-picrylhydrazyl (DPPH(•)) scavenging tests in dioxane/water or ethanol and (ii) tests involving multiphasic systems (lipid dispersion in water or cellulose film suspended in ethanol). These multiphasic systems were representative of food and packaging matrices in view of high-value applications. All lignins, in solution or in the film, effectively scavenged radicals. Moreover, they were competitive with a food commercial rosemary extract to protect linoleic acid against oxidation. Whereas the DPPH(•) test in dioxane was not discriminant, differences appeared between lignins when the test was performed in ethanol or with the multiphasic systems. Moreover, radical scavenging activity was preserved in the film even after its immersion in ethanol. Structural analysis of lignins revealed that low-molar-mass phenolics, namely p-hydroxycinnamic acids and lignin depolymerization products, governed lignin antioxidant properties in the multiphasic systems.

  3. 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.

  4. Applicability of an Arrhenius Model for the Combined Effect of Temperature and CO2 Packaging on the Spoilage Microflora of Fish

    Science.gov (United States)

    Koutsoumanis, Konstantinos P.; Taoukis, Petros S.; Drosinos, Eleftherios H.; Nychas, George-John E.

    2000-01-01

    The temperature behavior of the natural microflora on the Mediterranean fish red mullet (Mullus barbatus) was examined as a case study. The growth of the spoilage bacteria Pseudomonas spp., Shewanella putrefaciens, Brochothrix thermosphacta, and lactic acid bacteria was modeled as a function of temperature and the concentration of carbon dioxide in modified atmosphere packaging. Combined models were developed and comparatively assessed based on polynomial, Belehradek, and Arrhenius equations. The activation energy parameter of the Arrhenius model, EA, was independent of the packaging atmosphere and ranged from 75 to 85 kJ/mol for the different bacteria, whereas the preexponential constant decreased exponentially with the packaging CO2 concentration. We evaluated the applicability of the models developed by using experimental bacterial growth rates obtained from 42 independent experiments performed with three Mediterranean fish species and growth rates predicted from the models under the same temperature and packaging conditions. The accuracy factor and bias factor were used as statistical tools for evaluation, and the developed Arrhenius model and the Belehradek model were judged satisfactory overall. PMID:10919817

  5. Antioxidant BHT Modelling Migration from Food Packaging of High Density Polyethylene Plastics into the Food Simulant

    Directory of Open Access Journals (Sweden)

    Chi Haitao

    2015-09-01

    Full Text Available Made of High Density Polyethylene (HDPE films containing antioxidant 2, 6-di-tert-butyl-p-cresol (BHT, film samples were manufactured by plastic extrusion equipment, 95% ethanol aqueous solution simulating liquid was used for stimulant, using High Performance Liquid Chromatography (HPLC for the long-term migration test of 4 kinds of HDPE films containing different concentrations of antioxidant BHT. The migration data were processed by using Weibull model and then the migration model was specific under experimental conditions. Migration model was setup using the migrating data by Weibull model to fitting real experimental data. Using empirical formula reported FDA model formula and the diffusion coefficient constant D, calculated by the FDA model. Two kinds of model numerical after compared according to FDA model transfer numerical literature that is far lower than the actual test migration value. According to the actual test migration value, Weibull model numerical and experimental tests that the migration software fitting values are consistent.

  6. An Application of the Thermal Network Method to the Thermal Analysis of Multichip Packages (Proposal of a Simple Thermal Analysis Model)

    Science.gov (United States)

    Fukuoka, Yoshitaka; Ishizuka, Masaru

    1989-09-01

    In recent years, electronic circuits have been required to be smaller and lighter and to have greater complexity, more multifunctions and higher reliability. High-density multichip packaging technology has been used in order to meet these requirements. The higher the density scale, the larger the power dissipation per unit area will become. Therefore, thermal analysis becomes one of the most important design factors. However, the multichip package heat transport mode is very complex and its treatment is tedious and time consuming. This paper describes an application of the thermal network method and proposes a simple thermal analysis model for the thermal analysis of multichip packages as a preliminary thermal design tool. As a result, the validity of the thermal network method and the simple thermal analysis model can be confirmed.

  7. CH Packaging Program Guidance

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2007-12-13

    The purpose of this document is to provide the technical requirements for preparation for use, operation, inspection, and maintenance of a Transuranic Package Transporter Model II (TRUPACT-II), a HalfPACT shipping package, and directly related components. This document complies with the minimum requirements as specified in the TRUPACT-II Safety Analysis Report for Packaging (SARP), HalfPACT SARP, and U.S. Nuclear Regulatory Commission (NRC) Certificates of Compliance (C of C) 9218 and 9279, respectively. In the event of a conflict between this document and the SARP or C of C, the C of C shall govern. The C of Cs state: "each package must be prepared for shipment and operated in accordance with the procedures described in Chapter 7.0, Operating Procedures, of the application." They further state: "each package must be tested and maintained in accordance with the procedures described in Chapter 8.0, Acceptance Tests and Maintenance Program of the Application." Chapter 9.0 of the SARP charges the U.S. Department of Energy (DOE) or the Waste Isolation Pilot Plant (WIPP) management and operating (M&O) contractor with assuring packaging is used in accordance with the requirements of the C of C. Because the packaging is NRC-approved, users need to be familiar with Title 10 Code of Federal Regulations (CFR) §71.8. Any time a user suspects or has indications that the conditions of approval in the C of C were not met, the Carlsbad Field Office (CBFO) shall be notified immediately. The CBFO will evaluate the issue and notify the NRC if required.In accordance with 10 CFR Part 71, certificate holders, packaging users, and contractors or subcontractors who use, design, fabricate, test, maintain, or modify the packaging shall post copies of (1) 10 CFR Part 21 regulations, (2) Section 206 of the Energy Reorganization Act of 1974, and (3) NRC Form 3, Notice to Employees. These documents must be posted in a conspicuous location where the activities subject to these regulations are

  8. 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.

  9. 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

  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. Hidden Semi Markov Models for Multiple Observation Sequences: The mhsmm Package for R

    DEFF Research Database (Denmark)

    O'Connell, Jarad Michael; Højsgaard, Søren

    2011-01-01

    models only allow a geometrically distributed sojourn time in a given state, while hidden semi-Markov models extend this by allowing an arbitrary sojourn distribution. We demonstrate the software with simulation examples and an application involving the modelling of the ovarian cycle of dairy cows...

  12. Documentation of 'Care-Packages' for Children in OECD's 2003 Tax/Ben Model, December 2006

    DEFF Research Database (Denmark)

    Hansen, Hans

    This working paper contains documentation for the modelling of schemes implemented in OECD's 2003 Tax/Ben model for use in the 'Carearchitecture' project. The documentation also includes schemes already in the model and used in the calculations for the project. The documented schemes include pers...

  13. mizer: an R package for multispecies, trait-based and community size spectrum ecological modelling

    DEFF Research Database (Denmark)

    Scott, Finlay; Blanchard, Julia L.; Andersen, Ken Haste

    2014-01-01

    1. Size spectrum ecological models are representations of a community of individuals which grow and change trophic level. A key emergent feature of these models is the size spectrum; the total abundance of all individuals that scales negatively with size. The models we focus on are designed...

  14. 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.

  15. Underground Test Area Subproject Phase I Data Analysis Task. Volume VII - Tritium Transport Model Documentation Package

    Energy Technology Data Exchange (ETDEWEB)

    None

    1996-12-01

    Volume VII of the documentation for the Phase I Data Analysis Task performed in support of the current Regional Flow Model, Transport Model, and Risk Assessment for the Nevada Test Site Underground Test Area Subproject contains the tritium transport model documentation. Because of the size and complexity of the model area, a considerable quantity of data was collected and analyzed in support of the modeling efforts. The data analysis task was consequently broken into eight subtasks, and descriptions of each subtask's activities are contained in one of the eight volumes that comprise the Phase I Data Analysis Documentation.

  16. Underground Test Area Subproject Phase I Data Analysis Task. Volume VI - Groundwater Flow Model Documentation Package

    Energy Technology Data Exchange (ETDEWEB)

    None

    1996-11-01

    Volume VI of the documentation for the Phase I Data Analysis Task performed in support of the current Regional Flow Model, Transport Model, and Risk Assessment for the Nevada Test Site Underground Test Area Subproject contains the groundwater flow model data. Because of the size and complexity of the model area, a considerable quantity of data was collected and analyzed in support of the modeling efforts. The data analysis task was consequently broken into eight subtasks, and descriptions of each subtask's activities are contained in one of the eight volumes that comprise the Phase I Data Analysis Documentation.

  17. Automating calibration, sensitivity and uncertainty analysis of complex models using the R package Flexible Modeling Environment (FME): SWAT as an example

    Science.gov (United States)

    Wu, Y.; Liu, S.

    2012-01-01

    Parameter optimization and uncertainty issues are a great challenge for the application of large environmental models like the Soil and Water Assessment Tool (SWAT), which is a physically-based hydrological model for simulating water and nutrient cycles at the watershed scale. In this study, we present a comprehensive modeling environment for SWAT, including automated calibration, and sensitivity and uncertainty analysis capabilities through integration with the R package Flexible Modeling Environment (FME). To address challenges (e.g., calling the model in R and transferring variables between Fortran and R) in developing such a two-language coupling framework, 1) we converted the Fortran-based SWAT model to an R function (R-SWAT) using the RFortran platform, and alternatively 2) we compiled SWAT as a Dynamic Link Library (DLL). We then wrapped SWAT (via R-SWAT) with FME to perform complex applications including parameter identifiability, inverse modeling, and sensitivity and uncertainty analysis in the R environment. The final R-SWAT-FME framework has the following key functionalities: automatic initialization of R, running Fortran-based SWAT and R commands in parallel, transferring parameters and model output between SWAT and R, and inverse modeling with visualization. To examine this framework and demonstrate how it works, a case study simulating streamflow in the Cedar River Basin in Iowa in the United Sates was used, and we compared it with the built-in auto-calibration tool of SWAT in parameter optimization. Results indicate that both methods performed well and similarly in searching a set of optimal parameters. Nonetheless, the R-SWAT-FME is more attractive due to its instant visualization, and potential to take advantage of other R packages (e.g., inverse modeling and statistical graphics). The methods presented in the paper are readily adaptable to other model applications that require capability for automated calibration, and sensitivity and uncertainty

  18. Modeling & Simulation Education for the Acquisition and T&E Workforce: FY07 Deliverable Package

    Science.gov (United States)

    2007-12-01

    Malamed . 1998. Modern Simulation and Modeling, John Wiley and Sons, Canada. NPS-SE--08-M01 113 Zeigler, Bernard P., Tag Gon Kim, Herbert Praehofer...Reuven Y., Bemjamin Malamed . 1998. Modern Simulation and Modeling, John Wiley and Sons, Canada. NPS-SE--08-M01 116 Competency Level...and output analysis o simulation measures of effectiveness • Rubinstein, Reuven Y., Bemjamin Malamed . 1998. Modern Simulation and Modeling

  19. 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.

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

    Science.gov (United States)

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

    2016-12-01

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

  1. Report on first simulation model, that predicts the feasibility of communicative packaging concepts : Deliverable 6.14

    NARCIS (Netherlands)

    Canters, R.A.M.; Wienk, I.M.; Kreft-Pereira Da Silva, F.I.D.G.; Tromp, S.O.

    2005-01-01

    One of the objectives of this part of the SustainPack project (WP 6.3) is to facilitate the implementation process of communicative packaging in the chain of production, storage, distribution and use of packed products. New packaging concepts are more easily implemented if the benefits can be demons

  2. In-Package Chemistry Abstraction

    Energy Technology Data Exchange (ETDEWEB)

    E. Thomas

    2004-11-09

    This report was developed in accordance with the requirements in ''Technical Work Plan for: Regulatory Integration Modeling and Analysis of the Waste Form and Waste Package'' (BSC 2004 [DIRS 171583]). The purpose of the in-package chemistry model is to predict the bulk chemistry inside of a breached waste package and to provide simplified expressions of that chemistry as function of time after breach to Total Systems Performance Assessment for the License Application (TSPA-LA). The scope of this report is to describe the development and validation of the in-package chemistry model. The in-package model is a combination of two models, a batch reactor model that uses the EQ3/6 geochemistry-modeling tool, and a surface complexation model that is applied to the results of the batch reactor model. The batch reactor model considers chemical interactions of water with the waste package materials and the waste form for commercial spent nuclear fuel (CSNF) waste packages and codisposed waste packages that contain both high-level waste glass (HLWG) and DOE spent fuel. The surface complexation model includes the impact of fluid-surface interactions (i.e., surface complexation) on the resulting fluid composition. The model examines two types of water influx: (1) the condensation of water vapor that diffuses into the waste package, and (2) seepage water that enters the waste package from the drift as a liquid. (1) Vapor Influx Case: The condensation of vapor onto the waste package internals is simulated as pure H2O and enters at a rate determined by the water vapor pressure for representative temperature and relative humidity conditions. (2) Water Influx Case: The water entering a waste package from the drift is simulated as typical groundwater and enters at a rate determined by the amount of seepage available to flow through openings in a breached waste package. TSPA-LA uses the vapor influx case for the nominal scenario for simulations where the waste

  3. Application of Thermal Network Model to Transient Thermal Analysis of Power Electronic Package Substrate

    National Research Council Canada - National Science Library

    Ishizuka, Masaru; Hatakeyama, Tomoyuki; Funawatashi, Yuichi; Koizumi, katsuhiro

    2011-01-01

    .... This paper describes an application of the thermal network method to the transient thermal analysis of multichip modules and proposes a simple model for the thermal analysis of multichip modules as a preliminary thermal design tool. On the basis of the result of transient thermal analysis, the validity of the thermal network method and the simple thermal analysis model is confirmed.

  4. Variability in the Effectiveness of a Video Modeling Intervention Package for Children with Autism

    Science.gov (United States)

    Plavnick, Joshua B.; MacFarland, Mari C.; Ferreri, Summer J.

    2015-01-01

    Video modeling is an evidence-based instructional strategy for teaching a variety of skills to individuals with autism. Despite the effectiveness of this strategy, there is some uncertainty regarding the conditions under which video modeling is likely to be effective. The present investigation examined the differential effectiveness of video…

  5. Electromagnetic modeling and optimization of packaged photodetector modules for 100 Gbit/s applications

    DEFF Research Database (Denmark)

    Jiang, Chenhui; Krozer, Viktor; Bach, H-G;

    2008-01-01

    In this paper, we propose an accurate full 3D EM behavioral model of PD chips for the first time. The model, which is meshed at 130 GHz, runs for about 17 minutes on an Intel Core2 Duo CPU@3 GHz PC with 3.5 GB of RAM. The impact of various parameters in wire- bonding transitions for transmission...

  6. The ASTROID Simulator Software Package: Realistic Modelling of High-Precision High-Cadence Space-Based Imaging

    CERN Document Server

    Marcos-Arenal, P; De Ridder, J; Huygen, R; Aerts, C

    2014-01-01

    The preparation of a space-mission that carries out any kind of imaging to detect high-precision low-amplitude variability of its targets requires a robust model for the expected performance of its instruments. This model cannot be derived from simple addition of noise properties due to the complex interaction between the various noise sources. While it is not feasible to build and test a prototype of the imaging device on-ground, realistic numerical simulations in the form of an end-to-end simulator can be used to model the noise propagation in the observations. These simulations not only allow studying the performance of the instrument, its noise source response and its data quality, but also the instrument design verification for different types of configurations, the observing strategy and the scientific feasibility of an observing proposal. In this way, a complete description and assessment of the objectives to expect from the mission can be derived. We present a high-precision simulation software packag...

  7. ATLAS software packaging

    CERN Document Server

    Rybkin, G

    2012-01-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages - platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis pro...

  8. 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)

  9. Package Equivalent Reactor Networks as Reduced Order Models for Use with CAPE-OPEN Compliant Simulation

    Energy Technology Data Exchange (ETDEWEB)

    Meeks, E.; Chou, C. -P.; Garratt, T.

    2013-03-31

    Engineering simulations of coal gasifiers are typically performed using computational fluid dynamics (CFD) software, where a 3-D representation of the gasifier equipment is used to model the fluid flow in the gasifier and source terms from the coal gasification process are captured using discrete-phase model source terms. Simulations using this approach can be very time consuming, making it difficult to imbed such models into overall system simulations for plant design and optimization. For such system-level designs, process flowsheet software is typically used, such as Aspen Plus® [1], where each component where each component is modeled using a reduced-order model. For advanced power-generation systems, such as integrated gasifier/gas-turbine combined-cycle systems (IGCC), the critical components determining overall process efficiency and emissions are usually the gasifier and combustor. Providing more accurate and more computationally efficient reduced-order models for these components, then, enables much more effective plant-level design optimization and design for control. Based on the CHEMKIN-PRO and ENERGICO software, we have developed an automated methodology for generating an advanced form of reduced-order model for gasifiers and combustors. The reducedorder model offers representation of key unit operations in flowsheet simulations, while allowing simulation that is fast enough to be used in iterative flowsheet calculations. Using high-fidelity fluiddynamics models as input, Reaction Design’s ENERGICO® [2] software can automatically extract equivalent reactor networks (ERNs) from a CFD solution. For the advanced reduced-order concept, we introduce into the ERN a much more detailed kinetics model than can be included practically in the CFD simulation. The state-of-the-art chemistry solver technology within CHEMKIN-PRO allows that to be accomplished while still maintaining a very fast model turn-around time. In this way, the ERN becomes the basis for

  10. 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.

  11. The impact of packaging on product competition

    Directory of Open Access Journals (Sweden)

    Maryam Masoumi

    2012-09-01

    Full Text Available The primary objective of this paper is to detect important factors, which are influencing competitive advantage. The proposed model of this paper uses sampling technique to measure characteristics of society. There are eight independent variables for the proposed study of this paper including packaging endurance, easy distribution, customer promotion through packaging, packaging structure, packaging as silent advertiser, diversity of packaging, clean and healthy packaging and innovation in packaging. The proposed study uses structural equation modeling to either accept or reject all hypotheses associated with the proposed study of this paper. The population of this study includes all managers and experts who are involved in packaging products. We used simple sampling technique and chooses 300 from a population of 450 people who are considered as the population of this survey. Cronbach alpha was determined as 0.732, which is above the minimum acceptable level. The results confirm that all mentioned factors influence competitiveness, effectively.

  12. RPC Stereo Processor (rsp) - a Software Package for Digital Surface Model and Orthophoto Generation from Satellite Stereo Imagery

    Science.gov (United States)

    Qin, R.

    2016-06-01

    Large-scale Digital Surface Models (DSM) are very useful for many geoscience and urban applications. Recently developed dense image matching methods have popularized the use of image-based very high resolution DSM. Many commercial/public tools that implement matching methods are available for perspective images, but there are rare handy tools for satellite stereo images. In this paper, a software package, RPC (rational polynomial coefficient) stereo processor (RSP), is introduced for this purpose. RSP implements a full pipeline of DSM and orthophoto generation based on RPC modelled satellite imagery (level 1+), including level 2 rectification, geo-referencing, point cloud generation, pan-sharpen, DSM resampling and ortho-rectification. A modified hierarchical semi-global matching method is used as the current matching strategy. Due to its high memory efficiency and optimized implementation, RSP can be used in normal PC to produce large format DSM and orthophotos. This tool was developed for internal use, and may be acquired by researchers for academic and non-commercial purpose to promote the 3D remote sensing applications.

  13. 云存储智能多数据副本放置机制��%Intelligent Multiple Data Replica Placement Scheme for Cloud Storage

    Institute of Scientific and Technical Information of China (English)

    张榜; 王兴伟; 黄敏

    2014-01-01

    The data replica management scheme is a critical component of cloud storage system. In order to improve its scalability and reliability at the same time shorten user access time, the multiple data replica scheme should be adopted and the proper placement for each replica should be determined. Thus, this paper proposes an intelligent multiple data replica placement scheme for cloud storage. This scheme is based on p-center model with minimizing user access cost as its optimization objective. It uses genetic algorithm (GA) to find the optimal data replica placement solution and uses biogeography-based optimization (BBO) algorithm to optimally assign user access request to the specific data replica. The proposed scheme has been implemented based on CloudSim and performance evaluation has been done. The simulation results show that it is both feasible and effective.%数据副本管理机制是云存储系统的重要组成部分。为了提高云存储系统的可伸缩性、可靠性,同时改善用户访问时间,通常采用多数据副本机制,并且需要解决数据副本放置问题。为此,提出了一种用于云存储系统的智能多数据副本放置机制。该机制基于p-中心模型,以最小化访问代价为优化目标,基于遗传算法(genetic algorithm,GA)确定优化的数据副本放置方案,基于生物地理学优化(biogeography-based optimization,BBO)算法确定用户访问请求对数据副本的优化分配。基于CloudSim进行了仿真实现和性能评价,结果表明,云存储智能多数据副本放置机制是可行和有效的。

  14. The performance effect of the Lean package – a survey study using a structural equation model

    DEFF Research Database (Denmark)

    Kristensen, Thomas Borup; Israelsen, Poul

    practices. Furthermore, the paper provides evidence that supports the view that actions of middle management enhance performance in the system-wide approach to Lean. Originality/value - In contrast to previous surveys, our results support case studies describing the multiple interdependencies of Lean......Purpose - Our aim is to test and validate a system-wide approach using mediating relationships in a structural equation model in order to understand how the practices of Lean affect performance. Design/methodology/approach – A cross-sectional survey with 200 responding companies indicating...... that they use Lean. This is analyzed in a structural quation model setting. Findings - Previous quantitative research has shown mixed results for the performance of Lean because they have not addressed the system-wide mediating relations between Lean practices. We find that Companies using a system...

  15. Tracked Vehicle Dynamics Modeling and Simulation Methodology, with Control, using RecurDyn Software Package

    Science.gov (United States)

    2011-09-01

    track segment, with pins connecting each track segment. The modeler must align each segment properly with the track pins with the sprocket teeth and...representative track segment is copied and linked together using a simplified algorithm which assumes each track segment is identical, with force/ torque pairs...simulation, RecurDyn feeds CoLink the desired inputs (error term, speed, direction, etc), CoLink performs the programmed operation (generates torque

  16. 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.

  17. 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.

  18. A cost and technical efficiency analysis of two alternative models for implementing the basic package of health services in Afghanistan.

    Science.gov (United States)

    Blaakman, Aaron Philip; Salehi, Ahmad Shah; Boitard, Romain

    2014-01-01

    Since 2003, the Afghan Ministry of Public Health (MoPH) and international partners have directed a contracting-out model through which non-governmental organisations (NGOs) deliver the Basic Package of Health Services (BPHS) in 31 of the 34 Afghan provinces. The MoPH also managed health service delivery in three provinces under an alternative initiative entitled Strengthening Mechanisms (SM). In 2011, under the authority of the MoPH and Delegation of the European Union to Afghanistan, EPOS Health Management conducted a cost and technical efficiency study of the contracting-out and SM mechanisms in six provinces to examine economic trade-offs in the provision of the BPHS. The study provides analyses of all resource inputs and primary outputs of the BPHS in the six provinces during 2008 and 2009. The authors examined technical efficiency using Data Envelopment Analysis (DEA) at the BPHS facility level. Cost analysis results indicate that the weighted average cost per BPHS outpatient visit totalled $3.41 in the SM provinces and $5.39 in the NGO-led provinces in 2009. Furthermore, the data envelopment analyses (DEAs) indicate that facilities in the three NGO-led provinces scored 0.168 points higher on the DEA scale (0-1) than SM facilities. The authors conclude that an approximate 60% increase in costs yielded a 16.8% increase in technical efficiency in the delivery of the BPHS during 2009 in the six provinces.

  19. Developing a training package.

    Science.gov (United States)

    Minogue, Virginia; Donskoy, Anne-Laure

    2017-06-12

    Purpose The purpose of this paper is to outline the development of a training package for service users and carers with an interest in NHS health and social care research. It demonstrates how the developers used their unique experience and expertise as service users and carers to inform their work. Design/methodology/approach Service users and carers, NHS Research and Development Forum working group members, supported by health professionals, identified a need for research training that was tailored to other service user and carer needs. After reviewing existing provision and drawing on their training and support experience, they developed a training package. Sessions from the training package were piloted, which evaluated positively. In trying to achieve programme accreditation and training roll-out beyond the pilots, the group encountered several challenges. Findings The training package development group formed good working relationships and a co-production model that proved sustainable. However, challenges were difficult to overcome owing to external factors and financial constraints. Practical implications Lessons learnt by the team are useful for other service users and carer groups working with health service professionals. Training for service users and carers should be designed to meet their needs; quality and consistency are also important. The relationships between service user and carer groups, and professionals are important to understanding joint working. Recognising and addressing challenges at the outset can help develop strategies to overcome challenges and ensure project success. Originality/value The training package was developed by service users and carers for other service users and carers. Their unique health research experience underpinned the group's values and training development.

  20. Development of the Symbolic Manipulator Laboratory modeling package for the kinematic design and optimization of the Future Armor Rearm System robot. Ammunition Logistics Program

    Energy Technology Data Exchange (ETDEWEB)

    March-Leuba, S.; Jansen, J.F.; Kress, R.L.; Babcock, S.M. [Oak Ridge National Lab., TN (United States); Dubey, R.V. [Tennessee Univ., Knoxville, TN (United States). Dept. of Mechanical and Aerospace Engineering

    1992-08-01

    A new program package, Symbolic Manipulator Laboratory (SML), for the automatic generation of both kinematic and static manipulator models in symbolic form is presented. Critical design parameters may be identified and optimized using symbolic models as shown in the sample application presented for the Future Armor Rearm System (FARS) arm. The computer-aided development of the symbolic models yields equations with reduced numerical complexity. Important considerations have been placed on the closed form solutions simplification and on the user friendly operation. The main emphasis of this research is the development of a methodology which is implemented in a computer program capable of generating symbolic kinematic and static forces models of manipulators. The fact that the models are obtained trigonometrically reduced is among the most significant results of this work and the most difficult to implement. Mathematica, a commercial program that allows symbolic manipulation, is used to implement the program package. SML is written such that the user can change any of the subroutines or create new ones easily. To assist the user, an on-line help has been written to make of SML a user friendly package. Some sample applications are presented. The design and optimization of the 5-degrees-of-freedom (DOF) FARS manipulator using SML is discussed. Finally, the kinematic and static models of two different 7-DOF manipulators are calculated symbolically.

  1. Development of the Symbolic Manipulator Laboratory modeling package for the kinematic design and optimization of the Future Armor Rearm System robot

    Energy Technology Data Exchange (ETDEWEB)

    March-Leuba, S.; Jansen, J.F.; Kress, R.L.; Babcock, S.M. (Oak Ridge National Lab., TN (United States)); Dubey, R.V. (Tennessee Univ., Knoxville, TN (United States). Dept. of Mechanical and Aerospace Engineering)

    1992-08-01

    A new program package, Symbolic Manipulator Laboratory (SML), for the automatic generation of both kinematic and static manipulator models in symbolic form is presented. Critical design parameters may be identified and optimized using symbolic models as shown in the sample application presented for the Future Armor Rearm System (FARS) arm. The computer-aided development of the symbolic models yields equations with reduced numerical complexity. Important considerations have been placed on the closed form solutions simplification and on the user friendly operation. The main emphasis of this research is the development of a methodology which is implemented in a computer program capable of generating symbolic kinematic and static forces models of manipulators. The fact that the models are obtained trigonometrically reduced is among the most significant results of this work and the most difficult to implement. Mathematica, a commercial program that allows symbolic manipulation, is used to implement the program package. SML is written such that the user can change any of the subroutines or create new ones easily. To assist the user, an on-line help has been written to make of SML a user friendly package. Some sample applications are presented. The design and optimization of the 5-degrees-of-freedom (DOF) FARS manipulator using SML is discussed. Finally, the kinematic and static models of two different 7-DOF manipulators are calculated symbolically.

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2016-10-01

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

  5. 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.

  6. Numerical modeling and experimental validation of the acoustic transmission of aircraft's double-wall structures including sound package

    Science.gov (United States)

    Rhazi, Dilal

    to address this need. A numerical tool based on two approaches (Wave and Modal) is developed. It allows a fast computation of the vibroacoustic response for multilayer structures over full frequency spectrum and for various kinds of excitations (monople, rain on the roof, diffuse acoustic filed, turbulent boundary layer) . A comparison between results obtained by the developed model, experimental tests and the finite element method is given and discussed. The results are very promising with respect to the potential of such a model for industrial use as a prediction tool, and even for design. The code can be also integrated within an SEA (Statistical Energy Analysis) strategy in order to model a full vehicle by computing in particular the insertion loss and the equivalent damping added by the sound package. Keywords: Transfer Matrix Method, Wave Approach,Turbulent Boundary Layer, Rain on the Roof, Monopole, Insertion loss, Double-wall, Sound Package.

  7. 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.

  8. 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.

  9. Understanding Dynamics of Information Transmission in Drosophila melanogaster Using a Statistical Modeling Framework for Longitudinal Network Data (the RSiena Package)

    Science.gov (United States)

    Pasquaretta, Cristian; Klenschi, Elizabeth; Pansanel, Jérôme; Battesti, Marine; Mery, Frederic; Sueur, Cédric

    2016-01-01

    Social learning – the transmission of behaviors through observation or interaction with conspecifics – can be viewed as a decision-making process driven by interactions among individuals. Animal group structures change over time and interactions among individuals occur in particular orders that may be repeated following specific patterns, change in their nature, or disappear completely. Here we used a stochastic actor-oriented model built using the RSiena package in R to estimate individual behaviors and their changes through time, by analyzing the dynamic of the interaction network of the fruit fly Drosophila melanogaster during social learning experiments. In particular, we re-analyzed an experimental dataset where uninformed flies, left free to interact with informed ones, acquired and later used information about oviposition site choice obtained by social interactions. We estimated the degree to which the uninformed flies had successfully acquired the information carried by informed individuals using the proportion of eggs laid by uninformed flies on the medium their conspecifics had been trained to favor. Regardless of the degree of information acquisition measured in uninformed individuals, they always received and started interactions more frequently than informed ones did. However, information was efficiently transmitted (i.e., uninformed flies predominantly laid eggs on the same medium informed ones had learn to prefer) only when the difference in contacts sent between the two fly types was small. Interestingly, we found that the degree of reciprocation, the tendency of individuals to form mutual connections between each other, strongly affected oviposition site choice in uninformed flies. This work highlights the great potential of RSiena and its utility in the studies of interaction networks among non-human animals. PMID:27148146

  10. Understanding dynamics of information transmission in Drosophila melanogaster using a statistical modeling framework for longitudinal network data (the RSiena package

    Directory of Open Access Journals (Sweden)

    Cristian ePasquaretta

    2016-04-01

    Full Text Available Social learning – the transmission of behaviors through observation or interaction with conspecifics – can be viewed as a decision-making process driven by interactions among individuals. Animal group structures change over time and interactions among individuals occur in particular orders that may be repeated following specific patterns, change in their nature, or disappear completely. Here we used a stochastic actor-oriented model built using the RSiena package in R to estimate individual behaviors and their changes through time, by analyzing the dynamic of the interaction network of the fruit fly Drosophila melanogaster during social learning experiments. In particular, we re-analyzed an experimental dataset where uninformed flies, left free to interact with informed ones, acquired and later used information about oviposition site choice obtained by social interactions. We estimated the degree to which the uninformed flies had successfully acquired the information carried by informed individuals using the proportion of eggs laid by uninformed flies on the medium their conspecifics had been trained to favor. Regardless of the degree of information acquisition measured in uninformed individuals, they always received and started interactions more frequently than informed ones did. However, information was efficiently transmitted (i.e. uninformed flies predominantly laid eggs on the same medium informed ones had learn to prefer only when the difference in contacts sent between the two fly types was small. Interestingly, we found that the degree of reciprocation, the tendency of individuals to form mutual connections between each other, strongly affected oviposition site choice in uninformed flies. This work highlights the great potential of RSiena and its utility in the studies of interaction networks among non-human animals.

  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. 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....

  13. 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...

  14. Population stochastic modelling (PSM)-An R package for mixed-effects models based on stochastic differential equations

    DEFF Research Database (Denmark)

    Klim, Søren; Mortensen, Stig Bousgaard; Kristensen, Niels Rode

    2009-01-01

    likelihood estimation of a time-inhomogeneous stochastic differential model of glucose dynamics, Math. Med. Biol. 25 (June(2)) (2008) 141-155]. PK/PD models are traditionally based ordinary differential equations (ODES) with an observation link that incorporates noise. This state-space formulation only......The extension from ordinary to stochastic differential equations (SDEs) in pharmacokinetic and pharmacodynamic (PK/PD) modelling is an emerging field and has been motivated in a number of articles [N.R. Kristensen, H. Madsen, S.H. Ingwersen, Using stochastic differential equations for PK/PD model...... development, J. Pharmacokinet. Pharmacodyn. 32 (February(l)) (2005) 109-141; C.W. Tornoe, R.V Overgaard, H. Agerso, H.A. Nielsen, H. Madsen, E.N. Jonsson, Stochastic differential equations in NONMEM: implementation, application, and comparison with ordinary differential equations, Pharm. Res. 22 (August(8...

  15. DNA packaging by lambda-like bacteriophages: mutations broadening the packaging specificity of terminase, the lambda-packaging enzyme.

    Science.gov (United States)

    Feiss, Michael; Reynolds, Erin; Schrock, Morgan; Sippy, Jean

    2010-01-01

    The DNA-packaging specificities of phages lambda and 21 depend on the specific DNA interactions of the small terminase subunits, which have support helix-turn-recognition helix-wing DNA-binding motifs. lambda-Terminase with the recognition helix of 21 preferentially packages 21 DNA. This chimeric terminase's ability to package lambdaDNA is reduced approximately 20-fold. Phage lambda with the chimeric terminase is unable to form plaques, but pseudorevertants are readily obtained. Some pseudorevertants have trans-acting suppressors that change codons of the recognition helix. Some of these codons appear to remove an unfavorable base-pair contact; others appear to create a novel nonspecific DNA contact. Helper-packaging experiments show that these mutant terminases have lost the ability to discriminate between lambda and 21 during DNA packaging. Two cis-acting suppressors affect cosB, the small subunit's DNA-binding site. Each changes a cosB(lambda)-specific base pair to a cosB(21)-specific base pair. These cosB suppressors cause enhanced DNA packaging by 21-specific terminase and reduce packaging by lambda-terminase. Both the cognate support helix and turn are required for strong packaging discrimination. The wing does not contribute to cosB specificity. Evolution of packaging specificity is discussed, including a model in which lambda- and 21-packaging specificities diverged from a common ancestor phage with broad packaging specificity.

  16. DNA Packaging by λ-Like Bacteriophages: Mutations Broadening the Packaging Specificity of Terminase, the λ-Packaging Enzyme

    Science.gov (United States)

    Feiss, Michael; Reynolds, Erin; Schrock, Morgan; Sippy, Jean

    2010-01-01

    The DNA-packaging specificities of phages λ and 21 depend on the specific DNA interactions of the small terminase subunits, which have support helix-turn-recognition helix-wing DNA-binding motifs. λ-Terminase with the recognition helix of 21 preferentially packages 21 DNA. This chimeric terminase's ability to package λDNA is reduced ∼20-fold. Phage λ with the chimeric terminase is unable to form plaques, but pseudorevertants are readily obtained. Some pseudorevertants have trans-acting suppressors that change codons of the recognition helix. Some of these codons appear to remove an unfavorable base-pair contact; others appear to create a novel nonspecific DNA contact. Helper-packaging experiments show that these mutant terminases have lost the ability to discriminate between λ and 21 during DNA packaging. Two cis-acting suppressors affect cosB, the small subunit's DNA-binding site. Each changes a cosBλ-specific base pair to a cosB21-specific base pair. These cosB suppressors cause enhanced DNA packaging by 21-specific terminase and reduce packaging by λ-terminase. Both the cognate support helix and turn are required for strong packaging discrimination. The wing does not contribute to cosB specificity. Evolution of packaging specificity is discussed, including a model in which λ- and 21-packaging specificities diverged from a common ancestor phage with broad packaging specificity. PMID:19841094

  17. Aquarius - A Modelling Package for Groundwater Flow and Coupled Heat Transport in the Range 0.1 to 100 MPa and 0.1 to 1000 C

    Science.gov (United States)

    Cook, S. J.

    2009-05-01

    Aquarius is a Windows application that models fluid flow and heat transport under conditions in which fluid buoyancy can significantly impact patterns and magnitudes of fluid flow. The package is designed as a visualization tool through which users can examine flow systems in environments, both low temperature aquifers and regions with elevated PT regimes such as deep sedimentary basins, hydrothermal systems, and contact thermal aureoles. The package includes 4 components: (1) A finite-element mesh generator/assembler capable of representing complex geologic structures. Left-hand, right-hand and alternating linear triangles can be mixed within the mesh. Planer horizontal, planer vertical and cylindrical vertical coordinate sections are supported. (2) A menu-selectable system for setting properties and boundary/initial conditions. The design retains mathematical terminology for all input parameters such as scalars (e.g., porosity), tensors (e.g., permeability), and boundary/initial conditions (e.g., fixed potential). This makes the package an effective instructional aide by linking model requirements with the underlying mathematical concepts of partial differential equations and the solution logic of boundary/initial value problems. (3) Solution algorithms for steady-state and time-transient fluid flow/heat transport problems. For all models, the nonlinear global matrix equations are solved sequentially using over-relaxation techniques. Matrix storage design allows for large (e.g., 20000) element models to run efficiently on a typical PC. (4) A plotting system that supports contouring nodal data (e.g., head), vector plots for flux data (e.g., specific discharge), and colour gradient plots for elemental data (e.g., porosity), water properties (e.g., density), and performance measures (e.g., Peclet numbers). Display graphics can be printed or saved in standard graphic formats (e.g., jpeg). This package was developed from procedural codes in C written originally to

  18. 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.

  19. Entropy generation in Gaussian quantum transformations: applying the replica method to continuous-variable quantum information theory

    Science.gov (United States)

    Gagatsos, Christos N.; Karanikas, Alexandros I.; Kordas, Georgios; Cerf, Nicolas J.

    2016-02-01

    In spite of their simple description in terms of rotations or symplectic transformations in phase space, quadratic Hamiltonians such as those modelling the most common Gaussian operations on bosonic modes remain poorly understood in terms of entropy production. For instance, determining the quantum entropy generated by a Bogoliubov transformation is notably a hard problem, with generally no known analytical solution, while it is vital to the characterisation of quantum communication via bosonic channels. Here we overcome this difficulty by adapting the replica method, a tool borrowed from statistical physics and quantum field theory. We exhibit a first application of this method to continuous-variable quantum information theory, where it enables accessing entropies in an optical parametric amplifier. As an illustration, we determine the entropy generated by amplifying a binary superposition of the vacuum and a Fock state, which yields a surprisingly simple, yet unknown analytical expression.

  20. 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.

  1. 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....

  2. 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.

  3. PRIDE Surveillance Projects Data Packaging Project Information Package Specification Version 1.1

    Energy Technology Data Exchange (ETDEWEB)

    Kelleher, D. M.; Shipp, R. L.; Mason, J. D.

    2010-08-31

    Information Package Specification version 1.1 describes an XML document format called an information package that can be used to store information in information management systems and other information archives. An information package consists of package information, the context required to understand and use that information, package metadata that describes the information, and XML signatures that protect the information. The information package described in this specification was designed to store Department of Energy (DOE) and National Nuclear Security Administration (NNSA) information and includes the metadata required for that information: a unique package identifier, information marking that conforms to DOE and NNSA requirements, and access control metadata. It is an implementation of the Open Archival Information System (OAIS) Reference Model archival information package tailored to meet NNSA information storage requirements and designed to be used in the computing environments at the Y-12 National Security Complex and at other NNSA sites.

  4. Challenges in the Packaging of MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Malshe, A.P.; Singh, S.B.; Eaton, W.P.; O' Neal, C.; Brown, W.D.; Miller, W.M.

    1999-03-26

    gross lack of understanding between the package materials, induced stress, and the device performance. The material properties of these packaging materials are not well defined or understood. Modeling of these materials and processes is far from maturity. Current post-package yields are too low for commercial feasibility, and consumer operating environment reliability and compatibility are often difficult to simulate. With further understanding of the materials properties and behavior of the packaging materials, MEMS applications can be fully realized and integrated into countless commercial and military applications.

  5. Challenges in the Packaging of MEMS

    Energy Technology Data Exchange (ETDEWEB)

    Malshe, A.P.; Singh, S.B.; Eaton, W.P.; O' Neal, C.; Brown, W.D.; Miller, W.M.

    1999-03-26

    gross lack of understanding between the package materials, induced stress, and the device performance. The material properties of these packaging materials are not well defined or understood. Modeling of these materials and processes is far from maturity. Current post-package yields are too low for commercial feasibility, and consumer operating environment reliability and compatibility are often difficult to simulate. With further understanding of the materials properties and behavior of the packaging materials, MEMS applications can be fully realized and integrated into countless commercial and military applications.

  6. Long-term behaviour of concrete: development of operational model to predict the evolution of its containment performance. Application to cemented waste packages

    Energy Technology Data Exchange (ETDEWEB)

    Peycelon, H.; Le Bescop, P.; Richet, C. [CEA Saclay, Dept. de Physico-Chimie, DPC, 91 - Gif-sur-Yvette (France); Adenot, F. [CEA Cadarache, 13 - Saint Paul lez Durance (France). Dept. d' Entreposage et de Stockage des Dechets; Blanc, V. [Cogema, 78 - Saint Quentin en Yvelines (France)

    2001-07-01

    In order to describe the main phenomena during different stages of cement waste packages life-time and to predict the long-term behaviour (containment performance) of concrete, coupled experiments and modelling studies are achieved. With respect to logical methodology, improvement of these studies is accomplished. Degradation of concrete in low mineralized, carbonated and sulfated water lead to an evolution of chemical characteristics (dissolution/precipitation of solid phases) and of transport properties which must be included or coupled in retention/transport modelling of radio nuclides to predict containment performance. (author)

  7. Nonparametric Econometrics: The np Package

    Directory of Open Access Journals (Sweden)

    Tristen Hayfield

    2008-07-01

    Full Text Available We describe the R np package via a series of applications that may be of interest to applied econometricians. The np package implements a variety of nonparametric and semiparametric kernel-based estimators that are popular among econometricians. There are also procedures for nonparametric tests of significance and consistent model specification tests for parametric mean regression models and parametric quantile regression models, among others. The np package focuses on kernel methods appropriate for the mix of continuous, discrete, and categorical data often found in applied settings. Data-driven methods of bandwidth selection are emphasized throughout, though we caution the user that data-driven bandwidth selection methods can be computationally demanding.

  8. actuar: An R Package for Actuarial Science

    Directory of Open Access Journals (Sweden)

    Christophe Dutang

    2008-02-01

    Full Text Available actuar is a package providing additional Actuarial Science functionality to the R statistical system. The project was launched in 2005 and the package is available on the Comprehensive R Archive Network since February 2006. The current version of the package contains functions for use in the fields of loss distributions modeling, risk theory (including ruin theory, simulation of compound hierarchical models and credibility theory. This paper presents in detail but with few technical terms the most recent version of the package.

  9. Dissolved carbon dioxide and oxygen concentrations in purge of vacuum-packaged pork chops and the relationship to shelf life and models for estimating microbial populations.

    Science.gov (United States)

    Adams, K R; Niebuhr, S E; Dickson, J S

    2015-12-01

    The objectives of this study were to determine the dissolved CO2 and O2 concentrations in the purge of vacuum-packaged pork chops over a 60 day storage period, and to elucidate the relationship of dissolved CO2 and O2 to the microbial populations and shelf life. As the populations of spoilage bacteria increased, the dissolved CO2 increased and the dissolved O2 decreased in the purge. Lactic acid bacteria dominated the spoilage microflora, followed by Enterobacteriaceae and Brochothrix thermosphacta. The surface pH decreased to 5.4 due to carbonic acid and lactic acid production before rising to 5.7 due to ammonia production. A mathematical model was developed which estimated microbial populations based on dissolved CO2 concentrations. Scanning electron microscope images were also taken of the packaging film to observe the biofilm development. The SEM images revealed a two-layer biofilm on the packaging film that was the result of the tri-phase growth environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Analytic implementation of the GRAAL model: Application to a R7T7-type glass package in a geological disposal environment

    Energy Technology Data Exchange (ETDEWEB)

    Minet, Y., E-mail: yves.minet@cea.f [CEA Marcoule, DTCD/SECM/LCLT, BP 17171, 30207 Bagnols-sur-Ceze Cedex (France); Bonin, B. [CEA Saclay, DEN/DIR/DS, 91191 Gif-sur-Yvette Cedex (France); Gin, S.; Frugier, P. [CEA Marcoule, DTCD/SECM/LCLT, BP 17171, 30207 Bagnols-sur-Ceze Cedex (France)

    2010-09-30

    The Glass Reactivity with Allowance for the Alteration Layer Model (GRAAL) was proposed in 2008 to describe borosilicate nuclear glass alteration based on coupling an affinity law with the formation and dissolution of a passivating reactive interface. It is examined here in a simplified form in which only the affinity with respect to silicon is taken into account with a concentration at saturation C{sub sat}, and the precipitation of neoformed phases is described by an affine relation for silicon above a precipitation threshold C{sub sat}{sup '}. This simplified 'analytical GRAAL' model is capable of predicting the quantities of altered glass and the silicon and boron concentration variations in analytical or semi-analytical form, and thereby identify the main characteristic quantities of the system. The model was tested against a series of laboratory experiments lasting from a few days to a few years; its sensitivity to the parameter values was examined, and the model was validated with respect to SON68 glass alteration in initially pure water. It was then applied to the alteration of a glass package in a repository over periods of up to a million years, by means of exploratory calculations comprising a sensitivity study of the internal model parameters and extrapolation to the temperatures expected in a geological repository in order to identify the parameters and mechanisms having the greatest impact on the residual alteration rate. Alteration is controlled by the precipitation of neoformed phases in every case. The transient conditions are of very limited duration with respect to either silicon or boron (no more than a 100 years, with less than 0.01% alteration of the package). In the precipitation law used in the model, the residual alteration rate and total package lifetime are determined primarily by two parameters: k' (the precipitation kinetics) and {sigma}' (the precipitate surface area per unit volume in the geological barrier

  11. CH Packaging Operations Manual

    Energy Technology Data Exchange (ETDEWEB)

    Washington TRU Solutions LLC

    2005-06-13

    This procedure provides instructions for assembling the CH Packaging Drum payload assembly, Standard Waste Box (SWB) assembly, Abnormal Operations and ICV and OCV Preshipment Leakage Rate Tests on the packaging seals, using a nondestructive Helium (He) Leak Test.

  12. Dual Use Packaging Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA seeks down-weighted packaging compatible with microwave preparation and perhaps high hydrostatic pressure processing. New packaging must satisfy NASA's 3-year...

  13. Merganser Download Package

    Data.gov (United States)

    U.S. Environmental Protection Agency — This data download package contains an Esri 10.0 MXD, file geodatabase and copy of this FGDC metadata record. The data in this package are used in support of the...

  14. Comparative Packaging Study

    Science.gov (United States)

    Perchonok, Michele; Antonini, David

    2008-01-01

    This viewgraph presentation describes a comparative packaging study for use on long duration space missions. The topics include: 1) Purpose; 2) Deliverables; 3) Food Sample Selection; 4) Experimental Design Matrix; 5) Permeation Rate Comparison; and 6) Packaging Material Information.

  15. Directory of certificates of compliance for radioactive materials packages. Summary report of NRC approved packages

    Energy Technology Data Exchange (ETDEWEB)

    None

    1979-10-01

    This directory contains a Summary Report of NRC Approved Packages for radioactive material packages effective September 14, 1979. Purpose of this directory is to make available a convenient source of information on packagings which have been approved by the US Nuclear Regulatory Commission. To assist in identifying packaging, an index by Model Number and corresponding Certificate of Compliance number is included at the back of each volume of the directory. The Summary Report includes a listing of all users of each package design prior to the publication date of the directory.

  16. Materials for advanced packaging

    CERN Document Server

    Wong, CP

    2008-01-01

    Significant progress has been made in advanced packaging in recent years. Several new packaging techniques have been developed and new packaging materials have been introduced. This book provides a comprehensive overview of the recent developments in this industry, particularly in the areas of microelectronics, optoelectronics, digital health, and bio-medical applications. The book discusses established techniques, as well as emerging technologies, in order to provide readers with the most up-to-date developments in advanced packaging.

  17. Packaging Printing Today

    OpenAIRE

    Bolanča, Stanislav; Majnarić, Igor; Golubović, Kristijan

    2015-01-01

    Printing packaging covers today about 50% of all the printing products. Among the printing products there are printing on labels, printing on flexible packaging, printing on folding boxes, printing on the boxes of corrugated board, printing on glass packaging, synthetic and metal ones. The mentioned packaging are printed in flexo printing technique, offset printing technique, intaglio halftone process, silk – screen printing, ink ball printing, digital printing and hybrid print...

  18. ATLAS software packaging

    Science.gov (United States)

    Rybkin, Grigory

    2012-12-01

    Software packaging is indispensable part of build and prerequisite for deployment processes. Full ATLAS software stack consists of TDAQ, HLT, and Offline software. These software groups depend on some 80 external software packages. We present tools, package PackDist, developed and used to package all this software except for TDAQ project. PackDist is based on and driven by CMT, ATLAS software configuration and build tool, and consists of shell and Python scripts. The packaging unit used is CMT project. Each CMT project is packaged as several packages—platform dependent (one per platform available), source code excluding header files, other platform independent files, documentation, and debug information packages (the last two being built optionally). Packaging can be done recursively to package all the dependencies. The whole set of packages for one software release, distribution kit, also includes configuration packages and contains some 120 packages for one platform. Also packaged are physics analysis projects (currently 6) used by particular physics groups on top of the full release. The tools provide an installation test for the full distribution kit. Packaging is done in two formats for use with the Pacman and RPM package managers. The tools are functional on the platforms supported by ATLAS—GNU/Linux and Mac OS X. The packaged software is used for software deployment on all ATLAS computing resources from the detector and trigger computing farms, collaboration laboratories computing centres, grid sites, to physicist laptops, and CERN VMFS and covers the use cases of running all applications as well as of software development.

  19. Central heating: package boilers

    Energy Technology Data Exchange (ETDEWEB)

    Farahan, E.

    1977-05-01

    Performance and cost data for electrical and fossil-fired package boilers currently available from manufacturers are provided. Performance characteristics investigated include: unit efficiency, rated capacity, and average expected lifetime of units. Costs are tabulated for equipment and installation of various package boilers. The information supplied in this report will simplify the process of selecting package boilers required for industrial, commercial, and residential applications.

  20. Display system software for the integration of an ADAGE 3000 programmable display generator into the solid modeling package C.A.D. software

    Science.gov (United States)

    Montoya, R. J.; Lane, H. H., Jr.

    1986-01-01

    A software system that integrates an ADAGE 3000 Programmable Display Generator into a C.A.D. software package known as the Solid Modeling Program is described. The Solid Modeling Program (SMP) is an interactive program that is used to model complex solid object through the composition of primitive geomeentities. In addition, SMP provides extensive facilities for model editing and display. The ADAGE 3000 Programmable Display Generator (PDG) is a color, raster scan, programmable display generator with a 32-bit bit-slice, bipolar microprocessor (BPS). The modularity of the system architecture and the width and speed of the system bus allow for additional co-processors in the system. These co-processors combine to provide efficient operations on and rendering of graphics entities. The resulting software system takes advantage of the graphics capabilities of the PDG in the operation of SMP by distributing its processing modules between the host and the PDG. Initially, the target host computer was a PRIME 850, which was later substituted with a VAX-11/785. Two versions of the software system were developed, a phase 1 and a phase 2. In phase 1, the ADAGE 3000 is used as a frame buffer. In phase II, SMP was functionally partitioned and some of its functions were implemented in the ADAGE 3000 by means of ADAGE's SOLID 3000 software package.

  1. 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.

  2. MODFLOW-2000, the U.S. Geological Survey modular ground-water model -- Documentation of the Model-Layer Variable-Direction Horizontal Anisotropy (LVDA) capability of the Hydrogeologic-Unit Flow (HUF) package

    Science.gov (United States)

    Anderman, Evan R.; Kipp, K.L.; Hill, Mary C.; Valstar, Johan; Neupauer, R.M.

    2002-01-01

    This report documents the model-layer variable-direction horizontal anisotropy (LVDA) capability of the Hydrogeologic-Unit Flow (HUF) Package of MODFLOW-2000. The LVDA capability allows the principal directions of horizontal anisotropy to be different than the model-grid row and column directions, and for the directions to vary on a cell-by-cell basis within model layers. The HUF Package calculates effective hydraulic properties for model grid cells based on hydraulic properties of hydrogeologic units with thicknesses defined independently of the model layers. These hydraulic properties include, among other characteristics, hydraulic conductivity and a horizontal anisotropy ratio. Using the LVDA capability, horizontal anisotropy direction is defined for model grid cells within which one or more hydrogeologic units may occur. For each grid cell, the HUF Package calculates the effective horizontal hydraulic conductivity along the primary direction of anisotropy using the hydrogeologic-unit hydraulic conductivities, and calculates the effective horizontal hydraulic conductivity along the orthogonal anisotropy direction using the effective primary direction hydraulic conductivities and horizontal anisotropy ratios. The direction assigned to the model layer effective primary hydraulic conductivity is specified using a new data set defined by the LVDA capability, when active, to calculate coefficients needed to solve the ground-water flow equation. Use of the LVDA capability is illustrated in four simulation examples, which also serve to verify hydraulic heads, advective-travel paths, and sensitivities calculated using the LVDA capability. This version of the LVDA capability defines variable-direction horizontal anisotropy using model layers, not the hydrogeologic units defined by the HUF Package. This difference needs to be taken into account when designing model layers and hydrogeologic units to produce simulations that accurately represent a given field problem. This

  3. Simulation and Training Package on Corex Process

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A software package has been developed for simulation on the Corex process. The simulation and training package on the process of shaft furnace using Corex off gas were introduced. The package consists of three main modules, namely the numerical simulation, the system modeling and optimization, and the training module, which are integrated with graphical interfaces. In addition, the equipment starting and stopping operation and typical trouble-shooting were also included in the package, whereby a practical environment can be established for training of operation and management stuff.

  4. Active Packaging Coatings

    Directory of Open Access Journals (Sweden)

    Luis J. Bastarrachea

    2015-11-01

    Full Text Available Active food packaging involves the packaging of foods with materials that provide an enhanced functionality, such as antimicrobial, antioxidant or biocatalytic functions. This can be achieved through the incorporation of active compounds into the matrix of the commonly used packaging materials, or by the application of coatings with the corresponding functionality through surface modification. The latter option offers the advantage of preserving the packaging materials’ bulk properties nearly intact. Herein, different coating technologies like embedding for controlled release, immobilization, layer-by-layer deposition, and photografting are explained and their potential application for active food packaging is explored and discussed.

  5. PBM: a software package to create, display and manipulate interactively models of small molecules and proteins on IBM-compatible PCs.

    Science.gov (United States)

    Perrakis, A; Constantinides, C; Athanasiades, A; Hamodrakas, S J

    1995-04-01

    The PBM package was developed to create, display and conveniently manipulate protein and small molecule structures on IBM-compatible microcomputers. It consists of four modules: CREATE, SPHERE, RIBBON and CONVERT. CREATE includes commands to create or alter ('mutate') the primary and subsequently the tertiary structure of a given peptide or protein by defining phi and psi angles of residues at will, options to add, delete or alter atoms in a structure, utilities to choose easily between the most common rotamers of amino acid residue sidechains and options to analyse in various ways a protein conformation. SPHERE provides for an interactive manipulation of structures containing up to 2700 atoms which can belong up to six different molecules. All manipulations can be made with the use of an ordinary mouse, by choosing from a variety of pull-down menus. Three types of models can be implemented to display molecules on the computer screen or the plotter: skeletal, solid space-filling and wireframe space-filling models. RIBBON creates ribbon models of proteins and allows for a limited variety of interactive manipulations. CONVERT is a file converter, which is capable of converting files of atom coordinates of literally any format to Brookhaven Data Bank format files. The package produces very good results for protein molecules of reasonable sizes, both in terms of graphics quality and speed of operations, on an 80486 IBM PC-compatible machine equipped with a 1 MByte VGA display card and a colour VGA monitor, which is a recommended configuration.

  6. Kinetics Modeling of Hazelnut Quality Change under Nitrogen Packaging%充氮包装下榛子品质变化的动力学建模

    Institute of Scientific and Technical Information of China (English)

    王鹤腾; 董静

    2012-01-01

    The effect of packaging method on hazelnut quality was discussed. The results showed that nitrogen packaging has the best preservative effects. Kinetic models of peroxide value and acid value at different storage time and temperatures were established to predict and control the quality and shelf life of hazelnut during storage. The results showed that the peroxide value and acid value of hazelnut increases with storage time and storage temperature ; however, they increase slower because of good preservative performance of nitrogen packaging; the acid value and peroxide value has high fitting precision with the first order chemical reaction model and the Arrhenius equation.%探索了不同包装方式对榛子品质变化的影响,结果表明充氮包装保鲜效果最好。建立了充氮包装下酸价、过氧化值随贮藏温度和时间变化的动力学模型,以控制榛子在贮藏过程中的品质和货架期。结果表明,随着贮藏时间的延长和贮藏温度的升高,榛子的酸价和过氧化值不断增加,普通包装增加最快,充氮包装由于良好的保鲜性能而增长较慢。酸价、过氧化值对一级化学反应模型和Arrhenius方程具有很高的拟合精度。

  7. Edible packaging materials.

    Science.gov (United States)

    Janjarasskul, Theeranun; Krochta, John M

    2010-01-01

    Research groups and the food and pharmaceutical industries recognize edible packaging as a useful alternative or addition to conventional packaging to reduce waste and to create novel applications for improving product stability, quality, safety, variety, and convenience for consumers. Recent studies have explored the ability of biopolymer-based food packaging materials to carry and control-release active compounds. As diverse edible packaging materials derived from various by-products or waste from food industry are being developed, the dry thermoplastic process is advancing rapidly as a feasible commercial edible packaging manufacturing process. The employment of nanocomposite concepts to edible packaging materials promises to improve barrier and mechanical properties and facilitate effective incorporation of bioactive ingredients and other designed functions. In addition to the need for a more fundamental understanding to enable design to desired specifications, edible packaging has to overcome challenges such as regulatory requirements, consumer acceptance, and scaling-up research concepts to commercial applications.

  8. PNNL Technical Support to The Implementation of EMTA and EMTA-NLA Models in Autodesk® Moldflow® Packages

    Energy Technology Data Exchange (ETDEWEB)

    Nguyen, Ba Nghiep; Wang, Jin

    2012-12-01

    Under the Predictive Engineering effort, PNNL developed linear and nonlinear property prediction models for long-fiber thermoplastics (LFTs). These models were implemented in PNNL’s EMTA and EMTA-NLA codes. While EMTA is a standalone software for the computation of the composites thermoelastic properties, EMTA-NLA presents a series of nonlinear models implemented in ABAQUS® via user subroutines for structural analyses. In all these models, it is assumed that the fibers are linear elastic while the matrix material can exhibit a linear or typical nonlinear behavior depending on the loading prescribed to the composite. The key idea is to model the constitutive behavior of the matrix material and then to use an Eshelby-Mori-Tanaka approach (EMTA) combined with numerical techniques for fiber length and orientation distributions to determine the behavior of the as-formed composite. The basic property prediction models of EMTA and EMTA-NLA have been subject for implementation in the Autodesk® Moldflow® software packages. These models are the elastic stiffness model accounting for fiber length and orientation distributions, the fiber/matrix interface debonding model, and the elastic-plastic models. The PNNL elastic-plastic models for LFTs describes the composite nonlinear stress-strain response up to failure by an elastic-plastic formulation associated with either a micromechanical criterion to predict failure or a continuum damage mechanics formulation coupling damage to plasticity. All the models account for fiber length and orientation distributions as well as fiber/matrix debonding that can occur at any stage of loading. In an effort to transfer the technologies developed under the Predictive Engineering project to the American automotive and plastics industries, PNNL has obtained the approval of the DOE Office of Vehicle Technologies to provide Autodesk, Inc. with the technical support for the implementation of the basic property prediction models of EMTA and

  9. 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.

  10. 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.

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

    CERN Document Server

    Gil-Ley, Alejandro

    2015-01-01

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

  12. Optimization of Train Trip Package Operation Scheme

    Directory of Open Access Journals (Sweden)

    Lu Tong

    2015-01-01

    Full Text Available Train trip package transportation is an advanced form of railway freight transportation, realized by a specialized train which has fixed stations, fixed time, and fixed path. Train trip package transportation has lots of advantages, such as large volume, long distance, high speed, simple forms of organization, and high margin, so it has become the main way of railway freight transportation. This paper firstly analyzes the related factors of train trip package transportation from its organizational forms and characteristics. Then an optimization model for train trip package transportation is established to provide optimum operation schemes. The proposed model is solved by the genetic algorithm. At last, the paper tests the model on the basis of the data of 8 regions. The results show that the proposed method is feasible for solving operation scheme issues of train trip package.

  13. 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.

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

    Science.gov (United States)

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

    2009-05-07

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

  15. 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...

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. MODFLOW-2000, the U.S. Geological Survey modular ground-water model : user guide to the LMT6 package, the linkage with MT3DMS for multi-species mass transport modeling

    Science.gov (United States)

    Zheng, Chunmiao; Hill, Mary Catherine; Hsieh, Paul A.

    2001-01-01

    MODFLOW-2000, the newest version of MODFLOW, is a computer program that numerically solves the three-dimensional ground-water flow equation for a porous medium using a finite-difference method. MT3DMS, the successor to MT3D, is a computer program for modeling multi-species solute transport in three-dimensional ground-water systems using multiple solution techniques, including the finite-difference method, the method of characteristics (MOC), and the total-variation-diminishing (TVD) method. This report documents a new version of the Link-MT3DMS Package, which enables MODFLOW-2000 to produce the information needed by MT3DMS, and also discusses new visualization software for MT3DMS. Unlike the Link-MT3D Packages that coordinated previous versions of MODFLOW and MT3D, the new Link-MT3DMS Package requires an input file that, among other things, provides enhanced support for additional MODFLOW sink/source packages and allows list-directed (free) format for the flow model produced flow-transport link file. The report contains four parts: (a) documentation of the Link-MT3DMS Package Version 6 for MODFLOW-2000; (b) discussion of several issues related to simulation setup and input data preparation for running MT3DMS with MODFLOW-2000; (c) description of two test example problems, with comparison to results obtained using another MODFLOW-based transport program; and (d) overview of post-simulation visualization and animation using the U.S. Geological Survey?s Model Viewer.

  1. The extended Beer-Lambert theory for ray tracing modeling of LED chip-scaled packaging application with multiple luminescence materials

    Science.gov (United States)

    Yuan, Cadmus C. A.

    2015-12-01

    Optical ray tracing modeling applied Beer-Lambert method in the single luminescence material system to model the white light pattern from blue LED light source. This paper extends such algorithm to a mixed multiple luminescence material system by introducing the equivalent excitation and emission spectrum of individual luminescence materials. The quantum efficiency numbers of individual material and self-absorption of the multiple luminescence material system are considered as well. By this combination, researchers are able to model the luminescence characteristics of LED chip-scaled packaging (CSP), which provides simple process steps and the freedom of the luminescence material geometrical dimension. The method will be first validated by the experimental results. Afterward, a further parametric investigation has been then conducted.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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).

  7. 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.

  8. 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.

  9. 基于连锁超市的包装废弃物回收模型%Recycling Model of Waste Packaging Materials for Chain Supermarkets

    Institute of Scientific and Technical Information of China (English)

    黄勇; 邱丽艳

    2013-01-01

    阐述了包装废弃物回收的意义,基于资源整合与共享的理论思想,提出连锁超市的回收模式,即基于连锁超市的配送体系,在连锁超市合理选址的基础上,依超市建立回收站点,集中回收可再利用的包装;充分利用配送中心的网络资源,建立以达到降低物流成本,实现资源再利用为目的的模型.最后用模糊综合评价法对其进行了评价.%In this paper, we introduced the significance of the recycling of waste packaging materials and on the basis of the ideas of resource integration and sharing, proposed the recycling model of the chain supermarkets, which, on the basis of the reasonable location of the supermarkets, recycled reusable packaging materials in a centralized way and made full use of the network resource of the distribution centers to reduce logistics cost and realize resource reclamation. At the end, we evaluated the model using fuzzy comprehensive evaluation method.

  10. 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

  11. 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

  12. 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

  13. 黄鹤楼品牌个性化卷烟包装形态的造型设计%Modeling Design of Packaging form of Huanghelou Personalized Cigarette

    Institute of Scientific and Technical Information of China (English)

    孙明海; 于琳

    2012-01-01

    通过对黄鹤楼卷烟品牌的个性化包装造型的分析,总结出个性化烟包形态造型的设计法则,并阐述了个性化烟包设计对于消费者产生的心理效应,以此着手设计个性化烟包以达到吸引消费者,促进销售,并为品牌带来广阔市场的设计目的。%Through the analysis of the personalized packaging modeling of Huanghelou cigaretted,it summed up the design rules of personalized cigarette packaging,expounded the psychological effects of personalized cigarette packaging design for consumers,in order to design personalized cigarette packaging to attract consumers,promote the sale and bring the vast market for the brand.

  14. Packaging for Sustainability

    CERN Document Server

    Lewis, Helen; Fitzpatrick, Leanne

    2012-01-01

    The packaging industry is under pressure from regulators, customers and other stakeholders to improve packaging’s sustainability by reducing its environmental and societal impacts. This is a considerable challenge because of the complex interactions between products and their packaging, and the many roles that packaging plays in the supply chain. Packaging for Sustainability is a concise and readable handbook for practitioners who are trying to implement sustainability strategies for packaging. Industry case studies are used throughout the book to illustrate possible applications and scenarios. Packaging for Sustainability draws on the expertise of researchers and industry practitioners to provide information on business benefits, environmental issues and priorities, environmental evaluation tools, design for environment, marketing strategies, and challenges for the future.

  15. 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.

  16. 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.

  17. Grooming. Learning Activity Package.

    Science.gov (United States)

    Stark, Pamela

    This learning activity package on grooming for health workers is one of a series of 12 titles developed for use in health occupations education programs. Materials in the package include objectives, a list of materials needed, information sheets, reviews (self evaluations) of portions of the content, and answers to reviews. These topics are…

  18. Packaging issues: avoiding delamination.

    Science.gov (United States)

    Hall, R

    2005-10-01

    Manufacturers can minimise delamination occurrence by applying the appropriate packaging design and process features. The end user can minimise the impact of fibre tear and reduce subsequent delamination by careful package opening. The occasional inconvenient delamination is a small price to pay for the high level of sterility assurance that comes with the use of Tyvek.

  19. WASTE PACKAGE TRANSPORTER DESIGN

    Energy Technology Data Exchange (ETDEWEB)

    D.C. Weddle; R. Novotny; J. Cron

    1998-09-23

    The purpose of this Design Analysis is to develop preliminary design of the waste package transporter used for waste package (WP) transport and related functions in the subsurface repository. This analysis refines the conceptual design that was started in Phase I of the Viability Assessment. This analysis supports the development of a reliable emplacement concept and a retrieval concept for license application design. The scope of this analysis includes the following activities: (1) Assess features of the transporter design and evaluate alternative design solutions for mechanical components. (2) Develop mechanical equipment details for the transporter. (3) Prepare a preliminary structural evaluation for the transporter. (4) Identify and recommend the equipment design for waste package transport and related functions. (5) Investigate transport equipment interface tolerances. This analysis supports the development of the waste package transporter for the transport, emplacement, and retrieval of packaged radioactive waste forms in the subsurface repository. Once the waste containers are closed and accepted, the packaged radioactive waste forms are termed waste packages (WP). This terminology was finalized as this analysis neared completion; therefore, the term disposal container is used in several references (i.e., the System Description Document (SDD)) (Ref. 5.6). In this analysis and the applicable reference documents, the term ''disposal container'' is synonymous with ''waste package''.

  20. User friendly packaging

    DEFF Research Database (Denmark)

    Geert Jensen, Birgitte

    2010-01-01

    Most consumers have experienced occasional problems with opening packaging. Tomato sauce from the tinned mackerel splattered all over the kitchen counter, the unrelenting pickle jar lid, and the package of sliced ham that cannot be opened without a knife or a pair of scissors. The research project...

  1. The Development of Basic Animal Husbandry Learning Package

    OpenAIRE

    Sri Suryaningsih

    2015-01-01

    Pengembangan Paket Pembelajaran Dasar-dasar Peternakan Abstract: The purpose this research is to generate a package of learning development basics animal husbandry in accordance with the characteristics of the students and the subject and test the fea-sibility of the resulting learning package. The development of learning packages using the model of Dick, Carey & Carey (2001). The results of product assessment the package of learning the basics of animal husbandry is included in the quali...

  2. Adsorption of a Hard Sphere Fluid in a Disordered Polymerized Matrix: Application of the Replica Ornstein-Zernike Equations

    Science.gov (United States)

    Pizio; Trokhymchuk; Henderson; Labik

    1997-07-01

    A model of hard spheres adsorbed in disordered porous media is studied using the associative replica Ornstein-Zernike (ROZ) equations. Extending previous studies of adsorption in a hard sphere matrices, we investigate a polymerized matrix. We consider an associating fluid of hard spheres with two intracore attractive sites per particle; consequently chains consisting of overlapping hard spheres can be formed due to the chemical association. This is the generalization of the model with sites on the surface of Wertheim that has been studied in the bulk by Chang and Sandler. The matrix structure is obtained in the polymer Percus-Yevick approximation. We solve the ROZ equations in the associative hypernetted chain approximation. The pair distribution functions, the fluid compressibility, the equation of state and chemical potential of the adsorbed fluid are obtained and discussed. It is shown that the adsorption of a hard sphere fluid in a matrix at given density, but consisting of longer chains of overlapping hard spheres, is higher than the adsorption of this fluid in a hard sphere matrix.

  3. Development of a generic auto-calibration package for regional ecological modeling and application in the Central Plains of the United States

    Science.gov (United States)

    Wu, Yiping; Liu, Shuguang; Li, Zhengpeng; Dahal, Devendra; Young, Claudia J.; Schmidt, Gail L.; Liu, Jinxun; Davis, Brian; Sohl, Terry L.; Werner, Jeremy M.; Oeding, Jennifer

    2014-01-01

    Process-oriented ecological models are frequently used for predicting potential impacts of global changes such as climate and land-cover changes, which can be useful for policy making. It is critical but challenging to automatically derive optimal parameter values at different scales, especially at regional scale, and validate the model performance. In this study, we developed an automatic calibration (auto-calibration) function for a well-established biogeochemical model—the General Ensemble Biogeochemical Modeling System (GEMS)-Erosion Deposition Carbon Model (EDCM)—using data assimilation technique: the Shuffled Complex Evolution algorithm and a model-inversion R package—Flexible Modeling Environment (FME). The new functionality can support multi-parameter and multi-objective auto-calibration of EDCM at the both pixel and regional levels. We also developed a post-processing procedure for GEMS to provide options to save the pixel-based or aggregated county-land cover specific parameter values for subsequent simulations. In our case study, we successfully applied the updated model (EDCM-Auto) for a single crop pixel with a corn–wheat rotation and a large ecological region (Level II)—Central USA Plains. The evaluation results indicate that EDCM-Auto is applicable at multiple scales and is capable to handle land cover changes (e.g., crop rotations). The model also performs well in capturing the spatial pattern of grain yield production for crops and net primary production (NPP) for other ecosystems across the region, which is a good example for implementing calibration and validation of ecological models with readily available survey data (grain yield) and remote sensing data (NPP) at regional and national levels. The developed platform for auto-calibration can be readily expanded to incorporate other model inversion algorithms and potential R packages, and also be applied to other ecological models.

  4. Advanced flip chip packaging

    CERN Document Server

    Lai, Yi-Shao; Wong, CP

    2013-01-01

    Advanced Flip Chip Packaging presents past, present and future advances and trends in areas such as substrate technology, material development, and assembly processes. Flip chip packaging is now in widespread use in computing, communications, consumer and automotive electronics, and the demand for flip chip technology is continuing to grow in order to meet the need for products that offer better performance, are smaller, and are environmentally sustainable. This book also: Offers broad-ranging chapters with a focus on IC-package-system integration Provides viewpoints from leading industry executives and experts Details state-of-the-art achievements in process technologies and scientific research Presents a clear development history and touches on trends in the industry while also discussing up-to-date technology information Advanced Flip Chip Packaging is an ideal book for engineers, researchers, and graduate students interested in the field of flip chip packaging.

  5. Salvus: A flexible high-performance and open-source package for waveform modelling and inversion from laboratory to global scales

    Science.gov (United States)

    Afanasiev, Michael; Boehm, Christian; van Driel, Martin; Krischer, Lion; May, Dave; Rietmann, Max; Fichtner, Andreas

    2017-04-01

    Recent years have been witness to the application of waveform inversion to new and exciting domains, ranging from non-destructive testing to global seismology. Often, each new application brings with it novel wave propagation physics, spatial and temporal discretizations, and models of variable complexity. Adapting existing software to these novel applications often requires a significant investment of time, and acts as a barrier to progress. To combat these problems we introduce Salvus, a software package designed to solve large-scale full-waveform inverse problems, with a focus on both flexibility and performance. Currently based on an abstract implementation of high order finite (spectral) elements, we have built Salvus to work on unstructured quad/hex meshes in both 2 or 3 dimensions, with support for P1-P3 bases on triangles and tetrahedra. A diverse (and expanding) collection of wave propagation physics are supported (i.e. viscoelastic, coupled solid-fluid). With a focus on the inverse problem, functionality is provided to ease integration with internal and external optimization libraries. Additionally, a python-based meshing package is included to simplify the generation and manipulation of regional to global scale Earth models (quad/hex), with interfaces available to external mesh generators for complex engineering-scale applications (quad/hex/tri/tet). Finally, to ensure that the code remains accurate and maintainable, we build upon software libraries such as PETSc and Eigen, and follow modern software design and testing protocols. Salvus bridges the gap between research and production codes with a design based on C++ template mixins and Python wrappers that separates the physical equations from the numerical core. This allows domain scientists to add new equations using a high-level interface, without having to worry about optimized implementation details. Our goal in this presentation is to introduce the code, show several examples across the scales, and

  6. 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.

  7. 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.

  8. 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.

  9. 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...

  10. 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.

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

    DEFF Research Database (Denmark)

    Zhuang, Guisheng; Kutter, Jörg Peter

    2011-01-01

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

  12. Modular Packaging Development: Incorporating a modular perspective in the packaging design process

    OpenAIRE

    Karlsson, John

    2013-01-01

    This report presents the result of a research project conducted in 2012-2013 that aimed to adjust the existing modularity theories so that they could be used in packaging development. The study resulted in a model that can be incorporated into an existing packaging design process, thereby complementing this with aspects of modularity. The research project was conducted in close collaboration with Ericsson.

  13. Packaging Concerns/Techniques for Large Devices

    Science.gov (United States)

    Sampson, Michael J.

    2009-01-01

    This slide presentation reviews packaging challenges and options for electronic parts. The presentation includes information about non-hermetic packages, space challenges for packaging and complex package variations.

  14. PROSPECTS OF POLYMER PACKAGING MATERIALS

    Directory of Open Access Journals (Sweden)

    V. A. Sedykh

    2012-01-01

    Full Text Available The main types of materials used in the manufacture of packaging. Analyzed trends in further development of packaging materials. Shows how to improve the quality of plastic packaging materials in today's market.

  15. Consumer response to packaging design

    NARCIS (Netherlands)

    Steenis, Nigel D.; Herpen, van Erica; Lans, van der Ivo A.; Ligthart, Tom N.; Trijp, van Hans C.M.

    2017-01-01

    Building on theories of cue utilization, this paper investigates whether and how packaging sustainability influences consumer perceptions, inferences and attitudes towards packaged products. A framework is tested in an empirical study among 249 students using soup products varying in packaging

  16. Packaging Printing Today

    Directory of Open Access Journals (Sweden)

    Stanislav Bolanča

    2015-12-01

    Full Text Available Printing packaging covers today about 50% of all the printing products. Among the printing products there are printing on labels, printing on flexible packaging, printing on folding boxes, printing on the boxes of corrugated board, printing on glass packaging, synthetic and metal ones. The mentioned packaging are printed in flexo printing technique, offset printing technique, intaglio halftone process, silk – screen printing, ink ball printing, digital printing and hybrid printing process. The possibilities of particular printing techniques for optimal production of the determined packaging were studied in the paper. The problem was viewed from the technological and economical aspect. The possible printing quality and the time necessary for the printing realization were taken as key parameters. An important segment of the production and the way of life is alocation value and it had also found its place in this paper. The events in the field of packaging printing in the whole world were analyzed. The trends of technique developments and the printing technology for packaging printing in near future were also discussed.

  17. A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

    Energy Technology Data Exchange (ETDEWEB)

    Genser, Krzysztof [Fermilab; Hatcher, Robert [Fermilab; Perdue, Gabriel [Fermilab; Wenzel, Hans [Fermilab; Yarba, Julia [Fermilab; Kelsey, Michael [SLAC; Wright, Dennis H. [SLAC

    2016-11-10

    The Geant4 toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models are tuned to cover a large variety of possible applications. This raises the critical question of what uncertainties are associated with the Geant4 physics model, or group of models, involved in a simulation project. To address the challenge, we have designed and implemented a comprehen- sive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies. It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertain- ties associated with the simulation model choices. Key functionalities of the toolkit are presented in this paper and are illustrated with selected results.

  18. A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

    CERN Document Server

    Genser, Krzysztof; Perdue, Gabriel; Wenzel, Hans; Yarba, Julia; Kelsey, Michael; Wright, Dennis H

    2016-01-01

    The Geant4 toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models are tuned to cover a large variety of possible applications. This raises the critical question of what uncertainties are associated with the Geant4 physics model, or group of models, involved in a simulation project. To address the challenge, we have designed and implemented a comprehen- sive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies. It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertain- ties associated with the simulation model choices. Key functionalities of the toolkit are presented in this paper and are illustrated with selected results.

  19. Hermeticity of electronic packages

    CERN Document Server

    Greenhouse, Hal; Romenesco, Bruce

    2011-01-01

    This is a book about the integrity of sealed packages to resist foreign gases and liquids penetrating the seal or an opening (crack) in the packageùespecially critical to the reliability and longevity of electronics. The author explains how to predict the reliability and the longevity of the packages based on leak rate measurements and the assumptions of impurities. Non-specialists in particular will benefit from the author's long involvement in the technology. Hermeticity is a subject that demands practical experience, and solving one problem does not necessarily give one the background to so

  20. Optoelectronic packaging: A review

    Energy Technology Data Exchange (ETDEWEB)

    Carson, R.F.

    1993-09-01

    Optoelectronics and photonics hold great potential for high data-rate communication and computing. Wide using in computing applications was limited first by device technologies and now suffers due to the need for high-precision, mass-produced packaging. The use of phontons as a medium of communication and control implies a unique set of packaging constraints that was not present in traditional telecommunications applications. The state-of-the-art in optoelectronic packaging is now driven by microelectric techniques that have potential for low cost and high volume manufacturing.

  1. Hermeticity of electronic packages

    CERN Document Server

    Greenhouse, Hal

    2000-01-01

    This is a book about the integrity of sealed packages to resist foreign gases and liquids penetrating the seal or an opening (crack) in the package-especially critical to the reliability and longevity of electronics. The author explains how to predict the reliability and the longevity of the packages based on leak rate measurements and the assumptions of impurities. Non-specialists in particular will benefit from the author's long involvement in the technology. Hermeticity is a subject that demands practical experience, and solving one problem does not necessarily give one the background to so

  2. QSAR modeling: um novo pacote computacional open source para gerar e validar modelos QSAR QSAR modeling: a new open source computational package to generate and validate QSAR models

    Directory of Open Access Journals (Sweden)

    João Paulo A. Martins

    2013-01-01

    Full Text Available QSAR modeling is a novel computer program developed to generate and validate QSAR or QSPR (quantitative structure- activity or property relationships models. With QSAR modeling, users can build partial least squares (PLS regression models, perform variable selection with the ordered predictors selection (OPS algorithm, and validate models by using y-randomization and leave-N-out cross validation. An additional new feature is outlier detection carried out by simultaneous comparison of sample leverage with the respective Studentized residuals. The program was developed using Java version 6, and runs on any operating system that supports Java Runtime Environment version 6. The use of the program is illustrated. This program is available for download at lqta.iqm.unicamp.br.

  3. A combined mathematica--fortran program package for analytical calculation of the matrix elements of the microscopic cluster model

    CERN Document Server

    Varga, K

    1997-01-01

    We present a computer code that analytically evaluates the matrix elements of the microscopic nuclear Hamiltonian and unity operator between Slater determinants of displaced gaussian single particle orbits. Such matrix elements appear in the generator coordinate model and the resonating group model versions of the microscopic multicluster calculations.

  4. 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...

  5. A user's guide to the GoldSim/BLT-MS integrated software package:a low-level radioactive waste disposal performance assessment model.

    Energy Technology Data Exchange (ETDEWEB)

    Knowlton, Robert G.; Arnold, Bill Walter; Mattie, Patrick D.

    2007-03-01

    Sandia National Laboratories (Sandia), a U.S. Department of Energy National Laboratory, has over 30 years experience in the assessment of radioactive waste disposal and at the time of this publication is providing assistance internationally in a number of areas relevant to the safety assessment of radioactive waste disposal systems. In countries with small radioactive waste programs, international technology transfer program efforts are often hampered by small budgets, schedule constraints, and a lack of experienced personnel. In an effort to surmount these difficulties, Sandia has developed a system that utilizes a combination of commercially available software codes and existing legacy codes for probabilistic safety assessment modeling that facilitates the technology transfer and maximizes limited available funding. Numerous codes developed and endorsed by the United States Nuclear Regulatory Commission (NRC) and codes developed and maintained by United States Department of Energy are generally available to foreign countries after addressing import/export control and copyright requirements. From a programmatic view, it is easier to utilize existing codes than to develop new codes. From an economic perspective, it is not possible for most countries with small radioactive waste disposal programs to maintain complex software, which meets the rigors of both domestic regulatory requirements and international peer review. Therefore, revitalization of deterministic legacy codes, as well as an adaptation of contemporary deterministic codes, provides a credible and solid computational platform for constructing probabilistic safety assessment models. This document is a reference users guide for the GoldSim/BLT-MS integrated modeling software package developed as part of a cooperative technology transfer project between Sandia National Laboratories and the Institute of Nuclear Energy Research (INER) in Taiwan for the preliminary assessment of several candidate low

  6. 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.

  7. 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.

  8. Dual Use Packaging Project

    Data.gov (United States)

    National Aeronautics and Space Administration — NASA calculation that over a kg of packaging waste are generated per day for a 6 member crew. This represents over 1.5 metric tons of waste during a Mars mission....

  9. Materials for advanced packaging

    CERN Document Server

    Wong, CP

    2017-01-01

    This second edition continues to be the most comprehensive review on the developments in advanced electronic packaging technologies, with a focus on materials and processing. Recognized experts in the field contribute to 22 updated and new chapters that provide comprehensive coverage on various 3D package architectures, novel bonding and joining techniques, wire bonding, wafer thinning techniques, organic substrates, and novel approaches to make electrical interconnects between integrated circuit and substrates. Various chapters also address advances in several key packaging materials, including: Lead-free solders Flip chip underfills Epoxy molding compounds Conductive adhesives Die attach adhesives/films Thermal interface materials (TIMS) Materials for fabricating embedded passives including capacitors, inductors, and resistors Materials and processing aspects on wafer-level chip scale package (CSP) and MicroElectroMechanical system (MEMS) Contributors also review new and emerging technologies such as Light ...

  10. FLEXIBLE FOOD PACKAGING LABORATORY

    Data.gov (United States)

    Federal Laboratory Consortium — This laboratory contains equipment to fabricate and test prototype packages of many types and sizes (e.g., bags, pouches, trays, cartons, etc.). This equipment can...

  11. London 2012 packaging guidelines

    OpenAIRE

    2013-01-01

    These guidelines are intended to provide supplemental advice to suppliers and licensees regarding the provisions of the LOCOG Sustainable Sourcing Code that relate to packaging design and materials selection.

  12. Development of waste packages for tuff

    Energy Technology Data Exchange (ETDEWEB)

    Rothman, A.J.

    1982-09-20

    The objective of this program is to develop nuclear waste packages that meet the Nuclear Regulatory Commission`s requirements for a licensed repository in tuff at the Nevada Test Site. Selected accomplishments for FY82 are: (1) Selection, collection of rock, and characterization of suitable outcrops (for lab experiments); (2) Rock-water interactions (Bullfrog Tuff); (3) Corrosion tests of ferrous metals; (4) Thermal modeling of waste package in host rock; (5) Preliminary fabrication tests of alternate backfills (crushed tuff); (6) Reviewed Westinghouse conceptual waste package designs for tuff and began modification for unsaturated zone; and (7) Waste Package Codes (BARIER and WAPPA) now running on our computer. Brief discussions are presented for rock-water interactions, corrosion tests of ferrous metals, and thermal and radionuclide migration modelling.

  13. Lush Cosmetics packaging

    OpenAIRE

    Hudson, Frazer

    2014-01-01

    Frazer Hudson – Lush Cosmetics Packaging Commissioned by Suzie Hackney for Lush Cosmetics via illustration Agency - Debut Art - February 2014 I was approached in February 2014 via my London based Illustration agency Debut Art to create packaging illustration designs for the high street retailer and International cosmetics brand ‘Lush’. The illustrations would be used on an octagonal gift box set and be positioned amongst other bespoke gift box set designs within Lush Cosme...

  14. Galeri Matrix Generation Package

    Energy Technology Data Exchange (ETDEWEB)

    2006-09-01

    The Galeri package defines a collection of serial and distributed linear algebra objects to be used for software verification and validation. Galeri is used in several of the examples of the Amesos, IFPACK and ML packages, and in the Trilinos tutorial, Didasko. Galeri can be used for the generation of linear system with known propeties and data distribution for convergence analysis of interative solvers of Krylov type and domain decomposition and multigrid preconditioners.

  15. Interface free-energy exponent in the one-dimensional Ising spin glass with long-range interactions in both the droplet and broken replica symmetry regions

    Science.gov (United States)

    Aspelmeier, T.; Wang, Wenlong; Moore, M. A.; Katzgraber, Helmut G.

    2016-08-01

    The one-dimensional Ising spin-glass model with power-law long-range interactions is a useful proxy model for studying spin glasses in higher space dimensions and for finding the dimension at which the spin-glass state changes from having broken replica symmetry to that of droplet behavior. To this end we have calculated the exponent that describes the difference in free energy between periodic and antiperiodic boundary conditions. Numerical work is done to support some of the assumptions made in the calculations and to determine the behavior of the interface free-energy exponent of the power law of the interactions. Our numerical results for the interface free-energy exponent are badly affected by finite-size problems.

  16. The bacteriophage DNA packaging motor.

    Science.gov (United States)

    Rao, Venigalla B; Feiss, Michael

    2008-01-01

    An ATP-powered DNA translocation machine encapsidates the viral genome in the large dsDNA bacteriophages. The essential components include the empty shell, prohead, and the packaging enzyme, terminase. During translocation, terminase is docked on the prohead's portal protein. The translocation ATPase and the concatemer-cutting endonuclease reside in terminase. Remarkably, terminases, portal proteins, and shells of tailed bacteriophages and herpes viruses show conserved features. These DNA viruses may have descended from a common ancestor. Terminase's ATPase consists of a classic nucleotide binding fold, most closely resembling that of monomeric helicases. Intriguing models have been proposed for the mechanism of dsDNA translocation, invoking ATP hydrolysis-driven conformational changes of portal or terminase powering DNA motion. Single-molecule studies show that the packaging motor is fast and powerful. Recent advances permit experiments that can critically test the packaging models. The viral genome translocation mechanism is of general interest, given the parallels between terminases, helicases, and other motor proteins.

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

    Science.gov (United States)

    Cavalli, Andrea; Camilloni, Carlo; Vendruscolo, Michele

    2013-03-07

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

  18. RH Packaging Program Guidance

    Energy Technology Data Exchange (ETDEWEB)

    Washington TRU Solutions LLC

    2008-01-12

    The purpose of this program guidance document is to provide the technical requirements for use, operation, inspection, and maintenance of the RH-TRU 72-B Waste Shipping Package (also known as the "RH-TRU 72-B cask") and directly related components. This document complies with the requirements as specified in the RH-TRU 72-B Safety Analysis Report for Packaging (SARP), and Nuclear Regulatory Commission (NRC) Certificate of Compliance (C of C) 9212. If there is a conflict between this document and the SARP and/or C of C, the C of C shall govern. The C of C states: "...each package must be prepared for shipment and operated in accordance with the procedures described in Chapter 7.0, Operating Procedures, of the application." It further states: "...each package must be tested and maintained in accordance with the procedures described in Chapter 8.0, Acceptance Tests and Maintenance Program of the Application." Chapter 9.0 of the SARP tasks the Waste Isolation Pilot Plant (WIPP) Management and Operating (M&O) Contractor with assuring the packaging is used in accordance with the requirements of the C of C. Because the packaging is NRC-approved, users need to be familiar with Title 10 Code of Federal Regulations (CFR) §71.8, "Deliberate Misconduct." Any time a user suspects or has indications that the conditions of approval in the C of C were not met, the U.S. Department of Energy (DOE) Carlsbad Field Office (CBFO) shall be notified immediately. The CBFO will evaluate the issue and notify the NRC if required.In accordance with 10 CFR Part 71, "Packaging and Transportation of Radioactive Material," certificate holders, packaging users, and contractors or subcontractors who use, design, fabricate, test, maintain, or modify the packaging shall post copies of (1) 10 CFR Part 21, "Reporting of Defects and Noncompliance," regulations, (2) Section 206 of the Energy Reorganization Act of 1974, and (3) NRC Form 3, Notice to Employees. These documents must be posted in a

  19. RH Packaging Program Guidance

    Energy Technology Data Exchange (ETDEWEB)

    Washington TRU Solutions LLC

    2006-11-07

    The purpose of this program guidance document is to provide the technical requirements for use, operation, inspection, and maintenance of the RH-TRU 72-B Waste Shipping Package and directly related components. This document complies with the requirements as specified in the RH-TRU 72-B Safety Analysis Report for Packaging (SARP), and Nuclear Regulatory Commission (NRC) Certificate of Compliance (C of C) 9212. If there is a conflict between this document and the SARP and/or C of C, the C of C shall govern. The C of C states: "...each package must be prepared for shipment and operated in accordance with the procedures described in Chapter 7.0, Operating Procedures, of the application." It further states: "...each package must be tested and maintained in accordance with the procedures described in Chapter 8.0, Acceptance Tests and Maintenance Program of the Application." Chapter 9.0 of the SARP tasks the Waste Isolation Pilot Plant (WIPP) Management and Operating (M&O) Contractor with assuring the packaging is used in accordance with the requirements of the C of C. Because the packaging is NRC-approved, users need to be familiar with 10 Code of Federal Regulations (CFR) §71.8, "Deliberate Misconduct." Any time a user suspects or has indications that the conditions of approval in the C of C were not met, the U.S. Department of Energy (DOE) Carlsbad Field Office (CBFO) shall be notified immediately. CBFO will evaluate the issue and notify the NRC if required. In accordance with 10 CFR Part 71, "Packaging and Transportation of Radioactive Material," certificate holders, packaging users, and contractors or subcontractors who use, design, fabricate, test, maintain, or modify the packaging shall post copies of (1) 10 CFR Part 21, "Reporting of Defects and Noncompliance," regulations, (2) Section 206 of the Energy Reorganization Act of 1974, and (3) NRC Form 3, Notice to Employees. These documents must be posted in a conspicuous location where the activities subject to

  20. Modeling and optimization of sensory changes and shelf-life in vacuum-packaged cooked ham treated by E-beam irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Benedito, J., E-mail: jjbenedi@tal.upv.e [Grupo de Analisis y Simulacion de Procesos Agroalimentarios, Departamento Tecnologia de Alimentos, Universidad Politecnica de Valencia, Cami de Vera S/n, E46022 Valencia (Spain); Cambero, M.I. [Departamento de Nutricion, Bromatologia y Tecnologia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, E28040 Madrid (Spain); Ortuno, C. [Grupo de Analisis y Simulacion de Procesos Agroalimentarios, Departamento Tecnologia de Alimentos, Universidad Politecnica de Valencia, Cami de Vera S/n, E46022 Valencia (Spain); Cabeza, M.C.; Ordonez, J.A.; Hoz, L. de la [Departamento de Nutricion, Bromatologia y Tecnologia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, E28040 Madrid (Spain)

    2011-03-15

    The E-beam irradiation of vacuum-packaged RTE cooked ham was carried out to establish the dose required to achieve the food safety objective (FSO) and to minimize changes in selected sensory attributes. Cooked ham was irradiated with doses ranging 1-4 kGy. After the treatment, the microbial inactivation of Listeria monocytogenes, the shelf-life of the product and some sensory attributes (appearance, odor, and flavor) were determined. The inactivation of L. monocytogenes was satisfactorily described by a first-order kinetics equation (R2=0.99). The influence of the irradiation dose on appearance, odor, and flavor was modeled through Gompertz (R2=0.99, for appearance) and Activation/Inactivation (R2=0.99, for odor and flavor) equations. A model was also developed to determine the shelf-life of irradiated cooked ham depending on the irradiation dose (R2>0.91). The dose that maximized the scores of the sensory attributes was 0.96 kGy resulting in an acceptable sensory quality for 80 days. It is possible to apply up to 2 kGy to ensure microbial safety, while provoking no significant changes in the above mentioned sensory attributes.